Package: adductData Version: 1.27.0 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: 6191ee6b68b6108b32462ec943f31e7a 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: devel git_last_commit: 83b007b git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/adductData_1.27.0.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 dependencyCount: 65 Package: affycompData Version: 1.49.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp License: GPL (>= 2) MD5sum: 5202843862f7dea857111c6afa956e62 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: devel git_last_commit: e157cb1 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/affycompData_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: affycomp dependencyCount: 8 Package: affydata Version: 1.59.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Imports: methods Suggests: hgu95av2cdf, hgu133acdf License: GPL (>= 2) MD5sum: c593f63c29016a10f65b7747258559bb 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: devel git_last_commit: 760415f git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/affydata_1.59.0.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, affyPLM, Biostrings, gcrma, Harman, mimager, puma, pvac, TurboNorm, vsn dependencyCount: 12 Package: Affyhgu133A2Expr Version: 1.47.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 82cee7d9e5616afcf7fb6da2534f37e2 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: devel git_last_commit: 4ac565e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/Affyhgu133A2Expr_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: Affyhgu133aExpr Version: 1.49.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 83095369f8afd738bd2c7d2f17323656 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: devel git_last_commit: cad2b4c git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/Affyhgu133aExpr_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: Affyhgu133Plus2Expr Version: 1.45.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: db3e8d1b9fdd9e22c91eec315a5e2605 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: devel git_last_commit: 2a3d345 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/Affyhgu133Plus2Expr_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: AffymetrixDataTestFiles Version: 0.49.0 Depends: R (>= 2.5.0) License: LGPL-2.1 MD5sum: 8dfdbc91325f9b021242715ae94ce03d 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: devel git_last_commit: f2552d1 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/AffymetrixDataTestFiles_0.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: affxparser, affyILM, aroma.affymetrix dependencyCount: 0 Package: Affymoe4302Expr Version: 1.49.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: dde7f5080d36d634dbface8d394387e7 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: devel git_last_commit: 3db92ed git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/Affymoe4302Expr_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: airway Version: 1.31.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: knitr, GEOquery, markdown License: LGPL MD5sum: 5ab57c72b4df18109ebd45abf6b19a13 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: devel git_last_commit: f2865a6 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/airway_1.31.0.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: NetActivity suggestsMe: apeglm, awst, BioCor, CeTF, DelayedArray, DESeq2, DNEA, dominatR, EnhancedVolcano, ExperimentSubset, funOmics, geyser, gg4way, IHW, InteractiveComplexHeatmap, iSEEde, iSEEpathways, iSEEu, MLInterfaces, OPWeight, pathwayPCA, PCAtools, plyxp, ReducedExperiment, Rvisdiff, scToppR, SummarizedExperiment, tidybulk, tidyprint, tidySummarizedExperiment, TTMap, VISTA, weitrix, XAItest, IHWpaper, RegParallel, seqgendiff dependencyCount: 25 Package: ALL Version: 1.53.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Suggests: rpart License: Artistic-2.0 MD5