Package: adductData Version: 1.26.0 Depends: R (>= 3.6) Imports: ExperimentHub (>= 1.9.0), AnnotationHub (>= 2.13.10), stats (>= 3.5.0), utils (>= 3.5.0), methods (>= 3.5.0), datasets (>= 3.5.0) Suggests: knitr (>= 1.15.1), rmarkdown (>= 1.5) License: Artistic-2.0 MD5sum: c028bcccb06c5dc4bbcd74c00da66785 NeedsCompilation: no Title: Data from untargeted MS of modifications to Cys34 of serum albumin Description: mzXML files from Grigoryan et al 2016 (Anal Chem). biocViews: ExperimentData,MassSpectrometryData,ExperimentHub Author: Josie Hayes Maintainer: Josie Hayes VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/adductData git_branch: RELEASE_3_22 git_last_commit: 371b0e2 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/adductData_1.26.0.tar.gz vignettes: vignettes/adductData/inst/doc/adductData.html vignetteTitles: Raw mzXML data using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/adductData/inst/doc/adductData.R dependsOnMe: adductomicsR dependencyCount: 66 Package: affycompData Version: 1.48.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp License: GPL (>= 2) MD5sum: c1e9f944c1dfb8ca6fb268dc25c374bc NeedsCompilation: no Title: affycomp data Description: Data needed by the affycomp package. biocViews: MicroarrayData Author: Rafael A. Irizarry and Zhijin Wu with contributions from Simon Cawley Maintainer: Robert D Shear URL: https://bioconductor.org/packages/affycompData BugReports: https://github.com/rafalab/affyCompData/issues git_url: https://git.bioconductor.org/packages/affycompData git_branch: RELEASE_3_22 git_last_commit: 45dff8f git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/affycompData_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: affycomp dependencyCount: 8 Package: affydata Version: 1.58.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Imports: methods Suggests: hgu95av2cdf, hgu133acdf License: GPL (>= 2) MD5sum: 141c1ab0896f5759904c2ae9d5c94e61 NeedsCompilation: no Title: Affymetrix Data for Demonstration Purpose Description: Example datasets of a slightly large size. They represent 'real world examples', unlike the artificial examples included in the package affy. biocViews: ExperimentData, Tissue, MicroarrayData, TissueMicroarrayData Author: Laurent Gautier Maintainer: Robert D Shear URL: https://bioconductor.org/packages/affydata BugReports: https://github.com/rafalab/affydata/issues git_url: https://git.bioconductor.org/packages/affydata git_branch: RELEASE_3_22 git_last_commit: 10b07a5 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/affydata_1.58.0.tar.gz vignettes: vignettes/affydata/inst/doc/affydata.pdf vignetteTitles: affydata primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/affydata/inst/doc/affydata.R dependsOnMe: affyContam suggestsMe: affy, affycoretools, affyPLM, arrayMvout, Biostrings, gcrma, Harman, mimager, puma, pvac, TurboNorm, vsn dependencyCount: 12 Package: Affyhgu133A2Expr Version: 1.46.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 5c8e9378530cba9b8360f570998622ad NeedsCompilation: no Title: Affymetrix Human Genome U133A 2.0 Array (GPL571) Expression Data Package Description: Contains pre-built human (GPL571) databases of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133A2Expr git_branch: RELEASE_3_22 git_last_commit: 3087443 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/Affyhgu133A2Expr_1.46.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: Affyhgu133aExpr Version: 1.48.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 0cacc6506d9a7072384b41e394f195c4 NeedsCompilation: no Title: Affymetrix Human hgu133a Array (GPL96) Expression Data Package Description: Contains pre-built human (GPL96) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133aExpr git_branch: RELEASE_3_22 git_last_commit: 404c1b6 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/Affyhgu133aExpr_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: Affyhgu133Plus2Expr Version: 1.44.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 213d50673e66d370cc8d8da2077fb8da NeedsCompilation: no Title: Affyhgu133Plus2Expr (GPL570) Expression Data Package Description: Contains pre-built human (GPL570) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133Plus2Expr git_branch: RELEASE_3_22 git_last_commit: 2df08dd git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/Affyhgu133Plus2Expr_1.44.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: AffymetrixDataTestFiles Version: 0.48.0 Depends: R (>= 2.5.0) License: LGPL-2.1 MD5sum: 1637427f4bbfa1199f4c1ab02b8b2084 NeedsCompilation: no Title: Affymetrix Data Files (CEL, CDF, CHP, EXP, PGF, PSI) for Testing Description: This package contains annotation data files and sample data files of Affymetrix file formats. The files originate from the Affymetrix' Fusion SDK distribution and other official sources. biocViews: ExperimentData, MicroarrayData Author: Henrik Bengtsson [aut, cre], James Bullard [aut], Kasper Daniel Hansen [aut] Maintainer: Henrik Bengtsson git_url: https://git.bioconductor.org/packages/AffymetrixDataTestFiles git_branch: RELEASE_3_22 git_last_commit: d77ca79 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/AffymetrixDataTestFiles_0.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: affxparser, affyILM, aroma.affymetrix dependencyCount: 0 Package: Affymoe4302Expr Version: 1.48.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 717596fbb5b5167d47cef236d375889d NeedsCompilation: no Title: Affymetrix Mouse Genome 430 2.0 Array (GPL1261) Expression Data Package Description: Contains pre-built mouse (GPL1261) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Mus_musculus_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affymoe4302Expr git_branch: RELEASE_3_22 git_last_commit: 53202e1 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/Affymoe4302Expr_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: airway Version: 1.30.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: knitr, GEOquery, markdown License: LGPL MD5sum: 84a066da3b1ce2f3f1d0fc88ce57f29e NeedsCompilation: no Title: RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014 Description: This package provides a RangedSummarizedExperiment object of read counts in genes for an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. Details on the gene model and read counting procedure are provided in the package vignette. The citation for the experiment is: Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri R Jr, Tantisira KG, Weiss ST, Lu Q. 'RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells.' PLoS One. 2014 Jun 13;9(6):e99625. PMID: 24926665. GEO: GSE52778. biocViews: ExperimentData, SequencingData, RNASeqData, GEO Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/airway git_branch: RELEASE_3_22 git_last_commit: a6a39c3 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/airway_1.30.0.tar.gz vignettes: vignettes/airway/inst/doc/airway.html vignetteTitles: Airway smooth muscle cells hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/airway/inst/doc/airway.R dependsOnMe: rnaseqGene importsMe: consensusDE, NetActivity suggestsMe: apeglm, awst, biobroom, BioCor, BiocSet, CeTF, DelayedArray, DESeq2, DNEA, EnrichmentBrowser, ExperimentSubset, funOmics, geyser, gg4way, ideal, IHW, InteractiveComplexHeatmap, iSEEde, iSEEpathways, iSEEu, MLInterfaces, OPWeight, pathwayPCA, pcaExplorer, plyxp, progeny, ReducedExperiment, runibic, Rvisdiff, SummarizedExperiment, tidybulk, tidySummarizedExperiment, TTMap, weitrix, XAItest, IHWpaper, RegParallel, seqgendiff dependencyCount: 25 Package: ALL Version: 1.52.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Suggests: rpart License: Artistic-2.0 MD5sum: 40bd64aa3921b0009ced7f231972c7bd NeedsCompilation: no Title: A data package Description: Data of T- and B-cell Acute Lymphocytic Leukemia from the Ritz Laboratory at the DFCI (includes Apr 2004 versions) biocViews: ExperimentData, CancerData, LeukemiaCancerData Author: Xiaochun Li Maintainer: Robert Gentleman git_url: https://git.bioconductor.org/packages/ALL git_branch: RELEASE_3_22 git_last_commit: 0bc53bb git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/ALL_1.52.0.tar.gz vignettes: vignettes/ALL/inst/doc/ALLintro.pdf vignetteTitles: ALL data intro hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ALL/inst/doc/ALLintro.R importsMe: ConsensusClusterPlus, dGAselID, scRNAtools suggestsMe: a4, a4Base, a4Classif, a4Preproc, Biobase, BioNet, Category, CellMapper, ChromHeatMap, clipper, EnrichmentBrowser, esetVis, genefilter, GeneSelectMMD, GOstats, graphite, GSAR, GSEAlm, MLInterfaces, npGSEA, pathRender, ReportingTools, rScudo, SNAGEE, topGO, SNAGEEdata, MMDvariance, nlcv dependencyCount: 7 Package: ALLMLL Version: 1.50.0 Depends: R (>= 2.10), affy (>= 1.23.4) License: GPL-2 MD5sum: 842042655c3eea91d887e1145040509b NeedsCompilation: no Title: A subset of arrays from a large acute lymphoblastic leukemia (ALL) study Description: This package provides probe-level data for 20 HGU133A and 20 HGU133B arrays which are a subset of arrays from a large ALL study. The data is for the MLL arrays. This data was published in Mary E. Ross, Xiaodong Zhou, Guangchun Song, Sheila A. Shurtleff, Kevin Girtman, W. Kent Williams, Hsi-Che Liu, Rami Mahfouz, Susana C. Raimondi, Noel Lenny, Anami Patel, and James R. Downing (2003) Classification of pediatric acute lymphoblastic leukemia by gene expression profiling Blood 102: 2951-2959 biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData Author: B. M. Bolstad git_url: https://git.bioconductor.org/packages/ALLMLL git_branch: RELEASE_3_22 git_last_commit: 8af2a9d git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/ALLMLL_1.50.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: pvac dependencyCount: 12 Package: AmpAffyExample Version: 1.50.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Suggests: hgu133acdf License: LGPL (>= 2) MD5sum: 3ab21821413e4c18ae9a6cfc2a3ed032 NeedsCompilation: no Title: Example of Amplified Data Description: Six arrays. Three from amplified RNA, three from the typical procedure. biocViews: ExperimentData, MicroarrayData Author: Rafael A. Irizarry Maintainer: Robert D Shear URL: https://bioconductor.org/packages/AmpAffyExample BugReports: https://github.com/rafalab/AmpAffyExample/issues git_url: https://git.bioconductor.org/packages/AmpAffyExample git_branch: RELEASE_3_22 git_last_commit: ae15c93 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/AmpAffyExample_1.50.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: AffyRNADegradation dependencyCount: 12 Package: AneuFinderData Version: 1.38.0 Depends: R (>= 3.3) License: file LICENSE MD5sum: 6e7492c72a206535ae9e8d7f49d24fec NeedsCompilation: no Title: WGSCS Data for Demonstration Purposes Description: Whole-genome single cell sequencing data for demonstration purposes in the AneuFinder package. biocViews: CopyNumberVariationData, LungCancerData, Homo_sapiens_Data, SequencingData Author: Aaron Taudt Maintainer: Aaron Taudt PackageStatus: Deprecated git_url: https://git.bioconductor.org/packages/AneuFinderData git_branch: RELEASE_3_22 git_last_commit: 02b9cb8 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/AneuFinderData_1.38.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: antiProfilesData Version: 1.46.0 Depends: Biobase, Suggests: frma, GEOquery, GEOmetadb License: Artistic-2.0 MD5sum: cb7943884c486cfdb081bcc36572fea7 NeedsCompilation: no Title: Normal colon and cancer preprocessed affy data for antiProfile building. Description: Colon normal tissue and cancer samples used in Corrada Bravo, et al. gene expression anti-profiles paper: BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272. Measurements are z-scores obtained from the GeneExpression Barcode in the 'frma' package biocViews: ExperimentData, MicroarrayData, Tissue, CancerData, ColonCancerData Author: Hector Corrada Bravo, Matthew McCall and Rafael A. Irizarry Maintainer: Hector Corrada Bravo git_url: https://git.bioconductor.org/packages/antiProfilesData git_branch: RELEASE_3_22 git_last_commit: 63970b8 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/antiProfilesData_1.46.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: antiProfiles, epivizr, epivizrChart, messina dependencyCount: 7 Package: aracne.networks Version: 1.36.0 Depends: R (>= 3.3), viper License: file LICENSE MD5sum: 11cddeaba1a0c3ae4acb1cf3940f99ac NeedsCompilation: no Title: ARACNe-inferred gene networks from TCGA tumor datasets Description: This package contains ARACNe-inferred networks from TCGA tumor datasets. It also contains a function to export them into plain-text format. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData Author: Federico M. Giorgi Maintainer: Federico M. Giorgi , Mariano Alvarez git_url: https://git.bioconductor.org/packages/aracne.networks git_branch: RELEASE_3_22 git_last_commit: f3c9ed6 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/aracne.networks_1.36.0.tar.gz vignettes: vignettes/aracne.networks/inst/doc/aracne.networks.pdf vignetteTitles: Using aracne.networks hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/aracne.networks/inst/doc/aracne.networks.R dependencyCount: 88 Package: ARRmData Version: 1.46.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: 0fb9895c62700ac0fa7cf9a38a7b4a94 NeedsCompilation: no Title: Example dataset for normalization of Illumina 450k Methylation data Description: Raw Beta values from 36 samples across 3 groups from Illumina 450k methylation arrays biocViews: ExperimentData, MethylationArrayData Author: Jean-Philippe Fortin, Celia M.T. Greenwood, Aurelie Labbe Maintainer: Jean-Philippe Fortin git_url: https://git.bioconductor.org/packages/ARRmData git_branch: RELEASE_3_22 git_last_commit: 2d2dd34 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/ARRmData_1.46.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ARRmNormalization dependencyCount: 0 Package: AshkenazimSonChr21 Version: 1.40.0 Suggests: knitr, VariantAnnotation License: Artistic-2.0 MD5sum: ad3b8905b8f8cc3b758c6df35205cfba NeedsCompilation: no Title: Annotated variants on the chromosome 21, human genome 19, Ashkenazim Trio son sample Description: SonVariantsChr21 is a dataset of annotated genomic variants coming from Complete Genomics whole genome sequencing. Data comes from GIAB project, Ashkenazim Trio, sample HG002 run 1. Both vcf and annotated data frame are provided. biocViews: GenomicVariation, Sequencing, WholeGenome Author: Tomasz Stokowy Maintainer: Who to complain to VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/AshkenazimSonChr21 git_branch: RELEASE_3_22 git_last_commit: f019d7e git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/AshkenazimSonChr21_1.40.0.tar.gz vignettes: vignettes/AshkenazimSonChr21/inst/doc/AshkenazimSonChr21.pdf vignetteTitles: RareVariantVis hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/AshkenazimSonChr21/inst/doc/AshkenazimSonChr21.R dependencyCount: 0 Package: ASICSdata Version: 1.30.0 Depends: R (>= 3.5) Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 0ed2a2e7d86d72dbd149069f118525c8 NeedsCompilation: no Title: Example of 1D NMR spectra data for ASICS package Description: 1D NMR example spectra and additional data for use with the ASICS package. Raw 1D Bruker spectral data files were found in the MetaboLights database (https://www.ebi.ac.uk/metabolights/, study MTBLS1). biocViews: ExperimentData, Homo_sapiens_Data Author: Gaëlle Lefort [aut, cre], Rémi Servien [aut], Nathalie Villa-Vialaneix [aut] Maintainer: Gaëlle Lefort VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ASICSdata git_branch: RELEASE_3_22 git_last_commit: 84471d9 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/ASICSdata_1.30.0.tar.gz vignettes: vignettes/ASICSdata/inst/doc/ASICSdata.html vignetteTitles: ASICSdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ASICS dependencyCount: 0 Package: AssessORFData Version: 1.28.0 Depends: R (>= 3.5.0), RSQLite (>= 1.1) Imports: DECIPHER, utils Suggests: AssessORF, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 8e51de1bd19179b256ac1161b205ed5b NeedsCompilation: no Title: Data and Files for the AssessORF Package Description: This package provides access to mapping and results objects generated by the AssessORF package, as well as the genome sequences for the strains corresponding to those objects. biocViews: OrganismData, Bacillus_subtilis_Data, Escherichia_coli_Data, Pseudomonas_aeruginosa_Data, Staphylococcus_aureus_Data, Genome, Proteome, SequencingData Author: Deepank Korandla [aut], Nicholas Cooley [cre] (ORCID: ) Maintainer: Nicholas Cooley VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/AssessORFData git_branch: RELEASE_3_22 git_last_commit: 2cd0c9f git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/AssessORFData_1.28.0.tar.gz vignettes: vignettes/AssessORFData/inst/doc/AssessORFDataGuide.pdf vignetteTitles: Using AssessORFData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/AssessORFData/inst/doc/AssessORFDataGuide.R suggestsMe: AssessORF dependencyCount: 32 Package: AWAggregatorData Version: 1.0.0 Depends: ExperimentHub Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: e42325ecbc590b4030fba922105928e6 NeedsCompilation: no Title: Attribute-Weighted Aggregation Data Description: The AWAggregatorData package contains the data associated with the AWAggregator R package. It includes two pre-trained random forest models, one incorporating the average coefficient of variation as a feature, and the other one not including it. It also contains the PSMs in Benchmark Set 1~3 derived from the psm.tsv output files generated by FragPipe, which are used to train the random forest models. biocViews: ExperimentData, PackageTypeData, ExperimentHub, MassSpectrometryData, Proteome Author: Jiahua Tan [aut, cre] (ORCID: ), Gian L. Negri [aut] (ORCID: ), Gregg B. Morin [aut] (ORCID: ), David D. Y. Chen [aut] (ORCID: ) Maintainer: Jiahua Tan URL: https://github.com/Tan-Jiahua/AWAggregatorData VignetteBuilder: knitr BugReports: https://github.com/Tan-Jiahua/AWAggregatorData/issues git_url: https://git.bioconductor.org/packages/AWAggregatorData git_branch: RELEASE_3_22 git_last_commit: 536ce55 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/AWAggregatorData_1.0.0.tar.gz vignettes: vignettes/AWAggregatorData/inst/doc/AWAggregatorData-vignette.html vignetteTitles: AWAggregatorData vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/AWAggregatorData/inst/doc/AWAggregatorData-vignette.R suggestsMe: AWAggregator dependencyCount: 65 Package: bcellViper Version: 1.46.0 Depends: R(>= 2.14.0), Biobase, methods License: GPL (>=2) MD5sum: e082806ccb32f233953c7c594fd20aa3 NeedsCompilation: no Title: Human B-cell transcriptional interactome and normal human B-cell expression data Description: This package provides a human B-cell context-specific transcriptional regulatory network and a human normal B-cells dataset for the examples in package viper. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData Author: Mariano Javier Alvarez Maintainer: Mariano Javier Alvarez git_url: https://git.bioconductor.org/packages/bcellViper git_branch: RELEASE_3_22 git_last_commit: 3faf694 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/bcellViper_1.46.0.tar.gz vignettes: vignettes/bcellViper/inst/doc/bcellViper.pdf vignetteTitles: Using bcellViper hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bcellViper/inst/doc/bcellViper.R importsMe: dorothea suggestsMe: GenomicSuperSignature, pageRank, viper dependencyCount: 7 Package: beadarrayExampleData Version: 1.47.0 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>= 2.0.0) License: GPL-2 MD5sum: 05b4c55cf8582112c30c8cca2ed1ec47 NeedsCompilation: no Title: Example data for the beadarray package Description: An small dataset that can be used to run examples from the beadarray vignette and examples biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/beadarrayExampleData git_branch: devel git_last_commit: 40884e4 git_last_commit_date: 2025-04-15 Date/Publication: 2025-04-17 source.ver: src/contrib/beadarrayExampleData_1.47.0.tar.gz vignettes: vignettes/beadarrayExampleData/inst/doc/beadarrayExampleData.pdf vignetteTitles: beadarrayExampleData: example data for the beadarray package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/beadarrayExampleData/inst/doc/beadarrayExampleData.R suggestsMe: MiRaGE dependencyCount: 8 Package: BeadArrayUseCases Version: 1.47.0 Imports: beadarray (>= 2.3.18), limma, GEOquery Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db License: GPL-2 MD5sum: 4a7bb913de2014b09b8fb74bfbfe4820 NeedsCompilation: no Title: Analysing Illumina BeadArray expression data using Bioconductor Description: Example data files and use cases for processing Illumina BeadArray expression data using Bioconductor biocViews: MicroarrayData Author: Mark Dunning, Wei Shi, Andy Lynch, Mike Smith, Matt Ritchie Maintainer: Mike Smith git_url: https://git.bioconductor.org/packages/BeadArrayUseCases git_branch: devel git_last_commit: 9292245 git_last_commit_date: 2025-04-15 Date/Publication: 2025-04-17 source.ver: src/contrib/BeadArrayUseCases_1.47.0.tar.gz vignettes: vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.pdf vignetteTitles: BeadArrayUseCases.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.R dependencyCount: 76 Package: BeadSorted.Saliva.EPIC Version: 1.18.0 Depends: R (>= 4.1), minfi(>= 1.36.0), ExperimentHub Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 0e5b252a68cabcd066f9a90098c884f5 NeedsCompilation: no Title: Illumina EPIC data on BeadSorted child saliva cells Description: Raw data objects used to estimate saliva cell proportion estimates in ewastools. The FlowSorted.Saliva.EPIC object is constructed from samples assayed by Lauren Middleton et. al. (2021). biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData, Genome, MethylationArrayData, ExperimentHub Author: Jonah Fisher [aut, cre], Kelly Bakulski [aut], Lauren Middleton [aut] Maintainer: Jonah Fisher VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/BeadSorted.Saliva.EPIC git_branch: RELEASE_3_22 git_last_commit: 652ede4 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/BeadSorted.Saliva.EPIC_1.18.0.tar.gz vignettes: vignettes/BeadSorted.Saliva.EPIC/inst/doc/BeadSorted.Saliva.EPIC.html vignetteTitles: BeadSorted.Saliva.EPIC.html hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BeadSorted.Saliva.EPIC/inst/doc/BeadSorted.Saliva.EPIC.R dependencyCount: 151 Package: beta7 Version: 1.48.0 Depends: R (>= 2.4.0), marray License: LGPL MD5sum: 0c93b4b2fdcd335e2ca613fcce5a2d14 NeedsCompilation: no Title: Rodriguez et al. (2004) Differential Gene Expression by Memory/Effector T Helper Cells Bearing the Gut-Homing Receptor Integrin alpha4 beta7. Description: Data from 6 gpr files aims to identify differential expressed genes between the beta 7+ and beta 7- memory T helper cells. biocViews: ExperimentData, Homo_sapiens_Data, CGHData, MicroarrayData Author: Jean Yang Maintainer: Jean Yang git_url: https://git.bioconductor.org/packages/beta7 git_branch: RELEASE_3_22 git_last_commit: 9ae99c0 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/beta7_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 8 Package: BioImageDbs Version: 1.18.0 Depends: R (>= 4.1.0) Imports: ExperimentHub, AnnotationHub, markdown, rmarkdown, EBImage, magick, magrittr, filesstrings, animation, einsum Suggests: knitr, BiocStyle, purrr License: Artistic-2.0 MD5sum: e6dded43ca09584cb7a4091c444fed27 NeedsCompilation: no Title: Bio- and biomedical imaging dataset for machine learning and deep learning (for ExperimentHub) Description: The package provides a bioimage dataset for the image analysis using machine learning and deep learning. The dataset includes microscopy imaging data with supervised labels. The data is provided as R list data that can be loaded to Keras/tensorflow in R. biocViews: ExperimentHub, ExperimentData, CellCulture, Tissue Author: Satoshi Kume [aut, cre] (ORCID: ), Kozo Nishida [aut] (ORCID: ) Maintainer: Satoshi Kume URL: https://kumes.github.io/BioImageDbs/ VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/BioImageDbs git_branch: RELEASE_3_22 git_last_commit: cadf80b git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/BioImageDbs_1.18.0.tar.gz vignettes: vignettes/BioImageDbs/inst/doc/BioImageBbs_Datasets.html, vignettes/BioImageDbs/inst/doc/BioImageDbs.html vignetteTitles: The BioImageBbs Datasets, Providing Bioimage Dataset for ExperimentHub hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BioImageDbs/inst/doc/BioImageBbs_Datasets.R, vignettes/BioImageDbs/inst/doc/BioImageDbs.R dependencyCount: 102 Package: BioPlex Version: 1.15.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: BiocFileCache, GenomicRanges, GenomeInfoDb, GEOquery, graph, methods, utils Suggests: AnnotationDbi, AnnotationHub, BiocStyle, DEXSeq, ExperimentHub, GenomicFeatures, S4Vectors, depmap, knitr, rmarkdown License: Artistic-2.0 MD5sum: 9dce5b35fd3864028c4f2768943d3b59 NeedsCompilation: no Title: R-side access to BioPlex protein-protein interaction data Description: The BioPlex package implements access to the BioPlex protein-protein interaction networks and related resources from within R. Besides protein-protein interaction networks for HEK293 and HCT116 cells, this includes access to CORUM protein complex data, and transcriptome and proteome data for the two cell lines. Functionality focuses on importing the various data resources and storing them in dedicated Bioconductor data structures, as a foundation for integrative downstream analysis of the data. biocViews: CellCulture, ColonCancerData, ExperimentHub, ExpressionData, GEO, Genome, Homo_sapiens_Data, MassSpectrometryData, Proteome, ReproducibleResearch, RNASeqData Author: Ludwig Geistlinger [aut, cre], Robert Gentleman [aut] Maintainer: Ludwig Geistlinger URL: https://github.com/ccb-hms/BioPlex VignetteBuilder: knitr BugReports: https://github.com/ccb-hms/BioPlex/issues git_url: https://git.bioconductor.org/packages/BioPlex git_branch: devel git_last_commit: fde35b2 git_last_commit_date: 2025-04-15 Date/Publication: 2025-04-24 source.ver: src/contrib/BioPlex_1.15.0.tar.gz vignettes: vignettes/BioPlex/inst/doc/BasicChecks.html, vignettes/BioPlex/inst/doc/BioPlex.html vignetteTitles: 2. Data checks, 1. Data retrieval hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BioPlex/inst/doc/BasicChecks.R, vignettes/BioPlex/inst/doc/BioPlex.R dependencyCount: 88 Package: biotmleData Version: 1.34.0 Depends: R (>= 3.5.0) Suggests: Biobase, SummarizedExperiment License: file LICENSE MD5sum: 6298b1533b807d97b1af816d1ca0d0db NeedsCompilation: no Title: Example experimental microarray data set for the "biotmle" R package Description: Microarray data (from the Illumina Ref-8 BeadChips platform) and phenotype-level data from an epidemiological investigation of benzene exposure, packaged using "SummarizedExperiemnt", for use as an example with the "biotmle" R package. biocViews: GeneExpression, DifferentialExpression, Sequencing, Microarray, RNASeq Author: Nima Hejazi [aut, cre] Maintainer: Nima Hejazi git_url: https://git.bioconductor.org/packages/biotmleData git_branch: RELEASE_3_22 git_last_commit: b18a8d5 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/biotmleData_1.34.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: biotmle dependencyCount: 0 Package: biscuiteerData Version: 1.24.0 Depends: R (>= 4.1.0), ExperimentHub Imports: AnnotationHub, utils, curl, GenomicRanges Suggests: knitr, rmarkdown, markdown License: GPL-3 MD5sum: 90b394ddf5bddce028c1b58955acf9c5 NeedsCompilation: no Title: Data Package for Biscuiteer Description: Contains default datasets used by the Bioconductor package biscuiteer. biocViews: ExperimentHub, ExperimentData, Genome, Homo_sapiens_Data Author: Tim Triche, Jr. [aut, cre], Wanding Zhou [aut], Ben Johnson [aut], Jacob Morrison [aut], Lyong Heo [aut] Maintainer: "Jacob Morrison" VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/biscuiteerData git_branch: RELEASE_3_22 git_last_commit: 4399124 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/biscuiteerData_1.24.0.tar.gz vignettes: vignettes/biscuiteerData/inst/doc/biscuiteerData.html vignetteTitles: Biscuiteer User Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/biscuiteerData/inst/doc/biscuiteerData.R dependsOnMe: biscuiteer dependencyCount: 66 Package: bladderbatch Version: 1.48.0 Depends: Biobase License: Artistic-2.0 MD5sum: 0d9f1eefcf729bb007307d4257d5a8fb NeedsCompilation: no Title: Bladder gene expression data illustrating batch effects Description: This package contains microarray gene expression data on 57 bladder samples from 5 batches. The data are used as an illustrative example for the sva package. biocViews: ExperimentData, CancerData, MicroarrayData Author: Jeffrey T. Leek Maintainer: Jeffrey T. Leek git_url: https://git.bioconductor.org/packages/bladderbatch git_branch: RELEASE_3_22 git_last_commit: 2f7a931 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/bladderbatch_1.48.0.tar.gz vignettes: vignettes/bladderbatch/inst/doc/bladderbatch.pdf vignetteTitles: bladderbatchTutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bladderbatch/inst/doc/bladderbatch.R importsMe: RUVcorr suggestsMe: BatchQC, Harman, sva dependencyCount: 7 Package: blimaTestingData Version: 1.30.0 Depends: R(>= 3.0.0) Suggests: blima, beadarray, illuminaHumanv4.db, BiocStyle License: GPL-3 MD5sum: b8a14a73b000c6264e3f704634e83e2e NeedsCompilation: no Title: Data for testing of the package blima. Description: Experiment data package. The set were prepared using microarray images of human mesenchymal cells treated with various supplements. This package is intended to provide example data to test functionality provided by blima. biocViews: MicroarrayData, ExperimentData, GEO Author: Vojtech Kulvait Maintainer: Vojtech Kulvait URL: https://bitbucket.org/kulvait/blima git_url: https://git.bioconductor.org/packages/blimaTestingData git_branch: RELEASE_3_22 git_last_commit: e530fdf git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/blimaTestingData_1.30.0.tar.gz vignettes: vignettes/blimaTestingData/inst/doc/blimaTestingData.pdf vignetteTitles: blimaTestingData.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/blimaTestingData/inst/doc/blimaTestingData.R dependencyCount: 0 Package: BloodCancerMultiOmics2017 Version: 1.30.0 Depends: R (>= 3.5.0) Imports: beeswarm, Biobase, DESeq2, devtools, dplyr, ggdendro, ggplot2, glmnet, graphics, grDevices, grid, gtable, ipflasso, methods, RColorBrewer, reshape2, scales, stats, SummarizedExperiment, survival, tibble Suggests: BiocStyle, knitr, rmarkdown, abind, AnnotationDbi, biomaRt, broom, colorspace, cowplot, dendsort, doParallel, foreach, forestplot, genefilter, ggbeeswarm, ggtern, gridExtra, hexbin, limma, magrittr, Matrix, maxstat, nat, org.Hs.eg.db, pheatmap, piano, readxl, Rtsne, tidyr, xtable License: LGPL (>= 3) MD5sum: 135c7538c3bedbe84ae72bd03a015c0f NeedsCompilation: no Title: "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oleś M, Lu J et al. - experimental data and complete analysis Description: The package contains data of the Primary Blood Cancer Encyclopedia (PACE) project together with a complete executable transcript of the statistical analysis and reproduces figures presented in the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oleś M, Lu J et al., J. Clin. Invest. (2018) 128(1):427-445. doi:10.1172/JCI93801. biocViews: ExperimentData, ReproducibleResearch, CancerData, LeukemiaCancerData Author: Małgorzata Oleś, Sascha Dietrich, Junyan Lu, Britta Velten, Andreas Mock, Vladislav Kim, Wolfgang Huber Maintainer: Małgorzata Oleś VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/BloodCancerMultiOmics2017 git_branch: RELEASE_3_22 git_last_commit: f3bf310 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/BloodCancerMultiOmics2017_1.30.0.tar.gz vignettes: vignettes/BloodCancerMultiOmics2017/inst/doc/BloodCancerMultiOmics2017-dataOverview.html, vignettes/BloodCancerMultiOmics2017/inst/doc/BloodCancerMultiOmics2017.html vignetteTitles: BloodCancerMultiOmics2017 - data overview, BloodCancerMultiOmics2017 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BloodCancerMultiOmics2017/inst/doc/BloodCancerMultiOmics2017-dataOverview.R, vignettes/BloodCancerMultiOmics2017/inst/doc/BloodCancerMultiOmics2017.R dependencyCount: 156 Package: bodymapRat Version: 1.26.0 Depends: R (>= 3.6.0), SummarizedExperiment, ExperimentHub Imports: utils Suggests: rmarkdown, knitr, BiocStyle, testthat License: CC BY 4.0 MD5sum: 825fdbd656cc5bc24a37fd86356b6a06 NeedsCompilation: no Title: Experimental dataset from the rat BodyMap project Description: This package contains a SummarizedExperiment from the Yu et al. (2013) paper that performed the rat BodyMap across 11 organs and 4 developmental stages. Raw FASTQ files were downloaded and mapped using STAR. Data is available on ExperimentHub as a data package. biocViews: SequencingData, RNASeqData, ExpressionData, ExperimentData, ExperimentHub Author: Stephanie Hicks [aut, cre] (ORCID: ), Kwame Okrah [aut] Maintainer: Stephanie Hicks VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/bodymapRat git_branch: RELEASE_3_22 git_last_commit: e7d5321 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/bodymapRat_1.26.0.tar.gz vignettes: vignettes/bodymapRat/inst/doc/bodymapRat.html vignetteTitles: The bodymapRat data user's guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bodymapRat/inst/doc/bodymapRat.R suggestsMe: qsmooth dependencyCount: 76 Package: breakpointRdata Version: 1.28.0 Depends: R (>= 3.5) Suggests: knitr, BiocStyle, License: file LICENSE MD5sum: fa35347f784cb59fcdb71533c2ed892d NeedsCompilation: no Title: Strand-seq data for demonstration purposes Description: Strand-seq data to demonstrate functionalities of breakpointR package. biocViews: ExperimentData, Homo_sapiens_Data, SequencingData, DNASeqData, Genome, SingleCellData Author: David Porubsky, Aaron Taudt, Ashley Sanders Maintainer: David Porubsky URL: https://github.com/daewoooo/breakpointRdata VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/breakpointRdata git_branch: RELEASE_3_22 git_last_commit: f0520b3 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/breakpointRdata_1.28.0.tar.gz vignettes: vignettes/breakpointRdata/inst/doc/breakpointRdata-knitr.pdf vignetteTitles: Example data for breakpointR hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/breakpointRdata/inst/doc/breakpointRdata-knitr.R dependsOnMe: breakpointR dependencyCount: 0 Package: breastCancerMAINZ Version: 1.48.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 644b801af61355938b9e9d09dfe579b1 NeedsCompilation: no Title: Gene expression dataset published by Schmidt et al. [2008] (MAINZ). Description: Gene expression data from the breast cancer study published by Schmidt et al. in 2008, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerMAINZ git_branch: RELEASE_3_22 git_last_commit: 28f2680 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/breastCancerMAINZ_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: DART, genefu, MineICA dependencyCount: 0 Package: breastCancerNKI Version: 1.48.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 76fa8ccfbc888d74481f3d988ae081d6 NeedsCompilation: no Title: Genexpression dataset published by van't Veer et al. [2002] and van de Vijver et al. [2002] (NKI). Description: Genexpression data from a breast cancer study published by van't Veer et al. in 2002 and van de Vijver et al. in 2002, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, CGHData, MicroarrayData, OneChannelData, ChipOnChipData Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerNKI git_branch: RELEASE_3_22 git_last_commit: afcb1cb git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/breastCancerNKI_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, SigCheck, seventyGeneData dependencyCount: 0 Package: breastCancerTRANSBIG Version: 1.48.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: cb13abe4403a0071b6bbbbcbbe6d966e NeedsCompilation: no Title: Gene expression dataset published by Desmedt et al. [2007] (TRANSBIG). Description: Gene expression data from a breast cancer study published by Desmedt et al. in 2007, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerTRANSBIG git_branch: RELEASE_3_22 git_last_commit: c232dea git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/breastCancerTRANSBIG_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, GSgalgoR, MineICA dependencyCount: 0 Package: breastCancerUNT Version: 1.48.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: e30d5c6762430747a0371097007e5db5 NeedsCompilation: no Title: Gene expression dataset published by Sotiriou et al. [2007] (UNT). Description: Gene expression data from a breast cancer study published by Sotiriou et al. in 2007, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, TwoChannelData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerUNT git_branch: RELEASE_3_22 git_last_commit: 0d0ead6 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/breastCancerUNT_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu dependencyCount: 0 Package: breastCancerUPP Version: 1.48.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: b7e26ebad69f727a529a5118abd93024 NeedsCompilation: no Title: Gene expression dataset published by Miller et al. [2005] (UPP). Description: Gene expression data from a breast cancer study published by Miller et al. in 2005, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerUPP git_branch: RELEASE_3_22 git_last_commit: cc4bc3b git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/breastCancerUPP_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, GSgalgoR, MineICA, safe dependencyCount: 0 Package: breastCancerVDX Version: 1.48.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: a0573c86b9bcadf46d0e9da24ab2e5fd NeedsCompilation: no Title: Gene expression datasets published by Wang et al. [2005] and Minn et al. [2007] (VDX). Description: Gene expression data from a breast cancer study published by Wang et al. in 2005 and Minn et al. in 2007, provided as an eSet. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData, BreastCancerData, LungCancerData, MicroarrayData, OneChannelData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerVDX git_branch: RELEASE_3_22 git_last_commit: 7c5d586 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/breastCancerVDX_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: BAGS suggestsMe: AIMS, DART, genefu, MineICA dependencyCount: 0 Package: brgedata Version: 1.32.0 Depends: R (>= 3.5.0), Biobase Imports: SummarizedExperiment Suggests: minfi, MultiAssayExperiment, knitr, rmarkdown, rexposome, BiocStyle License: MIT + file LICENSE MD5sum: c0161d5a1d8d9193dee153b7fe69e687 NeedsCompilation: no Title: Exposures, Gene Expression and Methylation data for ilustration purpouses Description: This package contains several sets of omics data including Gene Expression (ExpressionSet), Methylation (GenomicRatioSet), Proteome and Exposome (ExposomeSet). This data is used in vignettes and exaples at MEAL, MultiDataSet and omicRexposome. biocViews: ExperimentData,Homo_sapiens_Data,MicroarrayData,MethylationArrayData Author: Dolors Pelegri-Siso [aut, cre], Carlos Ruiz-Arenas [aut], Carles Hernandez-Ferrer [aut], Juan R. Gonzalez [aut] Maintainer: Dolors Pelegri-Siso VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/brgedata git_branch: RELEASE_3_22 git_last_commit: bbf0386 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/brgedata_1.32.0.tar.gz vignettes: vignettes/brgedata/inst/doc/general_description.html vignetteTitles: brgedata -- data R package with three omic data-set and exposome data-set from the same Spanish pupulation hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/brgedata/inst/doc/general_description.R suggestsMe: MEAL, MultiDataSet, omicRexposome dependencyCount: 25 Package: bronchialIL13 Version: 1.48.0 Depends: R(>= 2.10.0), affy (>= 1.23.4) License: GPL-2 MD5sum: 15034b65fd67f5f5d0260c932655edc7 NeedsCompilation: no Title: time course experiment involving il13 Description: derived from CNMC (pepr.cnmcresearch.org) http://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=95 Human Bronchial Cell line A549 biocViews: ExperimentData, MicroarrayData Author: Vince Carey Maintainer: Vince Carey URL: http://www.biostat.harvard.edu/~carey git_url: https://git.bioconductor.org/packages/bronchialIL13 git_branch: RELEASE_3_22 git_last_commit: 818c46b git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/bronchialIL13_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 12 Package: bsseqData Version: 0.48.0 Depends: R (>= 3.5.0), bsseq (>= 1.16.0) License: Artistic-2.0 MD5sum: 31b372e16d1b973237af24163d0b9fad NeedsCompilation: no Title: Example whole genome bisulfite data for the bsseq package Description: Example whole genome bisulfite data for the bsseq package biocViews: Genome, CancerData, ColonCancerData, SequencingData Author: Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/bsseqData git_branch: RELEASE_3_22 git_last_commit: 9ebed48 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/bsseqData_0.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: bsseq, methylSig dependencyCount: 87 Package: bugphyzz Version: 1.4.0 Depends: R (>= 4.4) Imports: dplyr, utils, purrr, stringr, tidyr, tidyselect, BiocFileCache, httr2, tools, S4Vectors Suggests: DT, forcats, ggplot2, htmltools, knitr, rmarkdown, sessioninfo, testthat, EnrichmentBrowser, MicrobiomeBenchmarkData, mia, stats, rlang, limma, mgsub, methods, readr, crayon, tibble, magrittr, tidytext, BiocStyle License: Artistic-2.0 MD5sum: 75f1f75cc148fd969355f7864ecec8c6 NeedsCompilation: no Title: A harmonized data resource and software for enrichment analysis of microbial physiologies Description: bugphyzz is an electronic database of standardized microbial annotations. It facilitates the creation of microbial signatures based on shared attributes, which are utilized for bug set enrichment analysis. The data also includes annotations imputed with ancestra state reconstruction methods. biocViews: MicrobiomeData, ReproducibleResearch Author: Samuel Gamboa [aut, cre] (ORCID: ), Levi Waldron [aut] (ORCID: ), Kelly Eckenrode [aut], Jonathan Ye [aut], Jennifer Wokaty [aut] Maintainer: Samuel Gamboa URL: https://github.com/waldronlab/bugphyzz VignetteBuilder: knitr BugReports: https://github.com/waldronlab/bugphyzz/issues git_url: https://git.bioconductor.org/packages/bugphyzz git_branch: RELEASE_3_22 git_last_commit: 1ab92d5 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/bugphyzz_1.4.0.tar.gz vignettes: vignettes/bugphyzz/inst/doc/bugphyzz.html, vignettes/bugphyzz/inst/doc/sources.html vignetteTitles: bugphyzz, Sources hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bugphyzz/inst/doc/bugphyzz.R, vignettes/bugphyzz/inst/doc/sources.R dependencyCount: 47 Package: cancerdata Version: 1.48.0 Depends: R (>= 2.10.1), Biobase License: GPL (>= 2) MD5sum: 2ca7be70aa288d9b665f5c55a1040f40 NeedsCompilation: no Title: Development and validation of diagnostic tests from high-dimensional molecular data: Datasets Description: Dataset for the R package cancerclass biocViews: CancerData, MicroarrayData Author: Jan Budczies, Daniel Kosztyla Maintainer: Daniel Kosztyla git_url: https://git.bioconductor.org/packages/cancerdata git_branch: RELEASE_3_22 git_last_commit: d5f9e37 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/cancerdata_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: cancerclass dependencyCount: 7 Package: CardinalWorkflows Version: 1.42.0 Depends: R (>= 2.10), Cardinal, methods Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: e8808bc3cc9f03737d66e2a117ddc817 NeedsCompilation: no Title: Datasets and workflows for the Cardinal MSI Description: Datasets and workflows for Cardinal: DESI and MALDI examples including pig fetus, cardinal painting, and human RCC. biocViews: ExperimentData, MassSpectrometryData, ImagingMassSpectrometryData Author: Kylie A. Bemis Maintainer: Kylie A. Bemis VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/CardinalWorkflows git_branch: RELEASE_3_22 git_last_commit: d7ae39f git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/CardinalWorkflows_1.42.0.tar.gz vignettes: vignettes/CardinalWorkflows/inst/doc/MSI-classification.html, vignettes/CardinalWorkflows/inst/doc/MSI-segmentation.html, vignettes/CardinalWorkflows/inst/doc/MSI-testing.html vignetteTitles: 2. Classification: Supervised analysis workflow, 1. Segmentation: Unsupervised analysis workflow, 3. Class comparision: Statistical testing workflow hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CardinalWorkflows/inst/doc/MSI-classification.R, vignettes/CardinalWorkflows/inst/doc/MSI-segmentation.R, vignettes/CardinalWorkflows/inst/doc/MSI-testing.R dependencyCount: 67 Package: ccdata Version: 1.36.0 Depends: R (>= 3.3) License: MIT + file LICENSE MD5sum: 5820fb0bb2a8f11a46330cbcf5f00ed9 NeedsCompilation: no Title: Data for Combination Connectivity Mapping (ccmap) Package Description: This package contains microarray gene expression data generated from the Connectivity Map build 02 and LINCS l1000. The data are used by the ccmap package to find drugs and drug combinations to mimic or reverse a gene expression signature. biocViews: ExperimentData, MicroarrayData, ExpressionData Author: Alex Pickering Maintainer: Alex Pickering git_url: https://git.bioconductor.org/packages/ccdata git_branch: RELEASE_3_22 git_last_commit: f1f8d1c git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/ccdata_1.36.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: retriever dependencyCount: 0 Package: CCl4 Version: 1.48.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), limma License: Artistic-2.0 MD5sum: cfc9c3fa02259369155c8cda10d36489 NeedsCompilation: no Title: Carbon Tetrachloride (CCl4) treated hepatocytes Description: NChannelSet for rat hepatocytes treated with Carbon Tetrachloride (CCl4) data from LGC company. biocViews: ExperimentData, Genome, Rattus_norvegicus_Data, MicroarrayData Author: Audrey Kauffmann, Wolfgang Huber Maintainer: Audrey Kauffmann git_url: https://git.bioconductor.org/packages/CCl4 git_branch: RELEASE_3_22 git_last_commit: db6abcd git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/CCl4_1.48.0.tar.gz vignettes: vignettes/CCl4/inst/doc/CCl4.pdf vignetteTitles: CCl4 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CCl4/inst/doc/CCl4.R dependencyCount: 10 Package: celarefData Version: 1.28.0 Depends: R (>= 3.5.0) Suggests: ExperimentHub, knitr, rmarkdown License: GPL-3 MD5sum: 0f2c543bcd8aa4882fc1d4075d0dd0f8 NeedsCompilation: no Title: Processed scRNA data for celaref Vignette - cell labelling by reference Description: This experiment data contains some processed data used in the celaref package vignette. These are publically available datasets, that have been processed by celaref package, and can be manipulated further with it. biocViews: ExperimentData, SingleCellData, ExperimentHub Author: Sarah Williams [aut, cre] Maintainer: Sarah Williams VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/celarefData git_branch: RELEASE_3_22 git_last_commit: 718ab5d git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/celarefData_1.28.0.tar.gz vignettes: vignettes/celarefData/inst/doc/celarefData.html vignetteTitles: Manual hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/celarefData/inst/doc/celarefData.R dependencyCount: 0 Package: celldex Version: 1.20.0 Depends: SummarizedExperiment Imports: utils, methods, Matrix, ExperimentHub, AnnotationHub, AnnotationDbi, S4Vectors, DelayedArray, DelayedMatrixStats, gypsum, alabaster.base, alabaster.matrix, alabaster.se, DBI, RSQLite, jsonlite Suggests: testthat, knitr, rmarkdown, BiocStyle, DT, jsonvalidate, BiocManager, ensembldb License: GPL-3 MD5sum: 1eadf60bc18c8eb51a86ca0140bb9329 NeedsCompilation: no Title: Index of Reference Cell Type Datasets Description: Provides a collection of reference expression datasets with curated cell type labels, for use in procedures like automated annotation of single-cell data or deconvolution of bulk RNA-seq. biocViews: ExperimentHub, ExperimentData, ExpressionData, SequencingData, RNASeqData Author: Dvir Aran [aut], Aaron Lun [aut, cre, cph], Daniel Bunis [aut], Jared Andrews [aut], Friederike Dündar [aut] Maintainer: Aaron Lun URL: https://github.com/LTLA/celldex VignetteBuilder: knitr BugReports: https://support.bioconductor.org/ git_url: https://git.bioconductor.org/packages/celldex git_branch: RELEASE_3_22 git_last_commit: 4db42c8 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/celldex_1.20.0.tar.gz vignettes: vignettes/celldex/inst/doc/userguide.html vignetteTitles: Cell type references hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/celldex/inst/doc/userguide.R dependsOnMe: OSCA.basic, OSCA.workflows, SingleRBook importsMe: singleCellTK, scPipeline suggestsMe: ontoProc, scDiagnostics, scGraphVerse, SingleR, sketchR, tidySingleCellExperiment dependencyCount: 94 Package: CellMapperData Version: 1.36.0 Depends: ExperimentHub, CellMapper Suggests: BiocStyle License: Artistic-2.0 MD5sum: 2bae6c728f262cf6810e80c0757fe9f2 NeedsCompilation: no Title: Pre-processed data for use with the CellMapper package Description: Experiment data package. Contains microarray data from several large expression compendia that have been pre-processed for use with the CellMapper package. This pre-processed data is recommended for routine searches using the CellMapper package. biocViews: ExperimentData, MicroarrayData, ExpressionData Author: Brad Nelms Maintainer: Brad Nelms git_url: https://git.bioconductor.org/packages/CellMapperData git_branch: RELEASE_3_22 git_last_commit: 7ef858f git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/CellMapperData_1.36.0.tar.gz vignettes: vignettes/CellMapperData/inst/doc/CellMapperData.pdf vignetteTitles: CellMapperData Introduction hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CellMapperData/inst/doc/CellMapperData.R suggestsMe: CellMapper dependencyCount: 66 Package: CENTREprecomputed Version: 1.0.0 Depends: R (>= 4.5.0) Imports: ExperimentHub, RSQLite, DBI, BiocGenerics, methods Suggests: knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: 5a04e3e96c7d67365e3be804858fe41d NeedsCompilation: no Title: Hub package for the precomputed data of CENTRE and example data Description: Interface and documentation for the Experiment Hub records needed by the CENTRE Bioconductor software package. The Experiment Hub records contains the precomputed fisher combined p-values, CRUP correlations. Additionally, the records hold ChIP-seq and RNA-seq data used for the example of the software package. biocViews: ExperimentData, PackageTypeData, ExperimentHub, RNASeqData, ChIPSeqData, ChipOnChipData Author: Sara Lopez Ruiz de Vargas [aut, cre] (ORCID: ) Maintainer: Sara Lopez Ruiz de Vargas URL: https://github.com/slrvv/CENTREprecomputed VignetteBuilder: knitr BugReports: https://github.com/slrvv/CENTREprecomputed/issues git_url: https://git.bioconductor.org/packages/CENTREprecomputed git_branch: RELEASE_3_22 git_last_commit: 8836e4f git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/CENTREprecomputed_1.0.0.tar.gz vignettes: vignettes/CENTREprecomputed/inst/doc/CENTREprecomputed.html vignetteTitles: CENTRE ExperimentHub datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CENTREprecomputed/inst/doc/CENTREprecomputed.R dependencyCount: 65 Package: cfToolsData Version: 1.8.0 Depends: R (>= 4.3.0) Imports: utils, ExperimentHub Suggests: BiocStyle, knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0) License: file LICENSE MD5sum: 81d37c774c7126eaa9f5d76107a89aa6 NeedsCompilation: no Title: ExperimentHub data for the cfTools package Description: The cfToolsData package supplies the data for the cfTools package. It contains two pre-trained deep neural network (DNN) models for the cfSort function. Additionally, it includes the shape parameters of beta distribution characterizing methylation markers associated with four tumor types for the CancerDetector function, as well as the parameters characterizing methylation markers specific to 29 primary human tissue types for the cfDeconvolve function. biocViews: ExperimentHub, ExperimentData, ReproducibleResearch, DiseaseModel, CancerData, Tissue Author: Ran Hu [aut, cre] (ORCID: ), Shuo Li [aut] (ORCID: ), Xianghong Jasmine Zhou [aut] (ORCID: ), Wenyuan Li [aut] (ORCID: ) Maintainer: Ran Hu URL: https://github.com/jasminezhoulab/cfToolsData VignetteBuilder: knitr BugReports: https://github.com/jasminezhoulab/cfToolsData/issues git_url: https://git.bioconductor.org/packages/cfToolsData git_branch: RELEASE_3_22 git_last_commit: d98a4c0 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/cfToolsData_1.8.0.tar.gz vignettes: vignettes/cfToolsData/inst/doc/cfToolsData.html vignetteTitles: cfToolsData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/cfToolsData/inst/doc/cfToolsData.R importsMe: cfTools dependencyCount: 65 Package: ChAMPdata Version: 2.42.0 Depends: R (>= 3.5.0), GenomicRanges (>= 1.22.4), BiocGenerics (>= 0.16.1) License: GPL-3 MD5sum: ff746bdbeb7ff7fe54608cc46f6674ee NeedsCompilation: no Title: Data Packages for ChAMP package Description: Provides datasets needed for ChAMP including a test dataset and blood controls for CNA analysis. biocViews: ExperimentData Author: Yuan Tian [ctb,aut], Tiffany Morris [cre,aut], Lee Stirling [ctb] and Andrew Teschendorff [ctb] Maintainer: Yuan Tian git_url: https://git.bioconductor.org/packages/ChAMPdata git_branch: RELEASE_3_22 git_last_commit: 6d429ca git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/ChAMPdata_2.42.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ChAMP, methyLImp2 dependencyCount: 11 Package: ChimpHumanBrainData Version: 1.48.0 Depends: affy,qvalue,limma,hexbin,statmod Suggests: hgu95av2cdf License: MIT MD5sum: 89b9e3257d71ebd66fb485929db386af NeedsCompilation: no Title: Chimp and human brain data package Description: This data package contains chimp and human brain data extracted from the ArrayExpress accession E-AFMX-2. Both human and chimp RNAs were run on human hgu95av2 Affymetrix arrays. It is a useful dataset for tutorials. biocViews: Tissue, Homo_sapiens_Data, Pan_troglodytes_Data, MicroarrayData, TissueMicroarrayData, GEO Author: Roman Jaksik, Naomi Altman, and Sean Davis Maintainer: Sean Davis git_url: https://git.bioconductor.org/packages/ChimpHumanBrainData git_branch: RELEASE_3_22 git_last_commit: 8b57865 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/ChimpHumanBrainData_1.48.0.tar.gz vignettes: vignettes/ChimpHumanBrainData/inst/doc/DiffExpressVignette.pdf vignetteTitles: DiffExpressVignette.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ChimpHumanBrainData/inst/doc/DiffExpressVignette.R dependencyCount: 42 Package: ChIPDBData Version: 1.0.0 Imports: ExperimentHub Suggests: knitr, rmarkdown, BiocStyle, AnnotationHub, TFEA.ChIP, DESeq2, testthat (>= 3.0.0) License: GPL-3 MD5sum: 295a4c79c486d573ab64b69c2a917f0e NeedsCompilation: no Title: ChIP-seq Target Databases for TFEA.ChIP Description: Provides curated gene target databases derived from ChIP-seq datasets, formatted as ChIPDB objects for use with TFEA.ChIP. biocViews: ExperimentData, ExperimentHub, Homo_sapiens_Data, ENCODE, SequencingData Author: Yosra Berrouayel [aut, cre] (ORCID: ), Luis del Peso [aut] (ORCID: ) Maintainer: Yosra Berrouayel URL: https://github.com/yberda/ChIPDBData VignetteBuilder: knitr BugReports: https://github.com/yberda/ChIPDBData/issues git_url: https://git.bioconductor.org/packages/ChIPDBData git_branch: RELEASE_3_22 git_last_commit: 5162621 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/ChIPDBData_1.0.0.tar.gz vignettes: vignettes/ChIPDBData/inst/doc/using_chipdb.html vignetteTitles: Using ChIPDBData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ChIPDBData/inst/doc/using_chipdb.R dependencyCount: 65 Package: chipenrich.data Version: 2.34.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, BiocGenerics, methods, GenomicRanges, GenomeInfoDb, IRanges, readr, rtracklayer, S4Vectors, utils Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat, GO.db, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene License: GPL-3 MD5sum: 9ae260b2b8cced3fd2f469ca2d35c894 NeedsCompilation: no Title: Companion package to chipenrich Description: Supporting data for the chipenrich package. Includes pre-defined gene sets, gene locus definitions, and mappability estimates. biocViews: ChIPSeq, Epigenetics, FunctionalGenomics, GeneSetEnrichment, HistoneModification, Regression Author: Ryan P. Welch [aut, cph], Chee Lee [aut], Raymond G. Cavalcante [aut], Kai Wang [cre], Laura J. Scott [ths], Maureen A. Sartor [ths] Maintainer: Kai Wang VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/chipenrich.data git_branch: RELEASE_3_22 git_last_commit: cedd925 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/chipenrich.data_2.34.0.tar.gz vignettes: vignettes/chipenrich.data/inst/doc/chipenrich.data-vignette.html vignetteTitles: chipenrich.data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/chipenrich.data/inst/doc/chipenrich.data-vignette.R importsMe: chipenrich dependencyCount: 90 Package: ChIPexoQualExample Version: 1.34.0 Depends: R (>= 3.3) Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: fb7da1e295a4f3a31fae4ab479389168 NeedsCompilation: no Title: Example data for the ChIPexoQual package, which implements a quality control pipeline for ChIP-exo data Description: Data for the ChIPexoQual package, consisting of (3) chromosome 1 aligned reads from a ChIP-exo experiment for FoxA1 in mouse liver cell lines aligned to the mm9 genome. biocViews: ExperimentData, Genome Author: Rene Welch, Dongjun Chung, Sunduz Keles Maintainer: Rene Welch URL: http://www.github.com/keleslab/ChIPexoQualExample VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ChIPexoQualExample git_branch: RELEASE_3_22 git_last_commit: 320ba6e git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/ChIPexoQualExample_1.34.0.tar.gz vignettes: vignettes/ChIPexoQualExample/inst/doc/vignette.html vignetteTitles: ChIPexoQualExample hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ChIPexoQualExample/inst/doc/vignette.R suggestsMe: ChIPexoQual dependencyCount: 0 Package: chipseqDBData Version: 1.26.0 Imports: AnnotationHub, ExperimentHub, Rsamtools, S4Vectors Suggests: knitr, BiocStyle, rmarkdown License: CC BY 4.0 MD5sum: 02d0f6a84651149c704c509431eb8974 NeedsCompilation: no Title: Data for the chipseqDB Workflow Description: Sorted and indexed BAM files for ChIP-seq libraries, for use in the chipseqDB workflow. BAM indices are also included. biocViews: SequencingData, ChIPSeqData, ExperimentHub Author: Aaron Lun [aut, cre] Maintainer: Aaron Lun VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/chipseqDBData git_branch: RELEASE_3_22 git_last_commit: 05d1333 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/chipseqDBData_1.26.0.tar.gz vignettes: vignettes/chipseqDBData/inst/doc/chipseqDBData.html vignetteTitles: File manifest and statistics hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/chipseqDBData/inst/doc/chipseqDBData.R dependsOnMe: csawBook suggestsMe: chipseqDB dependencyCount: 78 Package: ChIPXpressData Version: 1.48.0 Depends: bigmemory License: GPL (>=2) MD5sum: 141472a85d958964e7b3c601f84f615a NeedsCompilation: no Title: ChIPXpress Pre-built Databases Description: Contains pre-built mouse (GPL1261) and human (GPL570) database of gene expression profiles to be used for ChIPXpress ranking. biocViews: Homo_sapiens_Data, Mus_musculus_Data, GEO Author: George Wu Maintainer: George Wu git_url: https://git.bioconductor.org/packages/ChIPXpressData git_branch: RELEASE_3_22 git_last_commit: d1a6774 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/ChIPXpressData_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ChIPXpress dependencyCount: 7 Package: chromstaRData Version: 1.36.0 Depends: R (>= 3.3) License: GPL-3 MD5sum: 1e988e76901f0fee8e11ac1a83d3285b NeedsCompilation: no Title: ChIP-seq data for Demonstration Purposes Description: ChIP-seq data for demonstration purposes in the chromstaR package. biocViews: Mus_musculus_Data, StemCell, ChIPSeqData Author: Aaron Taudt Maintainer: Aaron Taudt PackageStatus: Deprecated git_url: https://git.bioconductor.org/packages/chromstaRData git_branch: RELEASE_3_22 git_last_commit: 98b94a9 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/chromstaRData_1.36.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: epigraHMM dependencyCount: 0 Package: CLL Version: 1.50.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: LGPL MD5sum: 298e32fa59127eb55289cf6f71104007 NeedsCompilation: no Title: A Package for CLL Gene Expression Data Description: The CLL package contains the chronic lymphocytic leukemia (CLL) gene expression data. The CLL data had 24 samples that were either classified as progressive or stable in regards to disease progression. The data came from Dr. Sabina Chiaretti at Division of Hematology, Department of Cellular Biotechnologies and Hematology, University La Sapienza, Rome, Italy and Dr. Jerome Ritz at Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts. biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData Author: Elizabeth Whalen Maintainer: Robert Gentleman git_url: https://git.bioconductor.org/packages/CLL git_branch: RELEASE_3_22 git_last_commit: 86106a6 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/CLL_1.50.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: phenomis dependencyCount: 12 Package: CLLmethylation Version: 1.30.0 Depends: R (>= 3.5.0) Imports: SummarizedExperiment, ExperimentHub Suggests: BiocStyle, ggplot2, knitr, rmarkdown License: LGPL MD5sum: 5c75d23260ddd5a915be434d3bf1a6ad NeedsCompilation: no Title: Methylation data of primary CLL samples in PACE project Description: The package includes DNA methylation data for the primary Chronic Lymphocytic Leukemia samples included in the Primary Blood Cancer Encyclopedia (PACE) project. Raw data from the 450k DNA methylation arrays is stored in the European Genome-Phenome Archive (EGA) under accession number EGAS0000100174. For more information concerning the project please refer to the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) and R/Bioconductor package BloodCancerMultiOmics2017. biocViews: ExperimentData, DiseaseModel, CancerData, LeukemiaCancerData Author: Malgorzata Oles, Andreas Mock Maintainer: Malgorzata Oles , Andreas Mock VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/CLLmethylation git_branch: RELEASE_3_22 git_last_commit: 601a33b git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/CLLmethylation_1.30.0.tar.gz vignettes: vignettes/CLLmethylation/inst/doc/CLLmethylation.html vignetteTitles: CLLmethylation hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CLLmethylation/inst/doc/CLLmethylation.R dependencyCount: 76 Package: CluMSIDdata Version: 1.26.0 Depends: R (>= 3.6) License: MIT + file LICENSE MD5sum: f246197291d7d0ed8166387470c78022 NeedsCompilation: no Title: Data for the CluMSID package Description: This package contains various LC-MS/MS and GC-MS data that is used in vignettes and examples in the CluMSID package. biocViews: ExperimentData, MassSpectrometryData Author: Tobias Depke [aut, cre] Maintainer: Tobias Depke git_url: https://git.bioconductor.org/packages/CluMSIDdata git_branch: RELEASE_3_22 git_last_commit: 073a7ab git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/CluMSIDdata_1.26.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: CluMSID dependencyCount: 0 Package: clustifyrdatahub Version: 1.20.0 Depends: R (>= 4.0), ExperimentHub Imports: utils Suggests: clustifyr, Seurat, usethis, rmarkdown, knitr, tidyr, BiocStyle License: MIT + file LICENSE MD5sum: 601e70df7ea28b4be3a7a1a16c5302dd NeedsCompilation: no Title: External data sets for clustifyr in ExperimentHub Description: References made from external single-cell mRNA sequencing data sets, stored as average gene expression matrices. For use with clustifyr to assign cell type identities. biocViews: SingleCellData, SequencingData, MicroarrayData, ExperimentHub, RNASeqData, PackageTypeData, ExpressionData Author: Rui Fu [aut] (ORCID: ), Kent Riemondy [aut, cre] (ORCID: ), RNA Bioscience Initiative [fnd], Austin Gillen [ctb] (ORCID: ), Jay Hesselberth [ctb] (ORCID: ), Sidhant Puntambekar [ctb] Maintainer: Kent Riemondy URL: https://rnabioco.github.io/clustifyrdatahub/ VignetteBuilder: knitr BugReports: https://github.com/rnabioco/clustifyrdatahub/issues git_url: https://git.bioconductor.org/packages/clustifyrdatahub git_branch: RELEASE_3_22 git_last_commit: d009ec9 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/clustifyrdatahub_1.20.0.tar.gz vignettes: vignettes/clustifyrdatahub/inst/doc/clustifyrdatahub.html vignetteTitles: clustifyrdatahub hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/clustifyrdatahub/inst/doc/clustifyrdatahub.R dependencyCount: 65 Package: cMap2data Version: 1.46.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 20f78b173f29c2e53fb200108d0ad847 NeedsCompilation: no Title: Connectivity Map (version 2) Data Description: Data package which provides default drug profiles for the DrugVsDisease package as well as associated gene lists and data clusters used by the DrugVsDisease package. biocViews: Homo_sapiens_Data, MicroarrayData, GEO Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/cMap2data git_branch: RELEASE_3_22 git_last_commit: 54aa85c git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/cMap2data_1.46.0.tar.gz vignettes: vignettes/cMap2data/inst/doc/cMap2data.pdf vignetteTitles: cMap2data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cMap2data/inst/doc/cMap2data.R dependsOnMe: DrugVsDisease dependencyCount: 0 Package: cnvGSAdata Version: 1.46.0 Depends: R (>= 2.10), cnvGSA License: LGPL MD5sum: 7a8deb4733232ed05e27a3cfe3f6a69b NeedsCompilation: no Title: Data used in the vignette of the cnvGSA package Description: This package contains the data used in the vignette of the cnvGSA package. biocViews: ExperimentData, Genome, CopyNumberVariationData Author: Joseph Lugo Maintainer: Joseph Lugo git_url: https://git.bioconductor.org/packages/cnvGSAdata git_branch: RELEASE_3_22 git_last_commit: 240c53e git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/cnvGSAdata_1.46.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: cnvGSA dependencyCount: 21 Package: COHCAPanno Version: 1.46.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: bbcddeb690cddcc7e8d4080e1dc1a26e NeedsCompilation: no Title: Annotations for City of Hope CpG Island Analysis Pipeline Description: Provides genomic location, nearby CpG island and nearby gene information for common Illumina methylation array platforms biocViews: Homo_sapiens_Data, MicroarrayData, MethylationArrayData, CpGIslandData, GEO, ArrayExpress Author: Charles Warden Maintainer: Charles Warden git_url: https://git.bioconductor.org/packages/COHCAPanno git_branch: RELEASE_3_22 git_last_commit: 5c46a13 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/COHCAPanno_1.46.0.tar.gz vignettes: vignettes/COHCAPanno/inst/doc/COHCAPanno.pdf vignetteTitles: COHCAPanno Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/COHCAPanno/inst/doc/COHCAPanno.R dependencyCount: 0 Package: colonCA Version: 1.52.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: 680f2e1d80d016a50d53ef313a313e82 NeedsCompilation: no Title: exprSet for Alon et al. (1999) colon cancer data Description: exprSet for Alon et al. (1999) colon cancer data biocViews: ExperimentData, Tissue, CancerData, ColonCancerData, MicroarrayData, TissueMicroarrayData Author: Sylvia Merk Maintainer: W Sylvia Merk git_url: https://git.bioconductor.org/packages/colonCA git_branch: RELEASE_3_22 git_last_commit: 44fe793 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/colonCA_1.52.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: clustComp, copa dependencyCount: 7 Package: CONFESSdata Version: 1.38.0 Depends: R (>= 3.3) License: GPL-2 MD5sum: 386b7bb0ce9d707af0b35466f282b2cc NeedsCompilation: no Title: Example dataset for CONFESS package Description: Example text-converted C01 image files for use in the CONFESS Bioconductor package. biocViews: HighThroughputImagingData,CellCulture,Homo_sapiens_Data,ExpressionData Author: Diana LOW and Efthimios MOTAKIS Maintainer: Diana LOW git_url: https://git.bioconductor.org/packages/CONFESSdata git_branch: RELEASE_3_22 git_last_commit: 98e3733 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/CONFESSdata_1.38.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CONFESS dependencyCount: 0 Package: ConnectivityMap Version: 1.46.0 Depends: R (>= 2.15.1) Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: d6898ee09c8a5f206a37d883863dfbc6 NeedsCompilation: no Title: Functional connections between drugs, genes and diseases as revealed by common gene-expression changes Description: The Broad Institute's Connectivity Map (cmap02) is a "large reference catalogue of gene-expression data from cultured human cells perturbed with many chemicals and genetic reagents", containing more than 7000 gene expression profiles and 1300 small molecules. biocViews: ExperimentData, CancerData, MicroarrayData Author: Paul Shannon Maintainer: Paul Shannon git_url: https://git.bioconductor.org/packages/ConnectivityMap git_branch: RELEASE_3_22 git_last_commit: 184b3e3 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/ConnectivityMap_1.46.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: COPDSexualDimorphism.data Version: 1.46.0 License: LGPL-2.1 MD5sum: a8267a6ab7ec8e47d2017e19f4c5923c NeedsCompilation: no Title: Data to support sexually dimorphic and COPD differential analysis for gene expression and methylation. Description: Datasets to support COPDSexaulDimorphism Package. biocViews: ExperimentData, Tissue, COPDData Author: J Fah Sathirapongsasuti Maintainer: J Fah Sathirapongsasuti git_url: https://git.bioconductor.org/packages/COPDSexualDimorphism.data git_branch: RELEASE_3_22 git_last_commit: 572b6d3 git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/COPDSexualDimorphism.data_1.46.0.tar.gz vignettes: vignettes/COPDSexualDimorphism.data/inst/doc/lgrc_data.pdf vignetteTitles: SDCD Genes hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/COPDSexualDimorphism.data/inst/doc/lgrc_data.R dependencyCount: 0 Package: CopyhelpeR Version: 1.42.0 Depends: R (>= 3.5.0) Suggests: BiocStyle License: GPL-2 MD5sum: b9f5438729eae6249a8bca92eba497cc NeedsCompilation: no Title: Helper files for CopywriteR Description: This package contains the helper files that are required to run the Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content and mappability files for the reference genomes hg18, hg19, hg38, mm9 and mm10. In addition, it contains a blacklist filter to remove regions that display CNV. Files are stored as GRanges objects from the GenomicRanges Bioconductor package. biocViews: Homo_sapiens, GenomicSequence Author: Thomas Kuilman Maintainer: Oscar Krijgsman git_url: https://git.bioconductor.org/packages/CopyhelpeR git_branch: RELEASE_3_22 git_last_commit: f68a93d git_last_commit_date: 2025-10-29 Date/Publication: 2025-10-30 source.ver: src/contrib/CopyhelpeR_1.42.0.tar.gz vignettes: vignettes/CopyhelpeR/inst/doc/CopyhelpeR.pdf vignetteTitles: CopyhelpeR hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CopyhelpeR/inst/doc/CopyhelpeR.R dependencyCount: 0 Package: CopyNeutralIMA Version: 1.28.0 Depends: R (>= 3.5.0) Imports: ExperimentHub,Rdpack (>= 0.8) Suggests: BiocStyle,knitr,rmarkdown,minfi,conumee,minfiData License: Artistic-2.0 MD5sum: 65bb4adc70f2e05b8436f46748c5f1ae NeedsCompilation: no Title: Copy Neutral Illumina Methylation Arrays Description: Provides a set of genomic copy neutral samples hybridized using Illumina Methylation arrays (450k and EPIC). biocViews: ExperimentData,Homo_sapiens_Data,MicroarrayData,TwoChannelData,MethylationArrayData,GEO Author: Xavier Pastor Hostench [aut, cre], Moritz Przybilla [aut] Maintainer: Xavier Pastor Hostench VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/CopyNeutralIMA git_branch: RELEASE_3_22 git_last_commit: 5c282f0 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/CopyNeutralIMA_1.28.0.tar.gz vignettes: vignettes/CopyNeutralIMA/inst/doc/CopyNeutralIMA.html vignetteTitles: CopyNeutralIMA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CopyNeutralIMA/inst/doc/CopyNeutralIMA.R dependencyCount: 67 Package: CoSIAdata Version: 1.10.0 Depends: R (>= 4.3.0), ExperimentHub (>= 2.6.0), Suggests: BiocStyle (>= 2.26.0), utils (>= 4.3.0), AnnotationHub (>= 3.7.3), knitr (>= 1.42) License: MIT + file LICENSE MD5sum: 9eee619349e93785aa51951ccd8eeec6 NeedsCompilation: no Title: VST normalized RNA-Sequencing data with annotations for multiple species samples from Bgee Description: Variance Stabilized Transformation of Read Counts derived from Bgee RNA-Seq Expression Data. Expression Data includes annotations and is across 6 species (Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Drosophila melanogaster, and Caenorhabditis elegans) and across more than 132 tissues. The data is represented as a RData files and is available in ExperimentHub. biocViews: ExperimentHub, RNASeqData, ExperimentData, PackageTypeData, OrganismData, Tissue,Caenorhabditis_elegans_Data, Danio_rerio_Data, Drosophila_melanogaster_Data, Homo_sapiens_Data, Mus_musculus_Data, Rattus_norvegicus_Data, SequencingData, ExpressionData Author: Anisha Haldar [aut] (ORCID: ), Vishal H. Oza [aut] (ORCID: ), Amanda D. Clark [cre, aut] (ORCID: ), Nathaniel S. DeVoss [aut] (ORCID: ), Brittany N. Lasseigne [aut] (ORCID: ) Maintainer: Amanda D. Clark VignetteBuilder: knitr BugReports: https://github.com/lasseignelab/CoSIAdata/issues git_url: https://git.bioconductor.org/packages/CoSIAdata git_branch: RELEASE_3_22 git_last_commit: df39cc7 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/CoSIAdata_1.10.0.tar.gz vignettes: vignettes/CoSIAdata/inst/doc/CoSIAdata_vignette.html vignetteTitles: CoSIAdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/CoSIAdata/inst/doc/CoSIAdata_vignette.R dependencyCount: 65 Package: COSMIC.67 Version: 1.46.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, SummarizedExperiment, VariantAnnotation Suggests: testthat, BiocStyle, knitr License: GPL-3 MD5sum: e9ebd6fa9517d7ee8ab12d3807a9155d NeedsCompilation: no Title: COSMIC.67 Description: COSMIC: Catalogue Of Somatic Mutations In Cancer, version 67 (2013-10-24) biocViews: ExperimentData, Genome, CancerData Author: Julian Gehring Maintainer: Julian Gehring VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/COSMIC.67 git_branch: RELEASE_3_22 git_last_commit: 921cb75 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/COSMIC.67_1.46.0.tar.gz vignettes: vignettes/COSMIC.67/inst/doc/COSMIC.67.pdf vignetteTitles: COSMIC.67 - PDF hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/COSMIC.67/inst/doc/COSMIC.67.R importsMe: appreci8R dependencyCount: 78 Package: CRCL18 Version: 1.30.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 56724ce01989cfad8ef160ffa543c0b1 NeedsCompilation: no Title: CRC cell line dataset Description: colorectal cancer mRNA and miRNA on 18 cell lines biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/CRCL18 git_branch: RELEASE_3_22 git_last_commit: 96421a6 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/CRCL18_1.30.0.tar.gz vignettes: vignettes/CRCL18/inst/doc/CRCL18Vignette.pdf vignetteTitles: CRCL18 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CRCL18/inst/doc/CRCL18Vignette.R dependencyCount: 7 Package: crisprScoreData Version: 1.14.0 Depends: ExperimentHub Imports: AnnotationHub, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: a74750952b35b5b7e7ee386004f5fad7 NeedsCompilation: no Title: Pre-trained models for the crisprScore package Description: Provides an interface to access pre-trained models for on-target and off-target gRNA activity prediction algorithms implemented in the crisprScore package. Pre-trained model data are stored in the ExperimentHub database. Users should consider using the crisprScore package directly to use and load the pre-trained models. biocViews: ExperimentHub, Homo_sapiens_Data Author: Jean-Philippe Fortin [aut, cre, cph] Maintainer: Jean-Philippe Fortin URL: https://github.com/crisprVerse/crisprScoreData/issues VignetteBuilder: knitr BugReports: https://github.com/crisprVerse/crisprScoreData git_url: https://git.bioconductor.org/packages/crisprScoreData git_branch: RELEASE_3_22 git_last_commit: 68d44a6 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/crisprScoreData_1.14.0.tar.gz vignettes: vignettes/crisprScoreData/inst/doc/crisprScoreData.html vignetteTitles: crisprScoreData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/crisprScoreData/inst/doc/crisprScoreData.R dependsOnMe: crisprScore importsMe: crisprVerse dependencyCount: 65 Package: curatedAdipoArray Version: 1.22.0 Depends: R (>= 4.0) Suggests: knitr, rmarkdown, ExperimentHub, SummarizedExperiment License: GPL-3 + file LICENSE MD5sum: a1a16529ff9db703f420febf3c488521 NeedsCompilation: no Title: A Curated Microarrays Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Under Genetic and Pharmacological Perturbations Description: A curated dataset of Microarrays samples. The samples are MDI- induced pre-adipocytes (3T3-L1) at different time points/stage of differentiation under different types of genetic (knockdown/overexpression) and pharmacological (drug treatment) perturbations. The package documents the data collection and processing. In addition to the documentation, the package contains the scripts that was used to generated the data. biocViews: ExperimentData, ExperimentHub, GEO, MicroarrayData Author: Mahmoud Ahmed [aut, cre] (ORCID: ) Maintainer: Mahmoud Ahmed URL: https://github.com/MahShaaban/curatedAdipoArray VignetteBuilder: knitr BugReports: https://github.com/MahShaaban/curatedAdipoArray/issues git_url: https://git.bioconductor.org/packages/curatedAdipoArray git_branch: RELEASE_3_22 git_last_commit: abb63e0 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/curatedAdipoArray_1.22.0.tar.gz vignettes: vignettes/curatedAdipoArray/inst/doc/curatedAdipoArray.html vignetteTitles: Using curatedAdipoArray hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/curatedAdipoArray/inst/doc/curatedAdipoArray.R dependencyCount: 0 Package: curatedAdipoChIP Version: 1.26.0 Depends: R (>= 3.6), SummarizedExperiment, ExperimentHub Suggests: knitr, rmarkdown, GenomicFeatures, ChIPseeker, AnnotationDbi, S4Vectors, DESeq2, fastqcr, devtools, testthat, readr, dplyr, tidyr, ggplot2 License: GPL-3 MD5sum: a950d936851620cd86633792ff092793 NeedsCompilation: no Title: A Curated ChIP-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Description: A curated dataset of publicly available ChIP-sequencing of transcription factors, chromatin remodelers and histone modifications in the 3T3-L1 pre-adipocyte cell line. The package document the data collection, pre-processing and processing of the data. In addition to the documentation, the package contains the scripts that was used to generated the data. biocViews: ExperimentData, ExperimentHub, GEO, ChIPSeqData, SequencingData Author: Mahmoud Ahmed [aut, cre] (ORCID: ) Maintainer: Mahmoud Ahmed URL: https://github.com/MahShaaban/curatedAdipoChIP VignetteBuilder: knitr BugReports: https://github.com/MahShaaban/curatedAdipoChIP/issues git_url: https://git.bioconductor.org/packages/curatedAdipoChIP git_branch: RELEASE_3_22 git_last_commit: 21916dd git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/curatedAdipoChIP_1.26.0.tar.gz vignettes: vignettes/curatedAdipoChIP/inst/doc/curatedAdipoChIP.html vignetteTitles: Using curatedAdipoChIP hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedAdipoChIP/inst/doc/curatedAdipoChIP.R dependencyCount: 76 Package: curatedAdipoRNA Version: 1.26.0 Depends: R (>= 3.6), SummarizedExperiment Suggests: knitr, rmarkdown, DESeq2, fastqcr, devtools, testthat, readr, dplyr, tidyr, ggplot2, S4Vectors License: GPL-3 MD5sum: ec5d48c37723f2d2f2d480fa2f31a39d NeedsCompilation: no Title: A Curated RNA-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Description: A curated dataset of RNA-Seq samples. The samples are MDI-induced pre-phagocytes (3T3-L1) at different time points/stage of differentiation. The package document the data collection, pre-processing and processing. In addition to the documentation, the package contains the scripts that was used to generated the data. biocViews: ExperimentData, GEO, RNASeqData, SequencingData Author: Mahmoud Ahmed [aut, cre] (ORCID: ) Maintainer: Mahmoud Ahmed URL: https://github.com/MahShaaban/curatedAdipoRNA VignetteBuilder: knitr BugReports: https://github.com/MahShaaban/curatedAdipoRNA/issues git_url: https://git.bioconductor.org/packages/curatedAdipoRNA git_branch: RELEASE_3_22 git_last_commit: 4ad70e4 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/curatedAdipoRNA_1.26.0.tar.gz vignettes: vignettes/curatedAdipoRNA/inst/doc/curatedadiporna_vignette.html vignetteTitles: Using curatedAdipoRNA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedAdipoRNA/inst/doc/curatedadiporna_vignette.R dependencyCount: 25 Package: curatedBladderData Version: 1.46.0 Depends: R (>= 2.10.0), affy Suggests: BiocStyle, survival, xtable, sva, genefilter, logging License: Artistic-2.0 MD5sum: adc80b63e824799773e63eb0f8450c87 NeedsCompilation: no Title: Bladder Cancer Gene Expression Analysis Description: The curatedBladderData package provides relevant functions and data for gene expression analysis in patients with bladder cancer. biocViews: ExperimentData, CancerData, OvarianCancerData, MicroarrayData, ExpressionData Author: Markus Riester Maintainer: Markus Riester URL: https://github.com/lima1/curatedBladderData git_url: https://git.bioconductor.org/packages/curatedBladderData git_branch: RELEASE_3_22 git_last_commit: 3e9df6e git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/curatedBladderData_1.46.0.tar.gz vignettes: vignettes/curatedBladderData/inst/doc/curatedBladderData_vignette.pdf vignetteTitles: curatedBladderData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedBladderData/inst/doc/curatedBladderData_vignette.R suggestsMe: covEB dependencyCount: 12 Package: curatedBreastData Version: 2.38.0 Depends: R (>= 3.0.0), XML, ggplot2, impute, Biobase, BiocStyle Imports: methods, stats License: GPL (>= 2) MD5sum: a4b8bbab9b3141d149dfa8a717008789 NeedsCompilation: no Title: Curated breast cancer gene expression data with survival and treatment information Description: Curated human breast cancer tissue S4 ExpresionSet datasets from over 16 clinical trials comprising over 2,000 patients. All datasets contain at least one type of outcomes variable and treatment information (minimum level: whether they had chemotherapy and whether they had hormonal therapy). Includes code to post-process these datasets. biocViews: ExperimentData, ExpressionData, CancerData, Tissue, BreastCancerData, qPCRData, MicroarrayData, TissueMicroarrayData, GEO Author: Katie Planey Maintainer: Katie Planey git_url: https://git.bioconductor.org/packages/curatedBreastData git_branch: RELEASE_3_22 git_last_commit: aa38c0c git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/curatedBreastData_2.38.0.tar.gz vignettes: vignettes/curatedBreastData/inst/doc/curatedBreastData-manual.pdf vignetteTitles: Manual hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedBreastData/inst/doc/curatedBreastData-manual.R dependencyCount: 52 Package: curatedMetagenomicData Version: 3.17.4 Depends: R (>= 4.1.0), SummarizedExperiment, TreeSummarizedExperiment Imports: AnnotationHub, ExperimentHub, S4Vectors, dplyr, magrittr, mia, purrr, rlang, stringr, tibble, tidyr, tidyselect Suggests: BiocStyle, DT, knitr, readr, rmarkdown, scater, testthat, utils, uwot, vegan, OmicsMLRepoR, lefser License: Artistic-2.0 MD5sum: a56770f900655d964171509886053c7e NeedsCompilation: no Title: Curated Metagenomic Data of the Human Microbiome Description: The curatedMetagenomicData package provides standardized, curated human microbiome data for novel analyses. It includes gene families, marker abundance, marker presence, pathway abundance, pathway coverage, and relative abundance for samples collected from different body sites. The bacterial, fungal, and archaeal taxonomic abundances for each sample were calculated with MetaPhlAn3, and metabolic functional potential was calculated with HUMAnN3. The manually curated sample metadata and standardized metagenomic data are available as (Tree)SummarizedExperiment objects. biocViews: ExperimentHub, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch Author: Lucas schiffer [aut, cre] (ORCID: ), Levi Waldron [aut], Edoardo Pasolli [ctb], Jennifer Wokaty [ctb], Sean Davis [ctb], Audrey Renson [ctb], Chloe Mirzayi [ctb], Paolo Manghi [ctb], Samuel Gamboa-Tuz [ctb], Marcel Ramos [ctb], Valerie Obenchain [ctb], Kelly Eckenrode [ctb], Nicola Segata [ctb], Sehyun Oh [ctb], Yoon-Ji Jung [ctb] Maintainer: Lucas schiffer URL: https://github.com/waldronlab/curatedMetagenomicData VignetteBuilder: knitr BugReports: https://github.com/waldronlab/curatedMetagenomicData/issues git_url: https://git.bioconductor.org/packages/curatedMetagenomicData git_branch: devel git_last_commit: d23e876 git_last_commit_date: 2025-09-26 Date/Publication: 2025-10-02 source.ver: src/contrib/curatedMetagenomicData_3.17.4.tar.gz vignettes: vignettes/curatedMetagenomicData/inst/doc/curatedMetagenomicData.html vignetteTitles: curatedMetagenomicData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedMetagenomicData/inst/doc/curatedMetagenomicData.R suggestsMe: lefser dependencyCount: 182 Package: curatedOvarianData Version: 1.48.0 Depends: Biobase, R (>= 4.5.0) Imports: BiocGenerics Suggests: BiocStyle, futile.logger, genefilter, knitr, logging, metafor, rmarkdown, RUnit, survival, sva, xtable License: Artistic-2.0 MD5sum: dfc5ca2822e362a1f8a51c56a39761d2 NeedsCompilation: no Title: Clinically Annotated Data for the Ovarian Cancer Transcriptome Description: The curatedOvarianData package provides data for gene expression analysis in patients with ovarian cancer. biocViews: ExperimentData, RNASeqData, CancerData, OvarianCancerData, MicroarrayData Author: Benjamin Ganzfried [aut], Markus Riester [aut], Steve Skates [aut], Victoria Wang [aut], Thomas Risch [aut], Benjamin Haibe-Kains [aut], Svitlana Tyekucheva [aut], Jie Ding [aut], Ina Jazic [aut], Michael Birrer [aut], Giovanni Parmigiani [aut], Curtis Huttenhower [aut], Levi Waldron [aut, cre] (ORCID: ) Maintainer: Levi Waldron URL: http://bcb.dfci.harvard.edu/ovariancancer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/curatedOvarianData git_branch: RELEASE_3_22 git_last_commit: 27d3d92 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/curatedOvarianData_1.48.0.tar.gz vignettes: vignettes/curatedOvarianData/inst/doc/curatedOvarianData.html vignetteTitles: curatedOvarianData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedOvarianData/inst/doc/curatedOvarianData.R suggestsMe: doppelgangR, TOP dependencyCount: 7 Package: curatedPCaData Version: 1.5.0 Depends: R (>= 4.4.0), S4Vectors (>= 0.23.18), MultiAssayExperiment, RaggedExperiment Imports: ExperimentHub, AnnotationHub, utils, methods, rlang, stats, reshape2 Suggests: BiocStyle, knitr, ggplot2, rmarkdown, survival, survminer, ComplexHeatmap, corrplot, formatR License: CC BY 4.0 MD5sum: df1ceaf3118c4a14cbc4cd035861758e NeedsCompilation: no Title: Curated Prostate Cancer Data Description: The package curatedPCaData offers a selection of annotated prostate cancer datasets featuring multiple omics, manually curated metadata, and derived downstream variables. The studies are offered as MultiAssayExperiment (MAE) objects via ExperimentHub, and comprise of clinical characteristics tied to gene expression, copy number alteration and somatic mutation data. Further, downstream features computed from these multi-omics data are offered. Multiple vignettes help grasp characteristics of the various studies and provide example exploratory and meta-analysis of leveraging the multiple studies provided here-in. biocViews: ExperimentHub, ExperimentData, ProstateCancerData, CancerData, Homo_sapiens_Data, MicroarrayData, RNASeqData, ExpressionData, CopyNumberVariationData, Somatic, GEO, ReproducibleResearch Author: Teemu Daniel Laajala [aut, cre] (ORCID: ), Jordan Creed [ctb], Christelle Colin Leitzinger [ctb], Varsha Sreekanth [ctb], Federico Calboli [ctb], Kalaimathy Singaravelu [ctb], Michael Orman [ctb], Alex Soupir [ctb], Anni Halkola [ctb] Maintainer: Teemu Daniel Laajala URL: https://github.com/Syksy/curatedPCaData VignetteBuilder: knitr BugReports: https://github.com/Syksy/curatedPCaData/issues git_url: https://git.bioconductor.org/packages/curatedPCaData git_branch: devel git_last_commit: 638c642 git_last_commit_date: 2025-04-15 Date/Publication: 2025-04-17 source.ver: src/contrib/curatedPCaData_1.5.0.tar.gz vignettes: vignettes/curatedPCaData/inst/doc/overview.html vignetteTitles: Overview to curatedPCaData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedPCaData/inst/doc/overview.R dependencyCount: 81 Package: curatedTBData Version: 2.5.0 Depends: R (>= 4.3.0) Imports: AnnotationHub, ExperimentHub, MultiAssayExperiment, rlang, stats Suggests: BiocStyle, DT, dplyr, HGNChelper, knitr, methods, rmarkdown, SummarizedExperiment, sva, testthat License: MIT + file LICENSE MD5sum: cd77d947ac7e37b9d503d265c49cb0a4 NeedsCompilation: no Title: Curation of existing tuberculosis transcriptomic studies Description: The curatedTBData is an R package that provides standardized, curated tuberculosis(TB) transcriptomic studies. The initial release of the package contains 49 studies. The curatedTBData package allows users to access tuberculosis trancriptomic efficiently and to make efficient comparison for different TB gene signatures across multiple datasets. biocViews: ExperimentHub, GEO, Homo_sapiens_Data Author: Xutao Wang [aut, cre], W. Evan Johnson [aut], Prasad Patil [aut] Maintainer: Xutao Wang URL: https://github.com/compbiomed/curatedTBData VignetteBuilder: knitr BugReports: https://github.com/compbiomed/curatedTBData/issues git_url: https://git.bioconductor.org/packages/curatedTBData git_branch: devel git_last_commit: 9633353 git_last_commit_date: 2025-04-15 Date/Publication: 2025-04-17 source.ver: src/contrib/curatedTBData_2.5.0.tar.gz vignettes: vignettes/curatedTBData/inst/doc/curatedTBData.html vignetteTitles: curatedTBData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/curatedTBData/inst/doc/curatedTBData.R suggestsMe: BatchQC dependencyCount: 77 Package: curatedTCGAData Version: 1.31.3 Depends: R (>= 4.5.0), MultiAssayExperiment Imports: AnnotationHub, ExperimentHub, HDF5Array, methods, S4Vectors, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, RaggedExperiment, readr, rmarkdown, TCGAutils, testthat License: Artistic-2.0 MD5sum: 8d12e39c6f3718f22746abc2a0f52571 NeedsCompilation: no Title: Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects Description: This package provides publicly available data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects. MultiAssayExperiment integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. It also links assay barcodes with patient identifiers, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-'omics experiment. biocViews: Homo_sapiens_Data, ReproducibleResearch, CancerData, ExperimentHub Author: Marcel Ramos [aut, cre] (ORCID: ), Levi Waldron [ctb], Lucas Schiffer [ctb], Ludwig Geistlinger [ctb], Valerie Obenchain [ctb], Martin Morgan [ctb] Maintainer: Marcel Ramos VignetteBuilder: knitr BugReports: https://github.com/waldronlab/curatedTCGAData/issues git_url: https://git.bioconductor.org/packages/curatedTCGAData git_branch: devel git_last_commit: 29b8d6b git_last_commit_date: 2025-10-24 Date/Publication: 2025-10-28 source.ver: src/contrib/curatedTCGAData_1.31.3.tar.gz vignettes: vignettes/curatedTCGAData/inst/doc/curatedTCGAData.html vignetteTitles: curatedTCGAData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedTCGAData/inst/doc/curatedTCGAData.R importsMe: AMARETTO suggestsMe: CNVRanger, glmSparseNet, TCGAutils dependencyCount: 82 Package: CytoMethIC Version: 1.5.0 Depends: R (>= 4.4.0), ExperimentHub Imports: utils, stats, tools, sesame, methods, sesameData, BiocParallel, BiocManager Suggests: tibble, BiocStyle, randomForest, testthat, knitr, rmarkdown, e1071, xgboost, keras, tensorflow License: Artistic-2.0 MD5sum: 1eb1276d908dabe89c5e05a6fbe2f364 NeedsCompilation: no Title: DNA methylation-based machine learning models Description: This package provides model data and functions for easily using machine learning models that use data from the DNA methylome to classify cancer type and phenotype from a sample. The primary motivation for the development of this package is to abstract away the granular and accessibility-limiting code required to utilize machine learning models in R. Our package provides this abstraction for RandomForest, e1071 Support Vector, Extreme Gradient Boosting, and Tensorflow models. This is paired with an ExperimentHub component, which contains models developed for epigenetic cancer classification and predicting phenotypes. This includes CNS tumor classification, Pan-cancer classification, race prediction, cell of origin classification, and subtype classification models. The package links to our models on ExperimentHub. The package currently supports HM450, EPIC, EPICv2, MSA, and MM285. biocViews: ExperimentData, MicroarrayData, Genome, ExperimentHub, MethylationArrayData, CancerData, PackageTypeData Author: Wanding Zhou [aut] (ORCID: ), Jacob Fanale [aut, cre] (ORCID: ) Maintainer: Jacob Fanale URL: https://github.com/zhou-lab/CytoMethIC VignetteBuilder: knitr BugReports: https://github.com/zhou-lab/CytoMethIC/issues git_url: https://git.bioconductor.org/packages/CytoMethIC git_branch: devel git_last_commit: 88f8336 git_last_commit_date: 2025-04-15 Date/Publication: 2025-04-17 source.ver: src/contrib/CytoMethIC_1.5.0.tar.gz vignettes: vignettes/CytoMethIC/inst/doc/CytoMethIC.html, vignettes/CytoMethIC/inst/doc/Oncology.html vignetteTitles: 1. Basic Information, 2. CytoMethIC Oncology hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CytoMethIC/inst/doc/CytoMethIC.R, vignettes/CytoMethIC/inst/doc/Oncology.R dependencyCount: 110 Package: DAPARdata Version: 1.40.0 Depends: R (>= 4.4.0), MSnbase Imports: utils Suggests: knitr, DAPAR, BiocStyle License: GPL-2 MD5sum: bd0dbc1afa6ac55e49d9046975c17f80 NeedsCompilation: no Title: Data accompanying the DAPAR and Prostar packages Description: Mass-spectrometry based UPS proteomics data sets from Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssie D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianferani S, Ferro M, Dorssaeler AV, Burlet-Schiltz O, Schaeffer C, Coute Y, Gonzalez de Peredo A. Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods. Data Brief. 2015 Dec 17;6:286-94 and Giai Gianetto, Q., Combes, F., Ramus, C., Bruley, C., Coute, Y., Burger, T. (2016). Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments. Proteomics, 16(1), 29-32. biocViews: ExperimentData, MassSpectrometryData, Proteome Author: Samuel Wieczorek [cre,aut], Thomas Burger [aut], Enora Fremy [aut] Maintainer: Samuel Wieczorek URL: http://www.prostar-proteomics.org/ VignetteBuilder: knitr BugReports: https://github.com/edyp-lab/DAPARdata/issues git_url: https://git.bioconductor.org/packages/DAPARdata git_branch: RELEASE_3_22 git_last_commit: 27fe19a git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/DAPARdata_1.40.0.tar.gz vignettes: vignettes/DAPARdata/inst/doc/dapardata.html vignetteTitles: DAPARdata User Manual hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DAPARdata/inst/doc/dapardata.R importsMe: DAPAR, Prostar dependencyCount: 131 Package: davidTiling Version: 1.50.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db License: LGPL MD5sum: 0368bc66ae8cc1739780874abac76c16 NeedsCompilation: no Title: Data and analysis scripts for David, Huber et al. yeast tiling array paper Description: This package contains the data for the paper by L. David et al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix genechips, an ExpressionSet object with the raw feature data, a probe annotation data structure for the chip and the yeast genome annotation (GFF file) that was used. In addition, some custom-written analysis functions are provided, as well as R scripts in the scripts directory. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, MicroarrayData, ReproducibleResearch Author: Wolfgang Huber , Joern Toedling Maintainer: Wolfgang Huber URL: http://www.ebi.ac.uk/huber git_url: https://git.bioconductor.org/packages/davidTiling git_branch: RELEASE_3_22 git_last_commit: 576ac79 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/davidTiling_1.50.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 77 Package: depmap Version: 1.23.0 Depends: R (>= 4.1.0), methods, dplyr Imports: utils, ExperimentHub, AnnotationHub, BiocFileCache, httr2, curl, tibble Suggests: knitr, rmarkdown, BiocStyle, viridis, gridExtra, ggplot2, readr, stringr, tidyverse, magick License: Artistic-2.0 MD5sum: cfdff3918bcb75422f7004a3f41ca7af NeedsCompilation: no Title: Cancer Dependency Map Data Package Description: The depmap package is a data package that accesses datsets from the Broad Institute DepMap cancer dependency study using ExperimentHub. Datasets from the most current release are available, including RNAI and CRISPR-Cas9 gene knockout screens quantifying the genetic dependency for select cancer cell lines. Additional datasets are also available pertaining to the log copy number of genes for select cell lines, protein expression of cell lines as measured by reverse phase protein lysate microarray (RPPA), 'Transcript Per Million' (TPM) data, as well as supplementary datasets which contain metadata and mutation calls for the other datasets found in the current release. The 19Q3 release adds the drug_dependency dataset, that contains cancer cell line dependency data with respect to drug and drug-candidate compounds. The 20Q2 release adds the proteomic dataset that contains quantitative profiling of proteins via mass spectrometry. This package will be updated on a quarterly basis to incorporate the latest Broad Institute DepMap Public cancer dependency datasets. All data made available in this package was generated by the Broad Institute DepMap for research purposes and not intended for clinical use. This data is distributed under the Creative Commons license (Attribution 4.0 International (CC BY 4.0)). biocViews: ExperimentHub, ExperimentData, ReproducibleResearch, RepositoryData, AssayDomainData, CopyNumberVariationData, DiseaseModel, CancerData, BreastCancerData, ColonCancerData, KidneyCancerData, LeukemiaCancerData, LungCancerData, OvarianCancerData, ProstateCancerData, OrganismData, Homo_sapiens_Data, PackageTypeData, SpecimenSource, CellCulture, Genome, Proteome, StemCell, Tissue Author: Laurent Gatto [cre, aut] (ORCID: ), Theo Killian [aut], Alexander Peltzer [ctb] (ORCID: ) Maintainer: Laurent Gatto VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/depmap git_branch: devel git_last_commit: bc169e5 git_last_commit_date: 2025-04-15 Date/Publication: 2025-04-17 source.ver: src/contrib/depmap_1.23.0.tar.gz vignettes: vignettes/depmap/inst/doc/depmap.html, vignettes/depmap/inst/doc/using_depmap.html vignetteTitles: depmap, depmap use cases hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/depmap/inst/doc/depmap.R, vignettes/depmap/inst/doc/using_depmap.R importsMe: CBNplot, DeepTarget suggestsMe: mastR, BioPlex dependencyCount: 65 Package: derfinderData Version: 2.28.0 Depends: R (>= 3.5.0) Suggests: sessioninfo, knitr (>= 1.6), RefManageR, rmarkdown (>= 0.3.3), BiocStyle License: Artistic-2.0 MD5sum: 91c2ed2be46d72eec1fc292f5f2f704e NeedsCompilation: no Title: Processed BigWigs from BrainSpan for examples Description: Processed 22 samples from BrainSpan keeping only the information for chromosome 21. Data is stored in the BigWig format and is used for examples in other packages. biocViews: ExperimentData, Homo_sapiens_Data, RNASeqData Author: Leonardo Collado-Torres [aut, cre] (ORCID: ), Andrew Jaffe [aut] (ORCID: ), Jeffrey Leek [aut, ths] (ORCID: ) Maintainer: Leonardo Collado-Torres URL: https://github.com/leekgroup/derfinderData VignetteBuilder: knitr BugReports: https://github.com/leekgroup/derfinderData/issues git_url: https://git.bioconductor.org/packages/derfinderData git_branch: RELEASE_3_22 git_last_commit: 3940ba9 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/derfinderData_2.28.0.tar.gz vignettes: vignettes/derfinderData/inst/doc/derfinderData.html vignetteTitles: Introduction to derfinderData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/derfinderData/inst/doc/derfinderData.R suggestsMe: derfinder, derfinderPlot dependencyCount: 0 Package: DeSousa2013 Version: 1.46.0 Depends: R (>= 2.15), Imports: affy, frma, frmaTools, hgu133plus2.db, hgu133plus2frmavecs, sva, rgl, ConsensusClusterPlus, cluster, siggenes, ROCR, pamr, survival, gplots, AnnotationDbi, Biobase License: Artistic-2.0 MD5sum: 2ec3001f02efaa8b93abf1cedcebd1d1 NeedsCompilation: no Title: Poor prognosis colon cancer is defined by a molecularly distinct subtype and precursor lesion Description: This package reproduces the main pipeline to analyze the AMC-AJCCII-90 microarray data set in De Sousa et al. accepted by Nature Medicine in 2013. biocViews: CancerData, ColonCancerData, MicroarrayData Author: Xin Wang Maintainer: Xin Wang git_url: https://git.bioconductor.org/packages/DeSousa2013 git_branch: RELEASE_3_22 git_last_commit: 9a00f0d git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/DeSousa2013_1.46.0.tar.gz vignettes: vignettes/DeSousa2013/inst/doc/DeSousa2013-Vignette.pdf vignetteTitles: Main vignette:Poor prognosis colon cancer is defined by a molecular distinct subtype and develops from serrated precursor lesions hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DeSousa2013/inst/doc/DeSousa2013-Vignette.R dependencyCount: 124 Package: DExMAdata Version: 1.18.0 Depends: R (>= 4.1) Imports: Biobase Suggests: BiocStyle License: GPL-2 MD5sum: 797334b2261f710d95ee9125ce1ff570 NeedsCompilation: no Title: Data package for DExMA package Description: Data objects needed to allSameID() function of DExMA package. There are also some objects that are necessary to be able to apply the examples of the DExMA package, which illustrate package functionality. biocViews: ExperimentData, OrganismData, MicroarrayData Author: Juan Antonio Villatoro-García [aut, cre], Pedro Carmona-Sáez [aut] Maintainer: Juan Antonio Villatoro-García git_url: https://git.bioconductor.org/packages/DExMAdata git_branch: RELEASE_3_22 git_last_commit: ba363e3 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/DExMAdata_1.18.0.tar.gz vignettes: vignettes/DExMAdata/inst/doc/DExMAdata.pdf vignetteTitles: Data for DExMA package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DExMAdata/inst/doc/DExMAdata.R dependsOnMe: DExMA dependencyCount: 7 Package: diffloopdata Version: 1.38.0 Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 9360cc1a6df2925f1c9ad37568dbbd97 NeedsCompilation: no Title: Example ChIA-PET Datasets for the diffloop Package Description: ChIA-PET example datasets and additional data for use with the diffloop package. biocViews: ExperimentData, SequencingData Author: Caleb Lareau [aut], Martin Aryee [aut, cre] Maintainer: Caleb Lareau VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/diffloopdata git_branch: RELEASE_3_22 git_last_commit: e0b8f2c git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/diffloopdata_1.38.0.tar.gz vignettes: vignettes/diffloopdata/inst/doc/diffloopdata.html vignetteTitles: diffloopdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: diggitdata Version: 1.42.0 Depends: R(>= 2.14.0), Biobase, methods Imports: viper License: GPL (>=2) MD5sum: 55220b2c57c46b3a14b56561ff8c1f88 NeedsCompilation: no Title: Example data for the diggit package Description: This package provides expression profile and CNV data for glioblastoma from TCGA, and transcriptional and post-translational regulatory networks assembled with the ARACNe and MINDy algorithms, respectively. biocViews: ExperimentData, Cancer Author: Mariano Javier Alvarez Maintainer: Mariano Javier Alvarez git_url: https://git.bioconductor.org/packages/diggitdata git_branch: RELEASE_3_22 git_last_commit: 151b027 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/diggitdata_1.42.0.tar.gz vignettes: vignettes/diggitdata/inst/doc/diggitdata.pdf vignetteTitles: Using bcellViper hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/diggitdata/inst/doc/diggitdata.R suggestsMe: diggit dependencyCount: 88 Package: DLBCL Version: 1.50.0 Depends: R(>= 2.11.0), Biobase, graph License: GPL (>=2) MD5sum: 7082b2a7d31b68b82d986590cf9258e2 NeedsCompilation: no Title: Diffuse large B-cell lymphoma expression data Description: This package provides additional expression data on diffuse large B-cell lymphomas for the BioNet package. biocViews: ExperimentData, CancerData, MicroarrayData, ChipOnChipData Author: Marcus Dittrich and Daniela Beisser Maintainer: Marcus Dittrich URL: http://bionet.bioapps.biozentrum.uni-wuerzburg.de/ git_url: https://git.bioconductor.org/packages/DLBCL git_branch: RELEASE_3_22 git_last_commit: b6d1d8b git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/DLBCL_1.50.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: BioNet, mwcsr dependencyCount: 9 Package: DMRcatedata Version: 2.28.0 Depends: R (>= 4.0), ExperimentHub Imports: GenomicFeatures, Gviz, readxl, plyr, rtracklayer, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr License: GPL-3 MD5sum: 4c413bcd2857f948ae989ce3d4ec0525 NeedsCompilation: no Title: Data Package for DMRcate Description: This package contains 9 data objects supporting functionality and examples of the Bioconductor package DMRcate. biocViews: ExperimentHub, ExperimentData, SNPData, Homo_sapiens_Data, Mus_musculus_Data, SequencingData, MicroarrayData, Genome Author: Tim Peters Maintainer: Tim Peters VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DMRcatedata git_branch: RELEASE_3_22 git_last_commit: 54400d7 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/DMRcatedata_2.28.0.tar.gz vignettes: vignettes/DMRcatedata/inst/doc/DMRcatedata.pdf vignetteTitles: The DMRcate package user's guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DMRcatedata/inst/doc/DMRcatedata.R suggestsMe: DMRcate dependencyCount: 207 Package: DNAZooData Version: 1.10.0 Depends: R (>= 4.2), HiCExperiment Imports: BiocFileCache, S4Vectors, rjson, utils, tools Suggests: dplyr, testthat, methods, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 435237c95068e29feb06542f3046ed4f NeedsCompilation: no Title: DNA Zoo data package Description: DNAZooData is a data package giving programmatic access to genome assemblies and Hi-C contact matrices uniformly processed by the [DNA Zoo Consortium](https://www.dnazoo.org/). The matrices are available in the multi-resolution `.hic` format. A URL to corrected genome assemblies in `.fastq` format is also provided to the end-user. biocViews: ExperimentData, SequencingData Author: Jacques Serizay [aut, cre] Maintainer: Jacques Serizay URL: https://github.com/js2264/DNAZooData VignetteBuilder: knitr BugReports: https://github.com/js2264/DNAZooData/issues git_url: https://git.bioconductor.org/packages/DNAZooData git_branch: RELEASE_3_22 git_last_commit: af9776f git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/DNAZooData_1.10.0.tar.gz vignettes: vignettes/DNAZooData/inst/doc/DNAZooData.html vignetteTitles: DNAZooData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/DNAZooData/inst/doc/DNAZooData.R importsMe: OHCA dependencyCount: 86 Package: DonaPLLP2013 Version: 1.48.0 Depends: EBImage, parallel License: Artistic-2.0 MD5sum: 93a7706783009333bba76aa23a8a64ec NeedsCompilation: no Title: Supplementary data package for Dona et al. (2013) containing example images and tables Description: An experiment data package associated with the publication Dona et al. (2013). Package contains runnable vignettes showing an example image segmentation for one posterior lateral line primordium, and also the data table and code used to analyze tissue-scale lifetime-ratio statistics. biocViews: ExperimentData, Tissue Author: Erika Dona, Joseph D. Barry, Guillaume Valentin, Charlotte Quirin, Anton Khmelinskii, Andreas Kunze, Sevi Durdu, Lionel R. Newton, Ana Fernandez-Minan, Wolfgang Huber, Michael Knop, Darren Gilmour Maintainer: Joseph D. Barry git_url: https://git.bioconductor.org/packages/DonaPLLP2013 git_branch: RELEASE_3_22 git_last_commit: 613f650 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/DonaPLLP2013_1.48.0.tar.gz vignettes: vignettes/DonaPLLP2013/inst/doc/PLLPanalysis.pdf, vignettes/DonaPLLP2013/inst/doc/PLLPstatistics.pdf vignetteTitles: PLLP image analysis, PLLP tissue-scale ratio statistics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DonaPLLP2013/inst/doc/PLLPanalysis.R, vignettes/DonaPLLP2013/inst/doc/PLLPstatistics.R dependencyCount: 47 Package: DoReMiTra Version: 1.0.0 Depends: R (>= 4.5.0) Imports: ExperimentHub, SummarizedExperiment, AnnotationHub, utils, glue, S4Vectors, scater Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, DT License: MIT + file LICENSE MD5sum: 480142b1b562ec54418c78211f7ae355 NeedsCompilation: no Title: Orchestrating Blood Radiation Transcriptomic Data Description: DoReMiTra is an R data package providing access to curated transcriptomic datasets related to blood radiation, with a focus on neutron, x-ray, and gamma ray studies. It is designed to facilitate radiation biology research and support data exploration and reproducibility in radiation transcriptomics. All datasets are provided as SummarizedExperiment objects, allowing seamless integration with the Bioconductor ecosystem. biocViews: ExperimentData, RNASeqData, ExperimentHub, ExpressionData, GEO, PackageTypeData Author: Ahmed Salah [aut, cre] (ORCID: ), Federico Marini [aut] (ORCID: ) Maintainer: Ahmed Salah URL: https://github.com/AhmedSAHassan/DoReMiTra VignetteBuilder: knitr BugReports: https://github.com/AhmedSAHassan/DoReMiTra/issues git_url: https://git.bioconductor.org/packages/DoReMiTra git_branch: RELEASE_3_22 git_last_commit: 5d4d5e0 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/DoReMiTra_1.0.0.tar.gz vignettes: vignettes/DoReMiTra/inst/doc/DoReMiTra.html vignetteTitles: The DoReMiTra User's Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/DoReMiTra/inst/doc/DoReMiTra.R dependencyCount: 128 Package: dorothea Version: 1.22.0 Depends: R (>= 4.0) Imports: dplyr, magrittr, bcellViper, decoupleR, Suggests: Biobase, BiocStyle, OmnipathR, viper, knitr, pheatmap, pkgdown, rmarkdown, Seurat, SingleCellExperiment, SummarizedExperiment, testthat (>= 2.1.0), tibble, tidyr, utils License: GPL-3 + file LICENSE MD5sum: 2f2e788e050ec23dd4bae5f5c8b14674 NeedsCompilation: no Title: Collection Of Human And Mouse TF Regulons Description: DoRothEA is a gene regulatory network containing signed transcription factor (TF) - target gene interactions. DoRothEA regulons, the collection of a TF and its transcriptional targets, were curated and collected from different types of evidence for both human and mouse. A confidence level was assigned to each TF-target interaction based on the number of supporting evidence. biocViews: ExperimentData, Homo_sapiens_Data, Mus_musculus_Data Author: Pau Badia-i-Mompel [cre] (ORCID: ), Daniel Dimitrov [aut] (ORCID: ), Christian H. Holland [aut] (ORCID: ), Luz Garcia-Alonso [aut], Alberto Valdeolivas [ctb], Minoo Ashtiani [ctb], Attila Gabor [ctb] Maintainer: Pau Badia-i-Mompel URL: https://saezlab.github.io/dorothea/, https://github.com/saezlab/dorothea VignetteBuilder: knitr BugReports: https://github.com/saezlab/dorothea/issues git_url: https://git.bioconductor.org/packages/dorothea git_branch: RELEASE_3_22 git_last_commit: d467b8d git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/dorothea_1.22.0.tar.gz vignettes: vignettes/dorothea/inst/doc/dorothea.html vignetteTitles: DoRothEA regulons. hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/dorothea/inst/doc/dorothea.R importsMe: cosmosR, easier suggestsMe: epiregulon.extra, MethReg dependencyCount: 45 Package: dressCheck Version: 0.48.0 Depends: R (>= 2.10.1), methods, Biobase (>= 2.5.5) Suggests: survival, chron License: Artistic-2.0 MD5sum: 7fc4ca30553d2efc5aef04eab1d22b78 NeedsCompilation: no Title: data and software for checking Dressman JCO 25(5) 2007 Description: data and software for checking Dressman JCO 25(5) 2007 biocViews: ExperimentData, Genome Author: Vincent Carey Maintainer: Vincent Carey git_url: https://git.bioconductor.org/packages/dressCheck git_branch: RELEASE_3_22 git_last_commit: 806812f git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/dressCheck_0.48.0.tar.gz vignettes: vignettes/dressCheck/inst/doc/short.pdf vignetteTitles: short review of dressCheck contents hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/dressCheck/inst/doc/short.R dependencyCount: 7 Package: DropletTestFiles Version: 1.19.0 Imports: utils, ExperimentHub, AnnotationHub, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, testthat, DropletUtils License: GPL-3 MD5sum: 0d87165406a8cbaf21a13d89c77b98f8 NeedsCompilation: no Title: Test Files for Single-Cell Droplet Utilities Description: Assorted files generated from droplet-based single-cell protocols, to be used for testing functions in DropletUtils. Primarily intended for storing files that directly come out of processing pipelines like 10X Genomics' CellRanger software, prior to the formation of a SingleCellExperiment object. Unlike other packages, this is not designed to provide objects that are immediately ready for analysis. biocViews: ExperimentHub, ExperimentData, ExpressionData, SequencingData, RNASeqData, SingleCellData Author: Aaron Lun [ctb, cre] Maintainer: Aaron Lun VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DropletTestFiles git_branch: devel git_last_commit: 6baf794 git_last_commit_date: 2025-04-15 Date/Publication: 2025-04-17 source.ver: src/contrib/DropletTestFiles_1.19.0.tar.gz vignettes: vignettes/DropletTestFiles/inst/doc/motivation.html vignetteTitles: Test files for droplet-based single-cell utilities hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DropletTestFiles/inst/doc/motivation.R dependsOnMe: OSCA.advanced, OSCA.intro, OSCA.workflows suggestsMe: DropletUtils, TENxIO dependencyCount: 65 Package: DrugVsDiseasedata Version: 1.46.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: ccf3a524bf1ced6590e7d002c95e9213 NeedsCompilation: no Title: Drug versus Disease Data Description: Data package which provides default disease expression profiles, clusters and annotation information for use with the DrugVsDisease package. biocViews: Homo_sapiens_Data, MicroarrayData Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/DrugVsDiseasedata git_branch: RELEASE_3_22 git_last_commit: e477b51 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/DrugVsDiseasedata_1.46.0.tar.gz vignettes: vignettes/DrugVsDiseasedata/inst/doc/DrugVsDiseasedata.pdf vignetteTitles: DrugVsDiseasedata hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DrugVsDiseasedata/inst/doc/DrugVsDiseasedata.R dependsOnMe: DrugVsDisease dependencyCount: 0 Package: DuoClustering2018 Version: 1.27.0 Imports: ExperimentHub, utils, magrittr, dplyr, tidyr, mclust, ggplot2, purrr, reshape2, viridis, ggthemes, stats, methods Suggests: knitr, rmarkdown, BiocStyle, iSEE, scater, SingleCellExperiment, SummarizedExperiment, plyr License: GPL (>=2) MD5sum: cbcb32fdcb080421264325c50860cf22 NeedsCompilation: no Title: Data, Clustering Results and Visualization Functions From Duò et al (2018) Description: Preprocessed experimental and simulated scRNA-seq data sets used for evaluation of clustering methods for scRNA-seq data in Duò et al (2018). Also contains results from applying several clustering methods to each of the data sets, and functions for plotting method performance. biocViews: SingleCellData, ExperimentData Author: Angelo Duò, Charlotte Soneson Maintainer: Angelo Duò VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DuoClustering2018 git_branch: devel git_last_commit: 1bb0645 git_last_commit_date: 2025-04-15 Date/Publication: 2025-04-17 source.ver: src/contrib/DuoClustering2018_1.27.0.tar.gz vignettes: vignettes/DuoClustering2018/inst/doc/combine_data_clustering.html, vignettes/DuoClustering2018/inst/doc/plot_performance.html, vignettes/DuoClustering2018/inst/doc/run_clustering.html vignetteTitles: Visualize data sets and clustering results with iSEE, Plot performance summaries, Apply clustering method hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DuoClustering2018/inst/doc/combine_data_clustering.R, vignettes/DuoClustering2018/inst/doc/plot_performance.R, vignettes/DuoClustering2018/inst/doc/run_clustering.R suggestsMe: corral, scry dependencyCount: 82 Package: DvDdata Version: 1.46.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 5de8266caaceca395efd2897f737e903 NeedsCompilation: no Title: Drug versus Disease Data Description: Data package which provides default drug and disease expression profiles for the DvD package. biocViews: GEO Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/DvDdata git_branch: RELEASE_3_22 git_last_commit: 096e07b git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/DvDdata_1.46.0.tar.gz vignettes: vignettes/DvDdata/inst/doc/DvDdata.pdf vignetteTitles: DvDdata hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DvDdata/inst/doc/DvDdata.R dependencyCount: 0 Package: dyebiasexamples Version: 1.50.0 Depends: R (>= 1.4.1), marray, GEOquery Suggests: dyebias, convert, Biobase License: GPL-3 MD5sum: 8662597cc0c843ef8e9670fdd3ed9560 NeedsCompilation: no Title: Example data for the dyebias package, which implements the GASSCO method. Description: Data for the dyebias package, consisting of 4 self-self hybrizations of self-spotted yeast slides, as well as data from Array Express accession E-MTAB-32 biocViews: ExperimentData, SAGEData, CGHData, MicroarrayData, TwoChannelData, ArrayExpress Author: Philip Lijnzaad and Thanasis Margaritis Maintainer: Philip Lijnzaad URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad git_url: https://git.bioconductor.org/packages/dyebiasexamples git_branch: RELEASE_3_22 git_last_commit: 3580f3e git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/dyebiasexamples_1.50.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: dyebias dependencyCount: 76 Package: easierData Version: 1.16.0 Depends: R (>= 4.1.0) Imports: ExperimentHub, AnnotationHub, utils, SummarizedExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 1a4f2a4cb88b4a38b8b8efceebd7291e NeedsCompilation: no Title: easier internal data and exemplary dataset from IMvigor210CoreBiologies package Description: Access to internal data required for the functional performance of easier package and exemplary bladder cancer dataset with both processed RNA-seq data and information on response to ICB therapy generated by Mariathasan et al. "TGF-B attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells", published in Nature, 2018 [doi:10.1038/nature25501](https://doi.org/10.1038/nature25501). The data is made available via [`IMvigor210CoreBiologies`](http://research-pub.gene.com/IMvigor210CoreBiologies/) package under the CC-BY license. biocViews: RNASeqData, ExperimentHub, ReproducibleResearch, ImmunoOncologyData, CancerData, ExperimentData Author: Oscar Lapuente-Santana [aut, cre] (ORCID: ), Federico Marini [aut] (ORCID: ), Arsenij Ustjanzew [aut] (ORCID: ), Francesca Finotello [aut] (ORCID: ), Federica Eduati [aut] (ORCID: ) Maintainer: Oscar Lapuente-Santana VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/easierData git_branch: RELEASE_3_22 git_last_commit: 9ab91db git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/easierData_1.16.0.tar.gz vignettes: vignettes/easierData/inst/doc/easierData.html vignetteTitles: easier data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/easierData/inst/doc/easierData.R importsMe: easier dependencyCount: 76 Package: EatonEtAlChIPseq Version: 0.48.0 Depends: GenomicRanges (>= 1.5.42), ShortRead, rtracklayer License: Artistic 2.0 MD5sum: 26944018ba3f65d496e21cb7d11443e1 NeedsCompilation: no Title: ChIP-seq data of ORC-binding sites in Yeast excerpted from Eaton et al. 2010 Description: ChIP-seq analysis subset from "Conserved nucleosome positioning defines replication origins" (PMID 20351051) biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, ChIPSeqData, GEO Author: Patrick Aboyoun Maintainer: Patrick Aboyoun git_url: https://git.bioconductor.org/packages/EatonEtAlChIPseq git_branch: RELEASE_3_22 git_last_commit: 17b8b47 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/EatonEtAlChIPseq_0.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 69 Package: ecoliLeucine Version: 1.50.0 Depends: R (>= 1.9.0), affy (>= 1.23.4), ecolicdf License: GPL (>= 2) MD5sum: f4efddfd12186336fe4c617036a60cd8 NeedsCompilation: no Title: Experimental data with Affymetrix E. coli chips Description: Experimental data with Affymetrix E. coli chips, as reported in She-pin Hung, Pierre Baldi, and G. Wesley Hatfield, J. Biol. Chem., Vol. 277, Issue 43, 40309-40323, October 25, 2002 biocViews: ExperimentData, MicroarrayData Author: Laurent Gautier Maintainer: Laurent Gautier git_url: https://git.bioconductor.org/packages/ecoliLeucine git_branch: RELEASE_3_22 git_last_commit: 8136bb4 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/ecoliLeucine_1.50.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ecolitk dependencyCount: 48 Package: EGSEAdata Version: 1.38.0 Depends: R (>= 3.4) Suggests: EGSEA License: file LICENSE MD5sum: 0eb9690033a68af496638fb1eafdca42 NeedsCompilation: no Title: Gene set collections for the EGSEA package Description: This package includes gene set collections that are used for the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. It includes Human and Mouse versions of the MSidDB (Subramanian, et al. (2005) PNAS, 102(43):15545-15550) and GeneSetDB (Araki, et al. (2012) FEBS Open Bio, 2:76-82) collections. biocViews: ExperimentData, Homo_sapiens_Data, Mus_musculus_Data, Rattus_norvegicus_Data Author: Monther Alhamdoosh, Yifang Hu and Gordon K. Smyth Maintainer: Monther Alhamdoosh git_url: https://git.bioconductor.org/packages/EGSEAdata git_branch: RELEASE_3_22 git_last_commit: b03a3b9 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/EGSEAdata_1.38.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE importsMe: EGSEA dependencyCount: 0 Package: ELMER.data Version: 2.34.0 Depends: R (>= 3.5.0) Imports: GenomicRanges Suggests: BiocStyle, knitr, dplyr, devtools, DT, rmarkdown License: GPL-3 MD5sum: dbe4f8b94398217f6f2120bccd216443 NeedsCompilation: no Title: Data for the ELMER package Description: Supporting data for the ELMER package. It includes: - elmer.data.example.promoter: mae.promoter - elmer.data.example: data - EPIC.hg38.manifest - EPIC.hg19.manifest - hm450.hg38.manifest - hm450.hg19.manifest - hocomoco.table - human.TF - LUSC_meth_refined: Meth - LUSC_RNA_refined: GeneExp - Probes.motif.hg19.450K - Probes.motif.hg19.EPIC - Probes.motif.hg38.450K - Probes.motif.hg38.EPIC - TF.family - TF.subfamily - Human_genes__GRCh37_p13 - Human_genes__GRCh38_p12 - Human_genes__GRCh37_p13__tss - Human_genes__GRCh38_p12__tss biocViews: AssayDomainData, TechnologyData, OrganismData Author: Tiago Chedraoui Silva, Lijing Yao Simon Coetzee, Benjamin P. Berman Maintainer: Tiago Chedraoui Silva VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ELMER.data git_branch: RELEASE_3_22 git_last_commit: 9e171ea git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/ELMER.data_2.34.0.tar.gz vignettes: vignettes/ELMER.data/inst/doc/vignettes.html vignetteTitles: ELMER.data: Supporting data for the ELMER package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ELMER.data/inst/doc/vignettes.R dependsOnMe: ELMER importsMe: EpiMix dependencyCount: 11 Package: emtdata Version: 1.17.0 Depends: R (>= 4.1) Imports: edgeR, ExperimentHub, SummarizedExperiment Suggests: testthat (>= 3.0.0), stringr, plyr, prettydoc, BiocStyle, Homo.sapiens, RColorBrewer, rmarkdown, BiocFileCache, knitr License: GPL-3 MD5sum: 9296191cffe0ab1e87097a6c911ada63 NeedsCompilation: no Title: An ExperimentHub Package for data sets with an Epithelial to Mesenchymal Transition (EMT) Description: This package provides pre-processed RNA-seq data where the epithelial to mesenchymal transition was induced on cell lines. These data come from three publications Cursons et al. (2015), Cursons etl al. (2018) and Foroutan et al. (2017). In each of these publications, EMT was induces across multiple cell lines following treatment by TGFb among other stimulants. This data will be useful in determining the regulatory programs modified in order to achieve an EMT. Data were processed by the Davis laboratory in the Bioinformatics division at WEHI. biocViews: ExperimentHub, Homo_sapiens_Data, RNASeqData, ExpressionData Author: Malvika D. Kharbanda [aut, cre] (ORCID: ), Chin Wee Tan [aut] (ORCID: ), Dharmesh D. Bhuva [aut] (ORCID: ) Maintainer: Malvika D. Kharbanda URL: https://github.com/DavisLaboratory/emtdata VignetteBuilder: knitr BugReports: https://github.com/DavisLaboratory/emtdata/issues git_url: https://git.bioconductor.org/packages/emtdata git_branch: devel git_last_commit: 6c38e81 git_last_commit_date: 2025-04-15 Date/Publication: 2025-04-17 source.ver: src/contrib/emtdata_1.17.0.tar.gz vignettes: vignettes/emtdata/inst/doc/emtdataR.html vignetteTitles: emtdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/emtdata/inst/doc/emtdataR.R dependencyCount: 80 Package: eoPredData Version: 1.4.0 Depends: ExperimentHub Suggests: BiocStyle, knitr, rmarkdown, RefManageR, planet, mixOmics License: MIT + file LICENSE MD5sum: 26307e8618403f748306ad63b3d0533b NeedsCompilation: no Title: ExperimentHub package containing model data for predicting preeclampsia status for based on plcaental DNA methylation profile Description: Provides access to eoPred pretrained model hosted on ExperimentHub. Model was trained on placental DNA methylation preeclampsia samples using mixOmics splsda. There are two resources: 1. the model object, and 2. a testing data set used to demonstrate the function. biocViews: ExperimentData, ExperimentHub, GEO, Tissue, MethylationArrayData, Homo_sapiens_Data Author: Iciar Boyano [aut], Victor Yuan [aut, cre] Maintainer: Victor Yuan URL: https://github.com/wvictor14/eoPredData VignetteBuilder: knitr BugReports: https://github.com/wvictor14/eoPredData/issues git_url: https://git.bioconductor.org/packages/eoPredData git_branch: RELEASE_3_22 git_last_commit: 5f46a08 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/eoPredData_1.4.0.tar.gz vignettes: vignettes/eoPredData/inst/doc/eoPredData.html vignetteTitles: eoPredData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/eoPredData/inst/doc/eoPredData.R dependencyCount: 65 Package: EpiMix.data Version: 1.12.0 Depends: R (>= 4.2.0), ExperimentHub (>= 0.99.6) Suggests: rmarkdown, knitr License: GPL-3 MD5sum: 8d4eaa2e3c78a1b737a1d720adeb81d4 NeedsCompilation: no Title: Data for the EpiMix package Description: Supporting data for the EpiMix R package. It include: - HM450_lncRNA_probes.rda - HM450_miRNA_probes.rda - EPIC_lncRNA_probes.rda - EPIC_miRNA_probes.rda - EpigenomeMap.rda - LUAD.sample.annotation - TCGA_BatchData - MET.data - mRNA.data - microRNA.data - lncRNA.data - Sample_EpiMixResults_lncRNA - Sample_EpiMixResults_miRNA - Sample_EpiMixResults_Regular - Sample_EpiMixResults_Enhancer - lncRNA expression data of tumors from TCGA that are stored in the ExperimentHub. biocViews: ExperimentData, ExperimentHub, Genome, RNASeqData, ExpressionData Author: Yuanning Zheng [aut, cre] Maintainer: Yuanning Zheng VignetteBuilder: knitr BugReports: https://github.com/gevaertlab/EpiMix/issues git_url: https://git.bioconductor.org/packages/EpiMix.data git_branch: RELEASE_3_22 git_last_commit: 581330e git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/EpiMix.data_1.12.0.tar.gz vignettes: vignettes/EpiMix.data/inst/doc/RetrieveData.html vignetteTitles: vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/EpiMix.data/inst/doc/RetrieveData.R dependsOnMe: EpiMix dependencyCount: 65 Package: epimutacionsData Version: 1.13.0 Depends: R (>= 4.2.0) Suggests: rmarkdown, BiocStyle, knitr, ExperimentHub, minfi License: MIT + file LICENSE MD5sum: 6834b0a7cc1c91824669812daceed5ef NeedsCompilation: no Title: Data for epimutacions package Description: This package includes the data necessary to run functions and examples in epimutacions package. Collection of DNA methylation data. The package contains 2 datasets: (1) Control ( GEO: GSE104812), (GEO: GSE97362) case samples; and (2) reference panel (GEO: GSE127824). It also contains candidate regions to be epimutations in 450k methylation arrays. biocViews: ExperimentHub, Homo_sapiens_Data, MethylationArrayData, MicroarrayData Author: Leire Abarrategui [aut, cre], Juan R. Gonzalez [aut], Carlos Ruiz-Arenas [aut], Carles Hernandez-Ferrer [aut] Maintainer: Leire Abarrategui URL: https://github.com/LeireAbarrategui/epimutacionsData VignetteBuilder: knitr BugReports: https://github.com/LeireAbarrategui/epimutacionsData/issues git_url: https://git.bioconductor.org/packages/epimutacionsData git_branch: devel git_last_commit: d1f66b0 git_last_commit_date: 2025-04-15 Date/Publication: 2025-04-17 source.ver: src/contrib/epimutacionsData_1.13.0.tar.gz vignettes: vignettes/epimutacionsData/inst/doc/epimutacionsData.html vignetteTitles: data repository for epimutacions package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/epimutacionsData/inst/doc/epimutacionsData.R dependsOnMe: epimutacions dependencyCount: 0 Package: EpipwR.data Version: 1.4.0 Imports: ExperimentHub Suggests: knitr, rmarkdown, sessioninfo License: Artistic-2.0 MD5sum: 576d57c17aed0a4bab1ade6eb4c0a34a NeedsCompilation: no Title: EpipwR.data: Reference data for EpipwR Description: This package provides reference data for EpipwR. EpipwR is a fast and efficient power analysis for continuous and binary phenotypes of epigenomic-wide association studies. This package is only meant to be used in conjunction with EpipwR. biocViews: ExperimentHub, MethylationArrayData, MicroarrayData, TissueMicroarrayData, Tissue, ExperimentData Author: Jackson Barth [aut, cre] (ORCID: ), Austin Reynolds [aut] Maintainer: Jackson Barth URL: https://github.com/jbarth216/EpipwR.data VignetteBuilder: knitr BugReports: https://github.com/jbarth216/EpipwR.data git_url: https://git.bioconductor.org/packages/EpipwR.data git_branch: RELEASE_3_22 git_last_commit: fbead4a git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/EpipwR.data_1.4.0.tar.gz vignettes: vignettes/EpipwR.data/inst/doc/EpipwR.data.html vignetteTitles: EpipwR.data: Reference data for EpipwR hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/EpipwR.data/inst/doc/EpipwR.data.R importsMe: EpipwR dependencyCount: 65 Package: estrogen Version: 1.56.0 Suggests: affy, hgu95av2.db, hgu95av2cdf, vsn, knitr, genefilter License: LGPL MD5sum: 1827192f0836f204f45d3c2420490911 NeedsCompilation: no Title: Microarray dataset that can be used as example for 2x2 factorial designs Description: Data from 8 Affymetrix genechips, looking at a 2x2 factorial design (with 2 repeats per level). biocViews: ExperimentData, MicroarrayData Author: Wolfgang Huber, Robert Gentleman Maintainer: Wolfgang Huber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/estrogen git_branch: RELEASE_3_22 git_last_commit: 2596cbe git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/estrogen_1.56.0.tar.gz vignettes: vignettes/estrogen/inst/doc/estrogen.pdf vignetteTitles: estrogen hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/estrogen/inst/doc/estrogen.R suggestsMe: categoryCompare dependencyCount: 0 Package: etec16s Version: 1.38.0 Depends: R (>= 3.3), Biobase, metagenomeSeq(>= 1.12.0) License: Artistic-2.0 MD5sum: 72841a06e2f2b3b1aa0030bc7d8d168c NeedsCompilation: no Title: Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment Description: 16S rRNA gene sequencing data to study changes in the faecal microbiota of 12 volunteers during a human challenge study with ETEC (H10407) and subsequent treatment with ciprofloxacin. biocViews: ExperimentData, SequencingData, MicrobiomeData Author: Joseph N. Paulson Maintainer: Joseph N. Paulson git_url: https://git.bioconductor.org/packages/etec16s git_branch: RELEASE_3_22 git_last_commit: 1a8b9a8 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/etec16s_1.38.0.tar.gz vignettes: vignettes/etec16s/inst/doc/etec16s.pdf vignetteTitles: etec16s hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/etec16s/inst/doc/etec16s.R dependencyCount: 33 Package: ewceData Version: 1.17.0 Depends: R (>= 4.1), ExperimentHub Suggests: knitr, BiocStyle, ggplot2, cowplot, rmarkdown, markdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 3fd185efecc0022ce1251b5db3999c73 NeedsCompilation: no Title: The ewceData package provides reference data required for ewce Description: This package provides reference data required for ewce. Expression Weighted Celltype Enrichment (EWCE) is used to determine which cell types are enriched within gene lists. The package provides tools for testing enrichments within simple gene lists (such as human disease associated genes) and those resulting from differential expression studies. The package does not depend upon any particular Single Cell Transcriptome dataset and user defined datasets can be loaded in and used in the analyses. biocViews: ExperimentData, ExperimentHub, ExpressionData, Genome, Proteome, MicroarrayData, SequencingData, SingleCellData, RNASeqData Author: Alan Murphy [cre] (ORCID: ), Nathan Skene [aut] (ORCID: ) Maintainer: Alan Murphy URL: https://github.com/neurogenomics/ewceData VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ewceData git_branch: devel git_last_commit: 34a89b5 git_last_commit_date: 2025-04-15 Date/Publication: 2025-04-17 source.ver: src/contrib/ewceData_1.17.0.tar.gz vignettes: vignettes/ewceData/inst/doc/ewceData.html vignetteTitles: Data package for Expression Weighted Celltype Enrichment EWCE hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ewceData/inst/doc/ewceData.R importsMe: EWCE dependencyCount: 65 Package: faahKO Version: 1.50.0 Depends: R (>= 3.5) Imports: xcms (>= 4.5.4) Suggests: MSnbase (>= 2.33.3) License: LGPL MD5sum: 7515890b6ad1fdf121aac94b7ead7616 NeedsCompilation: no Title: Saghatelian et al. (2004) FAAH knockout LC/MS data Description: Positive ionization mode data in NetCDF file format. Centroided subset from 200-600 m/z and 2500-4500 seconds. Data originally reported in "Assignment of Endogenous Substrates to Enzymes by Global Metabolite Profiling" Biochemistry; 2004; 43(45). Also includes detected peaks in an xcmsSet. biocViews: ExperimentData, MassSpectrometryData Author: Colin A. Smith Maintainer: Steffen Neumann URL: http://dx.doi.org/10.1021/bi0480335 git_url: https://git.bioconductor.org/packages/faahKO git_branch: RELEASE_3_22 git_last_commit: e20d46a git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/faahKO_1.50.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: cosmiq suggestsMe: CAMERA, IPO, MAIT, peakPantheR, xcms dependencyCount: 140 Package: fabiaData Version: 1.48.0 Depends: R (>= 2.10.0), Biobase Imports: utils Suggests: fabia License: LGPL (>= 2.1) MD5sum: b53601ef361cca56b46a2dcb2ce9dacc NeedsCompilation: no Title: Data sets for FABIA (Factor Analysis for Bicluster Acquisition) Description: Supplying gene expression data sets for the demos of the biclustering method "Factor Analysis for Bicluster Acquisition" (FABIA). The following three data sets are provided: A) breast cancer (van't Veer, Nature, 2002), B) multiple tissues (Su, PNAS, 2002), and C) diffuse large-B-cell lymphoma (Rosenwald, N Engl J Med, 2002). biocViews: CancerData, BreastCancerData, MicroarrayData Author: Sepp Hochreiter Maintainer: Sepp Hochreiter URL: http://www.bioinf.jku.at/software/fabia/fabia.html git_url: https://git.bioconductor.org/packages/fabiaData git_branch: RELEASE_3_22 git_last_commit: d241882 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/fabiaData_1.48.0.tar.gz vignettes: vignettes/fabiaData/inst/doc/fabiaData.pdf vignetteTitles: fabiaData: Manual for the R Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/fabiaData/inst/doc/fabiaData.R dependencyCount: 7 Package: FANTOM3and4CAGE Version: 1.46.0 Depends: R (>= 2.15.0) License: GPL-3 MD5sum: 20a3e6971fc2dda6e80373506689d192 NeedsCompilation: no Title: CAGE data from FANTOM3 and FANTOM4 projects Description: CAGE (Cap Analysis Gene Expression) data from FANTOM3 and FANTOM4 projects produced by RIKEN Omics Science Center. biocViews: ExperimentData, Tissue Author: Vanja Haberle, Department of Biology, University of Bergen, Norway Maintainer: Vanja Haberle git_url: https://git.bioconductor.org/packages/FANTOM3and4CAGE git_branch: RELEASE_3_22 git_last_commit: ab85357 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/FANTOM3and4CAGE_1.46.0.tar.gz vignettes: vignettes/FANTOM3and4CAGE/inst/doc/FANTOM3and4CAGE.pdf vignetteTitles: FANTOM3and4CAGE hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FANTOM3and4CAGE/inst/doc/FANTOM3and4CAGE.R suggestsMe: CAGEr dependencyCount: 0 Package: ffpeExampleData Version: 1.48.0 Depends: R (>= 2.10.0), lumi Suggests: genefilter, affy License: GPL (>2) MD5sum: 5cac32b918421f9d0ed984e9ba8a0351 NeedsCompilation: no Title: Illumina DASL example microarray data Description: A subset of GSE17565 (April et al. 2009) containing 32 FFPE samples of Burkitts Lymphoma and Breast Adenocarcinoma, with a dilution series in technical duplicate. biocViews: Tissue, Genome, MicroarrayData, TissueMicroarrayData, GEO Author: Levi Waldron Maintainer: Levi Waldron git_url: https://git.bioconductor.org/packages/ffpeExampleData git_branch: RELEASE_3_22 git_last_commit: e5f9f29 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/ffpeExampleData_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ffpe dependencyCount: 165 Package: fibroEset Version: 1.52.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: 3aada58e5ef3ff02740e7fe2961f7786 NeedsCompilation: no Title: exprSet for Karaman et al. (2003) fibroblasts data Description: exprSet for Karaman et al. (2003) human, bonobo and gorilla fibroblasts data biocViews: ExperimentData, Genome, Homo_sapiens_Data, MicroarrayData, ChipOnChipData Author: Sylvia Merk Maintainer: Sylvia Merk git_url: https://git.bioconductor.org/packages/fibroEset git_branch: RELEASE_3_22 git_last_commit: cbae377 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/fibroEset_1.52.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: biocGraph, clusterStab, geneplotter dependencyCount: 7 Package: FieldEffectCrc Version: 1.19.0 Depends: utils Imports: BiocStyle, RUnit, SummarizedExperiment, ExperimentHub (>= 0.99.6), AnnotationHub, DESeq2 Suggests: knitr, rmarkdown, BiocGenerics, sva, BiocManager License: Artistic-2.0 MD5sum: de02eb5c26d43b0df36c824bda3a8e7b NeedsCompilation: no Title: Tumor, tumor-adjacent normal, and healthy colorectal transcriptomes as SummarizedExperiment objects Description: Processed RNA-seq data for 1,139 human primary colorectal tissue samples across three phenotypes, including tumor, normal adjacent-to-tumor, and healthy, available as Synapse ID syn22237139 on synapse.org. Data have been parsed into SummarizedExperiment objects available via ExperimentHub to facilitate reproducibility and extension of results from Dampier et al. (PMCID: PMC7386360, PMID: 32764205). biocViews: ExperimentData, ReproducibleResearch, Tissue, Homo_sapiens_Data, ColonCancerData, RNASeqData, ExpressionData, ExperimentHub, SequencingData Author: Christopher Dampier [aut, cre] (ORCID: ), Bioconductor Package Maintainer [ctb] Maintainer: Christopher Dampier URL: http://bioconductor.org/packages/release/bioc/html/FieldEffectCrc.html VignetteBuilder: knitr BugReports: https://github.com/Bioconductor/FieldEffectCrc/ git_url: https://git.bioconductor.org/packages/FieldEffectCrc git_branch: devel git_last_commit: 1d5c1c7 git_last_commit_date: 2025-04-15 Date/Publication: 2025-04-17 source.ver: src/contrib/FieldEffectCrc_1.19.0.tar.gz vignettes: vignettes/FieldEffectCrc/inst/doc/FieldEffectCrc.html vignetteTitles: SummarizedExperiments of colorectal transcriptomes hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FieldEffectCrc/inst/doc/FieldEffectCrc.R dependencyCount: 115 Package: FIs Version: 1.38.0 Depends: R (>= 3.3) License: GPL-3 MD5sum: 14cbe587cd98ae1b90cca5ac01298195 NeedsCompilation: no Title: Human Functional Interactions (FIs) for splineTimeR package Description: Data set containing two complete lists of identified functional interaction partners in Human. Data are derived from Reactome and BioGRID databases. biocViews: PathwayInteractionDatabase, Homo_sapiens_Data Author: Agata Michna Maintainer: Herbert Braselmann , Martin Selmansberger git_url: https://git.bioconductor.org/packages/FIs git_branch: RELEASE_3_22 git_last_commit: f7fb01f git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/FIs_1.38.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: splineTimeR dependencyCount: 0 Package: fission Version: 1.30.0 Depends: R (>= 2.10), SummarizedExperiment Suggests: knitr, markdown License: LGPL MD5sum: 08840fd77a7a54f108c681fbe8eb39dc NeedsCompilation: no Title: RangedSummarizedExperiment for time course RNA-Seq of fission yeast in response to stress, by Leong et al., Nat Commun 2014. Description: This package provides a RangedSummarizedExperiment object of read counts in genes for a time course RNA-Seq experiment of fission yeast (Schizosaccharomyces pombe) in response to oxidative stress (1M sorbitol treatment) at 0, 15, 30, 60, 120 and 180 mins. The samples are further divided between a wild-type group and a group with deletion of atf21. The read count matrix was prepared and provided by the author of the study: Leong HS, Dawson K, Wirth C, Li Y, Connolly Y, Smith DL, Wilkinson CR, Miller CJ. "A global non-coding RNA system modulates fission yeast protein levels in response to stress". Nat Commun 2014 May 23;5:3947. PMID: 24853205. GEO: GSE56761. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData, GEO Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/fission git_branch: RELEASE_3_22 git_last_commit: ae4955f git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/fission_1.30.0.tar.gz vignettes: vignettes/fission/inst/doc/fission.html vignetteTitles: Fission yeast time course hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/fission/inst/doc/fission.R dependsOnMe: ROCpAI, rnaseqGene dependencyCount: 25 Package: Fletcher2013a Version: 1.46.0 Depends: R (>= 2.15), limma Imports: Biobase ,VennDiagram, gplots,grid License: GPL (>= 2) MD5sum: d2a72223e684a934a8e5fcec6ff4a139 NeedsCompilation: no Title: Gene expression data from breast cancer cells under FGFR2 signalling perturbation Description: The package Fletcher2013a contains time-course gene expression data from MCF-7 cells treated under different experimental systems in order to perturb FGFR2 signalling. The data comes from Fletcher et al. (Nature Comms 4:2464, 2013) where further details about the background and the experimental design of the study can be found. biocViews: ExperimentData, ExpressionData, CancerData, BreastCancerData, MicroarrayData Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin Meyer. Maintainer: Mauro Castro URL: http://dx.doi.org/10.1038/ncomms3464 git_url: https://git.bioconductor.org/packages/Fletcher2013a git_branch: RELEASE_3_22 git_last_commit: 5f93ee4 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/Fletcher2013a_1.46.0.tar.gz vignettes: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.pdf vignetteTitles: Main vignette:Fletcher2013a hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.R dependsOnMe: Fletcher2013b suggestsMe: NetActivity dependencyCount: 21 Package: Fletcher2013b Version: 1.46.0 Depends: R (>= 2.15), Fletcher2013a, RTN (>= 1.1.2), RedeR (>= 1.8.1), igraph Imports: RColorBrewer License: GPL (>= 2) MD5sum: 5d4bd34d30131d89113f1285634e2548 NeedsCompilation: no Title: Master regulators of FGFR2 signalling and breast cancer risk Description: This package reproduces the systems biology analysis for the data in package Fletcher2013a using RTN. biocViews: ExperimentData, ChIPSeqData, CancerData, BreastCancerData, SNPData Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin Meyer. Maintainer: Mauro Castro URL: http://dx.doi.org/10.1038/ncomms3464 git_url: https://git.bioconductor.org/packages/Fletcher2013b git_branch: RELEASE_3_22 git_last_commit: 85a698b git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/Fletcher2013b_1.46.0.tar.gz vignettes: vignettes/Fletcher2013b/inst/doc/Fletcher2013b.pdf vignetteTitles: Main vignette:Fletcher2013b hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Fletcher2013b/inst/doc/Fletcher2013b.R suggestsMe: geneplast dependencyCount: 146 Package: flowPloidyData Version: 1.36.0 Suggests: knitr, rmarkdown, flowCore License: GPL-3 MD5sum: e095fc864bf2d9b7efc72b50ce51518c NeedsCompilation: no Title: Example Flow Cytometry Data Description: A collection of raw flow cytometry data for use in vignettes for the flowPloidy package. biocViews: FlowCytometryData Author: Tyler Smith Maintainer: Tyler Smith VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/flowPloidyData git_branch: RELEASE_3_22 git_last_commit: 241b58a git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/flowPloidyData_1.36.0.tar.gz vignettes: vignettes/flowPloidyData/inst/doc/flowPloidyData.html vignetteTitles: flowPloidy Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: flowPloidy dependencyCount: 0 Package: FlowSorted.Blood.450k Version: 1.48.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 0e9f5e7c16f1d5886eb5a8a824962483 NeedsCompilation: no Title: Illumina HumanMethylation data on sorted blood cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays, and an object depicting which CpGs on the array are associated with cell type. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Andrew E Jaffe Maintainer: Andrew E Jaffe git_url: https://git.bioconductor.org/packages/FlowSorted.Blood.450k git_branch: RELEASE_3_22 git_last_commit: 9e5687b git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/FlowSorted.Blood.450k_1.48.0.tar.gz vignettes: vignettes/FlowSorted.Blood.450k/inst/doc/FlowSorted.Blood.450k.pdf vignetteTitles: FlowSorted Blood 450k Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.Blood.450k/inst/doc/FlowSorted.Blood.450k.R dependsOnMe: methylCC, methylationArrayAnalysis suggestsMe: minfi, wateRmelon, FlowSorted.Blood.EPIC dependencyCount: 143 Package: FlowSorted.Blood.EPIC Version: 2.14.0 Depends: R (>= 3.5), minfi(>= 1.21.2), ExperimentHub Imports: genefilter, nlme, quadprog, graphics, stats, utils, AnnotationHub, SummarizedExperiment, S4Vectors Suggests: knitr,rmarkdown, FlowSorted.CordBlood.450k, FlowSorted.Blood.450k(>= 1.0.1), EpiDISH,FlowSorted.CordBloodNorway.450k, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Enhances: FlowSorted.CordBloodCombined.450k(>= 1.11.5) License: GPL-3 MD5sum: be980e595dc57da085e211855538385d NeedsCompilation: no Title: Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells Description: Raw data objects to be used for blood cell proportion estimation in minfi and similar packages. The FlowSorted.Blood.EPIC object is based in samples assayed by Brock Christensen and colleagues; for details see Salas et al. 2018. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, Genome, TissueMicroarrayData, MethylationArrayData Author: Lucas A. Salas [cre, aut], Devin C. Koestler [aut], Rondi A. Butler [ctb], Helen M. Hansen [ctb], John K. Wiencke [ctb], Karl T. Kelsey [ctb], Brock C. Christensen [ctb], Kasper Daniel Hansen [ctb] (author and maintainer of the original minfi estimateCellCounts and internal functions), Jean-Philippe Fortin [ctb] (contributor in the original minfi estimateCellCounts and internal functions), Shan V. Andrews [ctb] (contributor in the original minfi estimateCellCounts and internal functions), E. Andres Houseman [ctb] (author of the original quadratic programming function used for cell projection), Andrew E Jaffe [ctb] (author of the original estimateCellCounts and internal functions within minfi) Maintainer: Lucas A. Salas URL: https://github.com/immunomethylomics/FlowSorted.Blood.EPIC VignetteBuilder: knitr BugReports: https://github.com/immunomethylomics/FlowSorted.Blood.EPIC/issues. git_url: https://git.bioconductor.org/packages/FlowSorted.Blood.EPIC git_branch: RELEASE_3_22 git_last_commit: 317d4a4 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/FlowSorted.Blood.EPIC_2.14.0.tar.gz vignettes: vignettes/FlowSorted.Blood.EPIC/inst/doc/FlowSorted.Blood.EPIC.html vignetteTitles: FlowSorted.Blood.EPIC hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.Blood.EPIC/inst/doc/FlowSorted.Blood.EPIC.R importsMe: HiBED suggestsMe: DMRcate, wateRmelon, FlowSorted.CordBloodCombined.450k dependencyCount: 151 Package: FlowSorted.CordBlood.450k Version: 1.38.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 481c4383335fe86eebb2fac702ed6bc3 NeedsCompilation: no Title: Illumina 450k data on sorted cord blood cells Description: Raw data objects to be used for cord blood cell proportion estimation in minfi. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Shan V. Andrews [cre, aut], Kelly M. Bakulski [aut] Maintainer: Shan V. Andrews git_url: https://git.bioconductor.org/packages/FlowSorted.CordBlood.450k git_branch: RELEASE_3_22 git_last_commit: aacd0f3 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/FlowSorted.CordBlood.450k_1.38.0.tar.gz vignettes: vignettes/FlowSorted.CordBlood.450k/inst/doc/FlowSorted.CordBlood.450k.pdf vignetteTitles: Minfi Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: FlowSorted.Blood.EPIC dependencyCount: 143 Package: FlowSorted.CordBloodCombined.450k Version: 1.26.0 Depends: R (>= 3.6), minfi (>= 1.21.2), ExperimentHub(>= 1.9.1) Imports: SummarizedExperiment, IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b4.hg19, utils, AnnotationHub Suggests: FlowSorted.Blood.EPIC, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: GPL-3 MD5sum: 503d97d9a40b4d16079b71560036cf47 NeedsCompilation: no Title: Illumina 450k/EPIC data on FACS and MACS umbilical blood cells Description: Raw data objects to be used for umbilical cord blood cell proportion estimation in minfi and similar packages. The FlowSorted.CordBloodCombined.450k object is based in samples assayed by Bakulski et al, Gervin et al., de Goede et al., and Lin et al. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, Genome, TissueMicroarrayData, MethylationArrayData, ExperimentHub Author: Lucas A. Salas [cre, aut], Kristina Gervin [aut], Meaghan C. Jones [aut], Kelly M. Bakulski [ctb], Devin C. Koestler [ctb], John K. Wiencke [ctb], Karl T. Kelsey [ctb], Robert Lyle [ctb], Brock C. Christensen [ctb], Janine Felix [ctb] Maintainer: Lucas A. Salas URL: https://github.com/immunomethylomics/FlowSorted.CordBloodCombined.450k VignetteBuilder: knitr BugReports: https://github.com/immunomethylomics/FlowSorted.CordBloodCombined.450k/issues. git_url: https://git.bioconductor.org/packages/FlowSorted.CordBloodCombined.450k git_branch: RELEASE_3_22 git_last_commit: 0b402b3 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/FlowSorted.CordBloodCombined.450k_1.26.0.tar.gz vignettes: vignettes/FlowSorted.CordBloodCombined.450k/inst/doc/FlowSorted.CordBloodCombined.450k.html vignetteTitles: FlowSorted.CordBloodCombined.450k hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.CordBloodCombined.450k/inst/doc/FlowSorted.CordBloodCombined.450k.R dependencyCount: 153 Package: FlowSorted.CordBloodNorway.450k Version: 1.36.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 78795af66e2b04db52262fbb35c8817e NeedsCompilation: no Title: Illumina HumanMethylation data on sorted cord blood cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays, for cell type composition estimation. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: kristina gervin [cre, aut], Kasper Daniel Hansen [aut] Maintainer: kristina gervin URL: https://bitbucket.com/kasperdanielhansen/Illumina_CordBlood git_url: https://git.bioconductor.org/packages/FlowSorted.CordBloodNorway.450k git_branch: RELEASE_3_22 git_last_commit: a5da2ea git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/FlowSorted.CordBloodNorway.450k_1.36.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 143 Package: FlowSorted.DLPFC.450k Version: 1.46.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 86bef5e2aa7ad389cd9d2ccf8c7f1fde NeedsCompilation: no Title: Illumina HumanMethylation data on sorted frontal cortex cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Andrew E Jaffe, Zachary A. Kaminsky Maintainer: Andrew E Jaffe git_url: https://git.bioconductor.org/packages/FlowSorted.DLPFC.450k git_branch: RELEASE_3_22 git_last_commit: 21b2181 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/FlowSorted.DLPFC.450k_1.46.0.tar.gz vignettes: vignettes/FlowSorted.DLPFC.450k/inst/doc/FlowSorted.DLPFC.450k.pdf vignetteTitles: FlowSorted DLPFC 450k Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.DLPFC.450k/inst/doc/FlowSorted.DLPFC.450k.R importsMe: HiBED dependencyCount: 143 Package: flowWorkspaceData Version: 3.22.0 License: GPL-2 MD5sum: 28e573691dfe3430a4a8727f89510f1d NeedsCompilation: no Title: A data package containing two flowJo, one diva xml workspace and the associated fcs files as well as three GatingSets for testing the flowWorkspace, openCyto and CytoML packages. Description: The necessary external data to run the flowWorkspace and openCyto vignette is found in this package. biocViews: ExperimentData, FlowCytometryData Author: Greg Finak Maintainer: Mike Jiang git_url: https://git.bioconductor.org/packages/flowWorkspaceData git_branch: RELEASE_3_22 git_last_commit: 99bf675 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/flowWorkspaceData_3.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: COMPASS, CytoML, flowClust, flowCore, flowWorkspace, ggcyto, openCyto dependencyCount: 0 Package: fourDNData Version: 1.10.0 Depends: R (>= 4.2) Imports: BiocFileCache, HiCExperiment, GenomicRanges, IRanges, S4Vectors, utils, tools Suggests: rtracklayer, dplyr, testthat, methods, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: a290a61e4bb84153d034785c8a7723fc NeedsCompilation: no Title: 4DN data package Description: fourDNData is a data package giving programmatic access to Hi-C contact matrices uniformly processed by the [4DN consortium](https://www.4dnucleome.org/). The matrices are available in the multi-resolution `.mcool` format. biocViews: ExperimentData, SequencingData Author: Jacques Serizay [aut, cre] Maintainer: Jacques Serizay URL: https://github.com/js2264/fourDNData VignetteBuilder: knitr BugReports: https://github.com/js2264/fourDNData/issues git_url: https://git.bioconductor.org/packages/fourDNData git_branch: RELEASE_3_22 git_last_commit: 77a5348 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/fourDNData_1.10.0.tar.gz vignettes: vignettes/fourDNData/inst/doc/fourDNData.html vignetteTitles: fourDNData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/fourDNData/inst/doc/fourDNData.R importsMe: OHCA dependencyCount: 85 Package: frmaExampleData Version: 1.46.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 158364f60dd61c08f5aea729ef4fd0c9 NeedsCompilation: no Title: Frma Example Data Description: Data files used by the examples in frma and frmaTools packages biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/frmaExampleData git_branch: RELEASE_3_22 git_last_commit: def44a0 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/frmaExampleData_1.46.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: frma, frmaTools dependencyCount: 0 Package: furrowSeg Version: 1.38.0 Depends: R (>= 3.3), EBImage Imports: abind, dplyr, locfit, tiff Suggests: BiocStyle, ggplot2, knitr License: Artistic-2.0 MD5sum: 14f2cb5a0ee05dcc2e2ef76877e6bb14 NeedsCompilation: no Title: Furrow Segmentation Description: Image feature data and analysis codes for the Guglielmi, Barry et al. paper describing the application of an optogenetics tools to disrupt Drosophila embryo furrowing. biocViews: ExperimentData, Drosophila_melanogaster_Data, Tissue, ReproducibleResearch Author: Joseph Barry Maintainer: Joseph Barry VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/furrowSeg git_branch: RELEASE_3_22 git_last_commit: 6683afc git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/furrowSeg_1.38.0.tar.gz vignettes: vignettes/furrowSeg/inst/doc/exampleFurrowSegmentation.pdf, vignettes/furrowSeg/inst/doc/genPaperFigures.pdf vignetteTitles: Supplementary Methods - Example furrow segmentation, Supplementary Methods - Automatic generation of paper figures hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/furrowSeg/inst/doc/exampleFurrowSegmentation.R, vignettes/furrowSeg/inst/doc/genPaperFigures.R dependencyCount: 55 Package: gageData Version: 2.48.0 Depends: R (>= 2.10) Suggests: gage, pathview, genefilter License: GPL (>=2.0) MD5sum: 87789132308228c88c93b7474a23899e NeedsCompilation: no Title: Auxillary data for gage package Description: This is a supportive data package for the software package, gage. However, the data supplied here are also useful for gene set or pathway analysis or microarray data analysis in general. In this package, we provide two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and BMP6 (originally published as an demo dataset for GAGE, also registered as GSE13604 in GEO). This package also includes commonly used gene set data based on KEGG pathways and GO terms for major research species, including human, mouse, rat and budding yeast. Mapping data between common gene IDs for budding yeast are also included. biocViews: ExperimentData, StemCell, CancerData, BreastCancerData, MicroarrayData, GEO Author: Weijun Luo Maintainer: Weijun Luo git_url: https://git.bioconductor.org/packages/gageData git_branch: RELEASE_3_22 git_last_commit: 5d31f30 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/gageData_2.48.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: gage dependencyCount: 0 Package: gaschYHS Version: 1.48.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 20f242bfbb3e034319885130b0c278b8 NeedsCompilation: no Title: ExpressionSet for response of yeast to heat shock and other environmental stresses Description: Data from PMID 11102521 biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data Author: Audrey Gasch and colleagues Maintainer: Vince Carey URL: http://genome-www.stanford.edu/yeast_stress/data/rawdata/complete_dataset.txt git_url: https://git.bioconductor.org/packages/gaschYHS git_branch: RELEASE_3_22 git_last_commit: 8f92e00 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/gaschYHS_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: gcspikelite Version: 1.48.0 Depends: R (>= 2.5.0) License: LGPL MD5sum: d860bbe0d50d3d9d15d8ebb5e5d68f03 NeedsCompilation: no Title: Spike-in data for GC/MS data and methods within flagme Description: Spike-in data for GC/MS data and methods within flagme biocViews: MassSpectrometryData Author: Mark Robinson Maintainer: Mark Robinson git_url: https://git.bioconductor.org/packages/gcspikelite git_branch: RELEASE_3_22 git_last_commit: df05c64 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/gcspikelite_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: flagme suggestsMe: erah dependencyCount: 0 Package: gDNAinRNAseqData Version: 1.10.0 Depends: R (>= 4.3) Imports: RCurl, XML, ExperimentHub, BiocGenerics, Rsamtools Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 43d38aaefcc24cd85c1108d34731af57 NeedsCompilation: no Title: RNA-seq data with different levels of gDNA contamination Description: Provides access to BAM files generated from RNA-seq data produced with different levels of gDNA contamination. It currently allows one to download a subset of the data published by Li et al., BMC Genomics, 23:554, 2022. This subset of data is formed by BAM files with about 100,000 alignments with three different levels of gDNA contamination. biocViews: ExperimentHub, ExperimentData, ExpressionData, SequencingData, RNASeqData, Homo_sapiens_Data Author: Robert Castelo [aut, cre] (ORCID: ) Maintainer: Robert Castelo URL: https://github.com/functionalgenomics/gDNAinRNAseqData VignetteBuilder: knitr BugReports: https://github.com/functionalgenomics/gDNAinRNAseqData git_url: https://git.bioconductor.org/packages/gDNAinRNAseqData git_branch: RELEASE_3_22 git_last_commit: 2b1b649 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/gDNAinRNAseqData_1.10.0.tar.gz vignettes: vignettes/gDNAinRNAseqData/inst/doc/gDNAinRNAseqData.html vignetteTitles: RNA-seq data with different levels of gDNA contamination hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/gDNAinRNAseqData/inst/doc/gDNAinRNAseqData.R suggestsMe: gDNAx dependencyCount: 80 Package: gDRtestData Version: 1.8.0 Depends: R (>= 4.2) Imports: checkmate, data.table Suggests: BiocStyle, gDRstyle (>= 1.7.1), knitr, qs, reshape2, rmarkdown, SummarizedExperiment, testthat, yaml License: Artistic-2.0 MD5sum: 39e2b20012a76dda879594d7c7bc8782 NeedsCompilation: no Title: gDRtestData - R data package with testing dose response data Description: R package with internal dose-response test data. Package provides functions to generate input testing data that can be used as the input for gDR pipeline. It also contains qs files with MAE data processed by gDR. biocViews: ExperimentData, TechnologyData Author: Aleksander Chlebowski [aut], Bartosz Czech [aut] (ORCID: ), Arkadiusz Gladki [cre, aut] (ORCID: ), Marc Hafner [aut] (ORCID: ), Marcin Kamianowski [aut], Sergiu Mocanu [aut], Natalia Potocka [aut], Dariusz Scigocki [aut], Janina Smola [aut], Allison Voung [aut] Maintainer: Arkadiusz Gladki URL: https://github.com/gdrplatform/gDRtestData, https://gdrplatform.github.io/gDRtestData/ VignetteBuilder: knitr BugReports: https://github.com/gdrplatform/gDRtestData/issues git_url: https://git.bioconductor.org/packages/gDRtestData git_branch: RELEASE_3_22 git_last_commit: de7ea59 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/gDRtestData_1.8.0.tar.gz vignettes: vignettes/gDRtestData/inst/doc/gDRtestData.html vignetteTitles: gDRtestData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/gDRtestData/inst/doc/gDRtestData.R suggestsMe: gDR, gDRcore, gDRimport, gDRutils dependencyCount: 5 Package: geneLenDataBase Version: 1.46.0 Depends: R (>= 2.11.0) Imports: utils, rtracklayer, GenomicFeatures, txdbmaker License: LGPL (>= 2) MD5sum: 431c09197f66285a04401f72afd634d4 NeedsCompilation: no Title: Lengths of mRNA transcripts for a number of genomes Description: Length of mRNA transcripts for a number of genomes and gene ID formats, largely based on UCSC table browser. Data objects are provided as individual pieces of information to be retrieved and loaded. A variety of different gene identifiers and genomes is supported to ensure wide applicability. biocViews: ExperimentData, Genome Author: Matthew Young [aut], Nadia Davidson [aut], Federico Marini [ctb, cre] (ORCID: ) Maintainer: Federico Marini URL: https://github.com/federicomarini/geneLenDataBase BugReports: https://github.com/federicomarini/geneLenDataBase/issues git_url: https://git.bioconductor.org/packages/geneLenDataBase git_branch: RELEASE_3_22 git_last_commit: 0bae7f6 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/geneLenDataBase_1.46.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: goseq importsMe: SMITE dependencyCount: 100 Package: genomationData Version: 1.42.0 Suggests: knitr License: GPL-3 MD5sum: d89f5bcbc35c0c871968708190b990c9 NeedsCompilation: no Title: Experimental data for showing functionalities of the genomation package Description: The package contains Chip Seq, Methylation and Cage data, downloaded from Encode biocViews: ExperimentData, Genome, StemCell, SequencingData, ChIPSeqData, ChipOnChipData, ENCODE Author: Altuna Akalin, Vedran Franke Maintainer: Vedran Franke VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/genomationData git_branch: RELEASE_3_22 git_last_commit: 4a8c0fa git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/genomationData_1.42.0.tar.gz vignettes: vignettes/genomationData/inst/doc/genomationData-knitr.pdf vignetteTitles: genomationData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/genomationData/inst/doc/genomationData-knitr.R suggestsMe: genomation dependencyCount: 0 Package: GenomicDistributionsData Version: 1.18.0 Depends: R (>= 4.1) Imports: ExperimentHub (>= 1.14.0), AnnotationHub, AnnotationFilter, data.table, utils, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges, ensembldb Suggests: knitr, BiocStyle, rmarkdown License: BSD_2_clause + file LICENSE MD5sum: 657a9e7475a7b219fe000164d00b6a05 NeedsCompilation: no Title: Reference data for GenomicDistributions package Description: This package provides ready to use reference data for GenomicDistributions package. Raw data was obtained from ensembldb and processed with helper functions. Data files are available for the following genome assemblies: hg19, hg38, mm9 and mm10. biocViews: ExperimentHub, ExperimentData, Genome Author: Michal Stolarczyk [aut], Kristyna Kupkova [aut, cre], Jose Verdezoto [aut], John Lawson [ctb], Jason Smith [ctb], Nathan C. Sheffield [ctb] Maintainer: Kristyna Kupkova VignetteBuilder: knitr BugReports: http://github.com/databio/GenomicDistributionsData git_url: https://git.bioconductor.org/packages/GenomicDistributionsData git_branch: RELEASE_3_22 git_last_commit: 2c55533 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/GenomicDistributionsData_1.18.0.tar.gz vignettes: vignettes/GenomicDistributionsData/inst/doc/intro.html vignetteTitles: 1. Getting started with GenomicDistributionsData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/GenomicDistributionsData/inst/doc/intro.R suggestsMe: GenomicDistributions dependencyCount: 105 Package: GeuvadisTranscriptExpr Version: 1.38.0 Depends: R (>= 3.5.0) Suggests: limma, rtracklayer, GenomicRanges, Rsamtools, VariantAnnotation, tools, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: 78b351a472fa7c11d3ef77305803ed08 NeedsCompilation: no Title: Data package with transcript expression and bi-allelic genotypes from the GEUVADIS project Description: Provides transcript expression and bi-allelic genotypes corresponding to the chromosome 19 for CEU individuals from the GEUVADIS project, Lappalainen et al. biocViews: Homo_sapiens_Data, SNPData, Genome, RNASeqData, SequencingData, ExpressionData Author: Malgorzata Nowicka [aut, cre] Maintainer: Malgorzata Nowicka VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GeuvadisTranscriptExpr git_branch: RELEASE_3_22 git_last_commit: 5b748e8 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/GeuvadisTranscriptExpr_1.38.0.tar.gz vignettes: vignettes/GeuvadisTranscriptExpr/inst/doc/GeuvadisTranscriptExpr.pdf vignetteTitles: Preprocessing and preparation of transcript expression and genotypes from the GEUVADIS project for sQTL analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GeuvadisTranscriptExpr/inst/doc/GeuvadisTranscriptExpr.R suggestsMe: DRIMSeq dependencyCount: 0 Package: GIGSEAdata Version: 1.28.0 Depends: R (>= 3.5) Suggests: GIGSEA, knitr, rmarkdown License: LGPL-3 MD5sum: 597bcc2e10f419d3b41ca564b2d44d18 NeedsCompilation: no Title: Gene set collections for the GIGSEA package Description: The gene set collection used for the GIGSEA package. biocViews: ExperimentData, Homo_sapiens_Data Author: Shijia Zhu Maintainer: Shijia Zhu VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GIGSEAdata git_branch: RELEASE_3_22 git_last_commit: 6b89d9c git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/GIGSEAdata_1.28.0.tar.gz vignettes: vignettes/GIGSEAdata/inst/doc/GIGSEAdata_tutorial.pdf vignetteTitles: GIGSEAdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GIGSEAdata/inst/doc/GIGSEAdata_tutorial.R dependencyCount: 0 Package: golubEsets Version: 1.52.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: LGPL MD5sum: cbb8a2bcefde2e5a73934038bf6c6e1d NeedsCompilation: no Title: exprSets for golub leukemia data Description: representation of public golub data with some covariate data of provenance unknown to the maintainer at present; now employs ExpressionSet format biocViews: ExperimentData, Genome, CancerData, LeukemiaCancerData Author: Todd Golub Maintainer: Vince Carey git_url: https://git.bioconductor.org/packages/golubEsets git_branch: RELEASE_3_22 git_last_commit: d64fb88 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/golubEsets_1.52.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: adSplit, Biobase, biosigner, GlobalAncova, globaltest, idiogram, MLInterfaces, pvca, RDRToolbox, twilight dependencyCount: 7 Package: gpaExample Version: 1.22.0 Depends: R (>= 4.0.0) License: GPL (>= 2) MD5sum: 0d537e3b4fd543bff965f2bc39d55a8e NeedsCompilation: no Title: Example data for the GPA package (Genetic analysis incorporating Pleiotropy and Annotation) Description: Example data for the GPA package, consisting of the p-values of 1,219,805 SNPs for five psychiatric disorder GWAS from the psychiatric GWAS consortium (PGC), with the annotation data using genes preferentially expressed in the central nervous system (CNS). biocViews: ExperimentData, Homo_sapiens_Data, SNPData Author: Dongjun Chung, Carter Allen Maintainer: Dongjun Chung URL: http://dongjunchung.github.io/GPA/ git_url: https://git.bioconductor.org/packages/gpaExample git_branch: RELEASE_3_22 git_last_commit: 0141dbb git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/gpaExample_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GPA dependencyCount: 0 Package: grndata Version: 1.42.0 Depends: R (>= 2.10) Suggests: RUnit, BiocGenerics, knitr License: GPL-3 MD5sum: 92c17261063158a42019d3a8ec210c2e NeedsCompilation: no Title: Synthetic Expression Data for Gene Regulatory Network Inference Description: Simulated expression data for five large Gene Regulatory Networks from different simulators biocViews: ExperimentData, NetworkInference, GeneExpression, Microarray, GeneRegulation, Network Author: Pau Bellot, Catharina Olsen, Patrick E Meyer Maintainer: Pau Bellot VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/grndata git_branch: RELEASE_3_22 git_last_commit: 82edd20 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/grndata_1.42.0.tar.gz vignettes: vignettes/grndata/inst/doc/grndata.html vignetteTitles: GRNdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: GSBenchMark Version: 1.30.0 Depends: R (>= 2.13.1) License: GPL-2 MD5sum: 4b8eeea9622cfd98afe34f5641eab2a6 NeedsCompilation: no Title: Gene Set Benchmark Description: Benchmarks for Machine Learning Analysis of the Gene Sets. The package contains a list of pathways and gene expression data sets used in "Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)" (2010) by Eddy et al. biocViews: MicroarrayData Author: Bahman Afsari , Elana J. Fertig Maintainer: Bahman Afsari git_url: https://git.bioconductor.org/packages/GSBenchMark git_branch: RELEASE_3_22 git_last_commit: 3467623 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/GSBenchMark_1.30.0.tar.gz vignettes: vignettes/GSBenchMark/inst/doc/GSBenchMark.pdf vignetteTitles: Working with the GSBenchMark package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GSBenchMark/inst/doc/GSBenchMark.R suggestsMe: GSReg dependencyCount: 0 Package: GSE103322 Version: 1.16.0 Depends: Biobase, GEOquery Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown, SummarizedExperiment, SingleCellExperiment License: Artistic-2.0 MD5sum: 3cd0bb8c4c0d337b2722ea94bce3a3f0 NeedsCompilation: no Title: GEO accession data GSE103322 as a SingleCellExperiment Description: Single cell RNA-Seq data for 5902 cells from 18 patients with oral cavity head and neck squamous cell carcinoma available as GEO accession [GSE103322] (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE103322). GSE103322 data have been parsed into a SincleCellExperiment object available in ExperimentHub. biocViews: ExperimentData, Genome, DNASeqData, RNASeqData, ExperimentData, ExpressionData, RNASeqData, Homo_sapiens_Data, CancerData, SingleCellData, GEO, ExperimentHub Author: Mariano Alvarez [aut, cre] Maintainer: Mariano Alvarez VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GSE103322 git_branch: RELEASE_3_22 git_last_commit: 8ac31d6 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/GSE103322_1.16.0.tar.gz vignettes: vignettes/GSE103322/inst/doc/GSE103322.html vignetteTitles: scRNASeq HNSC data using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GSE103322/inst/doc/GSE103322.R dependencyCount: 75 Package: GSE13015 Version: 1.18.0 Depends: Biobase, GEOquery Imports: preprocessCore, SummarizedExperiment, GEOquery, Biobase Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown License: MIT License MD5sum: 095481c4e2500233400889a92a1a8434 NeedsCompilation: no Title: GEO accession data GSE13015_GPL6106 as a SummarizedExperiment Description: Microarray expression matrix platform GPL6106 and clinical data for 67 septicemic patients and made them available as GEO accession [GSE13015](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13015). GSE13015 data have been parsed into a SummarizedExperiment object available in ExperimentHub. This data data could be used as an example supporting BloodGen3Module R package. biocViews: ExperimentData, MicroarrayData,ExperimentHub Author: Darawan Rinchai [aut, cre] (ORCID: ) Maintainer: Darawan Rinchai VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GSE13015 git_branch: RELEASE_3_22 git_last_commit: 914bf11 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/GSE13015_1.18.0.tar.gz vignettes: vignettes/GSE13015/inst/doc/GSE13015.html vignetteTitles: Expression data from GSE13015 using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/GSE13015/inst/doc/GSE13015.R dependencyCount: 76 Package: GSE159526 Version: 1.16.0 Suggests: ExperimentHub, BiocStyle, RefManageR, knitr, rmarkdown, testthat, minfi, tibble, sessioninfo License: MIT + file LICENSE MD5sum: 7f59625a1c8bccb518f497e76a8c839d NeedsCompilation: no Title: Placental cell DNA methylation data from GEO accession GSE159526 Description: 19 term and 9 first trimester placental chorionic villi and matched cell-sorted samples ran on Illumina HumanMethylationEPIC DNA methylation microarrays. This data was made available on GEO accession [GSE159526](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159526). Both the raw and processed data has been made available on \code{ExperimentHub}. Raw unprocessed data formatted as an RGChannelSet object for integration and normalization using minfi and other existing Bioconductor packages. Processed normalized data is also available as a DNA methylation \code{matrix}, with a corresponding phenotype information as a \code{data.frame} object. biocViews: ExperimentData, ExperimentHub, GEO, Genome, Tissue, MethylationArrayData, Homo_sapiens_Data Author: Victor Yuan [aut, cre] (ORCID: ) Maintainer: Victor Yuan URL: https://github.com/wvictor14/GSE159526 VignetteBuilder: knitr BugReports: https://github.com/wvictor14/GSE159526/issues git_url: https://git.bioconductor.org/packages/GSE159526 git_branch: RELEASE_3_22 git_last_commit: 866ae75 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/GSE159526_1.16.0.tar.gz vignettes: vignettes/GSE159526/inst/doc/GSE159526.html vignetteTitles: Introduction to GSE159526 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/GSE159526/inst/doc/GSE159526.R dependencyCount: 0 Package: GSE62944 Version: 1.38.0 Depends: Biobase, GEOquery Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown, DESeq2 License: Artistic-2.0 MD5sum: ddbe52bb10a4dec62aaea170984dccc7 NeedsCompilation: no Title: GEO accession data GSE62944 as a SummarizedExperiment Description: TCGA processed RNA-Seq data for 9264 tumor and 741 normal samples across 24 cancer types and made them available as GEO accession [GSE62944](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944). GSE62944 data have been parsed into a SummarizedExperiment object available in ExperimentHub. biocViews: ExperimentData, Genome, DNASeqData, RNASeqData Author: Sonali Arora Maintainer: Bioconductor Package Maintainer URL: http://bioconductor.org/packages/release/bioc/html/GSE62944.html VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GSE62944 git_branch: RELEASE_3_22 git_last_commit: 000769a git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/GSE62944_1.38.0.tar.gz vignettes: vignettes/GSE62944/inst/doc/GSE62944.html vignetteTitles: Raw TCGA data using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GSE62944/inst/doc/GSE62944.R suggestsMe: GSEABenchmarkeR dependencyCount: 75 Package: GSVAdata Version: 1.46.0 Depends: R (>= 3.5), Biobase, GSEABase, hgu95a.db, SummarizedExperiment License: Artistic-2.0 MD5sum: fe05f9ccc119719dfb837e6f505b59c6 NeedsCompilation: no Title: Data employed in the vignette of the GSVA package Description: This package stores the data employed in the vignette of the GSVA package. These data belong to the following publications: Armstrong et al. Nat Genet 30:41-47, 2002; Cahoy et al. J Neurosci 28:264-278, 2008; Carrel and Willard, Nature, 434:400-404, 2005; Huang et al. PNAS, 104:9758-9763, 2007; Pickrell et al. Nature, 464:768-722, 2010; Skaletsky et al. Nature, 423:825-837; Verhaak et al. Cancer Cell 17:98-110, 2010; Costa et al. FEBS J, 288:2311-2331, 2021. biocViews: ExperimentData, RNASeqData, Homo_sapiens_Data, CancerData, LeukemiaCancerData Author: Robert Castelo Maintainer: Robert Castelo git_url: https://git.bioconductor.org/packages/GSVAdata git_branch: RELEASE_3_22 git_last_commit: 36517b7 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/GSVAdata_1.46.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: singleCellTK, RVA suggestsMe: GSAR, GSVA dependencyCount: 61 Package: GWASdata Version: 1.48.0 Depends: GWASTools Suggests: ncdf4 License: Artistic-2.0 MD5sum: dd340a75af821e72b2b7c4c48a306b5f NeedsCompilation: no Title: Data used in the examples and vignettes of the GWASTools package Description: Selected Affymetrix and Illlumina SNP data for HapMap subjects. Data provided by the Center for Inherited Disease Research at Johns Hopkins University and the Broad Institute of MIT and Harvard University. biocViews: ExperimentData, MicroarrayData, SNPData, HapMap Author: Stephanie Gogarten Maintainer: Stephanie Gogarten git_url: https://git.bioconductor.org/packages/GWASdata git_branch: RELEASE_3_22 git_last_commit: 1e9fcc4 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/GWASdata_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GENESIS, GWASTools dependencyCount: 96 Package: h5vcData Version: 2.30.0 Suggests: h5vc License: GPL (>= 3) MD5sum: cbd55c8fbffe7d9800914d0dd22c7a33 NeedsCompilation: no Title: Example data for the h5vc package Description: This package contains the data used in the vignettes and examples of the 'h5vc' package biocViews: CancerData Author: Paul Theodor Pyl Maintainer: Paul Theodor Pyl git_url: https://git.bioconductor.org/packages/h5vcData git_branch: RELEASE_3_22 git_last_commit: 1ba3cbe git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/h5vcData_2.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: h5vc suggestsMe: HDF5Array dependencyCount: 0 Package: hapmap100khind Version: 1.52.0 Suggests: oligo License: GPL MD5sum: c45be9dc0476b0a2258ebebe396edea3 NeedsCompilation: no Title: Sample data - Hapmap 100K HIND Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap100khind git_branch: RELEASE_3_22 git_last_commit: 0d3ec97 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/hapmap100khind_1.52.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmap100kxba Version: 1.52.0 Suggests: oligo License: GPL MD5sum: 1ddb5b887bc58d35690db6ea5c787f1c NeedsCompilation: no Title: Sample data - Hapmap 100K XBA Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap100kxba git_branch: RELEASE_3_22 git_last_commit: 8dc0617 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/hapmap100kxba_1.52.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligo dependencyCount: 0 Package: hapmap500knsp Version: 1.52.0 Suggests: oligo License: GPL MD5sum: 97bde9fe32e8cd55311ce455bbdc5e4d NeedsCompilation: no Title: Sample data - Hapmap 500K NSP Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap500knsp git_branch: RELEASE_3_22 git_last_commit: 7e3902e git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/hapmap500knsp_1.52.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmap500ksty Version: 1.52.0 Suggests: oligo License: GPL MD5sum: 096af5aa2b75dc501f024ff0bb9c4140 NeedsCompilation: no Title: Sample data - Hapmap 500K STY Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap500ksty git_branch: RELEASE_3_22 git_last_commit: 15e5963 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/hapmap500ksty_1.52.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmapsnp5 Version: 1.52.0 Suggests: oligo License: GPL MD5sum: ffbac9aaba5e80febb5609b92a38ba56 NeedsCompilation: no Title: Sample data - Hapmap SNP 5.0 Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData, SNPData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmapsnp5 git_branch: RELEASE_3_22 git_last_commit: f0cc9da git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/hapmapsnp5_1.52.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligoClasses dependencyCount: 0 Package: hapmapsnp6 Version: 1.52.0 Depends: R (>= 2.15) Suggests: oligo, oligoClasses License: GPL MD5sum: d2f41d4f0689739f729dc6a3ee6eab15 NeedsCompilation: no Title: Sample data - Hapmap SNP 6.0 Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, SNPData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmapsnp6 git_branch: RELEASE_3_22 git_last_commit: 92ba8c7 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/hapmapsnp6_1.52.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: crlmm, oligoClasses dependencyCount: 0 Package: harbChIP Version: 1.48.0 Depends: R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5), Biostrings Imports: methods, stats License: Artistic-2.0 MD5sum: 699ecebf9e0766d4c4ed0728e4eed043 NeedsCompilation: no Title: Experimental Data Package: harbChIP Description: data from a yeast ChIP-chip experiment biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/harbChIP git_branch: RELEASE_3_22 git_last_commit: f26dab5 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/harbChIP_1.48.0.tar.gz vignettes: vignettes/harbChIP/inst/doc/yeastUpstream.pdf vignetteTitles: upstream sequence management for yeast hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/harbChIP/inst/doc/yeastUpstream.R dependencyCount: 16 Package: HarmanData Version: 1.38.0 Depends: R (>= 3.5.0) Suggests: BiocGenerics, BiocStyle, knitr, rmarkdown, Harman (>= 1.23.3) License: GPL-3 MD5sum: ef512bbf9eded8f15e9b4f9d2af0feb3 NeedsCompilation: no Title: Data for the Harman package Description: Datasets of accompany Harman, a PCA and constrained optimisation based technique. Contains three example datasets: IMR90, Human lung fibroblast cells exposed to nitric oxide; NPM, an experiment to test skin penetration of metal oxide nanoparticles following topical application of sunscreens in non-pregnant mice; OLF; an experiment to gauge the response of human olfactory neurosphere-derived (hONS) cells to ZnO nanoparticles. Since version 1.24, this package also contains the Infinium5 dataset, a set of batch correction adjustments across 5 Illumina Infinium Methylation BeadChip datasets. This file does not contain methylation data, but summary statistics of 5 datasets after correction. There is also an EpiSCOPE_sample file as exampling for the new methylation clustering functionality in Harman. biocViews: ExpressionData, MicroarrayData, ExperimentData, Homo_sapiens_Data, Mus_musculus_Data Author: Yalchin Oytam [aut], Josh Bowden [aut], Jason Ross [aut, cre] Maintainer: Jason Ross URL: http://www.bioinformatics.csiro.au/harman/ VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/HarmanData git_branch: RELEASE_3_22 git_last_commit: f20fb7c git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/HarmanData_1.38.0.tar.gz vignettes: vignettes/HarmanData/inst/doc/HarmanData.html vignetteTitles: HarmanData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HarmanData/inst/doc/HarmanData.R suggestsMe: Harman dependencyCount: 0 Package: HarmonizedTCGAData Version: 1.32.0 Depends: R (>= 3.4.0) Imports: ExperimentHub Suggests: AnnotationHub, knitr, rmarkdown, igraph, survival, ANF, stats, testthat License: GPL-3 MD5sum: 111cfba5d0567203269177db90f476f6 NeedsCompilation: no Title: Processed Harmonized TCGA Data of Five Selected Cancer Types Description: This package contains the processed harmonized TCGA data of five cancer types used in "Tianle Ma and Aidong Zhang, Integrate Multi-omic Data Using Affinity Network Fusion (ANF) for Cancer Patient Clustering". biocViews: CancerData, ReproducibleResearch Author: Tianle Ma Maintainer: Tianle Ma VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/HarmonizedTCGAData git_branch: RELEASE_3_22 git_last_commit: 36dd1c5 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/HarmonizedTCGAData_1.32.0.tar.gz vignettes: vignettes/HarmonizedTCGAData/inst/doc/HarmonizedTCGAData.html vignetteTitles: Patient Affinity Matrices Derived from Harmonized TCGA Dataset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HarmonizedTCGAData/inst/doc/HarmonizedTCGAData.R dependencyCount: 65 Package: HCAData Version: 1.26.0 Depends: R (>= 3.6), SingleCellExperiment Imports: ExperimentHub, AnnotationHub, HDF5Array, utils Suggests: knitr, rmarkdown, BiocStyle, scran (>= 1.11.4), BiocSingular, scater, scuttle, Rtsne, igraph, iSEE, testthat License: MIT + file LICENSE MD5sum: 9ad9445999c76d33135ecf225862c90a NeedsCompilation: no Title: Accessing The Datasets Of The Human Cell Atlas in R/Bioconductor Description: This package allows a direct access to the dataset generated by the Human Cell Atlas project for further processing in R and Bioconductor, in the comfortable format of SingleCellExperiment objects (available in other formats here: http://preview.data.humancellatlas.org/). biocViews: RNASeqData, SingleCellData, ExperimentData, ExpressionData, ExperimentHub Author: Federico Marini [aut, cre] (ORCID: ) Maintainer: Federico Marini URL: https://github.com/federicomarini/HCAData VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/HCAData git_branch: RELEASE_3_22 git_last_commit: 2fcc634 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/HCAData_1.26.0.tar.gz vignettes: vignettes/HCAData/inst/doc/hcadata.html vignetteTitles: Accessing the Human Cell Atlas datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HCAData/inst/doc/hcadata.R dependsOnMe: OSCA.workflows dependencyCount: 82 Package: HCATonsilData Version: 1.8.0 Depends: R (>= 4.3.0) Imports: ExperimentHub, SingleCellExperiment, SpatialExperiment, HDF5Array, SummarizedExperiment, S4Vectors, htmltools, rmarkdown, base64enc, utils Suggests: knitr, ggplot2, testthat (>= 3.0.0), scater, Seurat, Signac, zellkonverter, iSEE, ggspavis, kableExtra, BiocStyle License: MIT + file LICENSE MD5sum: 9892747012d26e623740921e2b60a9f3 NeedsCompilation: no Title: Provide programmatic access to the tonsil cell atlas datasets Description: This package provides access to the scRNA-seq, scATAC-seq, multiome, CITE-seq and spatial transcriptomics (Visium) data generated by the tonsil cell atlas in the context of the Human Cell Atlas (HCA). The data is provided via the Bioconductor project in the form of SingleCellExperiments. Additionally, information on the whole compendium of identified cell types is provided in form of a glossary. biocViews: SingleCellData, ExperimentData, RNASeqData, ExperimentHub, ExpressionData, SpatialData Author: Ramon Massoni-Badosa [aut, cre] (ORCID: ), Federico Marini [aut] (ORCID: ), Alan O'Callaghan [aut], Helena L. Crowell [aut] (ORCID: ) Maintainer: Ramon Massoni-Badosa URL: https://github.com/massonix/HCATonsilData VignetteBuilder: knitr BugReports: https://github.com/massonix/HCATonsilData/issues git_url: https://git.bioconductor.org/packages/HCATonsilData git_branch: RELEASE_3_22 git_last_commit: a4a1e25 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/HCATonsilData_1.8.0.tar.gz vignettes: vignettes/HCATonsilData/inst/doc/HCATonsilData.html vignetteTitles: HCATonsilData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HCATonsilData/inst/doc/HCATonsilData.R dependencyCount: 100 Package: HD2013SGI Version: 1.50.0 Depends: R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots, limma, vcd, LSD,EBImage Suggests: BiocStyle License: Artistic-2.0 MD5sum: 08b4b3b4638830efc0be8042d4b6093e NeedsCompilation: no Title: Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping Description: This package contains the experimental data and a complete executable transcript (vignette) of the analysis of the HCT116 genetic interaction matrix presented in the paper "Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping" by C. Laufer, B. Fischer, M. Billmann, W. Huber, M. Boutros; Nature Methods (2013) 10:427-31. doi: 10.1038/nmeth.2436. biocViews: ExperimentData, CancerData, ColonCancerData, MicrotitrePlateAssayData, CellCulture, Homo_sapiens_Data, HighThroughputImagingData Author: Bernd Fischer Maintainer: Mike Smith SystemRequirements: GNU make git_url: https://git.bioconductor.org/packages/HD2013SGI git_branch: RELEASE_3_22 git_last_commit: b2b25f4 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/HD2013SGI_1.50.0.tar.gz vignettes: vignettes/HD2013SGI/inst/doc/HD2013SGI.pdf vignetteTitles: HD2013SGI hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HD2013SGI/inst/doc/HD2013SGI.R suggestsMe: splots dependencyCount: 88 Package: HDCytoData Version: 1.30.0 Depends: ExperimentHub, SummarizedExperiment, flowCore Imports: utils, methods Suggests: BiocStyle, knitr, rmarkdown, Rtsne, umap, ggplot2, FlowSOM, mclust License: MIT + file LICENSE MD5sum: ebd55893742d9cfdd113b87159a3f28c NeedsCompilation: no Title: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats Description: Data package containing a set of publicly available high-dimensional cytometry benchmark datasets, formatted into SummarizedExperiment and flowSet Bioconductor object formats, including all required metadata. Row metadata includes sample IDs, group IDs, patient IDs, reference cell population or cluster labels (where available), and labels identifying 'spiked in' cells (where available). Column metadata includes channel names, protein marker names, and protein marker classes (cell type or cell state). biocViews: ExperimentHub, ExperimentData, ExpressionData, FlowCytometryData, SingleCellData, Homo_sapiens_Data, ImmunoOncologyData Author: Lukas M. Weber [aut, cre], Charlotte Soneson [aut] Maintainer: Lukas M. Weber URL: https://github.com/lmweber/HDCytoData VignetteBuilder: knitr BugReports: https://github.com/lmweber/HDCytoData/issues git_url: https://git.bioconductor.org/packages/HDCytoData git_branch: RELEASE_3_22 git_last_commit: e43afbb git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/HDCytoData_1.30.0.tar.gz vignettes: vignettes/HDCytoData/inst/doc/Contribution_guidelines.html, vignettes/HDCytoData/inst/doc/Examples_and_use_cases.html, vignettes/HDCytoData/inst/doc/HDCytoData_package.html vignetteTitles: 3. Contribution guidelines, 2. Examples and use cases, 1. HDCytoData package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HDCytoData/inst/doc/Contribution_guidelines.R, vignettes/HDCytoData/inst/doc/Examples_and_use_cases.R, vignettes/HDCytoData/inst/doc/HDCytoData_package.R dependsOnMe: cytofWorkflow suggestsMe: CytoMDS, diffcyt, tidyFlowCore dependencyCount: 82 Package: healthyControlsPresenceChecker Version: 1.13.0 Depends: R (>= 4.0.0) Imports: xml2, GEOquery, geneExpressionFromGEO, magrittr Suggests: RUnit, BiocGenerics, markdown, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 82ff74c7d51a82d3d115431725197bf3 NeedsCompilation: no Title: Dowloads A Gene Expression Dataset From GEO And Checks If It Contains Data Of Healthy Controls Or Not Description: A function that reads in the GEO accession code of a gene expression dataset, retrieves its data from GEO, and checks if data of healthy controls are present in the dataset. It returns true if healthy controls data are found, and false otherwise. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL . biocViews: GEO, RepositoryData, ExpressionData Author: Davide Chicco [aut, cre] (ORCID: ) Maintainer: Davide Chicco URL: https://github.com/davidechicco/healthyControlsPresenceChecker VignetteBuilder: knitr BugReports: https://github.com/davidechicco/healthyControlsPresenceChecker/issues git_url: https://git.bioconductor.org/packages/healthyControlsPresenceChecker git_branch: devel git_last_commit: 18ed549 git_last_commit_date: 2025-04-15 Date/Publication: 2025-04-17 source.ver: src/contrib/healthyControlsPresenceChecker_1.13.0.tar.gz vignettes: vignettes/healthyControlsPresenceChecker/inst/doc/healthyControlsPresenceChecker.html vignetteTitles: healthyControlsPresenceChecker vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/healthyControlsPresenceChecker/inst/doc/healthyControlsPresenceChecker.R dependencyCount: 91 Package: healthyFlowData Version: 1.48.0 Depends: R (>= 2.15.0), flowCore Imports: methods License: Artistic-2.0 MD5sum: c6e85aba24442aef675e16ee2af66048 NeedsCompilation: no Title: Healthy dataset used by the flowMatch package Description: A healthy dataset with 20 flow cytometry samples used by the flowMatch package. biocViews: FlowCytometryData Author: Ariful Azad Maintainer: Ariful Azad git_url: https://git.bioconductor.org/packages/healthyFlowData git_branch: RELEASE_3_22 git_last_commit: fa78b51 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/healthyFlowData_1.48.0.tar.gz vignettes: vignettes/healthyFlowData/inst/doc/healthyFlowData.pdf vignetteTitles: healthyFlowData: A healthy dataset with 20 flow cytometry samples used by the flowMatch package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/healthyFlowData/inst/doc/healthyFlowData.R suggestsMe: flowMatch dependencyCount: 18 Package: HEEBOdata Version: 1.48.0 License: LGPL MD5sum: c758fb82c26f4ce0745d43dbacb8835f NeedsCompilation: no Title: HEEBO set and HEEBO controls. Description: R objects describing the HEEBO oligo set. biocViews: ExperimentData Author: Agnes Paquet Maintainer: Agnes Paquet URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/ git_url: https://git.bioconductor.org/packages/HEEBOdata git_branch: RELEASE_3_22 git_last_commit: 3ac4685 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/HEEBOdata_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQuality dependencyCount: 0 Package: HelloRangesData Version: 1.36.0 Suggests: BiocStyle License: GPL (>= 2) MD5sum: fabb20050433bd0bc427c370c9a257e0 NeedsCompilation: no Title: Data for the HelloRanges tutorial vignette Description: Provides the data that were used in the bedtools tutorial by Aaron Quinlan (http://quinlanlab.org/tutorials/bedtools/bedtools.html). Includes a subset of the DnaseI hypersensitivity data from "Maurano et al. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA. Science. 2012. Vol. 337 no. 6099 pp. 1190-1195." The rest of the tracks were originally downloaded from the UCSC table browser. See the HelloRanges vignette for a port of the bedtools tutorial to R. biocViews: ExperimentData, SequencingData Author: Michael Lawrence Maintainer: Michael Lawrence git_url: https://git.bioconductor.org/packages/HelloRangesData git_branch: RELEASE_3_22 git_last_commit: 2fa32d2 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/HelloRangesData_1.36.0.tar.gz vignettes: vignettes/HelloRangesData/inst/doc/intro.pdf vignetteTitles: HelloRanges Example Data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HelloRangesData/inst/doc/intro.R suggestsMe: HelloRanges, plyranges dependencyCount: 0 Package: hgu133abarcodevecs Version: 1.48.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 2c8896293a08a2fe6eb34f4027523d7d NeedsCompilation: no Title: hgu133a data for barcode Description: Data used by the barcode package for microarrays of type hgu133a. biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/hgu133abarcodevecs git_branch: RELEASE_3_22 git_last_commit: 94b504c git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/hgu133abarcodevecs_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hgu133plus2barcodevecs Version: 1.48.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: c8b65c87449f4f78861f29f1a1781619 NeedsCompilation: no Title: hgu133plus2 data for barcode Description: Data used by the barcode package for microarrays of type hgu133plus2. biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/hgu133plus2barcodevecs git_branch: RELEASE_3_22 git_last_commit: 01c98df git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/hgu133plus2barcodevecs_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hgu133plus2CellScore Version: 1.30.0 Depends: R (>= 3.5.0) Imports: Biobase (>= 2.39.1) Suggests: knitr License: GPL-3 MD5sum: 470f789de373dc3edcd1d0855e9c9d3e NeedsCompilation: no Title: CellScore Standard Cell Types Expression Dataset [hgu133plus2] Description: The CellScore Standard Dataset contains expression data from a wide variety of human cells and tissues, which should be used as standard cell types in the calculation of the CellScore. All data was curated from public databases such as Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) or ArrayExpress (https://www.ebi.ac.uk/arrayexpress/). This standard dataset only contains data from the Affymetrix GeneChip Human Genome U133 Plus 2.0 microarrays. Samples were manually annotated using the database information or consulting the publications in which the datasets originated. The sample annotations are stored in the phenoData slot of the expressionSet object. Raw data (CEL files) were processed with the affy package to generate present/absent calls (mas5calls) and background-subtracted values, which were then normalized by the R-package yugene to yield the final expression values for the standard expression matrix. The annotation table for the microarray was retrieved from the BioC annotation package hgu133plus2. All data are stored in an expressionSet object. biocViews: ExpressionData, MicroarrayData, GEO, ExperimentData, Homo_sapiens_Data, Genome, ArrayExpress Author: Nancy Mah, Katerina Taskova Maintainer: Nancy Mah VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/hgu133plus2CellScore git_branch: RELEASE_3_22 git_last_commit: 5267a8d git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/hgu133plus2CellScore_1.30.0.tar.gz vignettes: vignettes/hgu133plus2CellScore/inst/doc/hgu133plus2Vignette.pdf vignetteTitles: R packages: hgu133plus2CellScore hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/hgu133plus2CellScore/inst/doc/hgu133plus2Vignette.R dependencyCount: 7 Package: hgu2beta7 Version: 1.50.0 Depends: R (>= 2.0.0) License: Artistic-2.0 MD5sum: c7670999631833e377d9b465421dfcb3 NeedsCompilation: no Title: A data package containing annotation data for hgu2beta7 Description: Annotation data file for hgu2beta7 assembled using data from public data repositories biocViews: Genome Author: Chenwei Lin Maintainer: Bioconductor Package Maintainer git_url: https://git.bioconductor.org/packages/hgu2beta7 git_branch: RELEASE_3_22 git_last_commit: e2e616b git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/hgu2beta7_1.50.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: HiBED Version: 1.8.0 Depends: R (>= 3.5.0) Imports: dplyr, FlowSorted.Blood.EPIC, tibble, FlowSorted.DLPFC.450k, minfi, utils, AnnotationHub, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, IlluminaHumanMethylation450kmanifest License: GPL-3 MD5sum: 2df56917c24578ad6ccef9134e5a9b7e NeedsCompilation: no Title: HiBED Description: Hierarchical deconvolution for extensive cell type resolution in the human brain using DNA methylation. The HiBED deconvolution estimates proportions up to 7 cell types (GABAergic neurons, glutamatergic neurons, astrocytes, microglial cells, oligodendrocytes, endothelial cells, and stromal cells) in bulk brain tissues. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, Genome, MethylationArrayData, PackageTypeData Author: Ze Zhang [cre, aut] (ORCID: ), Lucas A. Salas [aut] Maintainer: Ze Zhang URL: https://github.com/SalasLab/HiBED VignetteBuilder: knitr BugReports: https://github.com/SalasLab/HiBED/issues. git_url: https://git.bioconductor.org/packages/HiBED git_branch: RELEASE_3_22 git_last_commit: 1b05c21 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/HiBED_1.8.0.tar.gz vignettes: vignettes/HiBED/inst/doc/HiBED.html vignetteTitles: HiBED hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HiBED/inst/doc/HiBED.R dependencyCount: 153 Package: HiCDataHumanIMR90 Version: 1.30.0 Depends: R (>= 3.5.0) Suggests: HiTC, BiocStyle License: GPL-3 MD5sum: 21ef242b4225d6207878ed16cf885e08 NeedsCompilation: no Title: Human IMR90 Fibroblast HiC data from Dixon et al. 2012 Description: The HiC data from Human Fibroblast IMR90 cell line (HindIII restriction) was retrieved from the GEO website, accession number GSE35156 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35156). The raw reads were processed as explained in Dixon et al. (Nature 2012). biocViews: ExperimentData, Genome, Homo_sapiens_Data, GEO Author: Nicolas Servant Maintainer: Nicolas Servant git_url: https://git.bioconductor.org/packages/HiCDataHumanIMR90 git_branch: RELEASE_3_22 git_last_commit: 7f037ad git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/HiCDataHumanIMR90_1.30.0.tar.gz vignettes: vignettes/HiCDataHumanIMR90/inst/doc/HiC_Human_IMR90.pdf vignetteTitles: HiC Data Human Fibroblast Dixon et al. 2012 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HiCDataHumanIMR90/inst/doc/HiC_Human_IMR90.R suggestsMe: HiTC dependencyCount: 0 Package: HiCDataLymphoblast Version: 1.46.0 Suggests: ShortRead License: GPL-3 MD5sum: ea989fcf492925ed307fe9763c22ea1c NeedsCompilation: no Title: Human lymphoblastoid HiC data from Lieberman-Aiden et al. 2009 Description: The HiC data from human lymphoblastoid cell line (HindIII restriction) was retrieved from the sequence read archive and two ends of the paired reads were aligned separately with bowtie. biocViews: ExperimentData, Homo_sapiens_Data Author: Borbala Mifsud Maintainer: Borbala Mifsud git_url: https://git.bioconductor.org/packages/HiCDataLymphoblast git_branch: RELEASE_3_22 git_last_commit: 529b631 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/HiCDataLymphoblast_1.46.0.tar.gz vignettes: vignettes/HiCDataLymphoblast/inst/doc/package_vignettes.pdf vignetteTitles: package_vignettes.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HiCDataLymphoblast/inst/doc/package_vignettes.R suggestsMe: GOTHiC dependencyCount: 0 Package: HiContactsData Version: 1.12.0 Depends: ExperimentHub Imports: BiocFileCache, AnnotationHub Suggests: testthat, methods, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: f417181429ad6ddd2014b5c8bcb34d61 NeedsCompilation: no Title: HiContacts companion data package Description: Provides a collection of Hi-C files (pairs, (m)cool and fastq). These datasets can be read into R and further investigated and visualized with the HiContacts package. Data includes yeast Hi-C data generated by the Koszul lab from the Pasteur Institute. biocViews: ExperimentHub, ExperimentData, SequencingData Author: Jacques Serizay [aut, cre] Maintainer: Jacques Serizay URL: https://github.com/js2264/HiContactsData VignetteBuilder: knitr BugReports: https://github.com/js2264/HiContactsData/issues git_url: https://git.bioconductor.org/packages/HiContactsData git_branch: RELEASE_3_22 git_last_commit: d1d5113 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/HiContactsData_1.12.0.tar.gz vignettes: vignettes/HiContactsData/inst/doc/HiContactsData.html vignetteTitles: HiContactsData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HiContactsData/inst/doc/HiContactsData.R importsMe: OHCA suggestsMe: HiCExperiment, HiContacts, plyinteractions dependencyCount: 65 Package: HighlyReplicatedRNASeq Version: 1.22.0 Depends: SummarizedExperiment, ExperimentHub Imports: S4Vectors Suggests: BiocStyle, BiocFileCache, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 65360c3c2e28443c3172f847358d1553 NeedsCompilation: no Title: Collection of Bulk RNA-Seq Experiments With Many Replicates Description: Gene-level count matrix data for bulk RNA-seq dataset with many replicates. The data are provided as easy to use SummarizedExperiment objects. The source data that is made accessible through this package comes from https://github.com/bartongroup/profDGE48. biocViews: ExperimentHub, ExperimentData, ExpressionData, SequencingData, RNASeqData Author: Constantin Ahlmann-Eltze [aut, cre] (ORCID: ) Maintainer: Constantin Ahlmann-Eltze URL: https://github.com/const-ae/HighlyReplicatedRNASeq VignetteBuilder: knitr BugReports: https://github.com/const-ae/HighlyReplicatedRNASeq/issues git_url: https://git.bioconductor.org/packages/HighlyReplicatedRNASeq git_branch: RELEASE_3_22 git_last_commit: a81f0c1 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/HighlyReplicatedRNASeq_1.22.0.tar.gz vignettes: vignettes/HighlyReplicatedRNASeq/inst/doc/HighlyReplicatedRNASeq.html vignetteTitles: Exploring the 86 bulk RNA-seq samples from the Schurch et al. (2016) study hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HighlyReplicatedRNASeq/inst/doc/HighlyReplicatedRNASeq.R dependencyCount: 76 Package: Hiiragi2013 Version: 1.46.0 Depends: R (>= 4.0.0), KEGGREST, affy, boot, clue, genefilter, geneplotter, gtools, mouse4302.db, xtable Imports: MASS, Biobase, RColorBrewer, cluster, gplots, grid, lattice, latticeExtra Suggests: BiocStyle License: Artistic-2.0 MD5sum: 10b46c19626e49780027b8e35ddf7ab8 NeedsCompilation: no Title: Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages Description: This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881." biocViews: ExperimentData, MicroarrayData, qPCRData, ReproducibleResearch Author: Andrzej Oles, Wolfgang Huber Maintainer: Wolfgang Huber git_url: https://git.bioconductor.org/packages/Hiiragi2013 git_branch: RELEASE_3_22 git_last_commit: db78820 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/Hiiragi2013_1.46.0.tar.gz vignettes: vignettes/Hiiragi2013/inst/doc/Hiiragi2013.pdf vignetteTitles: Hiiragi2013 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Hiiragi2013/inst/doc/Hiiragi2013.R dependencyCount: 77 Package: HIVcDNAvantWout03 Version: 1.50.0 License: GPL (>= 2) MD5sum: 9ea4be3a244e598846d189de16da7746 NeedsCompilation: no Title: T cell line infections with HIV-1 LAI (BRU) Description: The expression levels of approximately 4600 cellular RNA transcripts were assessed in CD4+ T cell lines at different times after infection with HIV-1BRU using DNA microarrays. This data corresponds to the first block of a 12 block array image (001030_08_1.GEL) in the first data set (2000095918 A) in the first experiment (CEM LAI vs HI-LAI 24hr). There are two data sets, which are part of a dye-swap experiment with replicates, representing the Cy3 (green) absorption intensities for channel 1 (hiv1raw) and the Cy5 (red) absorption intensities for channel 2 (hiv2raw). biocViews: ExperimentData, MicroarrayData, TwoChannelData, HIVData Author: Dr. Angelique van't Wout, Department of Microbiology, University of Washington Maintainer: Chris Fraley URL: http://expression.microslu.washington.edu/expression/vantwoutjvi2002.html git_url: https://git.bioconductor.org/packages/HIVcDNAvantWout03 git_branch: RELEASE_3_22 git_last_commit: 1ea6052 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/HIVcDNAvantWout03_1.50.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: HMP16SData Version: 1.30.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: AnnotationHub, ExperimentHub, S4Vectors, assertthat, dplyr, kableExtra, knitr, magrittr, methods, readr, stringr, tibble, utils Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, circlize, cowplot, dendextend, devtools, ggplot2, gridExtra, haven, phyloseq, rmarkdown, roxygen2, stats, testthat, tidyr License: Artistic-2.0 MD5sum: 59a2af07d9a34892d9187eb8a82eca20 NeedsCompilation: no Title: 16S rRNA Sequencing Data from the Human Microbiome Project Description: HMP16SData is a Bioconductor ExperimentData package of the Human Microbiome Project (HMP) 16S rRNA sequencing data for variable regions 1–3 and 3–5. Raw data files are provided in the package as downloaded from the HMP Data Analysis and Coordination Center. Processed data is provided as SummarizedExperiment class objects via ExperimentHub. biocViews: ExperimentData, ExperimentHub, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch, SequencingData Author: Lucas schiffer [aut, cre] (ORCID: ), Rimsha Azhar [aut], Marcel Ramos [ctb], Ludwig Geistlinger [ctb], Levi Waldron [aut] Maintainer: Lucas schiffer URL: https://github.com/waldronlab/HMP16SData VignetteBuilder: knitr BugReports: https://github.com/waldronlab/HMP16SData/issues git_url: https://git.bioconductor.org/packages/HMP16SData git_branch: RELEASE_3_22 git_last_commit: 473d35f git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/HMP16SData_1.30.0.tar.gz vignettes: vignettes/HMP16SData/inst/doc/HMP16SData.html vignetteTitles: HMP16SData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HMP16SData/inst/doc/HMP16SData.R dependencyCount: 109 Package: HMP2Data Version: 1.24.0 Depends: R (>= 3.6.0) Imports: AnnotationHub, assertthat, dplyr, ExperimentHub, kableExtra, knitr, magrittr, methods, readr, S4Vectors, SummarizedExperiment, phyloseq, MultiAssayExperiment, data.table Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, cowplot, devtools, ggplot2, gridExtra, haven, rmarkdown, roxygen2, stats, testthat, tibble, UpSetR License: Artistic-2.0 MD5sum: 524ef126d243df5575cf62b01450f6dc NeedsCompilation: no Title: 16s rRNA sequencing data from the Human Microbiome Project 2 Description: HMP2Data is a Bioconductor package of the Human Microbiome Project 2 (HMP2) 16S rRNA sequencing data. Processed data is provided as phyloseq, SummarizedExperiment, and MultiAssayExperiment class objects. Individual matrices and data.frames used for building these S4 class objects are also provided in the package. biocViews: ExperimentData, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch, SequencingData Author: John Stansfield , Ekaterina Smirnova , Ni Zhao , Jennifer Fettweis , Levi Waldron , Mikhail Dozmorov Maintainer: John Stansfield , Ekaterina Smirnova URL: https://github.com/jstansfield0/HMP2Data VignetteBuilder: knitr BugReports: https://github.com/jstansfield0/HMP2Data/issues git_url: https://git.bioconductor.org/packages/HMP2Data git_branch: RELEASE_3_22 git_last_commit: c79ed77 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/HMP2Data_1.24.0.tar.gz vignettes: vignettes/HMP2Data/inst/doc/hmp2data.html vignetteTitles: HMP2Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HMP2Data/inst/doc/hmp2data.R dependencyCount: 142 Package: homosapienDEE2CellScore Version: 1.5.0 Imports: Rtsne (>= 0.15), utils(>= 3.5.0), ExperimentHub, BiocGenerics, DESeq2, S4Vectors, SummarizedExperiment, getDEE2, MatrixGenerics Suggests: knitr, rmarkdown, devtools, Biobase (>= 2.39.1), BiocManager, AnnotationHubData, ExperimentHubData, AnnotationHub, CellScore (>= 1.21.4) License: GPL (>= 3) MD5sum: 059cfb347798eee07d49fb1b8386fa8a NeedsCompilation: no Title: Example Data Package for CellScore Description: This is a data package for normalised homosapien data downloaded from DEE2. The package both downloads, normalises, and filters the data, and provides a way to access the data from a canonical store without needing local processing. This package was built as a way to generate and store canonical test data for CellScore. biocViews: RNASeqData, Genome, ExperimentHub, ExpressionData Author: Justin Marsh [aut, cre] Maintainer: Justin Marsh VignetteBuilder: knitr BugReports: https://github.com/flaviusb/homosapienDEE2CellScore/issues git_url: https://git.bioconductor.org/packages/homosapienDEE2CellScore git_branch: devel git_last_commit: f5dd740 git_last_commit_date: 2025-04-15 Date/Publication: 2025-04-17 source.ver: src/contrib/homosapienDEE2CellScore_1.5.0.tar.gz vignettes: vignettes/homosapienDEE2CellScore/inst/doc/use-data-package.html vignetteTitles: Use the Data in this Data Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/homosapienDEE2CellScore/inst/doc/use-data-package.R dependencyCount: 101 Package: HSMMSingleCell Version: 1.30.0 Depends: R (>= 2.10) License: Artistic-2.0 MD5sum: 57d74fd30d6bac492b60c86e6f40ebd3 NeedsCompilation: no Title: Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM) Description: Skeletal myoblasts undergo a well-characterized sequence of morphological and transcriptional changes during differentiation. In this experiment, primary human skeletal muscle myoblasts (HSMM) were expanded under high mitogen conditions (GM) and then differentiated by switching to low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several hundred cells taken over a time-course of serum-induced differentiation. Between 49 and 77 cells were captured at each of four time points (0, 24, 48, 72 hours) following serum switch using the Fluidigm C1 microfluidic system. RNA from each cell was isolated and used to construct mRNA-Seq libraries, which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell. biocViews: ExperimentData, RNASeqData Author: Cole Trapnell Maintainer: Cole Trapnell git_url: https://git.bioconductor.org/packages/HSMMSingleCell git_branch: RELEASE_3_22 git_last_commit: 02d56cb git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/HSMMSingleCell_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: monocle dependencyCount: 0 Package: HumanAffyData Version: 1.36.0 Depends: ExperimentHub, Biobase, R (>= 3.3) Suggests: BiocStyle License: Artistic-2.0 MD5sum: 61f87a7bc00d2bcd1b29918ad9216205 NeedsCompilation: no Title: GEO accession GSE64985 and ArrayExpress accession E-MTAB-62 as ExpressionSet objects Description: Re-analysis of human gene expression data generated on the Affymetrix HG_U133PlusV2 (EH176) and Affymetrix HG_U133A (EH177) platforms. The original data were normalized using robust multiarray averaging (RMA) to obtain an integrated gene expression atlas across diverse biological sample types and conditions. The entire compendia comprisee 9395 arrays for EH176 and 5372 arrays for EH177. biocViews: ExperimentData, GEO, ArrayExpress, Homo_sapiens_Data, MicroarrayData, ExpressionData Author: Brad Nelms Maintainer: Brad Nelms git_url: https://git.bioconductor.org/packages/HumanAffyData git_branch: RELEASE_3_22 git_last_commit: 3b928f3 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/HumanAffyData_1.36.0.tar.gz vignettes: vignettes/HumanAffyData/inst/doc/HumanAffyData.pdf vignetteTitles: Intro to the HumanAffyData package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HumanAffyData/inst/doc/HumanAffyData.R suggestsMe: CellMapper dependencyCount: 65 Package: humanHippocampus2024 Version: 1.2.0 Depends: R (>= 4.4) Imports: ExperimentHub, SummarizedExperiment,SpatialExperiment Suggests: testthat (>= 3.0.0), sessioninfo, rmarkdown, knitr, BiocStyle, ExperimentHubData, AnnotationHubData, RefManageR License: Artistic-2.0 MD5sum: 5cd667093c8b4cbf5b58c74809af3fc4 NeedsCompilation: no Title: Access to SRT and snRNA-seq data from spatial_HPC project Description: This is an ExperimentHub Data package that helps to access the spatially-resolved transcriptomics and single-nucleus RNA sequencing data. The datasets are generated from adjacent tissue sections of the anterior human hippocampus across ten adult neurotypical donors. The datasets are based on [spatial_hpc](https://github.com/LieberInstitute/spatial_hpc) project by Lieber Institute for Brain Development (LIBD) researchers and collaborators. biocViews: ExperimentHub, SequencingData, SpatialData, ExpressionData, Tissue, RNASeqData Author: Christine Hou [aut, cre] (ORCID: ) Maintainer: Christine Hou URL: https://github.com/LieberInstitute/spatial_hpc, https://christinehou11.github.io/humanHippocampus2024/ VignetteBuilder: knitr BugReports: https://support.bioconductor.org/t/humanHippocampus2024 git_url: https://git.bioconductor.org/packages/humanHippocampus2024 git_branch: RELEASE_3_22 git_last_commit: 3942d0f git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/humanHippocampus2024_1.2.0.tar.gz vignettes: vignettes/humanHippocampus2024/inst/doc/humanHippocampus2024.html vignetteTitles: humanHippocampus2024 Tutorial hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/humanHippocampus2024/inst/doc/humanHippocampus2024.R dependencyCount: 81 Package: humanStemCell Version: 0.50.0 Depends: Biobase (>= 2.5.5), hgu133plus2.db License: Artistic-2.0 MD5sum: 914495f74e40e0ebc794fe6221bdd14c NeedsCompilation: no Title: Human Stem Cells time course experiment Description: Affymetrix time course experiment on human stem cells (two time points: undifferentiated and differentiated). biocViews: ExperimentData, Homo_sapiens_Data Author: R. Gentleman, N. Le Meur, M. Tewari Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/humanStemCell git_branch: RELEASE_3_22 git_last_commit: 7fc3573 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/humanStemCell_0.50.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MiRaGE, rtracklayer dependencyCount: 45 Package: IHWpaper Version: 1.38.0 Depends: R (>= 3.3), IHW Imports: Rcpp, stats, splines, methods, utils, DESeq2, SummarizedExperiment, fdrtool, genefilter, qvalue, Biobase, BiocGenerics, BiocParallel, dplyr, grid, ggplot2, cowplot LinkingTo: Rcpp Suggests: testthat, RColorBrewer, wesanderson, scales, gridExtra, BiocStyle, knitr, rmarkdown, airway, locfdr, tidyr, latex2exp License: Artistic-2.0 MD5sum: 6cb1dc5f39056040497bbb7904433bbe NeedsCompilation: yes Title: Reproduce figures in IHW paper Description: This package conveniently wraps all functions needed to reproduce the figures in the IHW paper (https://www.nature.com/articles/nmeth.3885) and the data analysis in https://rss.onlinelibrary.wiley.com/doi/10.1111/rssb.12411, cf. the arXiv preprint (http://arxiv.org/abs/1701.05179). Thus it is a companion package to the Bioconductor IHW package. biocViews: ReproducibleResearch, ExperimentData, RNASeqData, ExpressionData Author: Nikos Ignatiadis [aut, cre] Maintainer: Nikos Ignatiadis VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/IHWpaper git_branch: RELEASE_3_22 git_last_commit: 9d08436 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/IHWpaper_1.38.0.tar.gz vignettes: vignettes/IHWpaper/inst/doc/BH-explanation.html, vignettes/IHWpaper/inst/doc/explaining_tdr.html, vignettes/IHWpaper/inst/doc/grenander_vs_ecdf.html, vignettes/IHWpaper/inst/doc/hqtl_IHW_BY.html, vignettes/IHWpaper/inst/doc/IHW_bonferroni_simulations.html, vignettes/IHWpaper/inst/doc/real_data_examples_single_curve.html, vignettes/IHWpaper/inst/doc/real_data_examples.html, vignettes/IHWpaper/inst/doc/simulations_vignette.html, vignettes/IHWpaper/inst/doc/stratified_histograms.html, vignettes/IHWpaper/inst/doc/tdr_pvalue_rejection_thresholds.html, vignettes/IHWpaper/inst/doc/weights_vs_filtering.html vignetteTitles: "Various: BH explanation / visualization", "NMeth paper: Explaining tdr", "Various: Grenander Estimator as applied to IHW (vs ECDF)", "Stats paper: hQTL analysis with IHW-Benjamini-Yekutieli", "NMeth paper: IHW-Bonferroni simulations", "Various: Real data examples: 1-fold weight function", "NMeth paper: Real data examples", "NMeth paper: Simulation Figures", "NMeth paper: Stratified Histograms", "Various: tdr and pvalue rejection regions", "Various: Weights vs Independent Filtering" hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/IHWpaper/inst/doc/BH-explanation.R, vignettes/IHWpaper/inst/doc/explaining_tdr.R, vignettes/IHWpaper/inst/doc/grenander_vs_ecdf.R, vignettes/IHWpaper/inst/doc/hqtl_IHW_BY.R, vignettes/IHWpaper/inst/doc/IHW_bonferroni_simulations.R, vignettes/IHWpaper/inst/doc/real_data_examples_single_curve.R, vignettes/IHWpaper/inst/doc/real_data_examples.R, vignettes/IHWpaper/inst/doc/simulations_vignette.R, vignettes/IHWpaper/inst/doc/stratified_histograms.R, vignettes/IHWpaper/inst/doc/tdr_pvalue_rejection_thresholds.R, vignettes/IHWpaper/inst/doc/weights_vs_filtering.R dependencyCount: 99 Package: Illumina450ProbeVariants.db Version: 1.46.0 Depends: R (>= 3.0.1) License: GPL-3 MD5sum: bff5efe06f466b431df5c50e31cf5e69 NeedsCompilation: no Title: Annotation Package combining variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes Description: Includes details on variants for each probe on the 450k bead chip for each of the four populations (Asian, American, African and European) biocViews: Homo_sapiens_Data, CancerData, ChipOnChipData, SNPData Author: Lee Butcher Maintainer: Tiffany Morris git_url: https://git.bioconductor.org/packages/Illumina450ProbeVariants.db git_branch: RELEASE_3_22 git_last_commit: 5d24c32 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/Illumina450ProbeVariants.db_1.46.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: IlluminaDataTestFiles Version: 1.48.0 License: Artistic-2.0 MD5sum: ca1d2b1cc594a3ab2693e6122632b2d5 NeedsCompilation: no Title: Illumina microarray files (IDAT) for testing Description: Example data for Illumina microarray output files, for testing purposes biocViews: MicroarrayData Author: Kasper Daniel Hansen, Mike L. Smith Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/IlluminaDataTestFiles git_branch: RELEASE_3_22 git_last_commit: 7567e5f git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/IlluminaDataTestFiles_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: illuminaio dependencyCount: 0 Package: imcdatasets Version: 1.18.0 Depends: R (>= 4.4.0), SingleCellExperiment, SpatialExperiment, cytomapper, Imports: methods, utils, ExperimentHub, S4Vectors, DelayedArray, HDF5Array Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat License: GPL-3 + file LICENSE MD5sum: 3fe4e911ecbd662b8a1a7b6de71e6d5b NeedsCompilation: no Title: Collection of publicly available imaging mass cytometry (IMC) datasets Description: The imcdatasets package provides access to publicly available IMC datasets. IMC is a technology that enables measurement of > 40 proteins from tissue sections. The generated images can be segmented to extract single cell data. Datasets typically consist of three elements: a SingleCellExperiment object containing single cell data, a CytoImageList object containing multichannel images and a CytoImageList object containing the cell masks that were used to extract the single cell data from the images. biocViews: ExperimentData, ExperimentHub, SingleCellData, SpatialData, Homo_sapiens_Data, ImmunoOncologyData, TechnologyData, PackageTypeData, ReproducibleResearch, Tissue Author: Nicolas Damond [aut, cre] (ORCID: ), Nils Eling [ctb] (ORCID: ), Fischer Jana [ctb] (ORCID: ) Maintainer: Nicolas Damond URL: https://github.com/BodenmillerGroup/imcdatasets VignetteBuilder: knitr BugReports: https://github.com/BodenmillerGroup/imcdatasets/issues git_url: https://git.bioconductor.org/packages/imcdatasets git_branch: RELEASE_3_22 git_last_commit: 3f44c7c git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/imcdatasets_1.18.0.tar.gz vignettes: vignettes/imcdatasets/inst/doc/Guidelines_Contribution_Dataset-formatting.html, vignettes/imcdatasets/inst/doc/imcdatasets.html vignetteTitles: "Contributing guidelines and datasets format", "Accessing IMC datasets" hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/imcdatasets/inst/doc/Guidelines_Contribution_Dataset-formatting.R, vignettes/imcdatasets/inst/doc/imcdatasets.R importsMe: OSTA dependencyCount: 149 Package: iModMixData Version: 1.0.0 Imports: ExperimentHub Suggests: knitr, testthat License: GPL-3 MD5sum: a740228baaa7fcbe366b1c2827c366b1 NeedsCompilation: no Title: Data for iModMix Package Description: Provides example datasets for the iModMix package, including gene, protein, and metabolite partial correlation matrices derived from ccRCC4 and FloresData_K_TK studies. The data are preprocessed and ready to use for testing, demonstrating iModMix workflows, and exploring correlation networks. biocViews: ExperimentData, ExpressionData, MassSpectrometryData, ExperimentHub Author: Isis Narvaez-Bandera [aut, cre] (ORCID: ) Maintainer: Isis Narvaez-Bandera URL: https://github.com/biodatalab/iModMixData VignetteBuilder: knitr BugReports: https://github.com/biodatalab/iModMixData/issues git_url: https://git.bioconductor.org/packages/iModMixData git_branch: RELEASE_3_22 git_last_commit: 4b6ab7c git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/iModMixData_1.0.0.tar.gz vignettes: vignettes/iModMixData/inst/doc/iModMixData.html vignetteTitles: Using iModMixData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/iModMixData/inst/doc/iModMixData.R importsMe: iModMix dependencyCount: 65 Package: ITALICSData Version: 2.48.0 Depends: R (>= 2.0.0) License: GPL MD5sum: 2af71afb3bb666e5b9ff04864c2970cf NeedsCompilation: no Title: ITALICSData Description: Data needed to use the ITALICS package biocViews: ExperimentData, HapMap Author: Guillem Rigaill Maintainer: Guillem Rigaill URL: http://bioinfo.curie.fr git_url: https://git.bioconductor.org/packages/ITALICSData git_branch: RELEASE_3_22 git_last_commit: e11b5f9 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/ITALICSData_2.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ITALICS dependencyCount: 0 Package: Iyer517 Version: 1.52.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 8c57c7aa0a9592520abf467193d444d0 NeedsCompilation: no Title: exprSets for Iyer, Eisen et all 1999 Science paper Description: representation of public Iyer data from http://genome-www.stanford.edu/serum/clusters.html biocViews: ExperimentData Author: Vishy Iyer Maintainer: Vince Carey git_url: https://git.bioconductor.org/packages/Iyer517 git_branch: RELEASE_3_22 git_last_commit: aabf081 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/Iyer517_1.52.0.tar.gz vignettes: vignettes/Iyer517/inst/doc/Iyer517.pdf vignetteTitles: Iyer517 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Iyer517/inst/doc/Iyer517.R dependencyCount: 7 Package: JASPAR2014 Version: 1.46.0 Depends: R (>= 3.0.1), methods, Biostrings (>= 2.29.19) License: GPL-2 MD5sum: a636f09a88fbef80c4d4be0a3a7e0082 NeedsCompilation: no Title: Data package for JASPAR Description: Data package for JASPAR 2014. To search this databases, please use the package TFBSTools. biocViews: ExperimentData, SequencingData Author: Ge Tan Maintainer: Ge Tan URL: http://jaspar.genereg.net/ git_url: https://git.bioconductor.org/packages/JASPAR2014 git_branch: RELEASE_3_22 git_last_commit: a36b7fd git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/JASPAR2014_1.46.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MatrixRider, TFBSTools dependencyCount: 15 Package: JASPAR2016 Version: 1.38.0 Depends: R (>= 3.2.2), methods License: GPL-2 MD5sum: c34a2366afdf77e9cace2d70349ac5d7 NeedsCompilation: no Title: Data package for JASPAR 2016 Description: Data package for JASPAR 2016. To search this databases, please use the package TFBSTools (>= 1.8.1). biocViews: ExperimentData, MotifAnnotation, GeneRegulation Author: Ge Tan Maintainer: Ge Tan URL: http://jaspar.genereg.net/ git_url: https://git.bioconductor.org/packages/JASPAR2016 git_branch: RELEASE_3_22 git_last_commit: ce701a6 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/JASPAR2016_1.38.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: chromVAR, TFBSTools, CAGEWorkflow dependencyCount: 1 Package: JohnsonKinaseData Version: 1.6.0 Depends: R (>= 4.1.0) Imports: ExperimentHub, BiocParallel, checkmate, dplyr, stats, stringr, tidyr, purrr, utils Suggests: knitr, BiocStyle, ExperimentHubData, testthat (>= 3.0.0), rmarkdown License: MIT + file LICENSE MD5sum: 018a588542ba7725aea3050c47380ef9 NeedsCompilation: no Title: Kinase PWMs based on data published by Johnson et al. 2023 and Yaron-Barir et al. 2024 Description: The packages provides position specific weight matrices (PWMs) for 303 human serine/threonine and 93 tyrosine kinases originally published in Johnson et al. 2023 (doi:10.1038/s41586-022-05575-3) and Yaron-Barir et al. 2024 (doi:10.1038/s41586-024-07407-y). The package includes basic functionality to score user provided phosphosites. It also includes pre-computed PWM scores ("background scores") for a large collection of curated human phosphosites which can be used to rank PWM scores relative to the background scores ("percentile rank"). biocViews: ExperimentHub, Homo_sapiens_Data, Proteome Author: Florian Geier [aut, cre] (ORCID: ) Maintainer: Florian Geier URL: https://github.com/fgeier/JohnsonKinaseData/ VignetteBuilder: knitr BugReports: https://support.bioconductor.org/t/JohnsonKinaseData git_url: https://git.bioconductor.org/packages/JohnsonKinaseData git_branch: RELEASE_3_22 git_last_commit: 6ff1db4 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/JohnsonKinaseData_1.6.0.tar.gz vignettes: vignettes/JohnsonKinaseData/inst/doc/JohnsonKinaseData.html vignetteTitles: JohnsonKinaseData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/JohnsonKinaseData/inst/doc/JohnsonKinaseData.R dependencyCount: 76 Package: KEGGandMetacoreDzPathwaysGEO Version: 1.30.0 Depends: R (>= 2.15.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: 8869e7773c26a4e3f6bbd61790e321fb NeedsCompilation: no Title: Disease Datasets from GEO Description: This is a collection of 18 data sets for which the phenotype is a disease with a corresponding pathway in either KEGG or metacore database.This collection of datasets were used as gold standard in comparing gene set analysis methods. biocViews: ExperimentData, GEO Author: Gaurav Bhatti Maintainer: Gaurav Bhatti git_url: https://git.bioconductor.org/packages/KEGGandMetacoreDzPathwaysGEO git_branch: RELEASE_3_22 git_last_commit: 08b0d77 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/KEGGandMetacoreDzPathwaysGEO_1.30.0.tar.gz vignettes: vignettes/KEGGandMetacoreDzPathwaysGEO/inst/doc/KEGGandMetacoreDzPathwaysGEO.pdf vignetteTitles: KEGGandMetacoreDzPathwaysGEO Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/KEGGandMetacoreDzPathwaysGEO/inst/doc/KEGGandMetacoreDzPathwaysGEO.R importsMe: GSEABenchmarkeR dependencyCount: 7 Package: KEGGdzPathwaysGEO Version: 1.48.0 Depends: R (>= 2.13.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: 05c771182bf9cdb654c7f25cd7cf79c3 NeedsCompilation: no Title: KEGG Disease Datasets from GEO Description: This is a collection of 24 data sets for which the phenotype is a disease with a corresponding pathway in the KEGG database.This collection of datasets were used as gold standard in comparing gene set analysis methods by the PADOG package. biocViews: MicroarrayData, GEO, ExperimentData Author: Gaurav Bhatti, Adi L. Tarca Maintainer: Gaurav Bhatti git_url: https://git.bioconductor.org/packages/KEGGdzPathwaysGEO git_branch: RELEASE_3_22 git_last_commit: ff167f3 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/KEGGdzPathwaysGEO_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: PADOG importsMe: GSEABenchmarkeR dependencyCount: 7 Package: kidpack Version: 1.52.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5) License: GPL-2 MD5sum: 3e4967fa23d2e8e83c7a3b332dad1ea6 NeedsCompilation: no Title: DKFZ kidney package Description: kidney microarray data biocViews: ExperimentData, CancerData, KidneyCancerData, MicroarrayData, ArrayExpress Author: Wolfgang Huber Maintainer: Wolfgang Huber URL: http://www.dkfz.de/mga git_url: https://git.bioconductor.org/packages/kidpack git_branch: RELEASE_3_22 git_last_commit: 7992a32 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/kidpack_1.52.0.tar.gz vignettes: vignettes/kidpack/inst/doc/kidpack.pdf vignetteTitles: kidpack - overview over the DKFZ kidney data package hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/kidpack/inst/doc/kidpack.R dependencyCount: 7 Package: KOdata Version: 1.36.0 Depends: R (>= 3.3.0) License: MIT + file LICENSE MD5sum: e0a440255838c02751f9b363c9639e54 NeedsCompilation: no Title: LINCS Knock-Out Data Package Description: Contains consensus genomic signatures (CGS) for experimental cell-line specific gene knock-outs as well as baseline gene expression data for a subset of experimental cell-lines. Intended for use with package KEGGlincs. biocViews: ExpressionData, CancerData, Homo_sapiens_Data Author: Shana White Maintainer: Shana White git_url: https://git.bioconductor.org/packages/KOdata git_branch: RELEASE_3_22 git_last_commit: ee9254c git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/KOdata_1.36.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: KEGGlincs dependencyCount: 0 Package: leeBamViews Version: 1.46.0 Depends: R (>= 2.15.0), Biobase, Rsamtools (>= 0.1.50), BSgenome Imports: GenomicRanges, GenomicAlignments, methods, S4Vectors, parallel, IRanges Suggests: biomaRt, org.Sc.sgd.db, edgeR License: Artistic 2.0 MD5sum: 0ea6c77e199db1cafe79604ab4e9aa7a NeedsCompilation: no Title: leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009 Description: data from PMID 19096707; prototype for managing multiple NGS samples biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData, SNPData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/leeBamViews git_branch: RELEASE_3_22 git_last_commit: edd3062 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/leeBamViews_1.46.0.tar.gz vignettes: vignettes/leeBamViews/inst/doc/leeViews.pdf vignetteTitles: managing multiple NGS samples with bamViews hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/leeBamViews/inst/doc/leeViews.R suggestsMe: EDASeq dependencyCount: 58 Package: LegATo Version: 1.4.0 Depends: R (>= 4.4.0) Imports: animalcules, data.table, dplyr, ggplot2, magrittr, MultiAssayExperiment, plyr, rlang, S4Vectors, stringr, SummarizedExperiment, tibble, tidyr, tidyselect Suggests: BiocStyle, broom, broom.mixed, circlize, ComplexHeatmap, emmeans, geepack, ggalluvial, ggeffects, grDevices, knitr, lme4, lmerTest, methods, RColorBrewer, rmarkdown, spelling, TBSignatureProfiler, testthat (>= 3.0.0), TreeSummarizedExperiment, usethis, vegan License: MIT + file LICENSE MD5sum: 7a3de900d23f4cb9de980bd890c145be NeedsCompilation: no Title: LegATo: Longitudinal mEtaGenomic Analysis Toolkit Description: LegATo is a suite of open-source software tools for longitudinal microbiome analysis. It is extendable to several different study forms with optimal ease-of-use for researchers. Microbiome time-series data presents distinct challenges including complex covariate dependencies and variety of longitudinal study designs. This toolkit will allow researchers to determine which microbial taxa are affected over time by perturbations such as onset of disease or lifestyle choices, and to predict the effects of these perturbations over time, including changes in composition or stability of commensal bacteria. biocViews: MicrobiomeData, ReproducibleResearch, SequencingData Author: Aubrey Odom [aut, cre] (ORCID: ), Yilong Zhang [ctb] (Author of NMIT functions), Jared Pincus [csl] (ORCID: , other: Naming consultant of package), Jordan Pincus [art] (Artist of LegATo icon) Maintainer: Aubrey Odom URL: https://wejlab.github.io/LegATo-docs/ VignetteBuilder: knitr BugReports: https://github.com/wejlab/LegATo/issues git_url: https://git.bioconductor.org/packages/LegATo git_branch: RELEASE_3_22 git_last_commit: a90b8bd git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/LegATo_1.4.0.tar.gz vignettes: vignettes/LegATo/inst/doc/LegATo_vignette.html vignetteTitles: LegATo Tutorial hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/LegATo/inst/doc/LegATo_vignette.R dependencyCount: 191 Package: leukemiasEset Version: 1.46.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 802f7fea2d01c96fc8bb0a26db417ab7 NeedsCompilation: no Title: Leukemia's microarray gene expression data (expressionSet). Description: Expressionset containing gene expresion data from 60 bone marrow samples of patients with one of the four main types of leukemia (ALL, AML, CLL, CML) or non-leukemia. biocViews: Tissue, Genome, Homo_sapiens_Data, CancerData, LeukemiaCancerData, MicroarrayData, ChipOnChipData, TissueMicroarrayData, GEO Author: Sara Aibar, Celia Fontanillo and Javier De Las Rivas. Bioinformatics and Functional Genomics Group. Cancer Research Center (CiC-IBMCC, CSIC/USAL). Salamanca. Spain. Maintainer: Sara Aibar git_url: https://git.bioconductor.org/packages/leukemiasEset git_branch: RELEASE_3_22 git_last_commit: 68a2d04 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/leukemiasEset_1.46.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: geNetClassifier, multiclassPairs dependencyCount: 7 Package: LiebermanAidenHiC2009 Version: 0.48.0 Depends: KernSmooth, IRanges License: LGPL MD5sum: 2b52f501792f82b20d064bae90866f9f NeedsCompilation: no Title: Selected data from the HiC paper of E. Lieberman-Aiden et al. in Science (2009) Description: This package provides data that were presented in the article "Comprehensive mapping of long-range interactions reveals folding principles of the human genome", Science 2009 Oct 9;326(5950):289-93. PMID: 19815776 biocViews: ExperimentData, Genome, SequencingData, DNASeqData, ChIPSeqData, miRNAData, SmallRNAData, ChipOnChipData, GEO, NCI, ENCODE Author: Wolfgang Huber, Felix Klein Maintainer: Felix Klein git_url: https://git.bioconductor.org/packages/LiebermanAidenHiC2009 git_branch: RELEASE_3_22 git_last_commit: dd5e446 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/LiebermanAidenHiC2009_0.48.0.tar.gz vignettes: vignettes/LiebermanAidenHiC2009/inst/doc/LiebermanAidenHiC2009.pdf vignetteTitles: Exploration of HiC data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/LiebermanAidenHiC2009/inst/doc/LiebermanAidenHiC2009.R dependencyCount: 10 Package: ListerEtAlBSseq Version: 1.42.0 Depends: R (>= 3.1.1), methylPipe Suggests: BSgenome.Hsapiens.UCSC.hg18 License: Artistic 2.0 MD5sum: bd3ab763f773b70704418cc49a14cb18 NeedsCompilation: no Title: BS-seq data of H1 and IMR90 cell line excerpted from Lister et al. 2009 Description: Base resolution bisulfite sequencing data of Human DNA methylomes biocViews: ExperimentData, Homo_sapiens_Data, SequencingData Author: Mattia Pelizzola [aut], Kamal Kishore [aut], Mattia Furlan [ctb, cre] Maintainer: Mattia Furlan git_url: https://git.bioconductor.org/packages/ListerEtAlBSseq git_branch: RELEASE_3_22 git_last_commit: fafe5e3 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/ListerEtAlBSseq_1.42.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 160 Package: LRcellTypeMarkers Version: 1.18.0 Depends: R (>= 4.1) Imports: ExperimentHub Suggests: LRcell, BiocStyle, knitr, rmarkdown, roxygen2, testthat License: MIT + file LICENSE MD5sum: d4643766c00d738848251f39bc28092f NeedsCompilation: no Title: Marker gene information for LRcell R Bioconductor package Description: This is an external ExperimentData package for LRcell. This data package contains the gene enrichment scores calculated from scRNA-seq dataset which indicates the gene enrichment of each cell type in certain brain region. LRcell package is used to identify specific sub-cell types that drives the changes observed in a bulk RNA-seq differential gene expression experiment. For more details, please visit: https://github.com/marvinquiet/LRcell. biocViews: ExperimentData, ExperimentHub, RNASeqData, SingleCellData, ExpressionData, PackageTypeData Author: Wenjing Ma [cre, aut] (ORCID: ) Maintainer: Wenjing Ma VignetteBuilder: knitr BugReports: https://github.com/marvinquiet/LRcellTypeMarkers/issues git_url: https://git.bioconductor.org/packages/LRcellTypeMarkers git_branch: RELEASE_3_22 git_last_commit: f3c3066 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/LRcellTypeMarkers_1.18.0.tar.gz vignettes: vignettes/LRcellTypeMarkers/inst/doc/LRcellTypeMarkers-vignette.html vignetteTitles: LRcellTypeMarkers: Marker gene information for LRcell R Bioconductor package using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/LRcellTypeMarkers/inst/doc/LRcellTypeMarkers-vignette.R suggestsMe: LRcell dependencyCount: 65 Package: lumiBarnes Version: 1.50.0 Depends: R (>= 2.0), Biobase (>= 2.5.5), lumi (>= 1.1.0) License: LGPL MD5sum: acfa27e4510e98d426a0a0ae2fb83af6 NeedsCompilation: no Title: Barnes Benchmark Illumina Tissues Titration Data Description: The Barnes benchmark dataset can be used to evaluate the algorithms for Illumina microarrays. It measured a titration series of two human tissues, blood and placenta, and includes six samples with the titration ratio of blood and placenta as 100:0, 95:5, 75:25, 50:50, 25:75 and 0:100. The samples were hybridized on HumanRef-8 BeadChip (Illumina, Inc) in duplicate. The data is loaded as an LumiBatch Object (see documents in the lumi package). biocViews: ExperimentData, Tissue, MicroarrayData, ChipOnChipData Author: Pan Du Maintainer: Pan Du git_url: https://git.bioconductor.org/packages/lumiBarnes git_branch: RELEASE_3_22 git_last_commit: 51b3d66 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/lumiBarnes_1.50.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayMvout, lumi dependencyCount: 165 Package: LungCancerACvsSCCGEO Version: 1.46.0 Depends: R (>= 2.15.0) License: GPL-2 MD5sum: 4af9b5ca7ca0835c7bacb056d3f0044d NeedsCompilation: no Title: A lung cancer dataset that can be used with maPredictDSC package for developing outcome prediction models from Affymetrix CEL files. Description: This package contains 30 Affymetrix CEL files for 7 Adenocarcinoma (AC) and 8 Squamous cell carcinoma (SCC) lung cancer samples taken at random from 3 GEO datasets (GSE10245, GSE18842 and GSE2109) and other 15 samples from a dataset produced by the organizers of the IMPROVER Diagnostic Signature Challenge available from GEO (GSE43580). biocViews: CancerData, LungCancerData, MicroarrayData, GEO Author: Adi Laurentiu Tarca Maintainer: Adi Laurentiu Tarca URL: http://bioinformaticsprb.med.wayne.edu/ git_url: https://git.bioconductor.org/packages/LungCancerACvsSCCGEO git_branch: RELEASE_3_22 git_last_commit: 574147c git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/LungCancerACvsSCCGEO_1.46.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: LungCancerLines Version: 0.48.0 Imports: Rsamtools License: Artistic-2.0 MD5sum: 931e0d3f056e3c04a5c1d8684c526bea NeedsCompilation: no Title: Reads from Two Lung Cancer Cell Lines Description: Reads from an RNA-seq experiment between two lung cancer cell lines: H1993 (met) and H2073 (primary). The reads are stored as Fastq files and are meant for use with the TP53Genome object in the gmapR package. biocViews: ExperimentData, Genome, CancerData, LungCancerData, RNASeqData Author: Cory Barr, Michael Lawrence Maintainer: Michael Lawrence git_url: https://git.bioconductor.org/packages/LungCancerLines git_branch: RELEASE_3_22 git_last_commit: a9e2226 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/LungCancerLines_0.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: gmapR, VariantTools dependencyCount: 29 Package: lungExpression Version: 0.48.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 69de7275f9ac641b1f75f359435e4bcf NeedsCompilation: no Title: ExpressionSets for Parmigiani et al., 2004 Clinical Cancer Research paper Description: Data from three large lung cancer studies provided as ExpressionSets biocViews: ExperimentData, CancerData, LungCancerData Author: Robert Scharpf , Simens Zhong , Giovanni Parmigiani Maintainer: Robert Scharpf git_url: https://git.bioconductor.org/packages/lungExpression git_branch: RELEASE_3_22 git_last_commit: 57e47f5 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/lungExpression_0.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: globaltest dependencyCount: 7 Package: lydata Version: 1.36.0 License: MIT + file LICENSE MD5sum: 97ce5c2d091c398f3917ab7da48b3b26 NeedsCompilation: no Title: Example Dataset for crossmeta Package Description: Raw data downloaded from GEO for the compound LY294002. Raw data is from multiple platforms from Affymetrix and Illumina. This data is used to illustrate the cross-platform meta-analysis of microarray data using the crossmeta package. biocViews: ExperimentData, MicroarrayData Author: Alex Pickering Maintainer: Alex Pickering git_url: https://git.bioconductor.org/packages/lydata git_branch: RELEASE_3_22 git_last_commit: a5db459 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/lydata_1.36.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: M3DExampleData Version: 1.36.0 Depends: R (>= 3.3) License: GPL (>=2) MD5sum: 4e7db8a0583536646bd3f3a74f6a4da6 NeedsCompilation: no Title: M3Drop Example Data Description: Example data for M3Drop package. biocViews: Mus_musculus_Data, RNASeqData, ExpressionData, GEO, Tissue, ExperimentData Author: Tallulah Andrews Maintainer: Tallulah Andrews git_url: https://git.bioconductor.org/packages/M3DExampleData git_branch: RELEASE_3_22 git_last_commit: 11cd50e git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/M3DExampleData_1.36.0.tar.gz hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: celda, M3Drop dependencyCount: 0 Package: macrophage Version: 1.26.0 Depends: R (>= 3.5.0) Suggests: knitr, markdown License: GPL (>= 2) MD5sum: 62f0c5d4e13bd431fc32696f673b23f6 NeedsCompilation: no Title: Human macrophage immune response Description: This package provides the output of running Salmon on a set of 24 RNA-seq samples from Alasoo, et al. "Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response", published in Nature Genetics, January 2018. For details on version numbers and how the samples were processed see the package vignette. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/macrophage git_branch: RELEASE_3_22 git_last_commit: 8f32f2f git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/macrophage_1.26.0.tar.gz vignettes: vignettes/macrophage/inst/doc/macrophage.html vignetteTitles: Salmon quantifications for human macrophage immune response experiment hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/macrophage/inst/doc/macrophage.R suggestsMe: DeeDeeExperiment, fishpond, mosdef, quantiseqr, tximeta, fluentGenomics dependencyCount: 0 Package: MACSdata Version: 1.18.0 License: file LICENSE MD5sum: 4ccc5718fd89040d4e1fcbc2241a4fcf NeedsCompilation: no Title: Test datasets for the MACSr package Description: Test datasets from the MACS3 test examples are use in the examples of the `MACSr` package. All 9 datasets are uploaded to the `ExperimentHub`. The original data can be found at: https://github.com/macs3-project/MACS/. biocViews: ExperimentHub, ExperimentData, ChIPSeqData Author: Qiang Hu [aut, cre] Maintainer: Qiang Hu git_url: https://git.bioconductor.org/packages/MACSdata git_branch: RELEASE_3_22 git_last_commit: 05b6ac1 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/MACSdata_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: MACSr dependencyCount: 0 Package: mammaPrintData Version: 1.46.0 Depends: R (>= 2.13.0) Suggests: Biobase, readxl, limma License: Artistic-2.0 MD5sum: dc69dab7f30afdaa01b8d1a30d874b3e NeedsCompilation: no Title: RGLists from the Glas and Buyse breast cancer studies Description: Gene expression data for the two breast cancer cohorts published by Glas and Buyse in 2006. This cohorts were used to implement and validate the mammaPrint breast cancer test. biocViews: ExperimentData, ExpressionData, CancerData, BreastCancerData, MicroarrayData, TwoChannelData Author: Luigi Marchionni Maintainer: Luigi Marchionni URL: http://luigimarchionni.org/breastTSP.html git_url: https://git.bioconductor.org/packages/mammaPrintData git_branch: RELEASE_3_22 git_last_commit: f4ca7fb git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/mammaPrintData_1.46.0.tar.gz vignettes: vignettes/mammaPrintData/inst/doc/mammaPrintData.pdf vignetteTitles: Working with the mammaPrintData package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mammaPrintData/inst/doc/mammaPrintData.R dependencyCount: 0 Package: maqcExpression4plex Version: 1.54.0 Suggests: oligo, pdInfoBuilder License: GPL MD5sum: 854fb69c8b2f54401b97b14c8c76498c NeedsCompilation: no Title: Sample Expression Data - MAQC / HG18 - NimbleGen Description: Data from human (HG18) 4plex NimbleGen array. It has 24k genes with 3 60mer probes per gene. biocViews: ExperimentData, CancerData Author: NimbleGen Systems Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/maqcExpression4plex git_branch: RELEASE_3_22 git_last_commit: 36cac9c git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/maqcExpression4plex_1.54.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligo dependencyCount: 0 Package: MAQCsubset Version: 1.48.0 Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), lumi, methods Suggests: genefilter, codelink License: Artistic-2.0 MD5sum: aa8f62cf8128320a49c0c75d6fd64b1e NeedsCompilation: no Title: Experimental Data Package: MAQCsubset Description: Data Package automatically created on Sun Nov 19 15:59:29 2006. biocViews: ExperimentData, MicroarrayData, GEO Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/MAQCsubset git_branch: RELEASE_3_22 git_last_commit: da3b3ee git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/MAQCsubset_1.48.0.tar.gz vignettes: vignettes/MAQCsubset/inst/doc/maqcNotes.pdf vignetteTitles: MAQC notes hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MAQCsubset/inst/doc/maqcNotes.R suggestsMe: arrayMvout dependencyCount: 165 Package: marinerData Version: 1.10.0 Imports: utils, ExperimentHub Suggests: knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0) License: GPL-3 MD5sum: 78a0fd4c9589254a30664a24b64f1bbd NeedsCompilation: no Title: ExperimentHub data for the mariner package Description: Subsampled Hi-C in HEK cells expressing the NHA9 fusion with an F to S mutated IDR ("FS") or without any mutations to the IDR ("Wildtype" or "WT"). These files are used for testing mariner functions and some examples. biocViews: ExperimentHub, ExperimentData, SequencingData Author: Eric Davis [aut, cre] (ORCID: ) Maintainer: Eric Davis VignetteBuilder: knitr BugReports: https://support.bioconductor.org/t/marinerData git_url: https://git.bioconductor.org/packages/marinerData git_branch: RELEASE_3_22 git_last_commit: 7c5a67a git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/marinerData_1.10.0.tar.gz vignettes: vignettes/marinerData/inst/doc/marinerData.html vignetteTitles: marinerData package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/marinerData/inst/doc/marinerData.R suggestsMe: mariner dependencyCount: 65 Package: mCSEAdata Version: 1.30.0 Depends: R (>= 3.5) Imports: GenomicRanges Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 77fb578de54fe9867b69a8742af8a9c3 NeedsCompilation: no Title: Data package for mCSEA package Description: Data objects necessary to some mCSEA package functions. There are also example data objects to illustrate mCSEA package functionality. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData, ExperimentData Author: Jordi Martorell Marugán Maintainer: Jordi Martorell Marugán VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mCSEAdata git_branch: RELEASE_3_22 git_last_commit: 6c9906c git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/mCSEAdata_1.30.0.tar.gz vignettes: vignettes/mCSEAdata/inst/doc/mCSEAdata.html vignetteTitles: Data for mCSEA package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mCSEAdata/inst/doc/mCSEAdata.R dependencyCount: 11 Package: mcsurvdata Version: 1.28.0 Depends: R (>= 3.5), ExperimentHub Imports: AnnotationHub, Biobase Suggests: BiocStyle, knitr License: GPL (>=2) MD5sum: 52430434fd13d516acbadd1c04bcabc2 NeedsCompilation: no Title: Meta cohort survival data Description: This package stores two merged expressionSet objects that contain the gene expression profile and clinical information of -a- six breast cancer cohorts and -b- four colorectal cancer cohorts. Breast cancer data are employed in the vignette of the hrunbiased package for survival analysis of gene signatures. biocViews: ExperimentData, Homo_sapiens_Data, GEO, MicroarrayData Author: Adria Caballe Mestres [aut, cre], Antoni Berenguer Llergo [aut], Camille Stephan-Otto Attolini [aut] Maintainer: Adria Caballe Mestres URL: https://github.com/adricaba/mcsurvdata VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mcsurvdata git_branch: RELEASE_3_22 git_last_commit: 7cfc3cd git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/mcsurvdata_1.28.0.tar.gz vignettes: vignettes/mcsurvdata/inst/doc/mcsurvdata.html vignetteTitles: analysis vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mcsurvdata/inst/doc/mcsurvdata.R dependencyCount: 65 Package: MEDIPSData Version: 1.46.0 Depends: R (>= 3.5) Suggests: MEDIPS, GenomicRanges, qsea License: GPL (>= 2) MD5sum: 49134627ec6cea433bc6fffcee7327f6 NeedsCompilation: no Title: Example data for MEDIPS and QSEA packages Description: Example data for MEDIPS and QSEA packages, consisting of chromosome 22 MeDIP and control/Input sample data. Additionally, the package contains MeDIP seq data from 3 NSCLC samples and adjacent normal tissue (chr 20-22). All data has been aligned to human genome hg19. biocViews: ExperimentData, Genome, SequencingData Author: Lukas Chavez Maintainer: Lukas Chavez git_url: https://git.bioconductor.org/packages/MEDIPSData git_branch: RELEASE_3_22 git_last_commit: 1d8e5ae git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/MEDIPSData_1.46.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MEDIPS, qsea dependencyCount: 0 Package: MEEBOdata Version: 1.48.0 License: LGPL MD5sum: 7ff786603f2b35e107af3ad8aab62c05 NeedsCompilation: no Title: MEEBO set and MEEBO controls. Description: R objects describing the MEEBO set. biocViews: ExperimentData Author: Agnes Paquet Maintainer: Agnes Paquet URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/ git_url: https://git.bioconductor.org/packages/MEEBOdata git_branch: RELEASE_3_22 git_last_commit: 06cd6c6 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/MEEBOdata_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQuality dependencyCount: 0 Package: MerfishData Version: 1.12.0 Depends: R (>= 4.2.0), EBImage, SpatialExperiment Imports: grDevices, AnnotationHub, BumpyMatrix, ExperimentHub, S4Vectors, SingleCellExperiment, SummarizedExperiment, HDF5Array Suggests: grid, ggplot2, ggpubr, knitr, rmarkdown, scater, scattermore, terra, testthat, BiocStyle, DropletUtils License: Artistic-2.0 MD5sum: 5d1cfaa83bc9e3fb6413a01471c034d7 NeedsCompilation: no Title: Collection of public MERFISH datasets Description: MerfishData is an ExperimentHub package that serves publicly available datasets obtained with Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH). MERFISH is a massively multiplexed single-molecule imaging technology capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells. The scope of the package is to provide MERFISH data for benchmarking and analysis. biocViews: ExperimentHub, ExpressionData, HighThroughputImagingData, Mus_musculus_Data, SingleCellData, SpatialData Author: Ludwig Geistlinger [aut, cre] (ORCID: ), Tyrone Lee [ctb], Helena Crowell [ctb] (ORCID: ), Daniela Corbetta [ctb], Jeffrey Moffitt [aut], Robert Gentleman [aut] Maintainer: Ludwig Geistlinger URL: https://github.com/ccb-hms/MerfishData VignetteBuilder: knitr BugReports: https://github.com/ccb-hms/MerfishData/issues git_url: https://git.bioconductor.org/packages/MerfishData git_branch: RELEASE_3_22 git_last_commit: 42395d2 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/MerfishData_1.12.0.tar.gz vignettes: vignettes/MerfishData/inst/doc/Merfish_mouse_colon_ibd.html, vignettes/MerfishData/inst/doc/Merfish_mouse_hypothalamus.html, vignettes/MerfishData/inst/doc/Merfish_mouse_ileum.html vignetteTitles: Mouse colon ibd, Mouse hypothalamus, Mouse ileum hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MerfishData/inst/doc/Merfish_mouse_colon_ibd.R, vignettes/MerfishData/inst/doc/Merfish_mouse_hypothalamus.R, vignettes/MerfishData/inst/doc/Merfish_mouse_ileum.R dependencyCount: 109 Package: MetaGxBreast Version: 1.30.0 Depends: R (>= 3.6.0), Biobase, AnnotationHub, ExperimentHub Imports: stats, lattice, impute, SummarizedExperiment Suggests: testthat, xtable, tinytex License: Apache License (>= 2) MD5sum: fa92fca37813f7e4940a69c650902f89 NeedsCompilation: no Title: Transcriptomic Breast Cancer Datasets Description: A collection of Breast Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium. biocViews: ExpressionData, ExperimentHub, CancerData, Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData, ExperimentData Author: Michael Zon [aut], Deena M.A. Gendoo [aut], Christopher Eeles [ctb], Benjamin Haibe-Kains [aut, cre] Maintainer: Benjamin Haibe-Kains git_url: https://git.bioconductor.org/packages/MetaGxBreast git_branch: RELEASE_3_22 git_last_commit: 679360b git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/MetaGxBreast_1.30.0.tar.gz vignettes: vignettes/MetaGxBreast/inst/doc/MetaGxBreast.pdf vignetteTitles: MetaGxBreast: a package for breast cancer gene expression analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MetaGxBreast/inst/doc/MetaGxBreast.R dependencyCount: 77 Package: MetaGxPancreas Version: 1.30.0 Depends: SummarizedExperiment, ExperimentHub, R (>= 3.6.0) Imports: stats, impute, S4Vectors, AnnotationHub Suggests: testthat, knitr, BiocStyle, rmarkdown, markdown License: Artistic-2.0 MD5sum: 9e915e4c4ca131949b7868b56f7f2174 NeedsCompilation: no Title: Transcriptomic Pancreatic Cancer Datasets Description: A collection of pancreatic Cancer transcriptomic datasets that are part of the MetaGxData package compendium. This package contains multiple pancreas cancer datasets that have been downloaded from various resources and turned into SummarizedExperiment objects. The details of how the authors normalized the data can be found in the experiment data section of the objects. Additionally, the location the data was obtained from can be found in the url variables of the experiment data portion of each SE. biocViews: ExpressionData, ExperimentHub, CancerData, Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData, ExperimentData, SequencingData Author: Michael Zon [aut], Vandana Sandhu [aut], Christopher Eeles [ctb], Michael Tran Cao-Anh [ctb], Benjamin Haibe-Kains [aut, cre] Maintainer: Benjamin Haibe-Kains VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MetaGxPancreas git_branch: RELEASE_3_22 git_last_commit: 935c772 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/MetaGxPancreas_1.30.0.tar.gz vignettes: vignettes/MetaGxPancreas/inst/doc/MetaGxPancreas.html vignetteTitles: MetaGxPancreas: A Package for Pancreatic Cancer Gene Expression Analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MetaGxPancreas/inst/doc/MetaGxPancreas.R dependencyCount: 77 Package: metaMSdata Version: 1.46.0 License: GPL (>= 2) MD5sum: 5e1b8ccb160ab1dc7212a663d0ac1a3b NeedsCompilation: no Title: Example CDF data for the metaMS package Description: Example CDF data for the metaMS package biocViews: ExperimentData, MassSpectrometryData Author: Ron Wehrens [aut, cre], Pietro Franceschi [aut], Georg Weingart [ctb] Maintainer: Yann Guitton git_url: https://git.bioconductor.org/packages/metaMSdata git_branch: RELEASE_3_22 git_last_commit: 0852ef3 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/metaMSdata_1.46.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CluMSID, metaMS dependencyCount: 0 Package: MetaScope Version: 1.9.10 Depends: R (>= 4.1.0) Imports: BiocFileCache, Biostrings, data.table (>= 1.16.2), dplyr, ggplot2, magrittr, Matrix, MultiAssayExperiment, Rbowtie2, readr, rlang, Rsamtools, S4Vectors, stringr, SummarizedExperiment, taxonomizr, tibble, tidyr, tools Suggests: animalcules, BiocStyle, biomformat, GenomicRanges, IRanges, knitr, lintr, plyr, R.utils, RCurl, rmarkdown, Rsubread, spelling, sys, testthat, usethis Enhances: BiocParallel License: GPL (>= 3) MD5sum: a828f9d7153cfc2a61d59ca3b6ae4433 NeedsCompilation: no Title: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data Description: This package contains tools and methods for preprocessing microbiome data. Functionality includes library generation, demultiplexing, alignment, and microbe identification. It is in part an R translation of the PathoScope 2.0 pipeline. biocViews: MicrobiomeData, ReproducibleResearch, SequencingData Author: Sean Lu [aut, cre] (ORCID: ), Aubrey Odom [aut] (ORCID: ), Rahul Varki [aut] (ORCID: ), W. Evan Johnson [aut] (ORCID: ) Maintainer: Sean Lu URL: https://github.com/wejlab/metascope https://wejlab.github.io/metascope-docs/ VignetteBuilder: knitr BugReports: https://github.com/wejlab/MetaScope/issues git_url: https://git.bioconductor.org/packages/MetaScope git_branch: devel git_last_commit: 1f63097 git_last_commit_date: 2025-08-21 Date/Publication: 2025-08-26 source.ver: src/contrib/MetaScope_1.9.10.tar.gz vignettes: vignettes/MetaScope/inst/doc/MetaScope_vignette.html vignetteTitles: "Introduction to MetaScope" hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MetaScope/inst/doc/MetaScope_vignette.R dependencyCount: 100 Package: MethylAidData Version: 1.42.0 Depends: MethylAid, R (>= 3.2) Suggests: BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC License: GPL (>= 2) MD5sum: f9ebd7da5aa0bac59dcf57bef3c60335 NeedsCompilation: no Title: MethylAid-summarized data for 2800 Illumina 450k array samples and 2620 EPIC array samples Description: A data package containing summarized Illumina 450k array data on 2800 samples and summarized EPIC data for 2620 samples. The data can be use as a background data set in the interactive application. biocViews: ExperimentData, TechnologyData, MicroarrayData, MethylationArrayData Author: Davy Cats, Tyler J. Gorrie-Stone, Bastiaan T. Heijmans, John W. Holloway, BIOS Consortium, Maarten van Iterson, Faisal I. Rezwam, Leonard Schalkwyk Maintainer: M. van Iterson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MethylAidData git_branch: RELEASE_3_22 git_last_commit: 020dc02 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/MethylAidData_1.42.0.tar.gz vignettes: vignettes/MethylAidData/inst/doc/MethylAidData.pdf vignetteTitles: MethylAid-summarized data on 2800 Illumina 450k array samples hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MethylAidData/inst/doc/MethylAidData.R suggestsMe: MethylAid dependencyCount: 168 Package: methylclockData Version: 1.18.0 Imports: ExperimentHubData, ExperimentHub, utils Suggests: knitr, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: 42da993831c860de3cc40f854f234b36 NeedsCompilation: no Title: Data for methylclock package Description: Collection of 9 datasets, andrews and bakulski cord blood, blood gse35069, blood gse35069 chen, blood gse35069 complete, combined cord blood, cord bloo d gse68456, gervin and lyle cord blood, guintivano dlpfc and saliva gse48472". Data downloaded from [meffil](https://github.com/perishky/meffil/). Data used to estimate cell counts using Extrinsic epigenetic age acceleration (EEAA) method Collection of 12 datasets to use with MethylClock package to estimate chronological and gestational DNA methylationwith estimators to use wit different methylation clocks biocViews: SpecimenSource, ExperimentHub, Tissue, OrganismData, Homo_sapiens_Data Author: Juan R. Gonzalez [aut], Dolors Pelegri-Siso [aut, cre] Maintainer: Dolors Pelegri-Siso URL: https://github.com/isglobal-brge/methylclockData VignetteBuilder: knitr BugReports: https://github.com/isglobal-brge/methylclockData/issues git_url: https://git.bioconductor.org/packages/methylclockData git_branch: RELEASE_3_22 git_last_commit: d16e798 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/methylclockData_1.18.0.tar.gz vignettes: vignettes/methylclockData/inst/doc/methylcockData.html vignetteTitles: References for metilclock using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/methylclockData/inst/doc/methylcockData.R dependsOnMe: methylclock dependencyCount: 119 Package: MethylSeqData Version: 1.20.0 Depends: SummarizedExperiment Imports: ExperimentHub, HDF5Array, rhdf5, GenomeInfoDb, S4Vectors, GenomicRanges, stats, IRanges, utils Suggests: BiocFileCache, BiocStyle, data.table, knitr, rmarkdown License: CC0 MD5sum: c372fa0187560950c32441b6e978685a NeedsCompilation: no Title: Collection of Public DNA Methylation Sequencing Datasets Description: Base-level (i.e. cytosine-level) counts for a collection of public bisulfite-seq datasets (e.g., WGBS and RRBS), provided as SummarizedExperiment objects with sample- and base-level metadata. biocViews: ExperimentHub, ExperimentData, SequencingData, Homo_sapiens_Data, Mus_musculus_Data, MethylSeqData Author: Peter Hickey [aut, cre] Maintainer: Peter Hickey VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MethylSeqData git_branch: RELEASE_3_22 git_last_commit: 4dcd9e2 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/MethylSeqData_1.20.0.tar.gz vignettes: vignettes/MethylSeqData/inst/doc/MethylSeqData.html vignetteTitles: User's Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MethylSeqData/inst/doc/MethylSeqData.R dependencyCount: 83 Package: MicrobiomeBenchmarkData Version: 1.12.0 Depends: R (>= 4.2), SummarizedExperiment, TreeSummarizedExperiment Imports: BiocFileCache, tools, S4Vectors, ape, utils Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0), mia, ggplot2, tidyr, dplyr, magrittr, tibble, purrr License: Artistic-2.0 MD5sum: a5f43c9d33e392644339b9978ccf5c7e NeedsCompilation: no Title: Datasets for benchmarking in microbiome research Description: The MicrobiomeBenchmarkData package provides functionality to access microbiome datasets suitable for benchmarking. These datasets have some biological truth, which allows to have expected results for comparison. The datasets come from various published sources and are provided as TreeSummarizedExperiment objects. Currently, only datasets suitable for benchmarking differential abundance methods are available. biocViews: ExperimentData, MicrobiomeData, ReproducibleResearch, SequencingData Author: Samuel Gamboa [aut, cre] (ORCID: ), Levi Waldron [aut] (ORCID: ), Marcel Ramos [ctb] Maintainer: Samuel Gamboa URL: https://github.com/waldronlab/MicrobiomeBenchmarkData, http://waldronlab.io/MicrobiomeBenchmarkData/ VignetteBuilder: knitr BugReports: https://github.com/waldronlab/MicrobiomeBenchmarkData/issues git_url: https://git.bioconductor.org/packages/MicrobiomeBenchmarkData git_branch: RELEASE_3_22 git_last_commit: ba08baa git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/MicrobiomeBenchmarkData_1.12.0.tar.gz vignettes: vignettes/MicrobiomeBenchmarkData/inst/doc/datasets.html, vignettes/MicrobiomeBenchmarkData/inst/doc/MicrobiomeBenchmarkData.html, vignettes/MicrobiomeBenchmarkData/inst/doc/recalibrare_spikein_data.html vignetteTitles: Datasets in MicrobiomeBenchmarkData, MicrobiomeBenchmarkData, Recalibration of the Stammler_2016_16S_spikein dataset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MicrobiomeBenchmarkData/inst/doc/datasets.R, vignettes/MicrobiomeBenchmarkData/inst/doc/MicrobiomeBenchmarkData.R, vignettes/MicrobiomeBenchmarkData/inst/doc/recalibrare_spikein_data.R suggestsMe: bugphyzz dependencyCount: 85 Package: microbiomeDataSets Version: 1.18.0 Depends: R (>= 4.1), SummarizedExperiment, TreeSummarizedExperiment, MultiAssayExperiment Imports: methods, utils, BiocGenerics, ExperimentHub, Biostrings, ape Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, testthat License: CC0 MD5sum: 8350b261aa5afb204d20d4c7403f28ee NeedsCompilation: no Title: Experiment Hub based microbiome datasets Description: microbiomeDataSets is a collection of microbiome datasets loaded from Bioconductor'S ExperimentHub infrastructure. The datasets serve as reference for workflows and vignettes published adjacent to the microbiome analysis tools on Bioconductor. Additional datasets can be added overtime and additions from authors are welcome. biocViews: ExperimentHub, ExperimentData, MicrobiomeData, SequencingData Author: Leo Lahti [cre, aut] (ORCID: ), Felix G.M. Ernst [aut] (ORCID: ), Sudarshan Shetty [aut] (ORCID: ), Chouaib Benchraka [ctb] (ORCID: ), Yagmur Simsek [ctb] Maintainer: Leo Lahti VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/microbiomeDataSets git_branch: RELEASE_3_22 git_last_commit: 865d8fb git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/microbiomeDataSets_1.18.0.tar.gz vignettes: vignettes/microbiomeDataSets/inst/doc/microbiomeDataSets.html vignetteTitles: microbiomeDataSets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/microbiomeDataSets/inst/doc/microbiomeDataSets.R suggestsMe: mia dependencyCount: 97 Package: microRNAome Version: 1.32.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: BiocGenerics, RUnit License: GPL (>= 2) MD5sum: f75170d789acd6d15cfa463945c0af09 NeedsCompilation: no Title: SummarizedExperiment for the microRNAome project Description: This package provides a SummarizedExperiment object of read counts for microRNAs across tissues, cell-types, and cancer cell-lines. The read count matrix was prepared and provided by the author of the study: Towards the human cellular microRNAome. biocViews: ExperimentData, CellCulture, CancerData, SequencingData, RNASeqData, miRNAData Author: Matthew N. McCall , Marc K. Halushka , Arun H. Patil Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/microRNAome git_branch: RELEASE_3_22 git_last_commit: b62652f git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/microRNAome_1.32.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 25 Package: minfiData Version: 0.56.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2), IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 License: Artistic-2.0 MD5sum: dc7abebc8c3eaaa92a56c4f5c0e117bc NeedsCompilation: no Title: Example data for the Illumina Methylation 450k array Description: Data from 6 samples across 2 groups from 450k methylation arrays. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData Author: Kasper Daniel Hansen, Martin Aryee, Winston Timp Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/minfiData git_branch: RELEASE_3_22 git_last_commit: 7e79eee git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/minfiData_0.56.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: methylationArrayAnalysis suggestsMe: bigmelon, conumee, ENmix, funtooNorm, Harman, MEAL, MethylAid, minfi, missMethyl, MultiDataSet, recountmethylation, shinyepico, shinyMethyl, skewr, MethylAidData dependencyCount: 145 Package: minfiDataEPIC Version: 1.36.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2), IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: Artistic-2.0 MD5sum: b79c92114d2ba432e3af62b902d1dd0f NeedsCompilation: no Title: Example data for the Illumina Methylation EPIC array Description: Data from 3 technical replicates of the cell line GM12878 from the EPIC methylation array. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData Author: Jean-Philippe Fortin, Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/minfiDataEPIC git_branch: RELEASE_3_22 git_last_commit: b6347d8 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/minfiDataEPIC_1.36.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MethylAid, minfi, recountmethylation, REMP, MethylAidData dependencyCount: 145 Package: minionSummaryData Version: 1.40.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 39f891a909a26307c03b9d8b91ac37df NeedsCompilation: no Title: Summarised MinION sequencing data published by Ashton et al. 2015 Description: Summarised MinION sequencing data for Salmonella Typhi published by Ashton et al. in 2015. Three replicate runs are each provided as Fast5Summary objects. biocViews: ExperimentData, SequencingData Author: Mike Smith [aut, cre] Maintainer: Mike Smith VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/minionSummaryData git_branch: RELEASE_3_22 git_last_commit: d4fc529 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/minionSummaryData_1.40.0.tar.gz vignettes: vignettes/minionSummaryData/inst/doc/creating-Styphi-Dataset.html vignetteTitles: Creating example MinION summary dataset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/minionSummaryData/inst/doc/creating-Styphi-Dataset.R suggestsMe: IONiseR dependencyCount: 0 Package: miRcompData Version: 1.40.0 Depends: R (>= 3.2), Imports: utils License: GPL-3 | file LICENSE MD5sum: 4f6cfa622a54b3b796e26ab9db62fcbc NeedsCompilation: no Title: Data used in the miRcomp package Description: Raw amplification data from a large microRNA mixture / dilution study. These data are used by the miRcomp package to assess the performance of methods that estimate expression from the amplification curves. biocViews: ExperimentData, ExpressionData, qPCRData, Homo_sapiens_Data Author: Matthew N. McCall Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/miRcompData git_branch: RELEASE_3_22 git_last_commit: b216de5 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/miRcompData_1.40.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: miRcomp dependencyCount: 1 Package: miRNATarget Version: 1.48.0 Depends: R (>= 2.10), Biobase License: GPL MD5sum: 975053da55c096375cd6ea1b31f0e2d6 NeedsCompilation: no Title: gene target tabale of miRNA for human/mouse used for MiRaGE package Description: gene target tabale of miRNA for human/mouse used for MiRaGE package biocViews: ExperimentData, Homo_sapiens_Data Author: Y-h. Taguchi Maintainer: Y-h. Taguchi git_url: https://git.bioconductor.org/packages/miRNATarget git_branch: RELEASE_3_22 git_last_commit: 564aeb3 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/miRNATarget_1.48.0.tar.gz vignettes: vignettes/miRNATarget/inst/doc/miRNATarget.pdf vignetteTitles: miRNATargetTutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/miRNATarget/inst/doc/miRNATarget.R suggestsMe: MiRaGE dependencyCount: 7 Package: MMDiffBamSubset Version: 1.46.0 Suggests: MMDiff2 License: LGPL MD5sum: f26f8aa5b4d97281a2fc803f2db00b5b NeedsCompilation: no Title: Example ChIP-Seq data for the MMDiff package Description: Subset of BAM files, including WT_2.bam, Null_2.bam, Resc_2.bam, Input.bam from the "Cfp1" experiment (see Clouaire et al., Genes Dev. 2012). Data is available under ArrayExpress accession numbers E-ERAD-79. Additionally, corresponding subset of peaks called by MACS biocViews: ExperimentData, Genome, StemCell, Mus_musculus_Data, DNASeqData, ChIPSeqData, ArrayExpress Author: Gabriele Schweikert Maintainer: Gabriele Schweikert git_url: https://git.bioconductor.org/packages/MMDiffBamSubset git_branch: RELEASE_3_22 git_last_commit: 6bd89ce git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/MMDiffBamSubset_1.46.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MMDiff2 dependencyCount: 0 Package: MOFAdata Version: 1.26.0 Depends: R (>= 3.5) Suggests: knitr, MultiAssayExperiment, rmarkdown, BiocStyle License: LGPL-3 MD5sum: ad43d3bc27b7456fbdc4b8e8572bb046 NeedsCompilation: yes Title: Data package for Multi-Omics Factor Analysis (MOFA) Description: A collection of datasets to accompany the R package MOFA and illustrate running and analysing MOFA models. biocViews: ReproducibleResearch Author: Ricard Argelaguet, Britta Velten, Damien Arnol, Florian Buettner, Wolfgang Huber, Oliver Stegle Maintainer: Britta Velten VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MOFAdata git_branch: RELEASE_3_22 git_last_commit: c271962 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/MOFAdata_1.26.0.tar.gz vignettes: vignettes/MOFAdata/inst/doc/MOFAdata.html vignetteTitles: MOFAdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MOFAdata/inst/doc/MOFAdata.R importsMe: TDbasedUFE suggestsMe: TDbasedUFEadv, SUMO dependencyCount: 0 Package: mosaicsExample Version: 1.48.0 Depends: R (>= 2.11.1) License: GPL (>= 2) MD5sum: d932c88ee7e7e6a61afd95a7ba89dd5a NeedsCompilation: no Title: Example data for the mosaics package, which implements MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data for transcription factor binding and histone modification Description: Data for the mosaics package, consisting of (1) chromosome 22 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding and H3K4me3 modification in MCF7 cell line from ENCODE database (HG19) and (2) chromosome 21 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding, with mappability, GC content, and sequence ambiguity scores of human genome HG18. biocViews: ExperimentData, ChIPseqData, Homo_sapiens Author: Dongjun Chung, Pei Fen Kuan, Rene Welch, Sunduz Keles Maintainer: Dongjun Chung URL: http://groups.google.com/group/mosaics_user_group git_url: https://git.bioconductor.org/packages/mosaicsExample git_branch: RELEASE_3_22 git_last_commit: a221875 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/mosaicsExample_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: mosaics dependencyCount: 0 Package: mouse4302barcodevecs Version: 1.48.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 038f8d133bee9a3504424e530d827a82 NeedsCompilation: no Title: mouse4302 data for barcode Description: Data used by the barcode package for microarrays of type mouse4302. biocViews: Mus_musculus_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/mouse4302barcodevecs git_branch: RELEASE_3_22 git_last_commit: c2a4a8e git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/mouse4302barcodevecs_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: MouseAgingData Version: 1.6.0 Depends: R (>= 4.4.0), SingleCellExperiment Imports: AnnotationHub, ExperimentHub Suggests: BiocStyle, knitr, rmarkdown, scater License: Artistic-2.0 MD5sum: 1885170ed9055be0ba0a12ddfa4debab NeedsCompilation: no Title: Multi-omics data access for studies investigating the effects of aging Description: The MouseAgingData package provides analysis-ready data resources from different studies focused on aging and rejuvenation in mice. The package currently provides two 10x Genomics single-cell RNA-seq datasets. The first study profiled the aging mouse brain measured across 37,089 cells (Ximerakis et al., 2019). The second study investigated parabiosis by profiling a total of 105,329 cells (Ximerakis & Holton et al., 2023). The datasets are provided as SingleCellExperiment objects and provide raw UMI counts and cell metadata. biocViews: ExperimentData, ExpressionData, SequencingData, RNASeqData, SingleCellData, ExperimentHub, PackageTypeData, Mus_musculus_Data Author: Tram Nguyen [aut, cre] (ORCID: ), Kris Holton [aut], Tyrone Lee [aut], Nitesh Turaga [ctb], Ludwig Geistlinger [aut], Robert Gentleman [aut] Maintainer: Tram Nguyen URL: https://github.com/ccb-hms/MouseAgingData VignetteBuilder: knitr BugReports: https://github.com/ccb-hms/MouseAgingData/issues git_url: https://git.bioconductor.org/packages/MouseAgingData git_branch: RELEASE_3_22 git_last_commit: 4ab18d8 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/MouseAgingData_1.6.0.tar.gz vignettes: vignettes/MouseAgingData/inst/doc/MouseAgingData_parabiosis_droplet.html vignetteTitles: Accessing and Visualizing Parabiosis Droplet Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MouseAgingData/inst/doc/MouseAgingData_parabiosis_droplet.R dependencyCount: 77 Package: MouseGastrulationData Version: 1.24.0 Depends: R (>= 4.1), SingleCellExperiment, SummarizedExperiment, SpatialExperiment Imports: methods, ExperimentHub, BiocGenerics, S4Vectors, BumpyMatrix Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: ef5408483409bf0b3358b1ad108b8776 NeedsCompilation: no Title: Single-Cell -omics Data across Mouse Gastrulation and Early Organogenesis Description: Provides processed and raw count data for single-cell RNA sequencing, single-cell ATAC-seq, and seqFISH (spatial transcriptomic) experiments performed along a timecourse of mouse gastrulation and early organogenesis. biocViews: ExperimentData, ExpressionData, SequencingData, RNASeqData, SingleCellData, ExperimentHub, Mus_musculus_Data Author: Jonathan Griffiths [aut, cre], Aaron Lun [aut] Maintainer: Jonathan Griffiths URL: https://github.com/MarioniLab/MouseGastrulationData VignetteBuilder: knitr BugReports: https://github.com/MarioniLab/MouseGastrulationData/issues git_url: https://git.bioconductor.org/packages/MouseGastrulationData git_branch: RELEASE_3_22 git_last_commit: 61f2566 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/MouseGastrulationData_1.24.0.tar.gz vignettes: vignettes/MouseGastrulationData/inst/doc/MouseGastrulationData.html vignetteTitles: Available datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MouseGastrulationData/inst/doc/MouseGastrulationData.R dependsOnMe: OSCA.multisample suggestsMe: Coralysis, miloR dependencyCount: 82 Package: MouseThymusAgeing Version: 1.18.0 Depends: SingleCellExperiment, SummarizedExperiment Imports: ExperimentHub, methods, BiocGenerics, S4Vectors Suggests: knitr, scuttle, rmarkdown, BiocStyle License: GPL-3 MD5sum: 0f733aefae2698b2c99949d66fa401ba NeedsCompilation: no Title: Single-cell Transcriptomics Data of the Ageing Mouse Thymus Description: This package provides data access to counts matrices and meta-data for single-cell RNA sequencing data of thymic epithlial cells across mouse ageing using SMARTseq2 and 10X Genommics chemistries. Access is provided as a data package via ExperimentHub. It is designed to facilitate the re-use of data from Baran-Gale _et al._ in a consistent format that includes relevant and informative meta-data. biocViews: ExperimentHub, SingleCellData, ExpressionData, ExperimentData Author: Mike Morgan [aut, cre], Jeanette Baran-Gale [aut] Maintainer: Mike Morgan VignetteBuilder: knitr BugReports: https://github.com/MarioniLab/MouseThymusAgeing/issues git_url: https://git.bioconductor.org/packages/MouseThymusAgeing git_branch: RELEASE_3_22 git_last_commit: ad40f16 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/MouseThymusAgeing_1.18.0.tar.gz vignettes: vignettes/MouseThymusAgeing/inst/doc/MouseThymusAgeing.html vignetteTitles: Available datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MouseThymusAgeing/inst/doc/MouseThymusAgeing.R suggestsMe: miloR dependencyCount: 77 Package: msd16s Version: 1.30.0 Depends: R (>= 2.10), Biobase, metagenomeSeq, License: Artistic-2.0 MD5sum: d32ed1425d02282846d93f696af115ce NeedsCompilation: no Title: Healthy and moderate to severe diarrhea 16S expression data Description: Gut 16S sequencing expression data from 992 healthy and moderate-to-severe diarrhetic samples used in 'Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition'. biocViews: ExperimentData, SequencingData, MicrobiomeData Author: Joseph N. Paulson, Hector Corrada Bravo, Mihai Pop Maintainer: Joseph N. Paulson URL: http://www.cbcb.umd.edu/research/projects/GEMS-pathogen-discovery git_url: https://git.bioconductor.org/packages/msd16s git_branch: RELEASE_3_22 git_last_commit: ace6bd3 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/msd16s_1.30.0.tar.gz vignettes: vignettes/msd16s/inst/doc/msd16s.pdf vignetteTitles: msd16s hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/msd16s/inst/doc/msd16s.R suggestsMe: scTreeViz dependencyCount: 33 Package: msdata Version: 0.50.0 Depends: R (>= 3.5.0) Suggests: xcms, mzR, MSnbase License: GPL (>= 2) MD5sum: d8cb9351e410ea52dca527cad2392008 NeedsCompilation: no Title: Various Mass Spectrometry raw data example files Description: Ion Trap positive ionization mode data in mzML file format. Subset from 500-850 m/z and 1190-1310 seconds, incl. MS2 and MS3, intensity threshold 100.000. Extracts from FTICR Apex III, m/z 400-450. Subset of UPLC - Bruker micrOTOFq data, both mzML and mz5. LC-MSMS and MRM files from proteomics experiments. PSI mzIdentML example files for various search engines. biocViews: ExperimentData, MassSpectrometryData Author: Steffen Neumann , Laurent Gatto with contriutions from Johannes Rainer Maintainer: Steffen Neumann , Laurent Gatto git_url: https://git.bioconductor.org/packages/msdata git_branch: RELEASE_3_22 git_last_commit: c0d273d git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/msdata_0.50.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: MsQuality suggestsMe: Chromatograms, IPO, koinar, MetaboAnnotation, MsBackendSql, MsExperiment, MSnbase, mzR, peakPantheR, PSMatch, QFeatures, Spectra, SpectraQL, TargetDecoy, xcms, RforProteomics dependencyCount: 0 Package: msigdb Version: 1.18.0 Depends: R (>= 4.1) Imports: ExperimentHub, utils, GSEABase, org.Mm.eg.db, org.Hs.eg.db, AnnotationDbi, methods, stats, AnnotationHub Suggests: singscore, vissE, knitr, prettydoc, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocFileCache, GO.db, stringr, limma License: CC BY 4.0 MD5sum: 7ad7ff3ef11d2484277d8834571546c1 NeedsCompilation: no Title: An ExperimentHub Package for the Molecular Signatures Database (MSigDB) Description: This package provides the Molecular Signatures Database (MSigDB) in a R accessible objects. Signatures are stored in GeneSet class objects form the GSEABase package and the entire database is stored in a GeneSetCollection object. These data are then hosted on the ExperimentHub. Data used in this package was obtained from the MSigDB of the Broad Institute. Metadata for each gene set is stored along with the gene set in the GeneSet class object. biocViews: ExperimentHub, Homo_sapiens_Data, Mus_musculus_Data Author: Dharmesh D. Bhuva [aut, cre] (ORCID: ), Gordon K. Smyth [aut] (ORCID: ), Alexandra Garnham [aut] (ORCID: ) Maintainer: Dharmesh D. Bhuva URL: https://davislaboratory.github.io/msigdb VignetteBuilder: knitr BugReports: https://github.com/DavisLaboratory/msigdb/issues git_url: https://git.bioconductor.org/packages/msigdb git_branch: RELEASE_3_22 git_last_commit: a69837c git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/msigdb_1.18.0.tar.gz vignettes: vignettes/msigdb/inst/doc/msigdb.html vignetteTitles: msigdb hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/msigdb/inst/doc/msigdb.R importsMe: mastR, vissE suggestsMe: epiregulon.extra, escape dependencyCount: 72 Package: MSMB Version: 1.28.0 Depends: R (>= 3.5), tibble Suggests: knitr, BiocStyle License: LGPL MD5sum: 5dd8e9e1d58fa5c0ae7579db4230e855 NeedsCompilation: no Title: Data sets for the book 'Modern Statistics for Biology' Description: Data sets for the book 'Modern Statistics for Modern Biology', S.P. Holmes and W. Huber. biocViews: ExperimentData Author: Wolfgang Huber, Andrzej Oles, Mike Smith Maintainer: Wolfgang Huber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MSMB git_branch: RELEASE_3_22 git_last_commit: 5e7ffcb git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/MSMB_1.28.0.tar.gz vignettes: vignettes/MSMB/inst/doc/MSMB.html vignetteTitles: Data sets for the book 'Modern Statistics for Biology' hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MSMB/inst/doc/MSMB.R dependencyCount: 12 Package: msPurityData Version: 1.38.0 Suggests: knitr License: GPL (>= 2) MD5sum: 5a629fe0b540815ec92bbd0c39eb55f9 NeedsCompilation: no Title: Fragmentation spectral libraries and data to test the msPurity package Description: Fragmentation spectral libraries and data to test the msPurity package biocViews: ExperimentData, MassSpectrometryData Author: Thomas N. Lawson Maintainer: Thomas N. Lawson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/msPurityData git_branch: RELEASE_3_22 git_last_commit: 6d21374 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/msPurityData_1.38.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: msPurity dependencyCount: 0 Package: msqc1 Version: 1.38.0 Depends: R (>= 3.6), lattice, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, specL (>= 1.2) License: GPL MD5sum: 954e232ad5ba550d3af825437a203f41 NeedsCompilation: no Title: Sigma mix MSQC1 data Description: contains eight technical replicate data set and a three replicate dilution series of the MS Qual/Quant Quality Control Mix standard sample (Sigma-Aldrich, Buchs, Switzerland) measured on five different mass spectrometer platforms at the Functional Genomics Center Zurich. biocViews: ExperimentData, MassSpectrometryData, ReproducibleResearch Author: Tobias Kockmann [aut] (ORCID: ), Christian Trachsel [aut], Christian Panse [aut, cre] (ORCID: ) Maintainer: Christian Panse URL: https://panoramaweb.org/labkey/MSQC1.url, http://fgcz-bfabric.uzh.ch/bfabric/project.html?projectId=1959 VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/msqc1 git_branch: RELEASE_3_22 git_last_commit: 160df58 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/msqc1_1.38.0.tar.gz vignettes: vignettes/msqc1/inst/doc/poster.pdf, vignettes/msqc1/inst/doc/chromatography.html, vignettes/msqc1/inst/doc/msqc1.html vignetteTitles: ASMS 2016 poster (in portrait) abstract ID number: 282492, LC Observations - Retention Time Stability, Introducing msqc1 - A Mass Spec Data set for Targeted Proteomics Performance Evaluation hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/msqc1/inst/doc/chromatography.R, vignettes/msqc1/inst/doc/msqc1.R, vignettes/msqc1/inst/doc/poster.R suggestsMe: CalibraCurve dependencyCount: 6 Package: mtbls2 Version: 1.40.0 Depends: R (>= 2.10) Suggests: MSnbase, xcms (>= 3.13.8), CAMERA, knitr, Heatplus, pcaMethods, sp, rmarkdown, Biobase License: CC0 MD5sum: 585dec8984fb48136b6a15189fbf78a4 NeedsCompilation: no Title: MetaboLights MTBLS2: Comparative LC/MS-based profiling of silver nitrate-treated Arabidopsis thaliana leaves of wild-type and cyp79B2 cyp79B3 double knockout plants. Böttcher et al. (2004) Description: Indole-3-acetaldoxime (IAOx) represents an early intermediate of the biosynthesis of a variety of indolic secondary metabolites including the phytoanticipin indol-3-ylmethyl glucosinolate and the phytoalexin camalexin (3-thiazol-2'-yl-indole). Arabidopsis thaliana cyp79B2 cyp79B3 double knockout plants are completely impaired in the conversion of tryptophan to indole-3-acetaldoxime and do not accumulate IAOx-derived metabolites any longer. Consequently, comparative analysis of wild-type and cyp79B2 cyp79B3 plant lines has the potential to explore the complete range of IAOx-derived indolic secondary metabolites. biocViews: MassSpectrometryData, RepositoryData Author: Steffen Neumann Maintainer: Steffen Neumann URL: http://www.ebi.ac.uk/metabolights/MTBLS2, https://github.com/sneumann/mtbls2 VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mtbls2 git_branch: RELEASE_3_22 git_last_commit: 78b9c59 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/mtbls2_1.40.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: IPO, yamss dependencyCount: 0 Package: MUGAExampleData Version: 1.30.0 Depends: R (>= 2.10.0) License: GPL-3 MD5sum: d690168ec8f7872e00c56e8c92dce190 NeedsCompilation: no Title: Example {M}ouse {U}niversal {G}enotyping {A}rray data for genome reconstruction and quantitative trait locus mapping. Description: This package contains example data for the MUGA array that is used by the R package DOQTL. biocViews: ExperimentData, Mus_musculus_Data Author: Daniel Gatti Maintainer: Daniel Gatti git_url: https://git.bioconductor.org/packages/MUGAExampleData git_branch: RELEASE_3_22 git_last_commit: 19c5b40 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/MUGAExampleData_1.30.0.tar.gz vignettes: vignettes/MUGAExampleData/inst/doc/MUGAExampleData.pdf vignetteTitles: User Manual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MUGAExampleData/inst/doc/MUGAExampleData.R dependencyCount: 0 Package: muleaData Version: 1.6.0 Suggests: knitr, rmarkdown, ExperimentHub, dplyr License: MIT + file LICENSE MD5sum: 676f49d798a15dd8d009279c35680c40 NeedsCompilation: no Title: Genes Sets for Functional Enrichment Analysis with the 'mulea' R Package Description: ExperimentHubData package for the 'mulea' comprehensive overrepresentation and functional enrichment analyser R package. Here we provide ontologies (gene sets) in a data.frame for 27 different organisms, ranging from Escherichia coli to human, all acquired from publicly available data sources. Each ontology is provided with multiple gene and protein identifiers. Please see the NEWS file for a list of changes in each version. biocViews: ExperimentData, ExperimentHub, Arabidopsis_thaliana_Data, Bacillus_subtilis_Data, Caenorhabditis_elegans_Data, Danio_rerio_Data, Drosophila_melanogaster_Data, Escherichia_coli_Data, Homo_sapiens_Data, Pan_troglodytes_Data, Pseudomonas_aeruginosa_Data, Rattus_norvegicus_Data, Saccharomyces_cerevisiae_Data, Staphylococcus_aureus_Data, ChIPSeqData, DNASeqData, ExpressionData, miRNAData Author: Eszter Ari [aut, cre] (ORCID: ), Márton Ölbei [aut] (ORCID: ), Lejla Gul [aut], Balázs Bohár [aut] (ORCID: ), Tamás Stirling [aut] (ORCID: ) Maintainer: Eszter Ari URL: https://github.com/ELTEbioinformatics/muleaData VignetteBuilder: knitr BugReports: https://support.bioconductor.org/tag/muleaData/issues git_url: https://git.bioconductor.org/packages/muleaData git_branch: RELEASE_3_22 git_last_commit: 5d03e56 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/muleaData_1.6.0.tar.gz vignettes: vignettes/muleaData/inst/doc/muleaData.html vignetteTitles: muleaData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/muleaData/inst/doc/muleaData.R dependencyCount: 0 Package: multiWGCNAdata Version: 1.8.0 Depends: ExperimentHub Imports: utils Suggests: BiocStyle, knitr, multiWGCNA, rmarkdown, SummarizedExperiment License: Artistic-2.0 MD5sum: 728709d7c7b6c2f37320cfc33d97b1c3 NeedsCompilation: no Title: Data Package for multiWGCNA Description: Stores expression profiling data from experiments compatible with the multiWGCNA R package. This includes human postmortem microarray data from patients and controls (GSE28521), astrocyte Ribotag RNA-seq data from EAE and wildtype mice (GSE100329), and mouse RNA-seq data from tau pathology (rTg4510) and wildtype control mice (GSE125957). These data can be accessed using the ExperimentHub workflow (see multiWGCNA vignettes). biocViews: ExperimentHub, ExpressionData, Homo_sapiens_Data, Mus_musculus_Data, RNASeqData, MicroarrayData Author: Dario Tommasini [aut, cre] (ORCID: ) Maintainer: Dario Tommasini VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/multiWGCNAdata git_branch: RELEASE_3_22 git_last_commit: 42ab777 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/multiWGCNAdata_1.8.0.tar.gz vignettes: vignettes/multiWGCNAdata/inst/doc/multiWGCNAdata.html vignetteTitles: Loading data through ExperimentHub hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/multiWGCNAdata/inst/doc/multiWGCNAdata.R dependencyCount: 65 Package: muscData Version: 1.24.0 Depends: R (>= 3.6), ExperimentHub, SingleCellExperiment Imports: utils Suggests: BiocStyle, dplyr, DropletUtils, knitr, GEOquery, Matrix, matrixStats, methods, muscat, rmarkdown, R.utils, readxl, scater, scds, Seurat License: MIT + file LICENSE MD5sum: 3624d8ae077912985a0dc3e64d8b2ebe NeedsCompilation: no Title: Multi-sample multi-group scRNA-seq data Description: Data package containing a collection of multi-sample multi-group scRNA-seq datasets in SingleCellExperiment Bioconductor object format. biocViews: ExperimentHub, ExperimentData, ExpressionData, GEO, Homo_sapiens_Data, ImmunoOncologyData, SingleCellData Author: Helena L. Crowell [aut, cre] Maintainer: Helena L. Crowell URL: https://github.com/HelenaLC/muscData VignetteBuilder: knitr BugReports: https://github.com/HelenaLC/muscData/issues git_url: https://git.bioconductor.org/packages/muscData git_branch: RELEASE_3_22 git_last_commit: bf18664 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/muscData_1.24.0.tar.gz vignettes: vignettes/muscData/inst/doc/muscData.html vignetteTitles: Multi-sample multi-group scRNA-seq data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/muscData/inst/doc/muscData.R suggestsMe: dreamlet, glmGamPoi dependencyCount: 77 Package: muSpaData Version: 1.2.0 Depends: R (>= 4.5.0), ExperimentHub Suggests: SpatialExperiment, ggplot2, BiocStyle, knitr, rmarkdown, R.utils License: MIT + file LICENSE MD5sum: bbd753ac03b3704db7050e714a5ee47a NeedsCompilation: no Title: Multi-sample multi-group spatially resolved transcriptomic data Description: Data package containing a multi-sample multi-group spatial dataset in SpatialExperiment Bioconductor object format. biocViews: ExperimentHub, ExperimentData, ExpressionData, SpatialData, SingleCellData Author: Peiying Cai [aut, cre] (ORCID: ) Maintainer: Peiying Cai URL: https://github.com/peicai/muSpaData VignetteBuilder: knitr BugReports: https://github.com/peicai/muSpaData/issues git_url: https://git.bioconductor.org/packages/muSpaData git_branch: RELEASE_3_22 git_last_commit: a86afc5 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/muSpaData_1.2.0.tar.gz vignettes: vignettes/muSpaData/inst/doc/muSpaData.html vignetteTitles: Multi-sample multi-group spatial transcriptomics data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/muSpaData/inst/doc/muSpaData.R importsMe: OSTA suggestsMe: DESpace dependencyCount: 65 Package: mvoutData Version: 1.46.0 Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4), lumi License: Artistic-2.0 MD5sum: bbd1441a5626310574c7318f41f4ff5e NeedsCompilation: no Title: affy and illumina raw data for assessing outlier detector performance Description: affy and illumina raw data for assessing outlier detector performance biocViews: ExperimentData, MicroarrayData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/mvoutData git_branch: RELEASE_3_22 git_last_commit: bd9ace8 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/mvoutData_1.46.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayMvout dependencyCount: 165 Package: NanoporeRNASeq Version: 1.20.0 Depends: R(>= 4.0.0), ExperimentHub (>= 1.15.3) Suggests: knitr, bambu, ggbio, BSgenome.Hsapiens.NCBI.GRCh38, circlize, ComplexHeatmap, apeglm, rlang, rmarkdown, GenomicAlignments, Rsamtools Enhances: parallel License: GPL-3 + file LICENSE MD5sum: b55af18d54df8d69467a711d9fe37b93 NeedsCompilation: no Title: Nanopore RNA-Seq Example data Description: The NanoporeRNASeq package contains long read RNA-Seq data generated using Oxford Nanopore Sequencing. The data consists of 6 samples from two human cell lines (K562 and MCF7) that were generated by the SG-NEx project. Each of these cell lines has three replicates, with 1 direct RNA sequencing data and 2 cDNA sequencing data. Reads are aligned to chromosome 22 (Grch38) and stored as bam files. The original data is from the SG-NEx project. biocViews: ExperimentHub, ExperimentData, RNASeqData, Genome, SequencingData Author: Jonathan Goeke [aut], Ying Chen [cre], Yuk Kei Wan [aut] Maintainer: Ying Chen URL: https://github.com/GoekeLab/NanoporeRNASeq VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/NanoporeRNASeq git_branch: RELEASE_3_22 git_last_commit: 61dfc36 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/NanoporeRNASeq_1.20.0.tar.gz vignettes: vignettes/NanoporeRNASeq/inst/doc/NanoporeRNASeq.html vignetteTitles: NanoporeRNASeq hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/NanoporeRNASeq/inst/doc/NanoporeRNASeq.R suggestsMe: bambu dependencyCount: 65 Package: nanotubes Version: 1.26.0 Depends: R (>= 3.6) Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, rtracklayer, CAGEfightR License: GPL-3 MD5sum: 355593a27c1c0eba86a042803ac6d149 NeedsCompilation: no Title: Mouse nanotube CAGE data Description: Cap Analysis of Gene Expression (CAGE) data from "Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo" by Bornholdt et al. supplied as CAGE Transcription Start Sites (CTSSs). biocViews: ExperimentData, SequencingData, ExpressionData Author: Malte Thodberg Maintainer: Malte Thodberg URL: https://github.com/MalteThodberg/nanotubes VignetteBuilder: knitr BugReports: https://github.com/MalteThodberg/nanotubes/issues git_url: https://git.bioconductor.org/packages/nanotubes git_branch: RELEASE_3_22 git_last_commit: 79a9ca7 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/nanotubes_1.26.0.tar.gz vignettes: vignettes/nanotubes/inst/doc/nanotubes.html vignetteTitles: nanotubes hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/nanotubes/inst/doc/nanotubes.R dependsOnMe: CAGEWorkflow dependencyCount: 0 Package: NCIgraphData Version: 1.46.0 Depends: R (>= 2.10.0) Suggests: Rgraphviz License: GPL-3 MD5sum: 1827cc9747a011cba31b54f9df08eb23 NeedsCompilation: no Title: Data for the NCIgraph software package Description: Provides pathways from the NCI Pathways Database as R graph objects biocViews: NCI Author: Laurent Jacob Maintainer: Laurent Jacob git_url: https://git.bioconductor.org/packages/NCIgraphData git_branch: RELEASE_3_22 git_last_commit: d0095e6 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/NCIgraphData_1.46.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: NestLink Version: 1.26.0 Depends: R (>= 3.6), AnnotationHub (>= 2.15), ExperimentHub (>= 1.0), Biostrings (>= 2.51), gplots (>= 3.0), protViz (>= 0.4), ShortRead (>= 1.41) Imports: grDevices, graphics, stats, utils Suggests: BiocStyle (>= 2.2), DT, ggplot2, knitr, rmarkdown, testthat, specL, lattice, scales License: GPL MD5sum: 0d2dfc53c1b7305f060f84e748cf893c NeedsCompilation: no Title: NestLink an R data package to guide through Engineered Peptide Barcodes for In-Depth Analyzes of Binding Protein Ensembles Description: Provides next-generation sequencing (NGS) and mass spectrometry (MS) sample data, code snippets and replication material used for developing NestLink. The NestLink approach is a protein binder selection and identification technology able to biophysically characterize thousands of library members at once without handling individual clones at any stage of the process. Data were acquired on NGS and MS platforms at the Functional Genomics Center Zurich. biocViews: ExperimentHub, ExperimentData, SequencingData, MassSpectrometryData, ReproducibleResearch Author: Pascal Egloff [aut] (ORCID: ), Iwan Zimmermann [ctb] (ORCID: ), Fabian M. Arnold [ctb], Cedric A.J. Hutter [ctb] (ORCID: ), Lennart Opitz [aut, cre] (ORCID: ), Lucy Poveda [ctb] (ORCID: ), Hans-Anton Keserue [ctb], Christian Panse [aut, ctb] (ORCID: ), Bernd Roschitzki [aut] (ORCID: ), Markus Seeger [aut] (ORCID: ) Maintainer: Lennart Opitz VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/NestLink git_branch: RELEASE_3_22 git_last_commit: 81bfb69 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/NestLink_1.26.0.tar.gz vignettes: vignettes/NestLink/inst/doc/analyze-flycode-detectibilty.html, vignettes/NestLink/inst/doc/compare-predicted-observed-flycodes.html, vignettes/NestLink/inst/doc/link-nanobodies-flycodes.html, vignettes/NestLink/inst/doc/make-data.html, vignettes/NestLink/inst/doc/simulate-flycodes.html, vignettes/NestLink/inst/doc/supplement-note1.html vignetteTitles: 2. Analyze flycode detectability using ESP and SSRC prediction, 3. Compare Predicted and Observed flycodes hydrophobicity values using F255744., 1. Link high quality flycode and nanobody sequences by NGS filtering., 5. make-data, 0. Simulate flycode properties., 4. Control experiment to assess the robustness of protein detection via flycodes (NMETH-A35040 Suppl. notes 1). hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/NestLink/inst/doc/analyze-flycode-detectibilty.R, vignettes/NestLink/inst/doc/compare-predicted-observed-flycodes.R, vignettes/NestLink/inst/doc/link-nanobodies-flycodes.R, vignettes/NestLink/inst/doc/make-data.R, vignettes/NestLink/inst/doc/simulate-flycodes.R, vignettes/NestLink/inst/doc/supplement-note1.R dependencyCount: 106 Package: NetActivityData Version: 1.12.0 Depends: R (>= 4.2.0) Suggests: BiocStyle, knitr License: MIT + file LICENSE MD5sum: 619492746ac0a1a116acff346b024f7c NeedsCompilation: no Title: Data required for getting the gene set scores with NetActivity package Description: This package contains the weights from pre-trained shallow sparsely-connected autoencoders. This data is required for getting the gene set scores with NetActivity package. biocViews: ExperimentData, RepositoryData Author: Carlos Ruiz-Arenas [aut, cre] Maintainer: Carlos Ruiz-Arenas VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/NetActivityData git_branch: RELEASE_3_22 git_last_commit: 1dd59f8 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/NetActivityData_1.12.0.tar.gz vignettes: vignettes/NetActivityData/inst/doc/NetActivityData.html vignetteTitles: "NetActivityData" hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/NetActivityData/inst/doc/NetActivityData.R importsMe: NetActivity dependencyCount: 0 Package: Neve2006 Version: 0.48.0 Depends: R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0), hgu133a.db, annotate License: Artistic-2.0 MD5sum: 96c2e822422f2c470c867193990767e6 NeedsCompilation: no Title: expression and CGH data on breast cancer cell lines Description: Experimental organization of combined expression and CGH data biocViews: ExperimentData, CancerData, BreastCancerData Author: M. Neve et al. in Gray Lab at LBL Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/Neve2006 git_branch: RELEASE_3_22 git_last_commit: b16f1a4 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/Neve2006_0.48.0.tar.gz vignettes: vignettes/Neve2006/inst/doc/neve06notes.pdf vignetteTitles: Neve 2006: combined CGH and expression data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Neve2006/inst/doc/neve06notes.R dependencyCount: 48 Package: NGScopyData Version: 1.30.0 License: GPL (>=2) MD5sum: e5b965d62d75f8cfc3a27eba5de881ac NeedsCompilation: no Title: Subset of BAM files of human tumor and pooled normal sequencing data (Zhao et al. 2014) for the NGScopy package Description: Subset of BAM files of human lung tumor and pooled normal samples by targeted panel sequencing. [Zhao et al 2014. Targeted Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using the University of North Carolina (UNC) Sequencing Assay Captures Most Previously Described Genetic Aberrations in NSCLC. In preparation.] Each sample is a 10 percent random subsample drawn from the original sequencing data. The pooled normal sample has been rescaled accroding to the total number of normal samples in the "pool". Here provided is the subsampled data on chr6 (hg19). biocViews: ExperimentData, CancerData, LungCancerData, SequencingData Author: Xiaobei Zhao [aut, cre, cph] Maintainer: Xiaobei Zhao URL: http://www.bioconductor.org/packages/release/data/experiment/html/NGScopyData.html git_url: https://git.bioconductor.org/packages/NGScopyData git_branch: RELEASE_3_22 git_last_commit: c673704 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/NGScopyData_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: nmrdata Version: 1.0.0 Imports: ExperimentHub, Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 8355820d765acbdc1a23874f7be8765d NeedsCompilation: no Title: Example 1d NMR Data for Metabolic Profiling Description: Provides example one-dimensional proton NMR spectra of murine urine samples collected before and after bariatric or sham surgery (Roux-en-Y gastric bypass). The data are adapted from Jia V Li et al. (2011), "Metabolic surgery profoundly influences gut microbial-host metabolic cross-talk", Gut, 60(9), 1214–1223. . This package serves as example data for metabolomics analysis and teaching purposes. biocViews: ExperimentHub, ExperimentData Author: Torben Kimhofer [aut, cre] (ORCID: ) Maintainer: Torben Kimhofer URL: https://github.com/tkimhofer/nmrdata VignetteBuilder: knitr BugReports: https://github.com/tkimhofer/nmrdata/issues git_url: https://git.bioconductor.org/packages/nmrdata git_branch: RELEASE_3_22 git_last_commit: a43e0c7 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/nmrdata_1.0.0.tar.gz vignettes: vignettes/nmrdata/inst/doc/nmrdata.html vignetteTitles: nmrdata: Example 1D Proton NMR Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/nmrdata/inst/doc/nmrdata.R dependencyCount: 65 Package: nullrangesData Version: 1.16.0 Depends: R (>= 4.1.0), ExperimentHub, GenomicRanges, InteractionSet Imports: utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: f9ac146413d26934e2495cb024cca5e3 NeedsCompilation: no Title: ExperimentHub datasets for the nullranges package Description: Provides datasets for the nullranges package vignette, in particular example datasets for DNase hypersensitivity sites (DHS), CTCF binding sites, and CTCF genomic interactions. These are used to demonstrate generation of null hypothesis feature sets, either through block bootstrapping or matching, in the nullranges vignette. For more details, see the data object man pages, and the R scripts for object construction provided within the package. biocViews: ExperimentHub, Homo_sapiens_Data, SequencingData, ChIPSeqData, ENCODE Author: Michael Love [aut, cre] (ORCID: ), Wancen Mu [aut] (ORCID: ), Eric Davis [aut] (ORCID: ), Mikhail Dozmorov [aut] Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/nullrangesData git_branch: RELEASE_3_22 git_last_commit: 64c2eaf git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/nullrangesData_1.16.0.tar.gz vignettes: vignettes/nullrangesData/inst/doc/nullrangesData.html vignetteTitles: nullrangesData package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/nullrangesData/inst/doc/nullrangesData.R suggestsMe: iSEEhub, nullranges dependencyCount: 78 Package: NxtIRFdata Version: 1.16.0 Imports: ExperimentHub, BiocFileCache, rtracklayer, R.utils Suggests: testthat (>= 3.0.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: 58b78cd06976fa96084b996871727a2f NeedsCompilation: no Title: Data for NxtIRF Description: NxtIRFdata is a companion package for SpliceWiz, an interactive analysis and visualization tool for alternative splicing quantitation (including intron retention) for RNA-seq BAM files. NxtIRFdata contains Mappability files required for the generation of human and mouse references. NxtIRFdata also contains a synthetic genome reference and example BAM files used to demonstrate SpliceWiz's functionality. BAM files are based on 6 samples from the Leucegene dataset provided by NCBI Gene Expression Omnibus under accession number GSE67039. biocViews: ExperimentData, PackageTypeData, Genome, RNASeqData, ExpressionData, ExperimentHub Author: Alex Chit Hei Wong [aut, cre, cph], Ulf Schmitz [ctb] Maintainer: Alex Chit Hei Wong URL: https://github.com/alexchwong/NxtIRFdata VignetteBuilder: knitr BugReports: https://support.bioconductor.org/ git_url: https://git.bioconductor.org/packages/NxtIRFdata git_branch: RELEASE_3_22 git_last_commit: 50ae7e2 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/NxtIRFdata_1.16.0.tar.gz vignettes: vignettes/NxtIRFdata/inst/doc/NxtIRFdata.html vignetteTitles: NxtIRFdata: a data package for NxtIRF hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/NxtIRFdata/inst/doc/NxtIRFdata.R dependsOnMe: SpliceWiz dependencyCount: 99 Package: ObMiTi Version: 1.18.0 Depends: R (>= 4.1), SummarizedExperiment, ExperimentHub Suggests: knitr, rmarkdown, BiocManager, GenomicFeatures, S4Vectors, devtools, testthat License: GPL-3 MD5sum: 11c2f42b65ea148bde295d9e03750b73 NeedsCompilation: no Title: Ob/ob Mice Data on Normal and High Fat Diet Description: The package provide RNA-seq count for 2 strains of mus musclus; Wild type and Ob/Ob. Each strain was divided into two groups, and each group received either chow diet or high fat diet. RNA expression was measured after 20 weeks in 7 tissues. biocViews: ExperimentHub, GEO, RNASeqData Author: Omar Elashkar [aut, cre] (ORCID: ), Mahmoud Ahmed [aut] (ORCID: ) Maintainer: Omar Elashkar URL: https://github.com/OmarElAshkar/ObMiTi VignetteBuilder: knitr BugReports: https://github.com/OmarElAshkar/ObMiTi/issues git_url: https://git.bioconductor.org/packages/ObMiTi git_branch: RELEASE_3_22 git_last_commit: c957968 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/ObMiTi_1.18.0.tar.gz vignettes: vignettes/ObMiTi/inst/doc/ObMiTi.html vignetteTitles: Using ObMiTi hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ObMiTi/inst/doc/ObMiTi.R dependencyCount: 76 Package: oct4 Version: 1.26.0 Suggests: knitr, markdown License: GPL (>= 2) MD5sum: 34789afaa840a17dd74a9556e58acb83 NeedsCompilation: no Title: Conditional knockdown of OCT4 in mouse ESCs Description: This package provides the output of running Salmon on a set of 12 RNA-seq samples from King & Klose, "The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells", published in eLIFE, March 2017. For details on version numbers and how the samples were processed see the package vignette. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/oct4 git_branch: RELEASE_3_22 git_last_commit: 84d02cb git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/oct4_1.26.0.tar.gz vignettes: vignettes/oct4/inst/doc/oct4.html vignetteTitles: Salmon quantifications for condition OCT4 knockdown in mouse ESCs hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/oct4/inst/doc/oct4.R dependencyCount: 0 Package: octad.db Version: 1.12.0 Depends: R (>= 4.2.0), ExperimentHub Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: e182a923b8b7b38c5039abb2ee1b6e81 NeedsCompilation: no Title: Open Cancer TherApeutic Discovery (OCTAD) database Description: Open Cancer TherApeutic Discovery (OCTAD) package implies sRGES approach for the drug discovery. The essential idea is to identify drugs that reverse the gene expression signature of a disease by tamping down over-expressed genes and stimulating weakly expressed ones. The following package contains all required precomputed data for whole OCTAD pipeline computation. biocViews: ExperimentData, CancerData, ExperimentHub, SequencingData, ExpressionData Author: E. Chekalin [aut, cre], S. Paithankar [aut], B. Zeng [aut], B. Glicksberg [ctb], P. Newbury [ctb], J. Xing [ctb], K. Liu [ctb], A. Wen [ctb], D. Joseph [ctb], B. Chen [aut] Maintainer: E. Chekalin VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/octad.db git_branch: RELEASE_3_22 git_last_commit: ac5811e git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/octad.db_1.12.0.tar.gz vignettes: vignettes/octad.db/inst/doc/octad.db.html vignetteTitles: octad.db hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/octad.db/inst/doc/octad.db.R dependsOnMe: octad dependencyCount: 65 Package: OMICsPCAdata Version: 1.28.0 Depends: R (>= 3.5.0), MultiAssayExperiment Suggests: knitr, kableExtra, rmarkdown License: GPL-3 MD5sum: ed297f996ce341345d941f233b8f6a6c NeedsCompilation: no Title: Supporting data for package OMICsPCA Description: Supporting data for package OMICsPCA biocViews: RepositoryData, TechnologyData, ChIPSeqData, SequencingData, ExpressionData, ENCODE Author: Subhadeep Das Maintainer: Subhadeep Das VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/OMICsPCAdata git_branch: RELEASE_3_22 git_last_commit: 5613be2 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/OMICsPCAdata_1.28.0.tar.gz vignettes: vignettes/OMICsPCAdata/inst/doc/vignettes.html vignetteTitles: OMICsPCAdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/OMICsPCAdata/inst/doc/vignettes.R dependsOnMe: OMICsPCA dependencyCount: 46 Package: OnassisJavaLibs Version: 1.32.0 Depends: R (>= 3.4) Imports: rJava Suggests: BiocStyle, rmarkdown, knitr License: GPL-2 MD5sum: be134637e56c887c515ab93571fded7b NeedsCompilation: no Title: OnassisJavaLibs, java libraries to run conceptmapper and semantic similarity Description: A package that contains java libraries to call conceptmapper and compute semnatic similarity from R biocViews: ExperimentData Author: Eugenia Galeota Maintainer: Eugenia Galeota SystemRequirements: Java (>= 1.8) VignetteBuilder: rmarkdown, knitr git_url: https://git.bioconductor.org/packages/OnassisJavaLibs git_branch: RELEASE_3_22 git_last_commit: 28145a9 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/OnassisJavaLibs_1.32.0.tar.gz vignettes: vignettes/OnassisJavaLibs/inst/doc/OnassisJavaLibs.html vignetteTitles: OnassisJavaLibs: Java Libraries to support Onassis,, Ontology Annotation and Semantic Similarity software hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/OnassisJavaLibs/inst/doc/OnassisJavaLibs.R dependencyCount: 2 Package: optimalFlowData Version: 1.22.0 Depends: R (>= 4.0) Suggests: knitr, BiocStyle, rmarkdown, magick License: Artistic-2.0 MD5sum: 66c181f316a303a589fad28f713f1b39 NeedsCompilation: no Title: optimalFlowData Description: Data files used as examples and for testing of the software provided in the optimalFlow package. biocViews: ExperimentData, PackageTypeData, ImmunoOncologyData, FlowCytometryData Author: Hristo Inouzhe Maintainer: Hristo Inouzhe VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/optimalFlowData git_branch: RELEASE_3_22 git_last_commit: 1af9841 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/optimalFlowData_1.22.0.tar.gz vignettes: vignettes/optimalFlowData/inst/doc/optimalFlowData_vignette.html vignetteTitles: optimalFlow: optimal-transport approach to Flow Cytometry analysis hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/optimalFlowData/inst/doc/optimalFlowData_vignette.R dependsOnMe: optimalFlow dependencyCount: 0 Package: orthosData Version: 1.8.0 Imports: AnnotationHub, BiocFileCache, ExperimentHub, HDF5Array, stringr, SummarizedExperiment Suggests: BiocStyle, ggplot2, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 4201b7593093615e0e08a76f7a17204c NeedsCompilation: no Title: Data for the orthos package Description: `orthosData` is the companion ExperimentData package to the `orthos` R package for mechanistic studies using differential gene expression experiments. It provides functions for retrieval from ExperimentHub and local caching of the models and datasets used internally in orthos. biocViews: ExperimentData, RNASeqData, ExperimentHub Author: Panagiotis Papasaikas [aut, cre] (ORCID: ), Charlotte Soneson [aut] (ORCID: ), Michael Stadler [aut] (ORCID: ), Friedrich Miescher Institute for Biomedical Research [cph] Maintainer: Panagiotis Papasaikas URL: https://github.com/fmicompbio/orthosData VignetteBuilder: knitr BugReports: https://github.com/fmicompbio/orthosData/issues git_url: https://git.bioconductor.org/packages/orthosData git_branch: RELEASE_3_22 git_last_commit: 991a4e2 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/orthosData_1.8.0.tar.gz vignettes: vignettes/orthosData/inst/doc/orthosData.html vignetteTitles: 1. Introduction to orthos hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/orthosData/inst/doc/orthosData.R importsMe: orthos dependencyCount: 81 Package: pasilla Version: 1.38.0 Depends: R (>= 3.5.0), DEXSeq Suggests: rmarkdown, BiocStyle, knitr, roxygen2 License: LGPL MD5sum: 09056f70340cbecb24671fa8c40d5e71 NeedsCompilation: no Title: Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011. Description: This package provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in the article "Conservation of an RNA regulatory map between Drosophila and mammals" by Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR, Genome Res. 2011 Feb;21(2):193-202, Epub 2010 Oct 4, PMID: 20921232. The experiment studied the effect of RNAi knockdown of Pasilla, the Drosophila melanogaster ortholog of mammalian NOVA1 and NOVA2, on the transcriptome. The package vignette describes how the data provided here were derived from the RNA-Seq read sequence data that are provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. biocViews: ExperimentData, Genome, Drosophila_melanogaster_Data, RNASeqData Author: Wolfgang Huber, Alejandro Reyes Maintainer: Alejandro Reyes VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/pasilla git_branch: RELEASE_3_22 git_last_commit: 9f56232 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/pasilla_1.38.0.tar.gz vignettes: vignettes/pasilla/inst/doc/create_objects.html vignetteTitles: "Data preprocessing and creation of the data objects pasillaGenes and pasillaExons" hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pasilla/inst/doc/create_objects.R importsMe: blacksheepr suggestsMe: BADER, DEXSeq, gsean, regionReport, ReportingTools, tidybulk, pasillaBamSubset dependencyCount: 110 Package: pasillaBamSubset Version: 0.48.0 Suggests: pasilla License: LGPL MD5sum: 464625e27c246ee230f91fa3bb96db7b NeedsCompilation: no Title: Subset of BAM files from "Pasilla" experiment Description: Subset of BAM files untreated1.bam (single-end reads) and untreated3.bam (paired-end reads) from "Pasilla" experiment (Pasilla knock-down by Brooks et al., Genome Research 2011). See the vignette in the pasilla data package for how BAM files untreated1.bam and untreated3.bam were obtained from the RNA-Seq read sequence data that is provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. Also contains the DNA sequence for fly chromosome 4 to which the reads can be mapped. biocViews: ExperimentData, Genome, DNASeqData, RNASeqData Author: Hervé Pagès Maintainer: Hervé Pagès git_url: https://git.bioconductor.org/packages/pasillaBamSubset git_branch: RELEASE_3_22 git_last_commit: 0384ee4 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/pasillaBamSubset_0.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: DEXSeq, GenomicAlignments, GenomicFeatures, GenomicRanges, gmoviz, IRanges, karyoploteR, plyranges dependencyCount: 0 Package: PasillaTranscriptExpr Version: 1.38.0 Depends: R (>= 3.3.0) Suggests: rtracklayer, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: 3701c9ecf576f59317c66ec4835269a1 NeedsCompilation: no Title: Data package with transcript expression obtained with kallisto from pasilla knock-down RNA-Seq data from Brooks et al. Description: Provides kallisto workflow and transcript expression of RNA-Seq data from Brooks et al. biocViews: Drosophila_melanogaster_Data, Genome, RNASeqData, ExperimentData, SequencingData, ExpressionData, GEO Author: Malgorzata Nowicka [aut, cre] Maintainer: Malgorzata Nowicka VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/PasillaTranscriptExpr git_branch: RELEASE_3_22 git_last_commit: a655e3d git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/PasillaTranscriptExpr_1.38.0.tar.gz vignettes: vignettes/PasillaTranscriptExpr/inst/doc/PasillaTranscriptExpr.pdf vignetteTitles: Generation of transcript counts from pasilla dataset with kallisto hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/PasillaTranscriptExpr/inst/doc/PasillaTranscriptExpr.R suggestsMe: DRIMSeq dependencyCount: 0 Package: PathNetData Version: 1.46.0 Depends: R (>= 1.14.0) License: GPL-3 MD5sum: 00e6adce2e67ae85aa15c464cab439a7 NeedsCompilation: no Title: Experimental data for the PathNet package Description: This package contains the data employed in the vignette of the PathNet package. These data belong to the following publication: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J., Source Code for Biology and Medicine 2012 Sep 24;7(1):10. biocViews: ExperimentData, PathwayInteractionDatabase Author: Bhaskar Dutta , Anders Wallqvist , and Jaques Reifman Maintainer: Ludwig Geistlinger git_url: https://git.bioconductor.org/packages/PathNetData git_branch: RELEASE_3_22 git_last_commit: ceedf25 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/PathNetData_1.46.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PathNet dependencyCount: 0 Package: PCHiCdata Version: 1.38.0 Depends: R (>= 3.2), Chicago Suggests: testthat, BiocStyle, knitr License: Artistic-2.0 MD5sum: 1902acc5f680502fd75eb10390c36028 NeedsCompilation: no Title: Promoter Capture Hi-C data Description: Subsets of Promoter Capture Hi-C data conveniently packaged for Chicago users. Data includes interactions detected for chromosomes 20 and 21 in GM12878 cells and for chromosomes 18 and 19 in mESC. biocViews: ExperimentData, SequencingData, Homo_sapiens_Data, Mus_musculus_Data, StemCell Author: Paula Freire-Pritchett, Jonathan Cairns, Steven Wingett, Mikhail Spivakov Maintainer: Mikhail Spivakov VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/PCHiCdata git_branch: RELEASE_3_22 git_last_commit: 989d1fb git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/PCHiCdata_1.38.0.tar.gz vignettes: vignettes/PCHiCdata/inst/doc/PCHiCdata.html vignetteTitles: PCHiCdata Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/PCHiCdata/inst/doc/PCHiCdata.R suggestsMe: Chicago dependencyCount: 66 Package: pd.atdschip.tiling Version: 0.48.0 Depends: R (>= 3.5.0), methods, RSQLite (>= 0.10.0), oligoClasses (>= 1.15.58), oligo (>= 1.17.3), DBI Imports: Biostrings (>= 2.21.11), IRanges (>= 1.11.31), S4Vectors License: Artistic-2.0 MD5sum: 44f70cf7b2c0fc9fa6a4f758d2aa73e5 NeedsCompilation: no Title: Platform Design Info for Affymetrix Atdschip_tiling Description: Platform Design Info for Affymetrix Atdschip_tiling biocViews: Arabidopsis_thaliana_Data, MicroarrayData, SNPData Author: Kristof De Beuf Maintainer: Kristof De Beuf git_url: https://git.bioconductor.org/packages/pd.atdschip.tiling git_branch: RELEASE_3_22 git_last_commit: 9cc1e35 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/pd.atdschip.tiling_0.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 54 Package: pepDat Version: 1.30.0 Depends: R (>= 3.5.0) Imports: GenomicRanges Suggests: knitr License: Artistic-2.0 MD5sum: d3403d0f8913b857f8819bbd8b452ca5 NeedsCompilation: no Title: Peptide microarray data package Description: Provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV. biocViews: MicroarrayData Author: Renan Sauteraud, Raphael Gottardo Maintainer: Renan Sauteraud VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/pepDat git_branch: RELEASE_3_22 git_last_commit: b268acd git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/pepDat_1.30.0.tar.gz vignettes: vignettes/pepDat/inst/doc/pepDat.pdf vignetteTitles: The pepDat users guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pepDat/inst/doc/pepDat.R suggestsMe: pepStat, Pviz dependencyCount: 11 Package: PepsNMRData Version: 1.28.0 Depends: R (>= 3.5) Suggests: knitr, markdown, rmarkdown, BiocStyle License: GPL-2 | file LICENSE MD5sum: 364c7c92b7d59f82bd44a3de2fc6726d NeedsCompilation: no Title: Datasets for the PepsNMR package Description: This package contains all the datasets used in the PepsNMR package. biocViews: ExperimentData, OrganismData, Homo_sapiens_Data Author: Manon Martin [aut, cre], Bernadette Govaerts [aut, ths], Pascal de Tullio [dtc] Maintainer: Manon Martin BugReports: https://github.com/ManonMartin/PepsNMRData/issues git_url: https://git.bioconductor.org/packages/PepsNMRData git_branch: RELEASE_3_22 git_last_commit: 52f9bd5 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/PepsNMRData_1.28.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: PepsNMR dependencyCount: 0 Package: PhyloProfileData Version: 1.24.0 Depends: R (>= 4.5.0) Imports: ExperimentHub, Biostrings, BiocStyle Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: eebcac4275c79b2c5680ed21f56b1ca1 NeedsCompilation: yes Title: Data package for phylogenetic profile analysis using PhyloProfile tool Description: Two experimental datasets to illustrate running and analysing phylogenetic profiles with PhyloProfile package. biocViews: ExperimentData, ReproducibleResearch, ExperimentHub Author: Vinh Tran [aut, cre] (ORCID: ), Ingo Ebersberger [aut], Hannah Mülbaier [ctb], Arpit Jain [ctb] Maintainer: Vinh Tran URL: https://github.com/BIONF/PhyloProfileData VignetteBuilder: knitr BugReports: https://github.com/trvinh/PhyloProfileData/issues git_url: https://git.bioconductor.org/packages/PhyloProfileData git_branch: RELEASE_3_22 git_last_commit: 007af2f git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/PhyloProfileData_1.24.0.tar.gz vignettes: vignettes/PhyloProfileData/inst/doc/PhyloProfileData.html vignetteTitles: PhyloProfileData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/PhyloProfileData/inst/doc/PhyloProfileData.R dependencyCount: 81 Package: plotgardenerData Version: 1.16.0 Depends: R (>= 4.1.0) Suggests: rmarkdown, knitr License: MIT + file LICENSE MD5sum: 0984045897ad46547202fcdcdef675b3 NeedsCompilation: no Title: Datasets and test data files for the plotgardener package Description: This is a supplemental data package for the plotgardener package. Includes example datasets used in plotgardener vignettes and example raw data files. For details on how to use these datasets, see the plotgardener package vignettes. biocViews: ExperimentData, Homo_sapiens_Data, ExpressionData, Genome, ChIPSeqData, ENCODE Author: Nicole Kramer [aut, cre] (ORCID: ) Maintainer: Nicole Kramer URL: https://github.com/PhanstielLab/plotgardenerData, https://phanstiellab.github.io/plotgardener VignetteBuilder: knitr BugReports: https://github.com/PhanstielLab/plotgardenerData/issues git_url: https://git.bioconductor.org/packages/plotgardenerData git_branch: RELEASE_3_22 git_last_commit: cc953db git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/plotgardenerData_1.16.0.tar.gz vignettes: vignettes/plotgardenerData/inst/doc/plotgardenerData.html vignetteTitles: plotgardenerData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/plotgardenerData/inst/doc/plotgardenerData.R suggestsMe: plotgardener dependencyCount: 0 Package: prebsdata Version: 1.46.0 Depends: R (>= 2.14.0) License: Artistic-2.0 MD5sum: 4885bd9023a571e4944665890b77f769 NeedsCompilation: no Title: Data for 'prebs' package Description: This package contains data required to run examples in 'prebs' package. The data files include: 1) Small sample bam files for demonstration purposes 2) Probe sequence mappings for Custom CDF (taken from http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp) 3) Probe sequence mappings for manufacturer's CDF (manually created using bowtie) biocViews: ExperimentData, SequencingData, RNASeqData Author: Karolis Uziela and Antti Honkela Maintainer: Karolis Uziela git_url: https://git.bioconductor.org/packages/prebsdata git_branch: RELEASE_3_22 git_last_commit: cca999a git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/prebsdata_1.46.0.tar.gz vignettes: vignettes/prebsdata/inst/doc/prebsdata.pdf vignetteTitles: prebsdata User Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: prebs dependencyCount: 0 Package: preciseTADhub Version: 1.18.0 Depends: R (>= 4.1) Imports: ExperimentHub Suggests: knitr, rmarkdown, markdown, BiocStyle, preciseTAD License: MIT + file LICENSE MD5sum: 60983cb3a04a01c8deb153cd9736851f NeedsCompilation: no Title: Pre-trained random forest models obtained using preciseTAD Description: An experimentdata package to supplement the preciseTAD package containing pre-trained models and the variable importances of each genomic annotation used to build the model parsed into list objects and available in ExperimentHub. In total, preciseTADhub provides access to n=84 random forest classification models optimized to predict TAD/chromatin loop boundary regions and stored as .RDS files. The value, n, comes from the fact that we considered l=2 cell lines {GM12878, K562}, g=2 ground truth boundaries {Arrowhead, Peakachu}, and c=21 autosomal chromosomes {CHR1, CHR2, ..., CHR22} (omitting CHR9). Furthermore, each object is itself a two-item list containing: (1) the model object, and (2) the variable importances for CTCF, RAD21, SMC3, and ZNF143 used to predict boundary regions. Each model is trained via a "holdout" strategy, in which data from chromosomes {CHR1, CHR2, ..., CHRi-1, CHRi+1, ..., CHR22} were used to build the model and the ith chromosome was reserved for testing. See https://doi.org/10.1101/2020.09.03.282186 for more detail on the model building strategy. biocViews: ExperimentData, PackageTypeData, ExperimentHub, Genome Author: Spiro Stilianoudakis [aut], Mikhail Dozmorov [aut, cre] Maintainer: Mikhail Dozmorov URL: https://github.com/dozmorovlab/preciseTADhub VignetteBuilder: knitr BugReports: https://github.com/dozmorovlab/preciseTADhub/issues git_url: https://git.bioconductor.org/packages/preciseTADhub git_branch: RELEASE_3_22 git_last_commit: 1bc6256 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/preciseTADhub_1.18.0.tar.gz vignettes: vignettes/preciseTADhub/inst/doc/preciseTADhub.html vignetteTitles: preciseTADhub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/preciseTADhub/inst/doc/preciseTADhub.R dependencyCount: 65 Package: PREDAsampledata Version: 0.50.0 Depends: R (>= 2.10.0), methods, PREDA, Biobase, affy, annotate Suggests: hgu133plus2.db, hgu133plus2cdf License: Artistic-2.0 MD5sum: 81c417df8c29461badd1e35896e9873b NeedsCompilation: no Title: expression and copy number data on clear cell renal carcinoma samples Description: Sample data for PREDA package. (annotations objects synchronized with GeneAnnot custom CDFs version 2.2.0) biocViews: ExperimentData, Tissue, CancerData, KidneyCancerData, MicroarrayData, TissueMicroarrayData, ArrayExpress Author: I. Cifola et al. in Cristina Battaglia Lab, University of Milan Maintainer: Francesco Ferrari git_url: https://git.bioconductor.org/packages/PREDAsampledata git_branch: RELEASE_3_22 git_last_commit: 3bd7e24 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/PREDAsampledata_0.50.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PREDA dependencyCount: 60 Package: ProData Version: 1.48.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL MD5sum: 7030852c04a01b826458608bafe79855 NeedsCompilation: no Title: SELDI-TOF data of Breast cancer samples Description: A data package of SELDI-TOF protein mass spectrometry data of 167 breast cancer and normal samples. biocViews: ExperimentData, CancerData, BreastCancerData, MassSpectrometryData, NCI Author: Xiaochun Li Maintainer: Xiaochun Li git_url: https://git.bioconductor.org/packages/ProData git_branch: RELEASE_3_22 git_last_commit: 141570f git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/ProData_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CorrectedFDR dependencyCount: 7 Package: pRolocdata Version: 1.48.0 Depends: R (>= 3.6.3), MSnbase Imports: Biobase, utils Suggests: pRoloc (>= 1.13.8), testthat, SummarizedExperiment License: GPL-2 MD5sum: 1ee70f659fb47e6616b139fc25c3e930 NeedsCompilation: no Title: Data accompanying the pRoloc package Description: Mass-spectrometry based spatial proteomics data sets and protein complex separation data. Also contains the time course expression experiment from Mulvey et al. 2015. biocViews: ExperimentData, Homo_sapiens_Data, MassSpectrometryData, Arabidopsis_thaliana_Data, Drosophila_melanogaster_Data, Mus_musculus_Data, StemCell, Proteome Author: Laurent Gatto [aut] (ORCID: ), Oliver Crook [aut] (ORCID: ), Lisa Breckels [cre, aut] (ORCID: ) Maintainer: Lisa Breckels URL: https://github.com/lgatto/pRolocdata BugReports: https://github.com/lgatto/pRolocdata/issues git_url: https://git.bioconductor.org/packages/pRolocdata git_branch: RELEASE_3_22 git_last_commit: 4ec3932 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/pRolocdata_1.48.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: bandle suggestsMe: MSnbase, pRoloc, pRolocGUI, RforProteomics dependencyCount: 131 Package: prostateCancerCamcap Version: 1.38.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 72175f7526f47293bfd4e54c0977a9cb NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Ross-Adams (2015) Prostate Cancer dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerCamcap git_branch: RELEASE_3_22 git_last_commit: 80cdecf git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/prostateCancerCamcap_1.38.0.tar.gz vignettes: vignettes/prostateCancerCamcap/inst/doc/prostateCancerCamcap.pdf vignetteTitles: prostateCancerCamcap hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/prostateCancerCamcap/inst/doc/prostateCancerCamcap.R dependencyCount: 7 Package: prostateCancerGrasso Version: 1.38.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: ece89a4d95cefdff39a32eba635b5e7f NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Grasso (2012) Prostate Cancer dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerGrasso git_branch: RELEASE_3_22 git_last_commit: 5aa41bd git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/prostateCancerGrasso_1.38.0.tar.gz vignettes: vignettes/prostateCancerGrasso/inst/doc/prostateCancerGrasso.pdf vignetteTitles: prostateCancerGrasso hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/prostateCancerGrasso/inst/doc/prostateCancerGrasso.R dependencyCount: 7 Package: prostateCancerStockholm Version: 1.38.0 Depends: Biobase , R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 2153dab4022f66a83c7f462fbb3f89ac NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Stockholm dataset biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerStockholm git_branch: RELEASE_3_22 git_last_commit: 9edb36d git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/prostateCancerStockholm_1.38.0.tar.gz vignettes: vignettes/prostateCancerStockholm/inst/doc/prostateCancerStockholm.pdf vignetteTitles: prostateCancerStockholm hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/prostateCancerStockholm/inst/doc/prostateCancerStockholm.R dependencyCount: 7 Package: prostateCancerTaylor Version: 1.38.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery, org.Hs.eg.db License: Artistic-2.0 MD5sum: 0988045037864a2f72f6c12a55c8c405 NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Taylor et al (2010) dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerTaylor git_branch: RELEASE_3_22 git_last_commit: 4302fca git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/prostateCancerTaylor_1.38.0.tar.gz vignettes: vignettes/prostateCancerTaylor/inst/doc/prostateCancerTaylor.pdf vignetteTitles: prostateCancerTaylor hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/prostateCancerTaylor/inst/doc/prostateCancerTaylor.R dependencyCount: 7 Package: prostateCancerVarambally Version: 1.38.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 7b7df85985a4294b8cc399c1437653ac NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Varambally dataset biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerVarambally git_branch: RELEASE_3_22 git_last_commit: 5dd9c38 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/prostateCancerVarambally_1.38.0.tar.gz vignettes: vignettes/prostateCancerVarambally/inst/doc/prostateCancerVarambally.pdf vignetteTitles: prostateCancerVarambally hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/prostateCancerVarambally/inst/doc/prostateCancerVarambally.R dependencyCount: 7 Package: ProteinGymR Version: 1.4.0 Depends: R (>= 4.4.0) Imports: ExperimentHub, AnnotationHub, dplyr, purrr, queryup, spdl, tidyr, tidyselect, stringr, lifecycle, rlang, htmltools Suggests: tibble, BiocStyle, knitr, testthat (>= 3.0.0), ComplexHeatmap, circlize, pals, ggplot2 (>= 3.5.0), grDevices, ggExtra, bio3d, r3dmol, forcats, ggdist (>= 3.3.0) License: Artistic-2.0 MD5sum: 21b3bdcf812d25fef74fc11d8fb5b0fa NeedsCompilation: no Title: Programmatic access to ProteinGym datasets in R/Bioconductor Description: The ProteinGymR package provides analysis-ready data resources from ProteinGym, generated by Notin et al., 2023, as well as built-in functionality to visualize the data. ProteinGym comprises a collection of benchmarks for evaluating the performance of models predicting the effect of point mutations. This package provides access to 1. deep mutational scanning (DMS) scores from 217 assays measuring the impact of all possible amino acid substitutions across 186 proteins, 2. model performance metrics and prediction scores from 79 variant prediction models in the zero-shot setting and 12 models in the semi-supervised setting. biocViews: ExperimentData, ExperimentHub, PackageTypeData, Homo_sapiens_Data, ReproducibleResearch, CellCulture, SequencingData, Proteome Author: Tram Nguyen [aut, cre] (ORCID: ), Pascal Notin [aut], Aaron Kollasch [aut], Debora Marks [aut], Ludwig Geistlinger [aut] Maintainer: Tram Nguyen URL: https://github.com/ccb-hms/ProteinGymR VignetteBuilder: knitr BugReports: https://github.com/ccb-hms/ProteinGymR/issues git_url: https://git.bioconductor.org/packages/ProteinGymR git_branch: RELEASE_3_22 git_last_commit: a6ca341 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/ProteinGymR_1.4.0.tar.gz vignettes: vignettes/ProteinGymR/inst/doc/data_import_and_representation.html, vignettes/ProteinGymR/inst/doc/visualization_exploration.html vignetteTitles: Data access and representation, Visualization and exploration" hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ProteinGymR/inst/doc/data_import_and_representation.R, vignettes/ProteinGymR/inst/doc/visualization_exploration.R dependencyCount: 72 Package: ptairData Version: 1.18.0 Imports: rhdf5, signal, stats, graphics Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: f273f01d23444af426361bef8d990ef0 NeedsCompilation: no Title: PTR-TOF-MS volatolomics raw datasets from exhaled air and cell culture headspace Description: The package ptairData contains two raw datasets from Proton-Transfer-Reaction Time-of-Flight mass spectrometer acquisitions (PTR-TOF-MS), in the HDF5 format. One from the exhaled air of two volunteer healthy individuals with three replicates, and one from the cell culture headspace from two mycobacteria species and one control (culture medium only) with two replicates. Those datasets are used in the examples and in the vignette of the ptairMS package (PTR-TOF-MS data pre-processing). There are also used to gererate the ptrSet in the ptairMS data : exhaledPtrset and mycobacteriaSet biocViews: ExperimentData, MassSpectrometryData, CellCulture Author: camille Roquencourt [aut, cre] Maintainer: camille Roquencourt VignetteBuilder: knitr BugReports: https://github.com/camilleroquencourt/ptairData/issues git_url: https://git.bioconductor.org/packages/ptairData git_branch: RELEASE_3_22 git_last_commit: 641af11 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/ptairData_1.18.0.tar.gz vignettes: vignettes/ptairData/inst/doc/ptairData_vignette.html vignetteTitles: PTR-TOF-MS dataset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ptairData/inst/doc/ptairData_vignette.R suggestsMe: ptairMS dependencyCount: 10 Package: PtH2O2lipids Version: 1.36.0 Depends: R (>= 3.3), xcms, CAMERA, LOBSTAHS, methods, utils Suggests: gplots, RColorBrewer, cluster, vegan License: MIT + file LICENSE MD5sum: fe01c113e4dcf9d6ce742f63b148041c NeedsCompilation: no Title: P. tricornutum HPLC-ESI-MS Lipid Data from van Creveld et al. (2015) Description: Annotated HPLC-ESI-MS lipid data in positive ionization mode from an experiment in which cultures of the marine diatom Phaeodactylum tricornutum were treated with various concentrations of hydrogen peroxide (H2O2) to induce oxidative stress. The experiment is described in Graff van Creveld, et al., 2015, "Early perturbation in mitochondria redox homeostasis in response to environmental stress predicts cell fate in diatoms," ISME Journal 9:385-395. PtH2O2lipids consists of two objects: A CAMERA xsAnnotate object (ptH2O2lipids$xsAnnotate) and LOBSTAHS LOBSet object (ptH2O2lipids$xsAnnotate$LOBSet). The LOBSet includes putative compound assignments from the default LOBSTAHS database. Isomer annotation is recorded in three other LOBSet slots. biocViews: ReproducibleResearch, CellCulture, MassSpectrometryData, Phaeodactylum_tricornutum_data Author: Shiri Graff van Creveld [aut], Shilo Rosenwasser [aut], Daniella Schatz [aut], Ilan Koren [aut], Assaf Vardi [aut], James Collins [cre] Maintainer: James Collins URL: http://dx.doi.org/10.1038/ismej.2014.136, https://github.com/vanmooylipidomics/PtH2O2lipids, http://www.whoi.edu/page.do?pid=133616&tid=282&cid=192529 BugReports: https://github.com/vanmooylipidomics/PtH2O2lipids/issues/new git_url: https://git.bioconductor.org/packages/PtH2O2lipids git_branch: RELEASE_3_22 git_last_commit: 0adfb19 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/PtH2O2lipids_1.36.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: LOBSTAHS dependencyCount: 155 Package: pumadata Version: 2.46.0 Depends: R (>= 3.2.0), Biobase (>= 2.5.5),puma, oligo(>= 1.32.0) License: LGPL MD5sum: d8e4c43c8addb5607621563a2ca33b3d NeedsCompilation: no Title: Various data sets for use with the puma package Description: This is a simple data package including various data sets derived from the estrogen data for use with the puma (Propagating Uncertainty in Microarray Analysis) package. biocViews: ExperimentData, MicroarrayData, SNPData Author: Richard Pearson Maintainer: Xuejun liu URL: http://umber.sbs.man.ac.uk/resources/puma git_url: https://git.bioconductor.org/packages/pumadata git_branch: RELEASE_3_22 git_last_commit: 34644b0 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/pumadata_2.46.0.tar.gz vignettes: vignettes/pumadata/inst/doc/pumadata.pdf vignetteTitles: pumadata User Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pumadata/inst/doc/pumadata.R suggestsMe: puma dependencyCount: 57 Package: PWMEnrich.Dmelanogaster.background Version: 4.44.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: cabb779f6bd66edbc3706bd706cad8d0 NeedsCompilation: no Title: D. melanogaster background for PWMEnrich Description: PWMEnrich pre-compiled background objects for Drosophila melanogaster and MotifDb D. melanogaster motifs. biocViews: Drosophila_melanogaster_Data Author: Robert Stojnic Maintainer: Diego Diez git_url: https://git.bioconductor.org/packages/PWMEnrich.Dmelanogaster.background git_branch: RELEASE_3_22 git_last_commit: d433d33 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/PWMEnrich.Dmelanogaster.background_4.44.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 21 Package: PWMEnrich.Hsapiens.background Version: 4.44.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: 3583c97af32f8f8cbfe9a9e413de72b7 NeedsCompilation: no Title: H. sapiens background for PWMEnrich Description: PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs. biocViews: Homo_sapiens_Data, CGHData Author: Robert Stojnic Maintainer: Diego Diez git_url: https://git.bioconductor.org/packages/PWMEnrich.Hsapiens.background git_branch: RELEASE_3_22 git_last_commit: 98e080a git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/PWMEnrich.Hsapiens.background_4.44.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 21 Package: PWMEnrich.Mmusculus.background Version: 4.44.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: 9a1ecb29bf15cfad7914c3d2892ccf1f NeedsCompilation: no Title: M. musculus background for PWMEnrich Description: PWMEnrich pre-compiled background objects for M.musculus (mouse) and MotifDb M. musculus motifs. biocViews: Mus_musculus_Data Author: Robert Stojnic Maintainer: Diego Diez git_url: https://git.bioconductor.org/packages/PWMEnrich.Mmusculus.background git_branch: RELEASE_3_22 git_last_commit: 1673042 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/PWMEnrich.Mmusculus.background_4.44.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 21 Package: QDNAseq.hg19 Version: 1.40.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: 866e912e4993a067ccbd96fc3126f3ad NeedsCompilation: no Title: QDNAseq bin annotation for hg19 Description: This package provides QDNAseq bin annotations for the human genome build hg19. biocViews: ExperimentData, OrganismData, Homo_sapiens_Data Author: Daoud Sie [aut, cre] Maintainer: Daoud Sie URL: https://github.com/tgac-vumc/QDNAseq.hg19 BugReports: https://github.com/tgac-vumc/QDNAseq.hg19/issues git_url: https://git.bioconductor.org/packages/QDNAseq.hg19 git_branch: RELEASE_3_22 git_last_commit: b299eca git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/QDNAseq.hg19_1.40.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: biscuiteer, QDNAseq dependencyCount: 49 Package: QDNAseq.mm10 Version: 1.40.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: 85339d53a3e32fcede0b59e64e973548 NeedsCompilation: no Title: Bin annotation mm10 Description: This package provides QDNAseq bin annotations for the mouse genome build mm10. biocViews: ExperimentData, OrganismData, Mus_musculus_Data Author: Daoud Sie [aut, cre] Maintainer: Daoud Sie URL: https://github.com/tgac-vumc/QDNAseq.mm10 BugReports: https://github.com/tgac-vumc/QDNAseq.mm10/issues git_url: https://git.bioconductor.org/packages/QDNAseq.mm10 git_branch: RELEASE_3_22 git_last_commit: 8b406e2 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/QDNAseq.mm10_1.40.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: biscuiteer, QDNAseq dependencyCount: 49 Package: qPLEXdata Version: 1.27.0 Depends: R (>= 3.5), qPLEXanalyzer Imports: utils, knitr, MSnbase, dplyr Suggests: statmod License: GPL-2 MD5sum: 4a5d9d86577c1ce7228d15ce3e1d844a NeedsCompilation: no Title: Data accompanying qPLEXanalyzer package Description: qPLEX-RIME and Full proteome TMT mass spectrometry datasets. biocViews: ExperimentData, MassSpectrometryData, Proteome Author: Kamal Kishore Developer [aut, cre] Maintainer: Kamal Kishore Developer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/qPLEXdata git_branch: devel git_last_commit: 05e84b6 git_last_commit_date: 2025-04-15 Date/Publication: 2025-04-17 source.ver: src/contrib/qPLEXdata_1.27.0.tar.gz vignettes: vignettes/qPLEXdata/inst/doc/qPLEXdata.pdf vignetteTitles: qPLEXdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/qPLEXdata/inst/doc/qPLEXdata.R suggestsMe: qPLEXanalyzer dependencyCount: 145 Package: QUBICdata Version: 1.38.0 Depends: R (>= 3.1) Suggests: knitr, rmarkdown License: Unlimited | file LICENSE MD5sum: 7e806f94da4d95600bd6d9de19810b30 NeedsCompilation: no Title: Data employed in the vignette of the QUBIC package Description: The data employed in the vignette of the QUBIC package. These data belong to Many Microbe Microarrays Database and STRING v10. biocViews: Escherichia_coli_Data, OrganismData, ExperimentData Author: Yu Zhang [aut, cre], Qin Ma [aut] Maintainer: Yu Zhang URL: http://github.com/zy26/QUBICdata VignetteBuilder: knitr BugReports: http://github.com/zy26/QUBICdata/issues git_url: https://git.bioconductor.org/packages/QUBICdata git_branch: RELEASE_3_22 git_last_commit: 0acdb36 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/QUBICdata_1.38.0.tar.gz vignettes: vignettes/QUBICdata/inst/doc/qubic_data_vignette.pdf vignetteTitles: QUBIC Data Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/QUBICdata/inst/doc/qubic_data_vignette.R suggestsMe: QUBIC dependencyCount: 0 Package: raerdata Version: 1.8.0 Imports: ExperimentHub, Rsamtools, BiocGenerics, rtracklayer, SingleCellExperiment Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: cc8d84a7c1da1ed34864ab4d312d0b68 NeedsCompilation: no Title: A collection of datasets for use with raer package Description: raerdata is an ExperimentHub package that provides a collection of files useful for demostrating functionality in the raer package. Datasets include 10x genomics scRNA-seq, bulk RNA-seq, and paired whole-genome and RNA-seq data. Additionally databases of human and mouse RNA editing sites are provided. biocViews: SingleCellData, SequencingData, RNASeqData, ExperimentHub, PackageTypeData, ExpressionData Author: Kent Riemondy [aut, cre] (ORCID: ) Maintainer: Kent Riemondy URL: https://github.com/rnabioco/raerdata VignetteBuilder: knitr BugReports: https://github.com/rnabioco/raerdata/issues git_url: https://git.bioconductor.org/packages/raerdata git_branch: RELEASE_3_22 git_last_commit: 7f02dc2 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/raerdata_1.8.0.tar.gz vignettes: vignettes/raerdata/inst/doc/raerdata.html vignetteTitles: raerdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/raerdata/inst/doc/raerdata.R suggestsMe: raer dependencyCount: 97 Package: rcellminerData Version: 2.32.0 Depends: R (>= 3.5.0), Biobase Suggests: knitr, testthat, BiocStyle, rcellminer, rmarkdown License: LGPL-3 + file LICENSE MD5sum: 9ff1420eae7c52f33db08f120ffcf97b NeedsCompilation: no Title: rcellminerData: Molecular Profiles and Drug Response for the NCI-60 Cell Lines Description: The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data. biocViews: CancerData, CopyNumberVariationData, ExpressionData, SNPData, NCI, MicroarrayData, miRNAData Author: Augustin Luna, Vinodh Rajapakse, Fabricio Sousa Maintainer: Augustin Luna , Vinodh Rajapakse , Fathi Elloumi VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/rcellminerData git_branch: RELEASE_3_22 git_last_commit: 8b2dacc git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/rcellminerData_2.32.0.tar.gz vignettes: vignettes/rcellminerData/inst/doc/rcellminerDataUsage.html vignetteTitles: Accessing CellMiner Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/rcellminerData/inst/doc/rcellminerDataUsage.R dependsOnMe: rcellminer dependencyCount: 7 Package: RcisTarget.hg19.motifDBs.cisbpOnly.500bp Version: 1.30.0 Depends: R (>= 3.3) Imports: data.table License: GPL-3 MD5sum: 3ede8296dd0ab21abc1fa6605e3db42a NeedsCompilation: no Title: RcisTarget motif databases for human (hg19) - Subset of 4.6k motifs Description: RcisTarget databases: Gene-based motif rankings and annotation to transcription factors. This package contains a subset of 4.6k motifs (cisbp motifs), scored only within 500bp upstream and the TSS. See RcisTarget tutorial to download the full databases, containing 20k motifs and search space up to 10kbp around the TSS. biocViews: Homo_sapiens_Data Author: Sara Aibar, Gert Hulselmans, Stein Aerts. Laboratory of Computational Biology, KU Leuven Center for Human Genetics. Leuven, Belgium. Maintainer: Sara Aibar URL: http://scenic.aertslab.org git_url: https://git.bioconductor.org/packages/RcisTarget.hg19.motifDBs.cisbpOnly.500bp git_branch: RELEASE_3_22 git_last_commit: 2fb0481 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.30.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RcisTarget dependencyCount: 2 Package: ReactomeGSA.data Version: 1.24.0 Depends: R (>= 3.6), limma, edgeR, ReactomeGSA, Seurat License: Artistic-2.0 MD5sum: 11c24e29808cdd0af16a5219f9a507ae NeedsCompilation: no Title: Companion data package for the ReactomeGSA package Description: Companion data sets to showcase the functionality of the ReactomeGSA package. This package contains proteomics and RNA-seq data of the melanoma B-cell induction study by Griss et al. and scRNA-seq data from Jerby-Arnon et al. biocViews: ExpressionData, RNASeqData, Proteome, Homo_sapiens_Data Author: Johannes Griss [aut, cre] (ORCID: ) Maintainer: Johannes Griss URL: https://github.com/reactome/ReactomeGSA.data/issues BugReports: https://github.com/reactome/ReactomeGSA.data git_url: https://git.bioconductor.org/packages/ReactomeGSA.data git_branch: RELEASE_3_22 git_last_commit: c61ae33 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/ReactomeGSA.data_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ReactomeGSA dependencyCount: 185 Package: RegParallel Version: 1.28.0 Depends: doParallel, foreach, parallel, iterators, data.table, stringr, survival, arm, stats, utils, methods Suggests: RUnit, BiocGenerics, knitr, DESeq2, airway, magrittr, Biobase, GEOquery, biomaRt, survminer, survey, rmarkdown License: GPL-3 MD5sum: a18d0e0564ecc86f0d34a8dcfb051640 NeedsCompilation: no Title: Standard regression functions in R enabled for parallel processing over large data-frames Description: In many analyses, a large amount of variables have to be tested independently against the trait/endpoint of interest, and also adjusted for covariates and confounding factors at the same time. The major bottleneck in these is the amount of time that it takes to complete these analyses. With RegParallel, a large number of tests can be performed simultaneously. On a 12-core system, 144 variables can be tested simultaneously, with 1000s of variables processed in a matter of seconds via 'nested' parallel processing. Works for logistic regression, linear regression, conditional logistic regression, Cox proportional hazards and survival models, and Bayesian logistic regression. Also caters for generalised linear models that utilise survey weights created by the 'survey' CRAN package and that utilise 'survey::svyglm'. biocViews: DiseaseModel Author: Kevin Blighe [aut, cre], Sarega Gurudas [ctb], Jessica Lasky-Su [aut] Maintainer: Kevin Blighe URL: https://github.com/kevinblighe/RegParallel VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RegParallel git_branch: RELEASE_3_22 git_last_commit: be02caa git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RegParallel_1.28.0.tar.gz vignettes: vignettes/RegParallel/inst/doc/RegParallel.html vignetteTitles: Standard regression functions in R enabled for parallel processing over large data-frames hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RegParallel/inst/doc/RegParallel.R dependencyCount: 39 Package: RforProteomics Version: 1.48.0 Depends: R (>= 3.5), MSnbase (>= 2.35.2) Imports: R.utils, biocViews, BiocManager Suggests: AnnotationDbi, rpx (>= 2.0.3), DT, knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, MALDIquant (>= 1.12), MALDIquantForeign, readBrukerFlexData, Rdisop, OrgMassSpecR, SummarizedExperiment, BRAIN, rols, hpar, GO.db, org.Hs.eg.db, e1071, biomaRt, RColorBrewer, ggplot2, reshape2, xtable, lattice, mzID, pRoloc, pRolocdata, MSnID, msmsTests, msmsEDA, corrplot, beanplot, Heatplus, gplots, VennDiagram, protViz, genefilter, plotly, gridExtra, dplyr, lubridate, magick, cleaver License: Artistic-2.0 MD5sum: 5bfa2e3ab50e75895189e57de9c18912 NeedsCompilation: no Title: Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication Description: This package contains code to illustrate the 'Using R and Bioconductor for proteomics data analysis' and 'Visualisation of proteomics data using R and Bioconductor' manuscripts. The vignettes describe the code and data needed to reproduce the examples and figures described in the paper and functionality for proteomics visualisation. It also contain various function to discover R software for mass spectrometry and proteomics. biocViews: ExperimentData, MassSpectrometryData, ReproducibleResearch Author: Laurent Gatto [aut, cre], Sebastian Gibb [ctb], Vlad Petyuk [ctb], Thomas Pedersen Lin [ctb] Maintainer: Laurent Gatto URL: http://lgatto.github.com/RforProteomics/ VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RforProteomics git_branch: RELEASE_3_22 git_last_commit: eef7998 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RforProteomics_1.48.0.tar.gz vignettes: vignettes/RforProteomics/inst/doc/RforProteomics.html, vignettes/RforProteomics/inst/doc/RProtVis.html vignetteTitles: Using R for proteomics data analysis, Visualisation of proteomics data using R and Bioconductor hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RforProteomics/inst/doc/RforProteomics.R, vignettes/RforProteomics/inst/doc/RProtVis.R suggestsMe: MSstatsQC dependencyCount: 140 Package: RGMQLlib Version: 1.30.0 Depends: R(>= 3.4.2) Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 95c14978fb57f1bd5daf1995da7a92cd NeedsCompilation: no Title: RGMQLlib, java libraries to run GMQL scala API Description: A package that contains scala libraries to call GMQL from R used by RGMQL package. It contains a scalable data management engine written in Scala programming language. biocViews: ExperimentData,RepositoryData Author: Simone Pallotta [aut, cre], Marco Masseroli [aut] Maintainer: Simone Pallotta URL: http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/ VignetteBuilder: knitr PackageStatus: Deprecated git_url: https://git.bioconductor.org/packages/RGMQLlib git_branch: RELEASE_3_22 git_last_commit: f66617b git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RGMQLlib_1.30.0.tar.gz vignettes: vignettes/RGMQLlib/inst/doc/RGMQLlib.pdf vignetteTitles: RGMQLlib: scala Libraries to support GMQL hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: rheumaticConditionWOLLBOLD Version: 1.48.0 Depends: R (>= 2.10.0) Suggests: genefilter, Biobase, hgu133plus2.db License: Artistic-2.0 MD5sum: 6a70b17075da3277fe8aea6f454078be NeedsCompilation: no Title: Normalized gene expression dataset published by Wollbold et al. [2009] (WOLLBOLD). Description: Normalized gene expression data from rheumatic diseases from study published by Wollbold et al. in 2009, provided as an eSet. biocViews: ExperimentData, Tissue, MicroarrayData, MultiChannelData, ChipOnChipData, TissueMicroarrayData, GEO, ArrayExpress Author: Alejandro Quiroz-Zarate, John Quackenbush Maintainer: Alejandro Quiroz-Zarate URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/rheumaticConditionWOLLBOLD git_branch: RELEASE_3_22 git_last_commit: d33f4c1 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/rheumaticConditionWOLLBOLD_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: RITANdata Version: 1.34.0 Depends: R (>= 4.2) Suggests: knitr License: file LICENSE MD5sum: 0d7ff2789bbb462457a0d91613554d5d NeedsCompilation: no Title: This package contains reference annotation and network data sets Description: Data such as is contained in the two R data files in this package are required for the RITAN package examples. Users are highly encouraged to use their own or additional resources in conjunction with RITANdata. See the RITAN vignettes and RITAN.md for more information, such as gathering more up-to-date annotation data. biocViews: AnnotationData, Homo_sapiens Author: Michael Zimmermann [aut, cre] Maintainer: Michael Zimmermann VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RITANdata git_branch: RELEASE_3_22 git_last_commit: 43dbb26 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RITANdata_1.34.0.tar.gz vignettes: vignettes/RITANdata/inst/doc/RITANdata.html vignetteTitles: Vignette Title hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/RITANdata/inst/doc/RITANdata.R importsMe: RITAN dependencyCount: 0 Package: RMassBankData Version: 1.48.0 Suggests: RMassBank License: Artistic-2.0 MD5sum: 1fd3f95324ae7e2c5bf87428947a1474 NeedsCompilation: no Title: Test dataset for RMassBank Description: Example spectra, example compound list(s) and an example annotation list for a narcotics dataset; required to test RMassBank. The package is described in the man page for RMassBankData. Includes new XCMS test data. biocViews: ExperimentData, MassSpectrometryData Author: Michael Stravs, Emma Schymanski, Steffen Neumann Maintainer: Michael Stravs, Emma Schymanski git_url: https://git.bioconductor.org/packages/RMassBankData git_branch: RELEASE_3_22 git_last_commit: 01372ab git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RMassBankData_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RMassBank dependencyCount: 0 Package: RNAmodR.Data Version: 1.24.0 Depends: R (>= 3.6), ExperimentHub, ExperimentHubData (>= 1.9.2) Imports: utils Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, sessioninfo, testthat License: Artistic-2.0 MD5sum: 4309063631ce671868daa875931af863 NeedsCompilation: no Title: Example data for the RNAmodR package Description: RNAmodR.Data contains example data, which is used for vignettes and example workflows in the RNAmodR and dependent packages. biocViews: ExperimentData, SequencingData, RNASeqData Author: Felix G.M. Ernst [aut, cre], Denis L.J. Lafontaine [ctb, fnd] Maintainer: Felix G.M. Ernst URL: https://github.com/FelixErnst/RNAmodR.Data VignetteBuilder: knitr BugReports: https://github.com/FelixErnst/RNAmodR.Data/issues git_url: https://git.bioconductor.org/packages/RNAmodR.Data git_branch: RELEASE_3_22 git_last_commit: 2e7858d git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RNAmodR.Data_1.24.0.tar.gz vignettes: vignettes/RNAmodR.Data/inst/doc/RNAmodR.Data.html vignetteTitles: RNAmodR.Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RNAmodR.Data/inst/doc/RNAmodR.Data.R suggestsMe: RNAmodR, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq dependencyCount: 119 Package: RNAseqData.HNRNPC.bam.chr14 Version: 0.48.0 Suggests: GenomicAlignments, BiocManager License: LGPL MD5sum: 320a1d2871f6a3e1ffd44a63f67fca1e NeedsCompilation: no Title: Aligned reads from RNAseq experiment: Transcription profiling by high throughput sequencing of HNRNPC knockdown and control HeLa cells Description: The package contains 8 BAM files, 1 per sequencing run. Each BAM file was obtained by (1) aligning the reads (paired-end) to the full hg19 genome with TopHat2, and then (2) subsetting to keep only alignments on chr14. See accession number E-MTAB-1147 in the ArrayExpress database for details about the experiment, including links to the published study (by Zarnack et al., 2012) and to the FASTQ files. biocViews: ExperimentData, Genome, Homo_sapiens_Data, SequencingData, GEO, NCI, RNASeqData, ArrayExpress Author: Hervé Pagès Maintainer: Hervé Pagès URL: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1147/ git_url: https://git.bioconductor.org/packages/RNAseqData.HNRNPC.bam.chr14 git_branch: RELEASE_3_22 git_last_commit: 986efa9 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RNAseqData.HNRNPC.bam.chr14_0.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: sequencing suggestsMe: BiocParallel, cigarillo, GenomicAlignments, GenomicFiles, GenomicRanges, roar, Rsamtools, SplicingGraphs dependencyCount: 0 Package: RnaSeqSampleSizeData Version: 1.42.0 Depends: edgeR,R (>= 2.10) Suggests: BiocStyle, knitr License: GPL (>= 2) MD5sum: 09605564c021bb6c4aafb8e8b1e1d632 NeedsCompilation: no Title: RnaSeqSampleSizeData Description: RnaSeqSampleSizeData package provides the read counts and dispersion distribution from real RNA-seq experiments. It can be used by RnaSeqSampleSize package to estimate sample size and power for RNA-seq experiment design. biocViews: ExperimentData, CancerData, RNASeqData Author: Shilin Zhao, Chung-I Li, Yan Guo, Quanhu Sheng, Yu Shyr Maintainer: Shilin Zhao VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RnaSeqSampleSizeData git_branch: RELEASE_3_22 git_last_commit: 610f53f git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RnaSeqSampleSizeData_1.42.0.tar.gz vignettes: vignettes/RnaSeqSampleSizeData/inst/doc/RnaSeqSampleSizeData.pdf vignetteTitles: RnaSeqSampleSizeData: Read counts and dispersion distribution from real data for sample size estimation of RNA-seq experiments hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RnaSeqSampleSizeData/inst/doc/RnaSeqSampleSizeData.R dependsOnMe: RnaSeqSampleSize dependencyCount: 11 Package: RnBeads.hg19 Version: 1.42.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 49bca116d03a478e5589942ba60f1421 NeedsCompilation: no Title: RnBeads.hg19 Description: Automatically generated RnBeads annotation package for the assembly hg19. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.hg19 git_branch: RELEASE_3_22 git_last_commit: cb8d172 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RnBeads.hg19_1.42.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: MAGAR suggestsMe: RnBeads dependencyCount: 11 Package: RnBeads.hg38 Version: 1.42.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 98bb5a12771beaa1d9245477398f250e NeedsCompilation: no Title: RnBeads.hg38 Description: RnBeads annotation package for the assembly hg38. Author: RnBeads Team Maintainer: RnBeads Team git_url: https://git.bioconductor.org/packages/RnBeads.hg38 git_branch: RELEASE_3_22 git_last_commit: 79705b2 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RnBeads.hg38_1.42.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: MAGAR suggestsMe: RnBeads dependencyCount: 11 Package: RnBeads.mm10 Version: 2.18.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: b6af01e54bc3eb2c0f7fb43c8a003f43 NeedsCompilation: no Title: RnBeads.mm10 Description: Automatically generated RnBeads annotation package for the assembly mm10. Author: RnBeads Team Maintainer: RnBeads Team git_url: https://git.bioconductor.org/packages/RnBeads.mm10 git_branch: RELEASE_3_22 git_last_commit: f468d9a git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RnBeads.mm10_2.18.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 11 Package: RnBeads.mm9 Version: 1.42.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 7244cdba2bae02291e04d1c99ddfac59 NeedsCompilation: no Title: RnBeads.mm9 Description: Automatically generated RnBeads annotation package for the assembly mm9. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.mm9 git_branch: RELEASE_3_22 git_last_commit: c3692d0 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RnBeads.mm9_1.42.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RnBeads dependencyCount: 11 Package: RnBeads.rn5 Version: 1.42.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: ce5c4e5c2e5a87914fa29915f684068c NeedsCompilation: no Title: RnBeads.rn5 Description: Automatically generated RnBeads annotation package for the assembly rn5. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.rn5 git_branch: RELEASE_3_22 git_last_commit: 9ab3ab1 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RnBeads.rn5_1.42.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 11 Package: RRBSdata Version: 1.30.0 Depends: R (>= 3.5.0), BiSeq (>= 1.9.2) License: LGPL-3 MD5sum: 4b4bfc4b522b59c659e9ecc0f423522d NeedsCompilation: no Title: An RRBS data set with 12 samples and 10,000 simulated DMRs Description: RRBS data set comprising 12 samples with simulated differentially methylated regions (DMRs). biocViews: ExperimentData, CancerData, SequencingData, CpGIslandData Author: Katja Hebestreit, Hans-Ulrich Klein Maintainer: Katja Hebestreit git_url: https://git.bioconductor.org/packages/RRBSdata git_branch: RELEASE_3_22 git_last_commit: 57a8f34 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RRBSdata_1.30.0.tar.gz vignettes: vignettes/RRBSdata/inst/doc/RRBSdata.pdf vignetteTitles: An RRBS data set with 12 samples and 10,,000 simulated DMRs. hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RRBSdata/inst/doc/RRBSdata.R dependencyCount: 91 Package: rRDPData Version: 1.30.0 Depends: rRDP License: GPL-2 MD5sum: e6f94b6dfaa15b6be1967e3fd6ca6e2c NeedsCompilation: no Title: Databases for the Default RDP Classifier Description: The package provides the data for the RDP Classifier 2.14 released in August 2023. It contains the latest bacterial and archaeal taxonomy training set No. 19 as described in Wang Q, Cole JR. 2024. Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification. Microbiol Resour Announc 0:e01063-23. biocViews: SequencingData, MicrobiomeData, RNASeqData Author: Michael Hahsler [aut, cre] (ORCID: ), Nagar Anurag [aut] Maintainer: Michael Hahsler URL: https://github.com/mhahsler/rRDP PackageStatus: Deprecated git_url: https://git.bioconductor.org/packages/rRDPData git_branch: RELEASE_3_22 git_last_commit: e66bd54 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/rRDPData_1.30.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: rRDP dependencyCount: 17 Package: RTCGA.clinical Version: 20151101.40.0 Depends: R (>= 3.2.0), RTCGA Suggests: rmarkdown, knitr License: GPL-2 MD5sum: 4d5e34af9e7ad046b3df46a6b77878d4 NeedsCompilation: no Title: Clinical datasets from The Cancer Genome Atlas Project Description: Package provides clinical datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Clinical data format is explained here https://wiki.nci.nih.gov/display/TCGA/Clinical+Data+Overview. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.clinical git_branch: RELEASE_3_22 git_last_commit: 40c2ae3 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RTCGA.clinical_20151101.40.0.tar.gz vignettes: vignettes/RTCGA.clinical/inst/doc/downloading_clinical_datasets.html vignetteTitles: Using RTCGA to download clinical data as included in RTCGA.clinical hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.clinical/inst/doc/downloading_clinical_datasets.R suggestsMe: RTCGA, TDbasedUFEadv dependencyCount: 131 Package: RTCGA.CNV Version: 1.38.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 71b79a564b977a686ed9fec8bf0b642d NeedsCompilation: no Title: CNV (Copy-number variation) datasets from The Cancer Genome Atlas Project Description: Package provides CNV (based on Merge snp) datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Retrieving +Data+Using+the+Data+Matrix. Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Przemyslaw Biecek Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.CNV git_branch: RELEASE_3_22 git_last_commit: e019a4d git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RTCGA.CNV_1.38.0.tar.gz vignettes: vignettes/RTCGA.CNV/inst/doc/downloading_cnv_datasets.html, vignettes/RTCGA.CNV/inst/doc/frequency_of_cnv_for_mdm3.html vignetteTitles: Using RTCGA to download CNV data as included in RTCGA.CNV, Using RTCGA to estimate ratio of MDM2 duplications hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.CNV/inst/doc/downloading_cnv_datasets.R, vignettes/RTCGA.CNV/inst/doc/frequency_of_cnv_for_mdm3.R suggestsMe: RTCGA dependencyCount: 131 Package: RTCGA.methylation Version: 1.38.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 52782c2aaa15d5cfc9f54e8ea30766f9 NeedsCompilation: no Title: Methylation datasets from The Cancer Genome Atlas Project Description: Package provides methylation (humanmethylation27) datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/DNA+methylation Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Marcin Kosinski [aut, cre], Witold Chodor [aut] Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.methylation git_branch: RELEASE_3_22 git_last_commit: a179b6a git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RTCGA.methylation_1.38.0.tar.gz vignettes: vignettes/RTCGA.methylation/inst/doc/downloading_methylation_datasets.html vignetteTitles: Using RTCGA to download methylation data as included in RTCGA.methylation hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.methylation/inst/doc/downloading_methylation_datasets.R suggestsMe: RTCGA dependencyCount: 131 Package: RTCGA.miRNASeq Version: 1.38.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: fc2c3c1061f121a85afad47f2d190d75 NeedsCompilation: no Title: miRNASeq datasets from The Cancer Genome Atlas Project Description: Package provides miRNASeq datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/miRNASeq#miRNASeq-DataOverview Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.miRNASeq git_branch: RELEASE_3_22 git_last_commit: bb4e69b git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RTCGA.miRNASeq_1.38.0.tar.gz vignettes: vignettes/RTCGA.miRNASeq/inst/doc/downloading_miRNASeq_datasets.html vignetteTitles: Using RTCGA to download miRNASeq data as included in RTCGA.miRNASeq hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.miRNASeq/inst/doc/downloading_miRNASeq_datasets.R suggestsMe: RTCGA dependencyCount: 131 Package: RTCGA.mRNA Version: 1.38.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 2c313be50d258608903c5444341405ba NeedsCompilation: no Title: mRNA datasets from The Cancer Genome Atlas Project Description: Package provides mRNA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Gene+expression+data Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.mRNA git_branch: RELEASE_3_22 git_last_commit: a8b6385 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RTCGA.mRNA_1.38.0.tar.gz vignettes: vignettes/RTCGA.mRNA/inst/doc/downloading_mRNA_datasets.html vignetteTitles: Using RTCGA to download mRNA data as included in RTCGA.mRNA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.mRNA/inst/doc/downloading_mRNA_datasets.R suggestsMe: RTCGA dependencyCount: 131 Package: RTCGA.mutations Version: 20151101.40.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 65f68c297070947cfed96248303e3e0d NeedsCompilation: no Title: Mutations datasets from The Cancer Genome Atlas Project Description: Package provides mutations datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Mutations data format is explained here https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+(MAF)+Specification. There is extra one column with patients' barcodes. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.mutations git_branch: RELEASE_3_22 git_last_commit: 42ce965 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RTCGA.mutations_20151101.40.0.tar.gz vignettes: vignettes/RTCGA.mutations/inst/doc/downloading_mutations_datasets.html vignetteTitles: Using RTCGA to download mutations data as included in RTCGA.mutations hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.mutations/inst/doc/downloading_mutations_datasets.R suggestsMe: RTCGA dependencyCount: 131 Package: RTCGA.PANCAN12 Version: 1.38.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: ffba21e22b5350b91661e2dbb56c4659 NeedsCompilation: no Title: PanCan 12 from Genome Cancer Browser Description: Package provides clinical, expression, cnv and mutation data from Genome Cancer Browser. biocViews: AnnotationData Author: Przemyslaw Biecek Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.PANCAN12 git_branch: RELEASE_3_22 git_last_commit: ccec595 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RTCGA.PANCAN12_1.38.0.tar.gz vignettes: vignettes/RTCGA.PANCAN12/inst/doc/pancan12.html vignetteTitles: Using RTCGA.PANCAN12 to compare time to death hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.PANCAN12/inst/doc/pancan12.R suggestsMe: GOpro dependencyCount: 131 Package: RTCGA.rnaseq Version: 20151101.40.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: fa065a70f3c7d4bdfb8c34ae5253877c NeedsCompilation: no Title: Rna-seq datasets from The Cancer Genome Atlas Project Description: Package provides rna-seq datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Rna-seq data format is explained here https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2. Data source is illumina hiseq Level 3 RSEM normalized expression data. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.rnaseq git_branch: RELEASE_3_22 git_last_commit: 5188267 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RTCGA.rnaseq_20151101.40.0.tar.gz vignettes: vignettes/RTCGA.rnaseq/inst/doc/downloading_rnaseq_datasets.html vignetteTitles: Using RTCGA to download RNAseq data as included in RTCGA.rnaseq hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.rnaseq/inst/doc/downloading_rnaseq_datasets.R suggestsMe: RTCGA, TDbasedUFEadv, FSelectorRcpp dependencyCount: 131 Package: RTCGA.RPPA Version: 1.38.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 7db00bcd633b64533c95e1ef6e9e7c66 NeedsCompilation: no Title: RPPA datasets from The Cancer Genome Atlas Project Description: Package provides RPPA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Protein+Array +Data+Format+Specification?src=search biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.RPPA git_branch: RELEASE_3_22 git_last_commit: 1c3a1a7 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RTCGA.RPPA_1.38.0.tar.gz vignettes: vignettes/RTCGA.RPPA/inst/doc/downloading_RPPA_datasets.html vignetteTitles: Using RTCGA to download RPPA data as included in RTCGA.RPPA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.RPPA/inst/doc/downloading_RPPA_datasets.R suggestsMe: RTCGA dependencyCount: 131 Package: RUVnormalizeData Version: 1.30.0 Depends: R (>= 2.10.0), Biobase License: GPL-3 MD5sum: c36ea47d42e044af2ebc4f2e53175d0b NeedsCompilation: no Title: Gender data for the RUVnormalize package Description: Microarray gene expression data from the study of Vawter et al., 2004. biocViews: MicroarrayData Author: Laurent Jacob Maintainer: Laurent Jacob git_url: https://git.bioconductor.org/packages/RUVnormalizeData git_branch: RELEASE_3_22 git_last_commit: 61d09d2 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/RUVnormalizeData_1.30.0.tar.gz vignettes: vignettes/RUVnormalizeData/inst/doc/RUVnormalizeData.pdf vignetteTitles: RUVnormalizeData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RUVnormalizeData/inst/doc/RUVnormalizeData.R importsMe: RUVnormalize dependencyCount: 7 Package: sampleClassifierData Version: 1.34.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: BiocStyle License: Artistic-2.0 MD5sum: 7a24b40a861f975d42066773750f0608 NeedsCompilation: no Title: Pre-processed data for use with the sampleClassifier package Description: This package contains two microarray and two RNA-seq datasets that have been preprocessed for use with the sampleClassifier package. The RNA-seq data are derived from Fagerberg et al. (2014) and the Illumina Body Map 2.0 data. The microarray data are derived from Roth et al. (2006) and Ge et al. (2005). biocViews: ExperimentData, ExpressionData, MicroarrayData, SequencingData, RNASeqData, ArrayExpress Author: Khadija El Amrani Maintainer: Khadija El Amrani git_url: https://git.bioconductor.org/packages/sampleClassifierData git_branch: RELEASE_3_22 git_last_commit: fd9c843 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/sampleClassifierData_1.34.0.tar.gz vignettes: vignettes/sampleClassifierData/inst/doc/sampleClassifierData.pdf vignetteTitles: sampleClassifierData Introduction hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/sampleClassifierData/inst/doc/sampleClassifierData.R dependencyCount: 25 Package: SBGNview.data Version: 1.24.0 Depends: R (>= 3.6) Imports: knitr, rmarkdown, bookdown Suggests: SummarizedExperiment License: AGPL-3 MD5sum: 286eb1440d9a6fda440cd79b120e9f9c NeedsCompilation: no Title: Supporting datasets for SBGNview package Description: This package contains: 1. A microarray gene expression dataset from a human breast cancer study. 2. A RNA-Seq gene expression dataset from a mouse study on IFNG knockout. 3. ID mapping tables between gene IDs and SBGN-ML file glyph IDs. 4. Percent of orthologs detected in other species of the genes in a pathway. Cutoffs of this percentage for defining if a pathway exists in another species. 5. XML text of SBGN-ML files for all pre-collected pathways. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO, RNASeqData Author: Xiaoxi Dong*, Kovidh Vegesna*, Weijun Luo Maintainer: Weijun Luo VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/SBGNview.data git_branch: RELEASE_3_22 git_last_commit: b10eba8 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/SBGNview.data_1.24.0.tar.gz vignettes: vignettes/SBGNview.data/inst/doc/SBGNview.data.vignette.html vignetteTitles: Supporting Datasets for SBGNview Package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SBGNview.data/inst/doc/SBGNview.data.vignette.R dependsOnMe: SBGNview dependencyCount: 32 Package: scaeData Version: 1.6.0 Depends: R (>= 4.4.0) Imports: ExperimentHub Suggests: knitr, rmarkdown, markdown, SingleCellAlleleExperiment, Matrix, BiocStyle License: MIT + file LICENSE MD5sum: c9a3e89acea35a1c48c15cb79cb3bb6f NeedsCompilation: no Title: Data Package for SingleCellAlleleExperiment Description: Contains default datasets used by the Bioconductor package SingleCellAlleleExperiment. The raw FASTQ files were sourced from publicly accessible datasets provided by 10x Genomics. Subsequently, our scIGD snakemake workflow was employed to process these FASTQ files. The resulting output from scIGD constitutes to the contents of this data package. biocViews: ExperimentHub, ExperimentData, Homo_sapiens_Data, SingleCellData Author: Ahmad Al Ajami [aut, cre] (ORCID: ), Jonas Schuck [aut] (ORCID: ), Federico Marini [aut] (ORCID: ), Katharina Imkeller [aut] (ORCID: ) Maintainer: Ahmad Al Ajami URL: https://github.com/AGImkeller/scaeData VignetteBuilder: knitr BugReports: https://github.com/AGImkeller/scIGD/issues git_url: https://git.bioconductor.org/packages/scaeData git_branch: RELEASE_3_22 git_last_commit: 872aea7 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/scaeData_1.6.0.tar.gz vignettes: vignettes/scaeData/inst/doc/scaeData.html vignetteTitles: scaeData User Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/scaeData/inst/doc/scaeData.R suggestsMe: SingleCellAlleleExperiment dependencyCount: 65 Package: scanMiRData Version: 1.16.0 Depends: R (>= 4.0) Imports: scanMiR, utils Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 2107b9bb9400c3167812f2cd8bda7cf0 NeedsCompilation: no Title: miRNA Affinity models for the scanMiR package Description: This package contains companion data to the scanMiR package. It contains `KdModel` (miRNA 12-mer binding affinity models) collections corresponding to all human, mouse and rat mirbase miRNAs. See the scanMiR package for details. biocViews: miRNAData, ExperimentData, Homo_sapiens_Data, Mus_musculus_Data, Rattus_norvegicus_Data Author: Pierre-Luc Germain [cre, aut] (ORCID: ), Michael Soutschek [aut], Fridolin Gross [aut] Maintainer: Pierre-Luc Germain VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/scanMiRData git_branch: RELEASE_3_22 git_last_commit: 2035cf4 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/scanMiRData_1.16.0.tar.gz vignettes: vignettes/scanMiRData/inst/doc/scanMiRData.html vignetteTitles: scanMiRData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scanMiRData/inst/doc/scanMiRData.R importsMe: scanMiRApp dependencyCount: 49 Package: scATAC.Explorer Version: 1.16.0 Depends: R (>= 4.1), SingleCellExperiment, BiocFileCache, data.table, utils, S4Vectors, zellkonverter Imports: methods, Matrix Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 17174656722d3aa1dba3a5814ae70c32 NeedsCompilation: no Title: A Collection of Single-cell ATAC Sequencing Datasets and Corresponding Metadata Description: This package provides a tool to search and download a collection of publicly available single cell ATAC-seq datasets and their metadata. scATAC-Explorer aims to act as a single point of entry for users looking to study single cell ATAC-seq data. Users can quickly search available datasets using the metadata table and download datasets of interest for immediate analysis within R. biocViews: SingleCellData, SequencingData, ExpressionData, GEO, Tissue, Genome, PackageTypeData Author: Arrian Gibson-Khademi [aut], Erik Christensen [aut], Jonathan Wang [aut, cre], Parisa Shooshtari [aut] Maintainer: Jonathan Wang VignetteBuilder: knitr BugReports: https://github.com/shooshtarilab/scATACseq/issues git_url: https://git.bioconductor.org/packages/scATAC.Explorer git_branch: RELEASE_3_22 git_last_commit: 25c3354 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/scATAC.Explorer_1.16.0.tar.gz vignettes: vignettes/scATAC.Explorer/inst/doc/scATAC.Explorer.html vignetteTitles: scATAC.Explorer hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scATAC.Explorer/inst/doc/scATAC.Explorer.R dependencyCount: 75 Package: SCLCBam Version: 1.42.0 Depends: R(>= 2.10) Suggests: BiocStyle License: GPL-2 MD5sum: 15c7aec921dd8b73b03e374d517ded59 NeedsCompilation: no Title: Sequence data from chromosome 4 of a small-cell lung tumor Description: Whole-exome sequencing data from a murine small-cell lung tumor; only contains data of chromosome 4. biocViews: SequencingData, LungCancerData Author: Thomas Kuilman Maintainer: Oscar Krijgsman git_url: https://git.bioconductor.org/packages/SCLCBam git_branch: RELEASE_3_22 git_last_commit: 9c8603a git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/SCLCBam_1.42.0.tar.gz vignettes: vignettes/SCLCBam/inst/doc/SCLCBam.pdf vignetteTitles: SCLCBam hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SCLCBam/inst/doc/SCLCBam.R dependencyCount: 0 Package: scMultiome Version: 1.10.0 Depends: AnnotationHub, ExperimentHub (>= 2.8.1), MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment Imports: AzureStor, GenomicRanges, HDF5Array, S4Vectors, checkmate, methods, rhdf5, alabaster.matrix Suggests: BiocGenerics, IRanges, Matrix, knitr, rmarkdown, rstudioapi, testthat (>= 3.0.0), devtools, BiocStyle, ExperimentHubData License: CC BY-SA 4.0 MD5sum: 45e608c42164c04d71ce70db3584c357 NeedsCompilation: no Title: Collection of Public Single-Cell Multiome (scATAC + scRNAseq) Datasets Description: Single cell multiome data, containing chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) information analyzed with the ArchR package and presented as MultiAssayExperiment objects. biocViews: PackageTypeData, ExperimentHub, SingleCellData, ExpressionData, SequencingData, Homo_sapiens_Data, CellCulture, Tissue, GEO Author: Xiaosai Yao [cre, aut] (ORCID: ), Aleksander Chlebowski [aut], Aaron Lun [aut], Shiqi Xie [ctb], Tomasz Włodarczyk [aut] Maintainer: Xiaosai Yao VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/scMultiome git_branch: RELEASE_3_22 git_last_commit: 26da406 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/scMultiome_1.10.0.tar.gz vignettes: vignettes/scMultiome/inst/doc/scMultiome.html vignetteTitles: scMultiome tutorial hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scMultiome/inst/doc/scMultiome.R suggestsMe: epiregulon, epiregulon.extra dependencyCount: 100 Package: scpdata Version: 1.18.0 Depends: R (>= 4.2.0), QFeatures, ExperimentHub Imports: utils, AnnotationHub, SingleCellExperiment, S4Vectors Suggests: scp, magrittr, dplyr, knitr, BiocStyle, BiocCheck, rmarkdown, testthat License: GPL-2 MD5sum: d24e6b514a2a9556695ef42000d3c782 NeedsCompilation: no Title: Single-Cell Proteomics Data Package Description: The package disseminates mass spectrometry (MS)-based single-cell proteomics (SCP) datasets. The data were collected from published work and formatted using the `scp` data structure. The data sets contain quantitative information at spectrum, peptide and/or protein level for single cells or minute sample amounts. biocViews: ExperimentData, ExpressionData, ExperimentHub, ReproducibleResearch, MassSpectrometryData, Proteome, SingleCellData, PackageTypeData Author: Christophe Vanderaa [aut, cre] (ORCID: ), Laurent Gatto [aut] (ORCID: ), Enes Ayar [dtc] (ORCID: ), Samuel Grégoire [dtc] (ORCID: ) Maintainer: Christophe Vanderaa VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/scpdata git_branch: RELEASE_3_22 git_last_commit: 03bcf31 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/scpdata_1.18.0.tar.gz vignettes: vignettes/scpdata/inst/doc/contribution_guidelines.html, vignettes/scpdata/inst/doc/scpdata.html vignetteTitles: Contribution guidelines, Data Package for Single Cell Proteomics hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scpdata/inst/doc/contribution_guidelines.R, vignettes/scpdata/inst/doc/scpdata.R suggestsMe: scp dependencyCount: 120 Package: scRNAseq Version: 2.24.0 Depends: SingleCellExperiment Imports: utils, methods, Matrix, BiocGenerics, S4Vectors, SparseArray, DelayedArray, GenomicRanges, SummarizedExperiment, ExperimentHub (>= 2.3.4), AnnotationHub (>= 3.3.6), AnnotationDbi, ensembldb, GenomicFeatures, alabaster.base, alabaster.matrix, alabaster.sce, gypsum, jsonlite, DBI, RSQLite Suggests: BiocStyle, knitr, rmarkdown, testthat, jsonvalidate, BiocManager License: CC0 MD5sum: 0822979708e79b5ae78075d35ca19567 NeedsCompilation: no Title: Collection of Public Single-Cell RNA-Seq Datasets Description: Gene-level counts for a collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata. biocViews: ExperimentHub, ExperimentData, ExpressionData, SequencingData, RNASeqData, SingleCellData Author: Davide Risso [aut, cph], Michael Cole [aut], Aaron Lun [ctb, cre], Alan O'Callaghan [ctb], Jens Preussner [ctb], Charlotte Soneson [ctb], Stephany Orjuela [ctb], Daniel Bunis [ctb], Milan Malfait [ctb] Maintainer: Aaron Lun VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/scRNAseq git_branch: RELEASE_3_22 git_last_commit: 111920c git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/scRNAseq_2.24.0.tar.gz vignettes: vignettes/scRNAseq/inst/doc/scRNAseq.html vignetteTitles: User's Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scRNAseq/inst/doc/scRNAseq.R dependsOnMe: OSCA.advanced, OSCA.basic, OSCA.intro, OSCA.workflows, SingleRBook importsMe: singleCellTK suggestsMe: APL, BASiCS, batchelor, bluster, ccImpute, ClusterFoldSimilarity, Coralysis, CSOA, dittoSeq, Glimma, iSEE, iSEEfier, iSEEhex, iSEEindex, iSEEu, looking4clusters, miloR, miQC, mumosa, ReactomeGSA, scAnnotatR, scater, scDblFinder, scDiagnostics, scDotPlot, scFeatureFilter, scone, scran, scrapper, scTreeViz, scuttle, SingleCellExperiment, SingleR, SplineDV, UCell, velociraptor, zellkonverter, zinbwave, scStability, speakeasyR dependencyCount: 120 Package: scTHI.data Version: 1.22.0 Depends: R (>= 4.0) License: GPL-2 MD5sum: 8b4ff6b5d962006c3f1f025951e71c01 NeedsCompilation: no Title: The package contains examples of single cell data used in vignettes and examples of the scTHI package; data contain both tumor cells and immune cells from public dataset of glioma Description: Data for the vignette and tutorial of the package scTHI. biocViews: ExperimentData, SingleCellData Author: Francesca Pia Caruso [aut], Michele Ceccarelli [aut, cre] Maintainer: Michele Ceccarelli git_url: https://git.bioconductor.org/packages/scTHI.data git_branch: RELEASE_3_22 git_last_commit: a9dd6a5 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/scTHI.data_1.22.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: scTHI dependencyCount: 0 Package: seq2pathway.data Version: 1.42.0 Depends: R (>= 3.6.2) License: GPL (>= 2) MD5sum: 3e34561167f4db5731cc8778cbe3b75e NeedsCompilation: no Title: data set for R package seq2pathway Description: Supporting data for the seq2patheway package. Includes modified gene sets from MsigDB and org.Hs.eg.db; gene locus definitions from GENCODE project. biocViews: ExperimentData Author: Bin Wang Maintainer: Arjun Kinstlick git_url: https://git.bioconductor.org/packages/seq2pathway.data git_branch: RELEASE_3_22 git_last_commit: e8bca94 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/seq2pathway.data_1.42.0.tar.gz vignettes: vignettes/seq2pathway.data/inst/doc/seq2pathway.data.pdf vignetteTitles: An R data package for sequence hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: seqc Version: 1.44.0 Depends: R (>= 2.10) Imports: utils, Biobase License: GPL-3 MD5sum: 350ae3b9ac7b2f9d50faedb8ba765654 NeedsCompilation: no Title: RNA-seq data generated from SEQC (MAQC-III) study Description: The SEQC/MAQC-III Consortium has produced benchmark RNA-seq data for the assessment of RNA sequencing technologies and data analysis methods (Nat Biotechnol, 2014). Billions of sequence reads have been generated from ten different sequencing sites. This package contains the summarized read count data for ~2000 sequencing libraries. It also includes all the exon-exon junctions discovered from the study. TaqMan RT-PCR data for ~1000 genes and ERCC spike-in sequence data are included in this package as well. biocViews: ExperimentData, RNASeqData, qPCRData, SequencingData Author: Yang Liao and Wei Shi with contributions from Gordon K Smyth and Steve Lianoglou. Maintainer: Yang Liao and Wei Shi URL: http://bioconductor.org/packages/release/data/experiment/html/seqc.html git_url: https://git.bioconductor.org/packages/seqc git_branch: RELEASE_3_22 git_last_commit: e0fa160 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/seqc_1.44.0.tar.gz vignettes: vignettes/seqc/inst/doc/seqc.pdf vignetteTitles: SEQC Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/seqc/inst/doc/seqc.R dependencyCount: 7 Package: serumStimulation Version: 1.46.0 Depends: R (>= 2.10) License: GPL (>= 2) MD5sum: 8c1e043ee1c006945b9ac3124188d97e NeedsCompilation: no Title: serumStimulation is a data package which is used by examples in package pcaGoPromoter Description: Contains 13 micro array data results from a serum stimulation experiment biocViews: ExperimentData, MicroarrayData Author: Morten Hansen Maintainer: Morten Hansen, git_url: https://git.bioconductor.org/packages/serumStimulation git_branch: RELEASE_3_22 git_last_commit: cdc3700 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/serumStimulation_1.46.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: sesameData Version: 1.28.0 Depends: R (>= 4.2.0), ExperimentHub, AnnotationHub Imports: utils, readr, stringr, GenomicRanges (>= 1.61.1), S4Vectors, IRanges, Seqinfo Suggests: BiocGenerics, GenomeInfoDb, sesame, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: eeff4368537b03929881b9b9ab190535 NeedsCompilation: no Title: Supporting Data for SeSAMe Package Description: Provides supporting annotation and test data for SeSAMe package. This includes chip tango addresses, mapping information, performance annotation, and trained predictor for Infinium array data. This package provides user access to essential annotation data for working with many generations of the Infinium DNA methylation array. Current we support human array (HM27, HM450, EPIC), mouse array (MM285) and the HorvathMethylChip40 (Mammal40) array. biocViews: ExperimentData, MicroarrayData, Genome, ExperimentHub, MethylationArrayData Author: Wanding Zhou [aut, cre] (ORCID: ), Hui Shen [aut], Timothy Triche [ctb] Maintainer: Wanding Zhou URL: https://github.com/zwdzwd/sesame VignetteBuilder: knitr BugReports: https://github.com/zwdzwd/sesame/issue git_url: https://git.bioconductor.org/packages/sesameData git_branch: RELEASE_3_22 git_last_commit: 851657b git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/sesameData_1.28.0.tar.gz vignettes: vignettes/sesameData/inst/doc/sesameData.html vignetteTitles: sesameData User Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/sesameData/inst/doc/sesameData.R dependsOnMe: sesame importsMe: knowYourCG, MethReg, TENET, CytoMethIC suggestsMe: ELMER dependencyCount: 73 Package: seventyGeneData Version: 1.46.0 Depends: R (>= 2.13.0) Suggests: Biobase, limma, breastCancerNKI, knitr, rmarkdown, readxl, BiocStyle License: Artistic-2.0 MD5sum: e158487024756c5c4e543bbf084e91d7 NeedsCompilation: no Title: ExpressionSets from the van't Veer and Van de Vijver breast cancer studies Description: Gene expression data for the two breast cancer cohorts published by van't Veer and Van de Vijver in 2002. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData Author: Luigi Marchionni [aut, cre] (ORCID: ), Claudio Zanettini [aut, ctb], Lucio Queiroz [aut, ctb] (ORCID: ) Maintainer: Luigi Marchionni URL: https://bioconductor.org/packages/release/data/experiment/html/seventyGeneData.html VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/seventyGeneData git_branch: RELEASE_3_22 git_last_commit: 71f3661 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/seventyGeneData_1.46.0.tar.gz vignettes: vignettes/seventyGeneData/inst/doc/seventyGeneData.html vignetteTitles: 1. Working with the seventyGeneData package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/seventyGeneData/inst/doc/seventyGeneData.R dependencyCount: 0 Package: SFEData Version: 1.12.0 Depends: R (>= 4.1.0) Imports: BiocFileCache, AnnotationHub, ExperimentHub, utils Suggests: BiocStyle, knitr, rmarkdown, SeuratObject, SpatialFeatureExperiment, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: d132b6dd896bfce4cdd7bf5d53b5bd07 NeedsCompilation: no Title: Example SpatialFeatureExperiment datasets Description: Example spatial transcriptomics datasets with Simple Feature annotations as SpatialFeatureExperiment objects. Technologies include Visium, slide-seq, Nanostring CoxMX, Vizgen MERFISH, and 10X Xenium. Tissues include mouse skeletal muscle, human melanoma metastasis, human lung, breast cancer, and mouse liver. biocViews: ExperimentHub, ExpressionData, Mus_musculus_Data, Homo_sapiens_Data, SpatialData, Tissue, SingleCellData Author: Lambda Moses [aut, cre] (ORCID: ), Alik Huseynov [aut] (ORCID: ), Kayla Jackson [aut] (ORCID: ), Lior Pachter [aut, ths] (ORCID: ) Maintainer: Lambda Moses URL: https://github.com/pachterlab/SFEData VignetteBuilder: knitr BugReports: https://github.com/pachterlab/SFEData/issues git_url: https://git.bioconductor.org/packages/SFEData git_branch: RELEASE_3_22 git_last_commit: 6dcb2d3 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/SFEData_1.12.0.tar.gz vignettes: vignettes/SFEData/inst/doc/SFEData.html vignetteTitles: Example SpatialFeatureExperiment datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SFEData/inst/doc/SFEData.R importsMe: OSTA suggestsMe: alabaster.sfe, concordexR, jazzPanda, SpatialFeatureExperiment, Voyager, xenLite dependencyCount: 65 Package: shinyMethylData Version: 1.30.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: fd8f2ee9df31e0d7cf5b35317b3db910 NeedsCompilation: no Title: Example dataset of input data for shinyMethyl Description: Extracted data from 369 TCGA Head and Neck Cancer DNA methylation samples. The extracted data serve as an example dataset for the package shinyMethyl. Original samples are from 450k methylation arrays, and were obtained from The Cancer Genome Atlas (TCGA). 310 samples are from tumor, 50 are matched normals and 9 are technical replicates of a control cell line. biocViews: Genome, CancerData Author: Jean-Philippe Fortin [cre, aut], Kasper Daniel Hansen [aut] Maintainer: Jean-Philippe Fortin git_url: https://git.bioconductor.org/packages/shinyMethylData git_branch: RELEASE_3_22 git_last_commit: fa68252 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/shinyMethylData_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: shinyMethyl dependencyCount: 0 Package: signatureSearchData Version: 1.24.0 Depends: R (>= 3.6) Imports: ExperimentHub, utils, affy, limma, Biobase, magrittr, dplyr, R.utils, stats, rhdf5 Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 71b1eac92de8469273d28ddf8febcb43 NeedsCompilation: no Title: Datasets for signatureSearch package Description: CMAP/LINCS hdf5 databases and other annotations used for signatureSearch software package. biocViews: ExperimentHub, ExperimentData, ExpressionData Author: Yuzhu Duan , Brendan Gongol , Thomas Girke Maintainer: Brendan Gongol VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/signatureSearchData git_branch: RELEASE_3_22 git_last_commit: 7ab46d1 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/signatureSearchData_1.24.0.tar.gz vignettes: vignettes/signatureSearchData/inst/doc/signatureSearchData.html vignetteTitles: signatureSearchData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/signatureSearchData/inst/doc/signatureSearchData.R dependsOnMe: DFD suggestsMe: signatureSearch dependencyCount: 76 Package: SimBenchData Version: 1.18.0 Depends: ExperimentHub Imports: S4Vectors, utils Suggests: BiocStyle, knitr, rmarkdown, Seurat License: GPL-3 MD5sum: aec2e6976d8f608f7e6c917335902fe3 NeedsCompilation: no Title: SimBenchData: a collection of 35 single-cell RNA-seq data covering a wide range of data characteristics Description: The SimBenchData package contains a total of 35 single-cell RNA-seq datasets covering a wide range of data characteristics, including major sequencing protocols, multiple tissue types, and both human and mouse sources. biocViews: ExperimentHub, ExperimentData, SingleCellData, RNASeqData, Tissue, SequencingData Author: Yue Cao [aut, cre], Pengyi Yang [aut], Jean Yee Hwa Yang [aut] Maintainer: Yue Cao VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/SimBenchData git_branch: RELEASE_3_22 git_last_commit: 005996d git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/SimBenchData_1.18.0.tar.gz vignettes: vignettes/SimBenchData/inst/doc/SimBenchData-vignette.html vignetteTitles: SimBenchData: a collection of single-cell RNA-seq data covering a wide range of data characteristics hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SimBenchData/inst/doc/SimBenchData-vignette.R dependencyCount: 65 Package: simpIntLists Version: 1.46.0 License: GPL (>= 2) MD5sum: 5208739e1a07da9cbcf627d0999cb989 NeedsCompilation: no Title: The package contains BioGRID interactions for various organisms in a simple format Description: The package contains BioGRID interactions for arabidopsis(thale cress), c.elegans, fruit fly, human, mouse, yeast( budding yeast ) and S.pombe (fission yeast) . Entrez ids, official names and unique ids can be used to find proteins. The format of interactions are lists. For each gene/protein, there is an entry in the list with "name" containing name of the gene/protein and "interactors" containing the list of genes/proteins interacting with it. biocViews: ExperimentData, Arabidopsis_thaliana_Data Author: Kircicegi Korkmaz, Volkan Atalay, Rengul Cetin-Atalay Maintainer: Kircicegi Korkmaz git_url: https://git.bioconductor.org/packages/simpIntLists git_branch: RELEASE_3_22 git_last_commit: c1d9012 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/simpIntLists_1.46.0.tar.gz vignettes: vignettes/simpIntLists/inst/doc/simpIntLists.pdf vignetteTitles: simpIntLists hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/simpIntLists/inst/doc/simpIntLists.R dependsOnMe: ibh dependencyCount: 0 Package: Single.mTEC.Transcriptomes Version: 1.38.0 Depends: R (>= 3.5.0) Suggests: DESeq2, GenomicRanges, GenomicFeatures, genefilter, statmod, gdata, RColorBrewer, ggplot2, gplots, cluster, clue, grid, gridExtra, ggbio, Gviz, geneplotter, matrixStats, pheatmap, BiocStyle, knitr, BiocParallel License: LGPL MD5sum: 0d378587cd8a88ab4cf6f12fd42725f7 NeedsCompilation: no Title: Single Cell Transcriptome Data and Analysis of Mouse mTEC cells Description: This data package contains the code used to analyse the single-cell RNA-seq and the bulk ATAC-seq data from the manuscript titled: Single-cell transcriptome analysis reveals coordinated ectopic-gene expression patterns in medullary thymic epithelial cells. This paper was published in Nature Immunology 16,933-941(2015). The data objects provided in this package has been pre-processed: the raw data files can be downloaded from ArrayExpress under the accession identifiers E-MTAB-3346 and E-MTAB-3624. The vignette of this data package provides a documented and reproducible workflow that includes the code that was used to generate each statistic and figure from the manuscript. biocViews: ExperimentData Author: Alejandro Reyes Maintainer: Alejandro Reyes VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/Single.mTEC.Transcriptomes git_branch: RELEASE_3_22 git_last_commit: a2d5fc4 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/Single.mTEC.Transcriptomes_1.38.0.tar.gz vignettes: vignettes/Single.mTEC.Transcriptomes/inst/doc/mTECs.pdf vignetteTitles: Analysis of single cell mTEC data. hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Single.mTEC.Transcriptomes/inst/doc/mTECs.R dependencyCount: 0 Package: SingleCellMultiModal Version: 1.22.0 Depends: R (>= 4.2.0), MultiAssayExperiment Imports: AnnotationHub, BiocBaseUtils, BiocFileCache, ExperimentHub, graphics, HDF5Array, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, Matrix, methods, utils Suggests: BiocStyle, ggplot2, knitr, RaggedExperiment, rmarkdown, scater, scran, UpSetR, uwot License: Artistic-2.0 MD5sum: e400ebb19ca5a1d35d22409ac9fdcae1 NeedsCompilation: no Title: Integrating Multi-modal Single Cell Experiment datasets Description: SingleCellMultiModal is an ExperimentHub package that serves multiple datasets obtained from GEO and other sources and represents them as MultiAssayExperiment objects. We provide several multi-modal datasets including scNMT, 10X Multiome, seqFISH, CITEseq, SCoPE2, and others. The scope of the package is is to provide data for benchmarking and analysis. To cite, use the 'citation' function and see . biocViews: ExperimentData, SingleCellData, ReproducibleResearch, ExperimentHub, GEO Author: Marcel Ramos [aut, cre] (ORCID: ), Ricard Argelaguet [aut], Al Abadi [ctb], Dario Righelli [aut], Christophe Vanderaa [ctb], Kelly Eckenrode [aut], Ludwig Geistlinger [aut], Levi Waldron [aut] Maintainer: Marcel Ramos VignetteBuilder: knitr BugReports: https://github.com/waldronlab/SingleCellMultiModal/issues git_url: https://git.bioconductor.org/packages/SingleCellMultiModal git_branch: RELEASE_3_22 git_last_commit: d8abccb git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/SingleCellMultiModal_1.22.0.tar.gz vignettes: vignettes/SingleCellMultiModal/inst/doc/CITEseq.html, vignettes/SingleCellMultiModal/inst/doc/ECCITEseq.html, vignettes/SingleCellMultiModal/inst/doc/GTseq.html, vignettes/SingleCellMultiModal/inst/doc/scMultiome.html, vignettes/SingleCellMultiModal/inst/doc/scNMT.html, vignettes/SingleCellMultiModal/inst/doc/SCoPE2.html, vignettes/SingleCellMultiModal/inst/doc/seqFISH.html, vignettes/SingleCellMultiModal/inst/doc/SingleCellMultiModal.html vignetteTitles: CITEseq Cord Blood, ECCITEseq Peripheral Blood, GT-seq Mouse Embryo, scMultiome 10x PBMC, scNMT Mouse Gastrulation, SCoPE2: macrophage vs monocytes, seqFISH Mouse Visual Cortex, SingleCellMultiModal Introduction hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SingleCellMultiModal/inst/doc/CITEseq.R, vignettes/SingleCellMultiModal/inst/doc/ECCITEseq.R, vignettes/SingleCellMultiModal/inst/doc/GTseq.R, vignettes/SingleCellMultiModal/inst/doc/scMultiome.R, vignettes/SingleCellMultiModal/inst/doc/scNMT.R, vignettes/SingleCellMultiModal/inst/doc/SCoPE2.R, vignettes/SingleCellMultiModal/inst/doc/seqFISH.R, vignettes/SingleCellMultiModal/inst/doc/SingleCellMultiModal.R suggestsMe: decontX, MuData, StabMap dependencyCount: 87 Package: SingleMoleculeFootprintingData Version: 1.18.0 Imports: ExperimentHub, utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 5fbd165a063d4145e967eaf9b6b04448 NeedsCompilation: no Title: Data supporting the SingleMoleculeFootprinting pkg Description: This Data package contains data objcets relevanat for the SingleMoleculeFootprinting package. More specifically, it contains one example of aligned sequencing data (.bam & .bai) necessary to run the SingleMoleculeFootprinting vignette. Additionally, we provide data that are essential for some functions to work correctly such as BaitCapture() and SampleCorrelation(). biocViews: ExperimentHub, ExperimentData, SequencingData Author: Guido Barzaghi [aut, cre] (ORCID: ), Arnaud Krebs [aut] (ORCID: ), Mike Smith [ctb] (ORCID: ) Maintainer: Guido Barzaghi VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/SingleMoleculeFootprintingData git_branch: RELEASE_3_22 git_last_commit: 2069905 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/SingleMoleculeFootprintingData_1.18.0.tar.gz vignettes: vignettes/SingleMoleculeFootprintingData/inst/doc/SingleMoleculeFootprintingData.html vignetteTitles: SingleMoleculeFootprintingData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/SingleMoleculeFootprintingData/inst/doc/SingleMoleculeFootprintingData.R suggestsMe: SingleMoleculeFootprinting dependencyCount: 65 Package: smokingMouse Version: 1.8.0 Suggests: AnnotationHubData, BiocStyle, ExperimentHub, ExperimentHubData, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 462c0059e1336994d44e7e539a6628d0 NeedsCompilation: no Title: Provides access to smokingMouse project data Description: This is an ExperimentHub package that provides access to the data generated and analyzed in the [smoking-nicotine-mouse](https://github.com/LieberInstitute/smoking-nicotine-mouse/) LIBD project. The datasets contain the expression data of mouse genes, transcripts, exons, and exon-exon junctions across 208 samples from pup and adult mouse brain, and adult blood, that were exposed to nicotine, cigarette smoke, or controls. They also contain relevant metadata of these samples and gene expression features, such QC metrics, if they were used after filtering steps and also if the features were differently expressed in the different experiments. biocViews: ExperimentHub, ExpressionData, Mus_musculus_Data, RNASeqData Author: Daianna Gonzalez-Padilla [aut, cre] (ORCID: ) Maintainer: Daianna Gonzalez-Padilla URL: https://github.com/LieberInstitute/smokingMouse VignetteBuilder: knitr BugReports: https://support.bioconductor.org/tag/smokingMouse git_url: https://git.bioconductor.org/packages/smokingMouse git_branch: RELEASE_3_22 git_last_commit: c832af9 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/smokingMouse_1.8.0.tar.gz vignettes: vignettes/smokingMouse/inst/doc/smokingMouse.html vignetteTitles: Introduction to smokingMouse hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/smokingMouse/inst/doc/smokingMouse.R dependencyCount: 0 Package: SNAData Version: 1.56.0 Depends: R (>= 2.4.0), graph Suggests: Rgraphviz License: LGPL MD5sum: 2a8129b982930ba164733878ae8204bf NeedsCompilation: no Title: Social Networks Analysis Data Examples Description: Data from Wasserman & Faust (1999) "Social Network Analysis" biocViews: ExperimentData Author: Denise Scholtens Maintainer: Denise Scholtens git_url: https://git.bioconductor.org/packages/SNAData git_branch: RELEASE_3_22 git_last_commit: 57ae2ce git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/SNAData_1.56.0.tar.gz vignettes: vignettes/SNAData/inst/doc/SNAData.pdf vignetteTitles: SNAData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SNAData/inst/doc/SNAData.R dependencyCount: 8 Package: SNAGEEdata Version: 1.46.0 Depends: R (>= 2.6.0) Suggests: ALL, hgu95av2.db, SNAGEE License: Artistic-2.0 MD5sum: ad45caf17e866cdc96dd03647af9425b NeedsCompilation: no Title: SNAGEE data Description: SNAGEE data - gene list and correlation matrix biocViews: MicroarrayData Author: David Venet Maintainer: David Venet URL: http://fleming.ulb.ac.be/SNAGEE git_url: https://git.bioconductor.org/packages/SNAGEEdata git_branch: RELEASE_3_22 git_last_commit: 36029d4 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/SNAGEEdata_1.46.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: SNAGEE dependencyCount: 0 Package: SNPhoodData Version: 1.40.0 Depends: R (>= 3.2) Suggests: BiocStyle,knitr,rmarkdown License: LGPL (>= 3) MD5sum: 7df207ae36a10c225afab3a7a93f3fef NeedsCompilation: no Title: Additional and more complex example data for the SNPhood package Description: This companion package for SNPhood provides some example datasets of a larger size than allowed for the SNPhood package. They include full and real-world examples for performing analyses with the SNPhood package. biocViews: ExperimentData Author: Christian Arnold, Judith Zaugg Maintainer: Christian Arnold VignetteBuilder: knitr BugReports: christian.arnold@embl.de git_url: https://git.bioconductor.org/packages/SNPhoodData git_branch: RELEASE_3_22 git_last_commit: 3bb14ba git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/SNPhoodData_1.40.0.tar.gz vignettes: vignettes/SNPhoodData/inst/doc/SNPhoodData.html vignetteTitles: The *SNPhoodData* package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: SNPhood dependencyCount: 0 Package: SomatiCAData Version: 1.48.0 Depends: R (>= 2.14) License: Artistic-2.0 MD5sum: 836e031b356e36c5a5ef441418175933 NeedsCompilation: no Title: An example cancer whole genome sequencing data for the SomatiCA package Description: An example cancer whole genome sequencing data for the SomatiCA package biocViews: ExperimentData, Genome, CancerData, SequencingData Author: Mengjie Chen Maintainer: Mengjie Chen git_url: https://git.bioconductor.org/packages/SomatiCAData git_branch: RELEASE_3_22 git_last_commit: 62cdf84 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/SomatiCAData_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: SomaticCancerAlterations Version: 1.46.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, IRanges, S4Vectors Suggests: testthat, ggbio, ggplot2, knitr License: GPL-3 MD5sum: 7564511f77ac90020bb2c1edf535c6d8 NeedsCompilation: no Title: Somatic Cancer Alterations Description: Collection of somatic cancer alteration datasets biocViews: ExperimentData, Genome, CancerData, Project1000genomes, NCI Author: Julian Gehring Maintainer: Julian Gehring VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/SomaticCancerAlterations git_branch: RELEASE_3_22 git_last_commit: 22e826f git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/SomaticCancerAlterations_1.46.0.tar.gz vignettes: vignettes/SomaticCancerAlterations/inst/doc/SomaticCancerAlterations-html.html vignetteTitles: SomaticCancerAlterations - HTML hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SomaticCancerAlterations/inst/doc/SomaticCancerAlterations-html.R suggestsMe: SomaticSignatures dependencyCount: 11 Package: SpatialDatasets Version: 1.8.0 Depends: ExperimentHub, SpatialExperiment, Imports: utils Suggests: BiocStyle, knitr, rmarkdown, cytomapper License: GPL-3 MD5sum: 9cb422ef023f1a17e9c0c1e3758918f1 NeedsCompilation: no Title: Collection of spatial omics datasets Description: This is a collection of publically available spatial omics datasets. Where possible we have curated these datasets as either SpatialExperiments, MoleculeExperiments or CytoImageLists and included annotations of the sample characteristics. biocViews: ExperimentData, ExperimentHub, ReproducibleResearch, SingleCellData, SpatialData, Homo_sapiens_Data, Mus_musculus_Data Author: Farhan Ameen [aut], Nick Robertson [aut], Alex Qin [aut], Shreya Rao [aut], Elijah Willie [aut], Ellis Patrick [aut, cre] Maintainer: Ellis Patrick URL: https://github.com/SydneyBioX/SpatialDatasets VignetteBuilder: knitr BugReports: https://github.com/SydneyBioX/SpatialDatasets/issues git_url: https://git.bioconductor.org/packages/SpatialDatasets git_branch: RELEASE_3_22 git_last_commit: 32c4d40 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/SpatialDatasets_1.8.0.tar.gz vignettes: vignettes/SpatialDatasets/inst/doc/SpatialDatasets_overview.html vignetteTitles: The SpatialDataset package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SpatialDatasets/inst/doc/SpatialDatasets_overview.R suggestsMe: lisaClust, spicyR, spicyWorkflow dependencyCount: 81 Package: spatialDmelxsim Version: 1.16.0 Depends: R (>= 4.1), ExperimentHub, SummarizedExperiment Imports: utils Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: ba37a7d691aca5d7ee5dfab8b81f7c3d NeedsCompilation: no Title: Spatial allelic expression counts for fly cross embryo Description: Spatial allelic expression counts from Combs & Fraser (2018), compiled into a SummarizedExperiment object. This package contains data of allelic expression counts of spatial slices of a fly embryo, a Drosophila melanogaster x Drosophila simulans cross. See the CITATION file for the data source, and the associated script for how the object was constructed from publicly available data. biocViews: ExperimentHub, SequencingData, RNASeqData, ExpressionData, Drosophila_melanogaster_Data, GEO Author: Michael Love [aut, cre] Maintainer: Michael Love URL: https://github.com/mikelove/spatialDmelxsim VignetteBuilder: knitr BugReports: https://github.com/mikelove/spatialDmelxsim/issues git_url: https://git.bioconductor.org/packages/spatialDmelxsim git_branch: RELEASE_3_22 git_last_commit: 28f7c76 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/spatialDmelxsim_1.16.0.tar.gz vignettes: vignettes/spatialDmelxsim/inst/doc/spatialDmelxsim.html vignetteTitles: spatialDmelxsim hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/spatialDmelxsim/inst/doc/spatialDmelxsim.R dependencyCount: 76 Package: spatialLIBD Version: 1.22.0 Depends: SpatialExperiment (>= 1.3.3), R (>= 4.1) Imports: shiny, golem, ggplot2, cowplot, plotly, viridisLite, shinyWidgets, sessioninfo, grid, grDevices, methods, AnnotationHub, utils, png, scater, DT, ExperimentHub, SummarizedExperiment, stats, graphics, S4Vectors, IRanges, benchmarkme, SingleCellExperiment, BiocFileCache, jsonlite, tibble, rtracklayer, Matrix, BiocGenerics, GenomicRanges, magick, paletteer, scuttle, edgeR, limma, statmod, MatrixGenerics, rlang, dplyr, ComplexHeatmap, circlize Suggests: knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager, lobstr, DropletUtils, RColorBrewer License: Artistic-2.0 MD5sum: 5aa5d66b262ee59cf820941ea4da7567 NeedsCompilation: no Title: spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data Description: Inspect interactively the spatially-resolved transcriptomics data from the 10x Genomics Visium platform as well as data from the Maynard, Collado-Torres et al, Nature Neuroscience, 2021 project analyzed by Lieber Institute for Brain Development (LIBD) researchers and collaborators. biocViews: Homo_sapiens_Data, ExperimentHub, SequencingData, SingleCellData, ExpressionData, Tissue, PackageTypeData, SpatialData Author: Leonardo Collado-Torres [aut, cre] (ORCID: ), Kristen R. Maynard [ctb] (ORCID: ), Andrew E. Jaffe [ctb] (ORCID: ), Brenda Pardo [ctb] (ORCID: ), Abby Spangler [ctb] (ORCID: ), Jesús Vélez Santiago [ctb] (ORCID: ), Lukas M. Weber [ctb] (ORCID: ), Louise Huuki-Myers [ctb] (ORCID: ), Nicholas Eagles [ctb] (ORCID: ) Maintainer: Leonardo Collado-Torres URL: https://github.com/LieberInstitute/spatialLIBD VignetteBuilder: knitr BugReports: https://support.bioconductor.org/tag/spatialLIBD git_url: https://git.bioconductor.org/packages/spatialLIBD git_branch: RELEASE_3_22 git_last_commit: d06d43c git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/spatialLIBD_1.22.0.tar.gz vignettes: vignettes/spatialLIBD/inst/doc/guide_to_spatial_registration.html, vignettes/spatialLIBD/inst/doc/multi_gene_plots.html, vignettes/spatialLIBD/inst/doc/spatialLIBD.html, vignettes/spatialLIBD/inst/doc/TenX_data_download.html vignetteTitles: Guide to Spatial Registration, Guide to Multi-Gene Plots, Introduction to spatialLIBD, Using spatialLIBD with 10x Genomics public datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/spatialLIBD/inst/doc/guide_to_spatial_registration.R, vignettes/spatialLIBD/inst/doc/multi_gene_plots.R, vignettes/spatialLIBD/inst/doc/spatialLIBD.R, vignettes/spatialLIBD/inst/doc/TenX_data_download.R importsMe: DeconvoBuddies, visiumStitched, OSTA suggestsMe: Banksy, BatchSVG, BayesSpace, DESpace dependencyCount: 198 Package: SpikeIn Version: 1.52.0 Depends: R (>= 2.10), affy (>= 1.23.4) License: Artistic-2.0 MD5sum: d0fa73dfa0d85ed3b1c314891673d23e NeedsCompilation: no Title: Affymetrix Spike-In Experiment Data Description: Contains the HGU133 and HGU95 spikein experiment data. biocViews: ExperimentData, MicroarrayData Author: Rafael Irizarry Maintainer: Robert D Shear URL: https://bioconductor.org/packages/SpikeIn BugReports: https://github.com/rafalab/SpikeIn/issues git_url: https://git.bioconductor.org/packages/SpikeIn git_branch: RELEASE_3_22 git_last_commit: 9367cd3 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/SpikeIn_1.52.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PECA dependencyCount: 12 Package: SpikeInSubset Version: 1.50.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5), affy (>= 1.23.4) License: LGPL MD5sum: a51be81476b060e9d66e42c9deb0bd9d NeedsCompilation: no Title: Part of Affymetrix's Spike-In Experiment Data Description: Includes probe-level and expression data for the HGU133 and HGU95 spike-in experiments biocViews: ExperimentData, MicroarrayData Author: Rafael Irizarry and Zhijin Wu Maintainer: Robert D Shear URL: https://bioconductor.org/packages/SpikeInSubset BugReports: https://github.com/rafalab/SpikeInSubset/issues git_url: https://git.bioconductor.org/packages/SpikeInSubset git_branch: RELEASE_3_22 git_last_commit: 33c8bf1 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/SpikeInSubset_1.50.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 12 Package: spqnData Version: 1.22.0 Depends: R (>= 4.0), SummarizedExperiment License: Artistic-2.0 MD5sum: 502e2cc83ac8a5dd46b94cc3875f396a NeedsCompilation: no Title: Data for the spqn package Description: Bulk RNA-seq from GTEx on 4,000 randomly selected, expressed genes. Data has been processed for co-expression analysis. biocViews: Homo_sapiens_Data, ExpressionData, Tissue, RNASeqData Author: Yi Wang [cre, aut], Kasper Daniel Hansen [aut] Maintainer: Yi Wang git_url: https://git.bioconductor.org/packages/spqnData git_branch: RELEASE_3_22 git_last_commit: 30ae52d git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/spqnData_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: spqn dependencyCount: 25 Package: stemHypoxia Version: 1.46.0 Depends: R (>= 2.14.1) License: GPL (>=2) MD5sum: fe14af38cd074d51cc3b649e7ce5c7ff NeedsCompilation: no Title: Differentiation of Human Embryonic Stem Cells under Hypoxia gene expression dataset by Prado-Lopez et al. (2010) Description: Expression profiling using microarray technology to prove if 'Hypoxia Promotes Efficient Differentiation of Human Embryonic Stem Cells to Functional Endothelium' by Prado-Lopez et al. (2010) Stem Cells 28:407-418. Full data available at Gene Expression Omnibus series GSE37761. biocViews: ExperimentData, Tissue, StemCell, Homo_sapiens_Data, CancerData, MicroarrayData, TissueMicroarrayData, GEO Author: Cristobal Fresno and Elmer A. Fernandez Maintainer: Cristobal Fresno URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37761, http://onlinelibrary.wiley.com/doi/10.1002/stem.295/abstract git_url: https://git.bioconductor.org/packages/stemHypoxia git_branch: RELEASE_3_22 git_last_commit: 4100dd4 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/stemHypoxia_1.46.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: lmdme dependencyCount: 0 Package: STexampleData Version: 1.18.0 Depends: ExperimentHub, SingleCellExperiment, SpatialExperiment Imports: utils Suggests: BiocStyle, knitr, rmarkdown, BumpyMatrix, HDF5Array License: MIT + file LICENSE MD5sum: c324e1fc1c3bfd06c5f6b095ff5e5df4 NeedsCompilation: no Title: Collection of spatial transcriptomics datasets in SpatialExperiment Bioconductor format Description: Collection of spatial transcriptomics datasets stored in SpatialExperiment Bioconductor format, for use in examples, demonstrations, and tutorials. The datasets are from several different platforms and have been sourced from various publicly available sources. Several datasets include images and/or reference annotation labels. biocViews: ExperimentData, ExperimentHub, ReproducibleResearch, ExpressionData, SingleCellData, SpatialData, Homo_sapiens_Data, Mus_musculus_Data Author: Lukas M. Weber [aut, cre] (ORCID: ), Yixing E. Dong [aut] (ORCID: ) Maintainer: Lukas M. Weber URL: https://github.com/lmweber/STexampleData VignetteBuilder: knitr BugReports: https://github.com/lmweber/STexampleData/issues git_url: https://git.bioconductor.org/packages/STexampleData git_branch: RELEASE_3_22 git_last_commit: 2819726 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/STexampleData_1.18.0.tar.gz vignettes: vignettes/STexampleData/inst/doc/STexampleData_overview.html vignetteTitles: STexampleData overview hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/STexampleData/inst/doc/STexampleData_overview.R importsMe: OSTA suggestsMe: BulkSignalR, escheR, ggsc, ggspavis, nnSVG, poem, smoothclust, spatialSimGP, spoon, SpotSweeper, SVP, tpSVG dependencyCount: 81 Package: SubcellularSpatialData Version: 1.6.0 Depends: R (>= 4.4) Imports: dplyr, hexbin, Matrix, SpatialExperiment, stats Suggests: BiocStyle, ExperimentHub, ggplot2, knitr, prettydoc, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: 4f1ce0b473f994c73bbf0edd8b18118e NeedsCompilation: no Title: Annotated spatial transcriptomics datasets from 10x Xenium, NanoString CosMx and BGI STOmics. Description: This is a data package that hosts annotated sub-cellular localised datasets from the STOmics, Xenium and CosMx platforms. Specifically, it hosts datasets analysed in the publication Bhuva et. al, 2024 titled "Library size confounds biology in spatial transcriptomics data". Raw transcript detections are hosted and functions to convert them to SpatialExperiment objects have been implemented. biocViews: ExperimentHub, SpatialData, Homo_sapiens_Data, Mus_musculus_Data, LungCancerData Author: Dharmesh D. Bhuva [aut, cre] (ORCID: ) Maintainer: Dharmesh D. Bhuva URL: https://davislaboratory.github.io/SubcellularSpatialData VignetteBuilder: knitr BugReports: https://github.com/DavisLaboratory/SubcellularSpatialData/issues git_url: https://git.bioconductor.org/packages/SubcellularSpatialData git_branch: RELEASE_3_22 git_last_commit: f596e4d git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/SubcellularSpatialData_1.6.0.tar.gz vignettes: vignettes/SubcellularSpatialData/inst/doc/SubcellularSpatialData.html vignetteTitles: SubcellularSpatialData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SubcellularSpatialData/inst/doc/SubcellularSpatialData.R dependencyCount: 68 Package: SVM2CRMdata Version: 1.42.0 Depends: R(>= 3.2.0) License: LGPL (>= 2) MD5sum: 02e9e165b50788fdaaebbac111d822a7 NeedsCompilation: no Title: An example dataset for use with the SVM2CRM package Description: An example dataset for use with the SVM2CRM package. biocViews: ExperimentData, ChIPSeq, HistoneModification, Preprocessing, DataImport Author: Guidantonio Malagoli Tagliazucchi Maintainer: Guidantonio Malagoli Tagliazucchi git_url: https://git.bioconductor.org/packages/SVM2CRMdata git_branch: RELEASE_3_22 git_last_commit: 3100a16 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/SVM2CRMdata_1.42.0.tar.gz vignettes: vignettes/SVM2CRMdata/inst/doc/SVM2CRMdata.pdf vignetteTitles: The \Rpackage{SVM2CRMdata} Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SVM2CRMdata/inst/doc/SVM2CRMdata.R dependencyCount: 0 Package: systemPipeRdata Version: 2.14.0 Depends: R (>= 3.6.0) Imports: methods, Biostrings, BiocGenerics, jsonlite, remotes Suggests: GenomicFeatures, GenomicRanges, IRanges, Rsamtools, ShortRead, rtracklayer, RUnit, BiocStyle, knitr, rmarkdown, systemPipeR, kableExtra, magrittr, dplyr License: Artistic-2.0 MD5sum: dafa6204afb177d9d9888dc114ea2aaf NeedsCompilation: no Title: systemPipeRdata: Workflow templates and sample data Description: systemPipeRdata complements the systemPipeR workflow management system (WMS) by offering a collection of pre-designed data analysis workflow templates. These templates are easily accessible and can be readily loaded onto a user's system with a single command. Once loaded, the WMS can immediately utilize these templates for efficient end-to-end analysis, serving a wide range of data analysis needs. biocViews: Genetics, Infrastructure, DataImport, Sequencing, RNASeq, ChIPSeq, MethylSeq, SNP, GeneExpression, Coverage, GeneSetEnrichment, Alignment, QualityControl, ImmunoOncology, RiboSeq, WorkflowStep Author: Thomas Girke Maintainer: Thomas Girke URL: https://github.com/tgirke/systemPipeRdata VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/systemPipeRdata git_branch: RELEASE_3_22 git_last_commit: 388f9b8 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/systemPipeRdata_2.14.0.tar.gz vignettes: vignettes/systemPipeRdata/inst/doc/new.html, vignettes/systemPipeRdata/inst/doc/SPblast.html, vignettes/systemPipeRdata/inst/doc/SPcheminfo.html, vignettes/systemPipeRdata/inst/doc/SPscrna.html, vignettes/systemPipeRdata/inst/doc/systemPipeChIPseq.html, vignettes/systemPipeRdata/inst/doc/systemPipeRdata.html, vignettes/systemPipeRdata/inst/doc/systemPipeRIBOseq.html, vignettes/systemPipeRdata/inst/doc/systemPipeRNAseq.html, vignettes/systemPipeRdata/inst/doc/systemPipeVARseq.html vignetteTitles: WF: Basic Generic Template, WF: BLAST Template, WF: Cheminformatics Drug Similarity Template, WF: Basic Single Cell Template, WF: ChIP-Seq Workflow Template, systemPipeRdata: Workflow templates and sample data, WF: RIBO-Seq Workflow Template, WF: RNA-Seq Workflow Template, WF: VAR-Seq Template hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/systemPipeRdata/inst/doc/new.R, vignettes/systemPipeRdata/inst/doc/SPblast.R, vignettes/systemPipeRdata/inst/doc/SPcheminfo.R, vignettes/systemPipeRdata/inst/doc/SPscrna.R, vignettes/systemPipeRdata/inst/doc/systemPipeChIPseq.R, vignettes/systemPipeRdata/inst/doc/systemPipeRdata.R, vignettes/systemPipeRdata/inst/doc/systemPipeRIBOseq.R, vignettes/systemPipeRdata/inst/doc/systemPipeRNAseq.R, vignettes/systemPipeRdata/inst/doc/systemPipeVARseq.R suggestsMe: systemPipeR, systemPipeShiny dependencyCount: 17 Package: TabulaMurisData Version: 1.28.0 Depends: R (>= 3.5) Imports: ExperimentHub, utils Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran, scater, iSEE, testthat License: MIT + file LICENSE MD5sum: f9b42bced5b21ff1f994692871369c56 NeedsCompilation: no Title: 10x And SmartSeq2 Data From The Tabula Muris Consortium Description: Access to processed 10x (droplet) and SmartSeq2 (on FACS-sorted cells) single-cell RNA-seq data from the Tabula Muris consortium (http://tabula-muris.ds.czbiohub.org/). biocViews: SingleCellData, ExperimentData, RNASeqData Author: Charlotte Soneson [aut, cre] (ORCID: ) Maintainer: Charlotte Soneson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TabulaMurisData git_branch: RELEASE_3_22 git_last_commit: 0fbb88d git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/TabulaMurisData_1.28.0.tar.gz vignettes: vignettes/TabulaMurisData/inst/doc/TabulaMurisData.html vignetteTitles: Tabula Muris data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TabulaMurisData/inst/doc/TabulaMurisData.R dependencyCount: 65 Package: TabulaMurisSenisData Version: 1.16.0 Imports: ExperimentHub, SingleCellExperiment, HDF5Array, SummarizedExperiment, gdata, AnnotationHub Suggests: ggplot2, testthat, knitr, rmarkdown, iSEE, BiocStyle License: MIT + file LICENSE MD5sum: e92ec5d004026b6583dce1519fac5457 NeedsCompilation: no Title: Bulk and single-cell RNA-seq data from the Tabula Muris Senis project Description: This package provides access to RNA-seq data generated by the Tabula Muris Senis project via the Bioconductor project. The data is made available without restrictions by the Chan Zuckerberg Biohub. It is provided here without further processing, collected in the form of SingleCellExperiment objects. biocViews: SingleCellData, ExperimentData, RNASeqData, ExperimentHub Author: Charlotte Soneson [aut, cre] (ORCID: ), Dania Machlab [aut] (ORCID: ), Federico Marini [aut] (ORCID: ), Stefania Astrologo [aut] (ORCID: ) Maintainer: Charlotte Soneson URL: https://github.com/fmicompbio/TabulaMurisSenisData VignetteBuilder: knitr BugReports: https://github.com/fmicompbio/TabulaMurisSenisData/issues git_url: https://git.bioconductor.org/packages/TabulaMurisSenisData git_branch: RELEASE_3_22 git_last_commit: 5a0bd7a git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/TabulaMurisSenisData_1.16.0.tar.gz vignettes: vignettes/TabulaMurisSenisData/inst/doc/TabulaMurisSenisData.html vignetteTitles: TabulaMurisSenisData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TabulaMurisSenisData/inst/doc/TabulaMurisSenisData.R suggestsMe: SETA, SPOTlight dependencyCount: 84 Package: TargetScoreData Version: 1.46.0 Suggests: TargetScore, gplots License: GPL-2 MD5sum: fcfa48b7647edf6d69bbab6ae728a412 NeedsCompilation: no Title: TargetScoreData Description: Precompiled and processed miRNA-overexpression fold-changes from 84 Gene Expression Omnibus (GEO) series corresponding to 6 platforms, 77 human cells or tissues, and 113 distinct miRNAs. Accompanied with the data, we also included in this package the sequence feature scores from TargetScanHuman 6.1 including the context+ score and the probabilities of conserved targeting for each miRNA-mRNA interaction. Thus, the user can use these static sequence-based scores together with user-supplied tissue/cell-specific fold-change due to miRNA overexpression to predict miRNA targets using the package TargetScore (download separately) biocViews: ExperimentData, RNASeqData, miRNAData Author: Yue Li Maintainer: Yue Li git_url: https://git.bioconductor.org/packages/TargetScoreData git_branch: RELEASE_3_22 git_last_commit: 9090a03 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/TargetScoreData_1.46.0.tar.gz vignettes: vignettes/TargetScoreData/inst/doc/TargetScoreData.pdf vignetteTitles: Processed human microRNA-overexpression data from GEO,, and sequence information from TargetScan,, and targetScore from TargetScore hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TargetScoreData/inst/doc/TargetScoreData.R suggestsMe: TargetScore dependencyCount: 0 Package: TargetSearchData Version: 1.48.0 License: GPL (>= 2) MD5sum: b3a941511571ca158665cc92c80de8a0 NeedsCompilation: no Title: Example GC-MS data for TargetSearch Package Description: Example files of GC-MS data for the TargetSearch Package. The package contains raw NetCDF files from a E.coli salt stress experiment, extracted peak lists, and sample metadata required for a GC-MS analysis. The raw data has been restricted for demonstration purposes. biocViews: ExperimentData, Escherichia_coli_Data Author: Alvaro Cuadros-Inostroza [aut, cre], Jan Lisec [aut], Henning Redestig [aut], Matt Hannah [aut] Maintainer: Alvaro Cuadros-Inostroza URL: https://github.com/acinostroza/TargetSearchData BugReports: https://github.com/acinostroza/TargetSearchData/issues git_url: https://git.bioconductor.org/packages/TargetSearchData git_branch: RELEASE_3_22 git_last_commit: b687cef git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/TargetSearchData_1.48.0.tar.gz vignettes: vignettes/TargetSearchData/inst/doc/TargetSearchData.pdf vignetteTitles: The TargetSearchData Package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TargetSearchData/inst/doc/TargetSearchData.R suggestsMe: TargetSearch dependencyCount: 0 Package: tartare Version: 1.24.0 Depends: R (>= 4.1), AnnotationHub (>= 2.16), ExperimentHub (>= 1.0) Imports: utils Suggests: BiocStyle, knitr, rmarkdown, testthat, tools License: GPL-3 MD5sum: 84990105a98a575e6d46c90a71717c2e NeedsCompilation: no Title: Raw ground spectra recorded on Thermo Fisher Scientific mass spectrometers Description: Provides raw files recorded on different Liquid Chromatography Mass Spectrometry (LC-MS) instruments. All included MS instruments are manufactured by Thermo Fisher Scientific and belong to the Orbitrap Tribrid or Q Exactive Orbitrap family of instruments. Despite their common origin and shared hardware components, e.g., Orbitrap mass analyser, the above instruments tend to write data in different "dialects" in a shared binary file format (.raw). The intention behind tartare is to provide complex but slim real-world files that can be used to make code robust with respect to this diversity. In other words, it is intended for enhanced unit testing. The package is considered to be used with the rawrr package and the Spectra MsBackends. biocViews: ExperimentData, MassSpectrometryData, ExperimentHub Author: Christian Panse [aut, cre] (ORCID: ), Tobias Kockmann [aut] (ORCID: ) Maintainer: Christian Panse URL: https://github.com/cpanse/tartare VignetteBuilder: knitr BugReports: https://github.com/cpanse/tartare/issues git_url: https://git.bioconductor.org/packages/tartare git_branch: RELEASE_3_22 git_last_commit: f1dc67a git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/tartare_1.24.0.tar.gz vignettes: vignettes/tartare/inst/doc/tartare.html vignetteTitles: make and use tartare data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tartare/inst/doc/tartare.R suggestsMe: MsBackendRawFileReader, rawDiag, rawrr dependencyCount: 65 Package: TBX20BamSubset Version: 1.46.0 Depends: Rsamtools (>= 1.9.8) Imports: xtable License: LGPL MD5sum: 643ae75fef853bb1653fe8dc0cc66f8d NeedsCompilation: no Title: Subset of BAM files from the "TBX20" experiment Description: Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. A subset of the RNA-Seq data. biocViews: ExperimentData, SequencingData, RNASeqData Author: D. Bindreither Maintainer: D. Bindreither git_url: https://git.bioconductor.org/packages/TBX20BamSubset git_branch: RELEASE_3_22 git_last_commit: 815d015 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/TBX20BamSubset_1.46.0.tar.gz vignettes: vignettes/TBX20BamSubset/inst/doc/TBX20BamSubset.pdf vignetteTitles: TBX20 RNA-Seq data subset hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TBX20BamSubset/inst/doc/TBX20BamSubset.R importsMe: Rmmquant suggestsMe: magpie dependencyCount: 30 Package: TCGAbiolinksGUI.data Version: 1.30.0 Depends: R (>= 3.5.0) Suggests: BiocStyle, knitr, rmarkdown, readr, DT License: GPL-3 MD5sum: 9bc34b80673f6e1e25a5435bcc7b4a1a NeedsCompilation: no Title: Data for the TCGAbiolinksGUI package Description: Supporting data for the TCGAbiolinksGUI package. biocViews: AssayDomainData, TechnologyData, OrganismData Author: Tiago Chedraoui Silva Maintainer: Tiago Chedraoui Silva URL: https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data VignetteBuilder: knitr BugReports: https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data/issues git_url: https://git.bioconductor.org/packages/TCGAbiolinksGUI.data git_branch: RELEASE_3_22 git_last_commit: 985dc7c git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/TCGAbiolinksGUI.data_1.30.0.tar.gz vignettes: vignettes/TCGAbiolinksGUI.data/inst/doc/vignettes.html vignetteTitles: Supporting data for the TCGAbiolinksGUI package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TCGAbiolinksGUI.data/inst/doc/vignettes.R importsMe: TCGAbiolinks dependencyCount: 0 Package: TCGAcrcmiRNA Version: 1.30.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: cdf5c0a187e5b0f4f9520d1ac02d5c3d NeedsCompilation: no Title: TCGA CRC 450 miRNA dataset Description: colorectal cancer miRNA profile provided by TCGA biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/TCGAcrcmiRNA git_branch: RELEASE_3_22 git_last_commit: fc0a6ef git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/TCGAcrcmiRNA_1.30.0.tar.gz vignettes: vignettes/TCGAcrcmiRNA/inst/doc/TcgaCrcVignette.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TCGAcrcmiRNA/inst/doc/TcgaCrcVignette.R dependencyCount: 7 Package: TCGAcrcmRNA Version: 1.30.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 52d49d0ad0ee8c2d1007c153d8de6e7f NeedsCompilation: no Title: TCGA CRC 450 mRNA dataset Description: colorectal cancer mRNA profile provided by TCGA biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/TCGAcrcmRNA git_branch: RELEASE_3_22 git_last_commit: ae085f4 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/TCGAcrcmRNA_1.30.0.tar.gz vignettes: vignettes/TCGAcrcmRNA/inst/doc/TcgaCrcVignette.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TCGAcrcmRNA/inst/doc/TcgaCrcVignette.R dependencyCount: 7 Package: TCGAMethylation450k Version: 1.46.0 License: GPL-2 MD5sum: 9d554691f250808d6ad61c76e47cfee0 NeedsCompilation: no Title: The Cancer Genome Atlas Illumina 450k methylation example data Description: The Cancer Genome Atlas (TCGA) is applying genomics technologies to over 20 different types of cancer. This package contains a small set of 450k array data in idat format. biocViews: Genome, CancerData, MethylationArrayData Author: Sean Davis Maintainer: Sean Davis git_url: https://git.bioconductor.org/packages/TCGAMethylation450k git_branch: RELEASE_3_22 git_last_commit: f7532f0 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/TCGAMethylation450k_1.46.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: methylumi dependencyCount: 0 Package: TCGAWorkflowData Version: 1.34.0 Depends: R (>= 3.5.0) Imports: SummarizedExperiment Suggests: knitr, rmarkdown, pander, testthat, BiocStyle License: GPL-3 MD5sum: d93ece4f65703d800b404e94e12b0c74 NeedsCompilation: no Title: Data for TCGA Workflow Description: This experimental data package contains 11 data sets necessary to follow the "TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages". biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData, CancerData Author: Tiago Chedraoui Silva Maintainer: Tiago Chedraoui Silva URL: https://f1000research.com/articles/5-1542/v2 VignetteBuilder: knitr BugReports: https://github.com/BioinformaticsFMRP/TCGAWorkflow/issues git_url: https://git.bioconductor.org/packages/TCGAWorkflowData git_branch: RELEASE_3_22 git_last_commit: 25ba292 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/TCGAWorkflowData_1.34.0.tar.gz vignettes: vignettes/TCGAWorkflowData/inst/doc/TCGAWorkflowData.html vignetteTitles: 'Example data for TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages' hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TCGAWorkflowData/inst/doc/TCGAWorkflowData.R dependencyCount: 25 Package: TENET.ExperimentHub Version: 1.2.0 Depends: R (>= 4.5), ggplot2 (>= 4.0) Imports: ExperimentHub, SummarizedExperiment, MultiAssayExperiment, GenomicRanges, methods Suggests: TENET, ExperimentHubData, testthat (>= 3.0.0), BiocManager, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 0f8c9341a86697b49ed969e879d24e45 NeedsCompilation: no Title: Experiment data for the TENET package Description: ExperimentHub package containing datasets for use in the TENET package's vignette and function examples. These include a variety of different objects to illustrate different datasets used in TENET functions. Where applicable, all datasets are aligned to the hg38 human genome. biocViews: ExperimentHub, ExperimentData, Homo_sapiens_Data, CancerData, BreastCancerData, MicroarrayData, ExpressionData, RNASeqData, MethylationArrayData, Genome, CellCulture, Tissue Author: Rhie Lab at the University of Southern California [cre], Daniel Mullen [aut] (ORCID: ), Zexun Wu [aut] (ORCID: ), Ethan Nelson-Moore [aut] (ORCID: ), Suhn Rhie [aut] (ORCID: ) Maintainer: Rhie Lab at the University of Southern California URL: https://github.com/rhielab/TENET.ExperimentHub VignetteBuilder: knitr BugReports: https://github.com/rhielab/TENET.ExperimentHub/issues git_url: https://git.bioconductor.org/packages/TENET.ExperimentHub git_branch: RELEASE_3_22 git_last_commit: e681368 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/TENET.ExperimentHub_1.2.0.tar.gz vignettes: vignettes/TENET.ExperimentHub/inst/doc/TENET.ExperimentHub_vignette.html vignetteTitles: Using the TENET.ExperimentHub datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TENET.ExperimentHub/inst/doc/TENET.ExperimentHub_vignette.R importsMe: TENET dependencyCount: 86 Package: TENxBrainData Version: 1.30.0 Depends: SingleCellExperiment, HDF5Array Imports: AnnotationHub (>= 2.9.22), ExperimentHub Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel, data.table, rmarkdown License: CC BY 4.0 MD5sum: be8fa8d7b1c3fb8576fedd459d2b7ebb NeedsCompilation: no Title: Data from the 10X 1.3 Million Brain Cell Study Description: Single-cell RNA-seq data for 1.3 million brain cells from E18 mice, generated by 10X Genomics. biocViews: SequencingData, RNASeqData, ExpressionData, SingleCellData Author: Aaron Lun [aut], Martin Morgan [aut], Bioconductor Package Maintainer [cre] Maintainer: Bioconductor Package Maintainer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TENxBrainData git_branch: RELEASE_3_22 git_last_commit: 185f337 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/TENxBrainData_1.30.0.tar.gz vignettes: vignettes/TENxBrainData/inst/doc/TENxBrainData.html vignetteTitles: Exploring the 1.3 million brain cell scRNA-seq data from 10X Genomics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TENxBrainData/inst/doc/TENxBrainData.R dependsOnMe: OSCA.advanced suggestsMe: h5mread, HDF5Array dependencyCount: 82 Package: TENxBUSData Version: 1.24.0 Imports: ExperimentHub, AnnotationHub, utils, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle License: BSD_2_clause + file LICENSE MD5sum: 2aa465ba53fe61cea788aaabf22f01bb NeedsCompilation: no Title: Single cell dataset from 10x in BUS format Description: Download Barcode, UMI, and Set (BUS) format of 10x datasets from within R. This package accompanies the package BUSpaRse, which can load BUS format into R as a sparse matrix, and which has utility functions related to using the C++ command line package bustools. biocViews: SingleCellData, SequencingData, ExperimentHub, ExperimentData, ExpressionData Author: Lambda Moses [aut, cre] (ORCID: ) Maintainer: Lambda Moses URL: https://github.com/BUStools/TENxBUSData VignetteBuilder: knitr BugReports: https://github.com/BUStools/TENxBUSData/issues git_url: https://git.bioconductor.org/packages/TENxBUSData git_branch: RELEASE_3_22 git_last_commit: f0a01ef git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/TENxBUSData_1.24.0.tar.gz vignettes: vignettes/TENxBUSData/inst/doc/downloading-10x-hgmm-data.html vignetteTitles: Downloading BUS data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TENxBUSData/inst/doc/downloading-10x-hgmm-data.R suggestsMe: BUSpaRse dependencyCount: 65 Package: TENxPBMCData Version: 1.28.0 Depends: SingleCellExperiment, HDF5Array Imports: AnnotationHub, ExperimentHub Suggests: rmarkdown, knitr, BiocStyle, snow, BiocFileCache, BiocParallel License: CC BY 4.0 MD5sum: 441ad05a194d2adccc086db6bb20497a NeedsCompilation: no Title: PBMC data from 10X Genomics Description: Single-cell RNA-seq data for on PBMC cells, generated by 10X Genomics. biocViews: SequencingData, RNASeqData, ExpressionData, ExperimentHub, ExperimentData, SingleCellData Author: Kasper D. Hansen [aut], Davide Risso [aut], Milan Malfait [ctb], Jeroen Gilis [ctb], Theodore Killian [ctb], Murat Cem Kose [ctb], Chong Tang [ctb], Teun van den Brand [ctb], Dania Machlab [ctb], Stephanie Hicks [aut, cre] Maintainer: Stephanie Hicks VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TENxPBMCData git_branch: RELEASE_3_22 git_last_commit: 11a0abc git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/TENxPBMCData_1.28.0.tar.gz vignettes: vignettes/TENxPBMCData/inst/doc/TENxPBMCData.html vignetteTitles: Obtaining scRNA-seq data on PBMCs from 10X Genomics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TENxPBMCData/inst/doc/TENxPBMCData.R dependsOnMe: OSCA.multisample, SingleRBook importsMe: singleCellTK suggestsMe: adverSCarial, ASURAT, celda, concordexR, decontX, ExperimentSubset, glmGamPoi, GSVA, iSEE, mbkmeans, scGraphVerse, schex, scone, scry, sketchR, transformGamPoi dependencyCount: 82 Package: TENxVisiumData Version: 1.18.0 Depends: ExperimentHub, SpatialExperiment Imports: utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: a220e92e705d58fae5f9baf644021f4a NeedsCompilation: no Title: Visium spatial gene expression data by 10X Genomics Description: Collection of Visium spatial gene expression datasets by 10X Genomics, formatted into objects of class SpatialExperiment. Data cover various organisms and tissues, and include: single- and multi-section experiments, as well as single sections subjected to both whole transcriptome and targeted panel analysis. Datasets may be used for testing of and as examples in packages, for tutorials and workflow demonstrations, or similar purposes. biocViews: ExperimentHub, ExpressionData, ExperimentData, Homo_sapiens_Data, Mus_musculus_Data, ReproducibleResearch Author: Helena L. Crowell [aut, cre] (ORCID: ) Maintainer: Helena L. Crowell URL: https://github.com/helenalc/TENxVisiumData VignetteBuilder: knitr BugReports: https://github.com/helenalc/TENxVisiumData/issues git_url: https://git.bioconductor.org/packages/TENxVisiumData git_branch: RELEASE_3_22 git_last_commit: a24265a git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/TENxVisiumData_1.18.0.tar.gz vignettes: vignettes/TENxVisiumData/inst/doc/vignette.html vignetteTitles: TENxVisiumData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TENxVisiumData/inst/doc/vignette.R suggestsMe: SPOTlight dependencyCount: 81 Package: TENxXeniumData Version: 1.6.0 Depends: ExperimentHub Imports: SpatialExperiment, SpatialFeatureExperiment, BumpyMatrix, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 788d348360bc26683061d2fadfdfc2f3 NeedsCompilation: no Title: Collection of Xenium spatial data by 10X genomics Description: Collection of Xenium spatial transcriptomics datasets provided by 10x Genomics, formatted into the Bioconductor classes, the SpatialExperiment or SpatialFeatureExperiment (SFE), to facilitate seamless integration into various applications, including examples, demonstrations, and tutorials. The constructed data objects include gene expression profiles, per-transcript location data, centroid, segmentation boundaries (e.g., cell or nucleus boundaries), and image. biocViews: ExperimentData, ExperimentHub, SpatialData Author: Matineh Rahmatbakhsh [aut, cre], Monica Ge [aut] Maintainer: Matineh Rahmatbakhsh URL: https://github.com/mrbakhsh/TENxXeniumData VignetteBuilder: knitr BugReports: https://github.com/mrbakhsh/TENxXeniumData/issues git_url: https://git.bioconductor.org/packages/TENxXeniumData git_branch: RELEASE_3_22 git_last_commit: ce89f83 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/TENxXeniumData_1.6.0.tar.gz vignettes: vignettes/TENxXeniumData/inst/doc/TENxXeniumData.html vignetteTitles: TENxXeniumData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TENxXeniumData/inst/doc/TENxXeniumData.R suggestsMe: jazzPanda dependencyCount: 165 Package: timecoursedata Version: 1.20.0 Depends: R (>= 4.0), SummarizedExperiment Suggests: testthat (>= 1.0.0), knitr, rmarkdown, markdown, covr, BiocStyle License: BSD 3-clause License + file LICENSE MD5sum: 8084bb0cab948fed4a43e05a5ca21388 NeedsCompilation: no Title: A data package for timecourse RNA-seq and microarray gene expression data sets Description: This data package contains timecourse gene expression data sets. The first dataset, from Shoemaker et al, consists of microarray samples from lung tissue of mice exposed to different influenzy strains from 14 timepoints. The two other datasets are leaf and root samples from sorghum crops exposed to pre- and post-flowering drought stress and a control condition, sampled across the plants lifetime. biocViews: ExpressionData, MicroarrayData, RNASeqData Author: Elizabeth Purdom [aut] (ORCID: ), Nelle Varoquaux [aut, cre] (ORCID: ) Maintainer: Nelle Varoquaux VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/timecoursedata git_branch: RELEASE_3_22 git_last_commit: 73ba2a1 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/timecoursedata_1.20.0.tar.gz vignettes: vignettes/timecoursedata/inst/doc/documentation.html vignetteTitles: timecoursedata: Time course gene expression datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/timecoursedata/inst/doc/documentation.R suggestsMe: moanin dependencyCount: 25 Package: TimerQuant Version: 1.39.0 Depends: shiny Imports: ggplot2, grid, gridExtra, deSolve, dplyr, locfit Suggests: BiocStyle, reshape2, knitr, shinyBS License: Artistic-2.0 MD5sum: b686aa8ae23be9eae2a83877dadf0688 NeedsCompilation: no Title: Timer Quantification Description: Supplementary Data package for tandem timer methods paper by Barry et al. (2015) including TimerQuant shiny applications. biocViews: ExperimentData, Danio_rerio_Data, HighThroughputImagingData, Tissue Author: Joseph Barry Maintainer: Joseph Barry VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TimerQuant git_branch: devel git_last_commit: 23a5364 git_last_commit_date: 2025-04-15 Date/Publication: 2025-04-17 source.ver: src/contrib/TimerQuant_1.39.0.tar.gz vignettes: vignettes/TimerQuant/inst/doc/genPaperFigures.pdf, vignettes/TimerQuant/inst/doc/mathematicalDerivations.pdf vignetteTitles: Supplementary Methods - automatic generation of paper figures, Supplementary Methods - mathematical derivations hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TimerQuant/inst/doc/genPaperFigures.R, vignettes/TimerQuant/inst/doc/mathematicalDerivations.R dependencyCount: 58 Package: tinesath1cdf Version: 1.48.0 License: Artistic-2.0 MD5sum: fd7d0e08a2af7bb77c93365b8a42ce46 NeedsCompilation: no Title: tinesath1cdf Description: A package containing an environment represeting the newcdf/tinesATH1.cdf.cdf file. biocViews: Arabidopsis_thaliana_Data, ChipOnChipData Author: Tine Casneuf Maintainer: Tine Casneuf git_url: https://git.bioconductor.org/packages/tinesath1cdf git_branch: RELEASE_3_22 git_last_commit: f4c210d git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/tinesath1cdf_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: XhybCasneuf dependencyCount: 0 Package: tinesath1probe Version: 1.48.0 Depends: R (>= 1.6), AnnotationDbi (>= 1.11.9) License: LGPL MD5sum: 2b3d421dcf8359ed83590857d2d0c81c NeedsCompilation: no Title: Probe sequence data for microarrays of type tinesath1 Description: This package was automatically created by package matchprobes version 1.4.0. The probe sequence data was obtained from http://www.affymetrix.com. biocViews: Arabidopsis_thaliana_Data, SequencingData, MicroarrayData Author: The Bioconductor Project www.bioconductor.org Maintainer: Tine Casneuf git_url: https://git.bioconductor.org/packages/tinesath1probe git_branch: RELEASE_3_22 git_last_commit: ec33445 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/tinesath1probe_1.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 43 Package: tissueTreg Version: 1.30.0 Depends: R (>= 3.5) Suggests: BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq, SummarizedExperiment, ggplot2, reshape2 License: GPL (>= 2) MD5sum: 658558f88fc56108784e033c3a895c43 NeedsCompilation: no Title: TWGBS and RNA-seq data from tissue T regulatory cells from mice Description: The package provides ready to use epigenomes (obtained from TWGBS) and transcriptomes (RNA-seq) from various tissues as obtained in the study (Delacher and Imbusch 2017, PMID: 28783152). Regulatory T cells (Treg cells) perform two distinct functions: they maintain self-tolerance, and they support organ homeostasis by differentiating into specialized tissue Treg cells. The underlying dataset characterises the epigenetic and transcriptomic modifications for specialized tissue Treg cells. biocViews: ExperimentData, Tissue, Mus_musculus_Data, SequencingData, RNASeqData Author: Charles Imbusch [aut, cre], Michael Delacher [aut], Markus Feuerer [aut], Benedikt Brors [aut] Maintainer: Charles Imbusch URL: https://github.com/cimbusch/tissueTreg VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tissueTreg git_branch: RELEASE_3_22 git_last_commit: c10eab0 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/tissueTreg_1.30.0.tar.gz vignettes: vignettes/tissueTreg/inst/doc/tissueTreg.html vignetteTitles: tissueTreg hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tissueTreg/inst/doc/tissueTreg.R suggestsMe: DMRcate dependencyCount: 0 Package: TMExplorer Version: 1.20.0 Depends: R (>= 4.1), SingleCellExperiment, BiocFileCache Imports: methods, Matrix Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 571424591e3f1afba18dbe9c53f2b32a NeedsCompilation: no Title: A Collection of Tumour Microenvironment Single-cell RNA Sequencing Datasets and Corresponding Metadata Description: This package provides a tool to search and download a collection of tumour microenvironment single-cell RNA sequencing datasets and their metadata. TMExplorer aims to act as a single point of entry for users looking to study the tumour microenvironment at the single cell level. Users can quickly search available datasets using the metadata table and then download the ones they are interested in for analysis. biocViews: CancerData, SingleCellData, RNASeqData, SequencingData, ExpressionData, GEO, PackageTypeData Author: Erik Christensen [aut, cre], Alaine Naidas [aut], David Chen [aut], Parisa Shooshtari [aut] Maintainer: Erik Christensen VignetteBuilder: knitr BugReports: https://github.com/shooshtarilab/TMExplorer/issues git_url: https://git.bioconductor.org/packages/TMExplorer git_branch: RELEASE_3_22 git_last_commit: e6877cc git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/TMExplorer_1.20.0.tar.gz vignettes: vignettes/TMExplorer/inst/doc/TMExplorer.html vignetteTitles: TMExplorer hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TMExplorer/inst/doc/TMExplorer.R dependencyCount: 63 Package: tofsimsData Version: 1.38.0 Depends: R (>= 3.2.0) Suggests: knitr, rmarkdown, tools License: GPL-3 MD5sum: 21a6263edabc22c453df0b1fd2ce7c6f NeedsCompilation: no Title: Import, process and analysis of ToF-SIMS imaging data Description: This packages contains data to be used with the 'tofsims' package. biocViews: ExperimentData, MassSpectrometry, ImagingMassSpectrometry, DataImport Author: Lorenz Gerber, Viet Mai Hoang Maintainer: Lorenz Gerber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tofsimsData git_branch: RELEASE_3_22 git_last_commit: 0519797 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/tofsimsData_1.38.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: topdownrdata Version: 1.32.0 Depends: topdownr License: GPL (>= 3) MD5sum: 752adbaadbdfd384edc37a8e16e69af4 NeedsCompilation: no Title: Example Files for the topdownr R Package Description: Example data for the topdownr package generated on a Thermo Orbitrap Fusion Lumos MS device. biocViews: ExperimentData, MassSpectrometryData Author: Sebastian Gibb [aut, cre], Pavel Shliaha [aut], Ole Nørregaard Jensen [aut] Maintainer: Sebastian Gibb URL: https://codeberg.org/sgibb/topdownrdata/ BugReports: https://codeberg.org/sgibb/topdownrdata/issues/ git_url: https://git.bioconductor.org/packages/topdownrdata git_branch: RELEASE_3_22 git_last_commit: 50139a6 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/topdownrdata_1.32.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: topdownr dependencyCount: 134 Package: TransOmicsData Version: 1.6.0 Imports: S4Vectors, utils Suggests: BiocStyle, knitr, rmarkdown, RefManageR, sessioninfo, testthat, ExperimentHub License: GPL-3 + file LICENSE MD5sum: d2a174c02da66d1e5c56f7ecea575343 NeedsCompilation: no Title: A collection of trans-omics datasets across various biological systems Description: Contains a collection of trans-omics datasets generated using various sequencing technologies such as RNA-seq, Mass spectrometry and ChIP-seq. Modalities include the bulk profiling of the phosphoproteome, proteome, transcriptome and epigenome. Data reflects the timecourses of different developmental systems from the mouse or human. biocViews: ExperimentHub, MassSpectrometryData, RNASeqData, ChIPSeqData, Tissue, SequencingData Author: Carissa Chen [aut] (ORCID: ), Di Xiao [aut, cre] (ORCID: ), Pengyi Yang [aut] (ORCID: ) Maintainer: Di Xiao URL: https://github.com/PYangLab/TransOmicsData VignetteBuilder: knitr BugReports: https://support.bioconductor.org/t/TransOmicsData git_url: https://git.bioconductor.org/packages/TransOmicsData git_branch: RELEASE_3_22 git_last_commit: 848dce3 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/TransOmicsData_1.6.0.tar.gz vignettes: vignettes/TransOmicsData/inst/doc/TransOmicsData-vignette.html vignetteTitles: TransOmicsData: A collection of trans-omics datasets across various biological systems hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TransOmicsData/inst/doc/TransOmicsData-vignette.R dependencyCount: 8 Package: tuberculosis Version: 1.16.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: AnnotationHub, ExperimentHub, S4Vectors, dplyr, magrittr, purrr, rlang, stringr, tibble, tidyr Suggests: BiocStyle, ggplot2, knitr, readr, rmarkdown, scater, usethis, utils License: Artistic-2.0 MD5sum: f5420af4bd0f60062bc566e4e1cd1575 NeedsCompilation: no Title: Tuberculosis Gene Expression Data for Machine Learning Description: The tuberculosis R/Bioconductor package features tuberculosis gene expression data for machine learning. All human samples from GEO that did not come from cell lines, were not taken postmortem, and did not feature recombination have been included. The package has more than 10,000 samples from both microarray and sequencing studies that have been processed from raw data through a hyper-standardized, reproducible pipeline. biocViews: ExperimentHub, ExpressionData, Homo_sapiens_Data, MicroarrayData, SequencingData, ReproducibleResearch Author: Lucas Schiffer [aut, cre] (ORCID: ) Maintainer: Lucas Schiffer URL: https://github.com/schifferl/tuberculosis VignetteBuilder: knitr BugReports: https://github.com/schifferl/tuberculosis/issues git_url: https://git.bioconductor.org/packages/tuberculosis git_branch: RELEASE_3_22 git_last_commit: 1b28e51 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/tuberculosis_1.16.0.tar.gz vignettes: vignettes/tuberculosis/inst/doc/tuberculosis.html vignetteTitles: tuberculosis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tuberculosis/inst/doc/tuberculosis.R dependencyCount: 76 Package: TumourMethData Version: 1.8.0 Depends: R (>= 4.2), SummarizedExperiment Imports: ExperimentHub, GenomicRanges, HDF5Array, R.utils, rhdf5 Suggests: ggplot2, knitr, rmarkdown License: Artistic-2.0 MD5sum: 772132a3c375eac882055f0b791ce993 NeedsCompilation: no Title: A Collection of DNA Methylation Datasets for Human Tumour Samples and Matching Normal Samples Description: TumourMethData collects tumour methylation data from a variety of different tumour types (and also matching normal samples where available) and produced with different technologies (e.g. WGBS, RRBS and methylation arrays) and provides them as RangedSummarizedExperiments. This facilitates easy extraction of methylation data for regions of interest across different tumour types and studies. biocViews: ExperimentData, ExperimentHub, MethylSeqData, CancerData, Homo_sapiens_Data, Author: Richard Heery [aut, cre] (ORCID: ) Maintainer: Richard Heery URL: https://github.com/richardheery/TumourMethData VignetteBuilder: knitr BugReports: https://support.bioconductor.org/tag/TumourMethData git_url: https://git.bioconductor.org/packages/TumourMethData git_branch: RELEASE_3_22 git_last_commit: 9cade98 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/TumourMethData_1.8.0.tar.gz vignettes: vignettes/TumourMethData/inst/doc/getting_tumour_methylation_from_TumourMethData.html vignetteTitles: getting_tumour_methylation_from_TumourMethData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TumourMethData/inst/doc/getting_tumour_methylation_from_TumourMethData.R importsMe: methodical dependencyCount: 84 Package: tweeDEseqCountData Version: 1.48.0 Depends: Biobase, R (>= 4.3.0) Suggests: knitr, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: b42acec96ff0cc596fba9da0da1917e9 NeedsCompilation: no Title: RNA-seq count data employed in the vignette of the tweeDEseq package Description: RNA-seq count data from Pickrell et al. (2010) employed to illustrate the use of the Poisson-Tweedie family of distributions with the tweeDEseq package. biocViews: Genome, Homo_sapiens_Data, RNASeqData Author: Dolors Pelegri-Siso [aut, cre] (ORCID: ), Juan R. Gonzalez [aut] (ORCID: ), Mikel Esnaola [aut], Robert Castelo [aut] Maintainer: Dolors Pelegri-Siso URL: https://github.com/isglobal-brge/tweeDEseqCountData/ VignetteBuilder: knitr BugReports: https://github.com/isglobal-brge/tweeDEseqCountData/issues git_url: https://git.bioconductor.org/packages/tweeDEseqCountData git_branch: RELEASE_3_22 git_last_commit: fbfe9fa git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/tweeDEseqCountData_1.48.0.tar.gz vignettes: vignettes/tweeDEseqCountData/inst/doc/tweeDEseqCountData.html vignetteTitles: RNA-seq count data employed in the vignette of the tweeDEseq package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tweeDEseqCountData/inst/doc/tweeDEseqCountData.R suggestsMe: GSAR, missMethyl, tweeDEseq, zenith dependencyCount: 7 Package: tximportData Version: 1.38.0 Suggests: knitr, markdown License: GPL (>= 2) MD5sum: f7006aaacb3c9f61eda3d8ae1b4fc531 NeedsCompilation: no Title: tximportData Description: This package provides the output of running various transcript abundance quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project. The quantifiers were Cufflinks, RSEM, kallisto, Salmon and Sailfish. alevin example output is also included. Forr details on version numbers, sample information, and details on calls, see the package vignette. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tximportData git_branch: RELEASE_3_22 git_last_commit: 5c04cae git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/tximportData_1.38.0.tar.gz vignettes: vignettes/tximportData/inst/doc/tximportData.html vignetteTitles: Sample output files for tximport hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tximportData/inst/doc/tximportData.R importsMe: TDbasedUFE suggestsMe: DESeq2, eds, fishpond, tximeta, tximport, variancePartition dependencyCount: 0 Package: VariantToolsData Version: 1.34.0 Depends: R (>= 3.5.0), VariantAnnotation (>= 1.7.35) Imports: BiocGenerics, GenomicRanges Suggests: VariantTools (>= 1.3.4), gmapR (>= 1.3.3), BiocStyle License: Artistic-2.0 MD5sum: bbfb3a537000992a90acd815526f222a NeedsCompilation: no Title: Data for the VariantTools tutorial Description: Data from the sequencing of a 50/50 mixture of HapMap trio samples NA12878 (CEU) and NA19240 (YRI), subset to the TP53 region. biocViews: ExperimentData, SequencingData, HapMap, SNPData Author: Michael Lawrence Maintainer: Michael Lawrence git_url: https://git.bioconductor.org/packages/VariantToolsData git_branch: RELEASE_3_22 git_last_commit: 4bab3d5 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/VariantToolsData_1.34.0.tar.gz vignettes: vignettes/VariantToolsData/inst/doc/intro.pdf vignetteTitles: VariantTools Example Data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/VariantToolsData/inst/doc/intro.R dependencyCount: 78 Package: VectraPolarisData Version: 1.14.0 Depends: ExperimentHub, SpatialExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, dplyr License: Artistic-2.0 MD5sum: 8e3d8d9f8c537bebe3226e665b21b1d2 NeedsCompilation: no Title: Vectra Polaris and Vectra 3 multiplex single-cell imaging data Description: Provides two multiplex imaging datasets collected on Vectra instruments at the University of Colorado Anschutz Medical Campus. Data are provided as a Spatial Experiment objects. Data is provided in tabular form and has been segmented and phenotyped using Inform software. Raw .tiff files are not included. biocViews: ExperimentHub, ExperimentData, SpatialData, SingleCellData, Homo_sapiens_Data, ReproducibleResearch Author: Wrobel Julia [aut, cre] (ORCID: ), Tusharkanti Ghosh [aut] Maintainer: Wrobel Julia URL: https://github.com/julia-wrobel/VectraPolarisData VignetteBuilder: knitr BugReports: https://support.bioconductor.org/t/VectraPolarisData git_url: https://git.bioconductor.org/packages/VectraPolarisData git_branch: RELEASE_3_22 git_last_commit: 6947fa7 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/VectraPolarisData_1.14.0.tar.gz vignettes: vignettes/VectraPolarisData/inst/doc/VectraPolarisData.html vignetteTitles: VectraPolarisData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/VectraPolarisData/inst/doc/VectraPolarisData.R dependencyCount: 81 Package: vulcandata Version: 1.32.0 Imports: utils Suggests: viper License: LGPL-3 MD5sum: 2823fd7b11c7ca4882fbda1dafa1bc90 NeedsCompilation: no Title: VirtUaL ChIP-Seq data Analysis using Networks, dummy dataset Description: This package provides a dummy regulatory network and ChIP-Seq dataset for running examples in the vulcan package biocViews: ExperimentData, Homo_sapiens_Data, CancerData, ChIPSeqData Author: Federico M. Giorgi, Andrew N. Holding, Florian Markowetz Maintainer: Federico M. Giorgi git_url: https://git.bioconductor.org/packages/vulcandata git_branch: RELEASE_3_22 git_last_commit: 41aa5dd git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/vulcandata_1.32.0.tar.gz vignettes: vignettes/vulcandata/inst/doc/vulcandata.pdf vignetteTitles: Vulcan: VirtUaL ChIP-Seq Analysis through Networks,, dummy datasets hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/vulcandata/inst/doc/vulcandata.R suggestsMe: vulcan dependencyCount: 1 Package: WeberDivechaLCdata Version: 1.12.0 Depends: ExperimentHub, SpatialExperiment, SingleCellExperiment Imports: utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 18a74fe672eeb84d59fde44d09ce4b7f NeedsCompilation: no Title: Spatially-resolved transcriptomics and single-nucleus RNA-sequencing data from the locus coeruleus (LC) in postmortem human brain samples Description: Spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from the locus coeruleus (LC) in postmortem human brain samples. Data were generated with the 10x Genomics Visium SRT and 10x Genomics Chromium snRNA-seq platforms. Datasets are stored in SpatialExperiment and SingleCellExperiment formats. biocViews: ExperimentData, ExperimentHub, ReproducibleResearch, ExpressionData, SequencingData, RNASeqData, SingleCellData, SpatialData, Homo_sapiens_Data Author: Lukas M. Weber [aut, cre] (ORCID: ), Heena R. Divecha [aut] (ORCID: ) Maintainer: Lukas M. Weber URL: https://github.com/lmweber/WeberDivechaLCdata VignetteBuilder: knitr BugReports: https://github.com/lmweber/WeberDivechaLCdata/issues git_url: https://git.bioconductor.org/packages/WeberDivechaLCdata git_branch: RELEASE_3_22 git_last_commit: 7286965 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/WeberDivechaLCdata_1.12.0.tar.gz vignettes: vignettes/WeberDivechaLCdata/inst/doc/WeberDivechaLCdata.html vignetteTitles: WeberDivechaLCdata package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/WeberDivechaLCdata/inst/doc/WeberDivechaLCdata.R suggestsMe: nnSVG dependencyCount: 81 Package: WES.1KG.WUGSC Version: 1.42.0 License: GPL-2 MD5sum: d5a2e87b3a44d4c4eeef6edb90305da0 NeedsCompilation: no Title: Whole Exome Sequencing (WES) of chromosome 22 401st to 500th exon from the 1000 Genomes (1KG) Project by the Washington University Genome Sequencing Center (WUGSC). Description: The assembled .bam files of whole exome sequencing data from the 1000 Genomes Project. 46 samples sequenced by the Washington University Genome Sequencing Center are included. biocViews: ExperimentData, Project1000genomes, SequencingData, DNASeqData, Homo_sapiens_Data Author: Yuchao Jiang, Nancy R. Zhang Maintainer: Yuchao Jiang git_url: https://git.bioconductor.org/packages/WES.1KG.WUGSC git_branch: RELEASE_3_22 git_last_commit: 80ba88e git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/WES.1KG.WUGSC_1.42.0.tar.gz vignettes: vignettes/WES.1KG.WUGSC/inst/doc/WES.1KG.WUGSC_vignettes.pdf vignetteTitles: Using CODEX hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CODEX, iCNV dependencyCount: 0 Package: WGSmapp Version: 1.22.0 Depends: R (>= 3.6.0), GenomicRanges License: GPL-2 MD5sum: e868f142ee3a3df2e5ce23688b3eb349 NeedsCompilation: no Title: Mappability tracks of Whole-genome Sequencing from the ENCODE Project Description: This package provides whole-genome mappability tracks on human hg19/hg38 assembly. We employed the 100-mers mappability track from the ENCODE Project and computed weighted average of the mappability scores if multiple ENCODE regions overlap with the same bin. “Blacklist” bins, including segmental duplication regions and gaps in reference assembly from telomere, centromere, and/or heterochromatin regions are included. The dataset consists of three assembled .bam files of single-cell whole genome sequencing from 10X for illustration purposes. biocViews: ExperimentData, SequencingData, DNASeqData, SingleCellData, Homo_sapiens_Data, Genome, ENCODE Author: Rujin Wang Maintainer: Rujin Wang git_url: https://git.bioconductor.org/packages/WGSmapp git_branch: RELEASE_3_22 git_last_commit: f6fe54e git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/WGSmapp_1.22.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: SCOPE dependencyCount: 11 Package: xcoredata Version: 1.14.0 Depends: R (>= 4.2) Imports: ExperimentHub (>= 2.2.0), utils (>= 4.2.0) Suggests: BiocGenerics (>= 0.40.0), data.table (>= 1.14.2), GenomeInfoDb (>= 1.30.0), GenomicRanges (>= 1.46.1), IRanges (>= 2.28.0), knitr (>= 1.37), rmarkdown (>= 2.11), Matrix (>= 1.3.4), stringr (>= 1.4.0), S4Vectors (>= 0.32.3), TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.14.0), xcore License: GPL-2 MD5sum: 9ef984265921c0020b4aca7b86bd2fb0 NeedsCompilation: no Title: data package for xcore Description: Provides data to use with xcore package. biocViews: ExperimentHub, ExperimentData, Homo_sapiens_Data Author: Maciej Migdał [aut, cre] (ORCID: ), Bogumił Kaczkowski [aut] (ORCID: ) Maintainer: Maciej Migdał VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/xcoredata git_branch: RELEASE_3_22 git_last_commit: 7fc5b40 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/xcoredata_1.14.0.tar.gz vignettes: vignettes/xcoredata/inst/doc/xcoredata.html vignetteTitles: xcoredata hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/xcoredata/inst/doc/xcoredata.R suggestsMe: xcore dependencyCount: 65 Package: XhybCasneuf Version: 1.48.0 Depends: R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf , RColorBrewer , methods, grid License: Artistic-2.0 MD5sum: 90c0adbfa15e8cdbb2da64264d9ae25d NeedsCompilation: no Title: EBI/PSB cross-hybridisation study package Description: Cross-hybridisation study on the ATH1 Affymetrix GeneChip biocViews: ExperimentData, Tissue, MicroarrayData, TissueMicroarrayData Author: Tineke Casneuf Maintainer: Tineke Casneuf git_url: https://git.bioconductor.org/packages/XhybCasneuf git_branch: RELEASE_3_22 git_last_commit: cd755c7 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/XhybCasneuf_1.48.0.tar.gz vignettes: vignettes/XhybCasneuf/inst/doc/Xhyb.pdf vignetteTitles: Xhyb hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/XhybCasneuf/inst/doc/Xhyb.R dependencyCount: 51 Package: yeastCC Version: 1.50.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: b2cde5ed5f007c60ad449fbb2d17fcef NeedsCompilation: no Title: Spellman et al. (1998) and Pramila/Breeden (2006) yeast cell cycle microarray data Description: ExpressionSet for Spellman et al. (1998) yeast cell cycle microarray experiment biocViews: ExperimentData, CellCulture, Saccharomyces_cerevisiae_Data, CancerData, MicroarrayData, OneChannelData, GEO Author: Sandrine Dudoit Maintainer: Sandrine Dudoit git_url: https://git.bioconductor.org/packages/yeastCC git_branch: RELEASE_3_22 git_last_commit: 7987c0e git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/yeastCC_1.50.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: LiquidAssociation suggestsMe: fastLiquidAssociation, ibh dependencyCount: 7 Package: yeastExpData Version: 0.56.0 Depends: R (>= 2.4), graph (>= 1.9.26) Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db License: GPL MD5sum: 9b38929933a994a0d8f76c0997eba0f6 NeedsCompilation: no Title: Yeast Experimental Data Description: A collection of different sets of experimental data from yeast. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data Author: R. Gentleman Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/yeastExpData git_branch: RELEASE_3_22 git_last_commit: fffb325 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/yeastExpData_0.56.0.tar.gz vignettes: vignettes/yeastExpData/inst/doc/yeastExample.pdf vignetteTitles: Yeast PPI Example hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/yeastExpData/inst/doc/yeastExample.R dependsOnMe: PPInfer suggestsMe: ClusterJudge dependencyCount: 8 Package: yeastGSData Version: 0.48.0 License: Artistic-2.0 MD5sum: a86c30c75a4873c77f1d2a7b14434c9a NeedsCompilation: no Title: Yeast Gold Standard Data Description: A collection of so-called gold (and other) standard data sets biocViews: ExperimentData, Saccharomyces_cerevisiae_Data Author: R. Gentleman Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/yeastGSData git_branch: RELEASE_3_22 git_last_commit: e3700d6 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/yeastGSData_0.48.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: yeastNagalakshmi Version: 1.46.0 License: Artistic-2.0 MD5sum: eebe3e567c470af7a62bdacd4137489f NeedsCompilation: no Title: Yeast genome RNA sequencing data based on Nagalakshmi et. al. Description: The yeast genome data was retrieved from the sequence read archive, aligned with bwa, and converted to BAM format with samtools. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, SequencingData, BiocViews, ChIPSeqData Author: Martin Morgan Maintainer: Bioconductor Package Maintainer git_url: https://git.bioconductor.org/packages/yeastNagalakshmi git_branch: RELEASE_3_22 git_last_commit: 15fac50 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/yeastNagalakshmi_1.46.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ShortRead dependencyCount: 0 Package: yeastRNASeq Version: 0.48.0 Depends: R (>= 2.4) Suggests: Biobase, ShortRead, IRanges License: GPL MD5sum: e5ff2799362ba9099067bf21ad75192e NeedsCompilation: no Title: Yeast RNA-Seq Experimental Data from Lee et al. 2008 Description: A selection of RNA-Seq data from a yeast transcriptome experiment. biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData Author: James H. Bullard and Kasper D. Hansen Maintainer: J. Bullard git_url: https://git.bioconductor.org/packages/yeastRNASeq git_branch: RELEASE_3_22 git_last_commit: 63a51a6 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/yeastRNASeq_0.48.0.tar.gz vignettes: vignettes/yeastRNASeq/inst/doc/yeastRNASeq.pdf vignetteTitles: An overview of yeastRNASeq hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/yeastRNASeq/inst/doc/yeastRNASeq.R suggestsMe: EDASeq dependencyCount: 0 Package: zebrafishRNASeq Version: 1.30.0 Depends: R (>= 2.10) Suggests: BiocStyle, knitr License: GPL MD5sum: 3634f28e1c205d355a4f581e5af0c2e1 NeedsCompilation: no Title: Zebrafish RNA-Seq Experimental Data from Ferreira et al. (2014) Description: Gene-level read counts from RNA-Seq for gallein-treated and control zebrafish. biocViews: ExperimentData, Danio_rerio_Data, RNASeqData Author: Davide Risso Maintainer: Davide Risso VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/zebrafishRNASeq git_branch: RELEASE_3_22 git_last_commit: 2cb20d4 git_last_commit_date: 2025-10-29 Date/Publication: 2025-11-04 source.ver: src/contrib/zebrafishRNASeq_1.30.0.tar.gz vignettes: vignettes/zebrafishRNASeq/inst/doc/preprocessing.html vignetteTitles: Pre-Processing for the Zebrafish RNA-Seq Gene-Level Counts hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/zebrafishRNASeq/inst/doc/preprocessing.R suggestsMe: RUVSeq, sva dependencyCount: 0 Package: curatedCRCData Version: 2.42.0 Depends: R (>= 2.10.0), nlme Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle License: Artistic-2.0 Title: Colorectal Cancer Gene Expression Analysis Description: The curatedCRC package provides relevant functions and data for gene expression analysis in patients with colorectal cancer. biocViews: Colorectal, Cancer, TCGA, ExperimentData, RNAExpressionData Author: Princy Parsana, Markus Riester, Curtis Huttenhower, Levi Waldron Maintainer: Princy Parsana URL: https://bitbucket.org/biobakery/curatedcrcdata PackageStatus: Deprecated Package: MetaGxOvarian Version: 1.30.0 Depends: Biobase, AnnotationHub, ExperimentHub, SummarizedExperiment, R (>= 3.6.0) Imports: stats, lattice, impute Suggests: testthat, xtable, rmarkdown, knitr, BiocStyle, markdown License: Artistic-2.0 NeedsCompilation: no Title: Transcriptomic Ovarian Cancer Datasets Description: A collection of Ovarian Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium. biocViews: ExpressionData, ExperimentHub, CancerData, Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData, ExperimentData Author: Michael Zon [aut], Vandana Sandhu [aut], Christopher Eeles [ctb], Benjamin Haibe-Kains [aut, cre] Maintainer: Benjamin Haibe-Kains VignetteBuilder: knitr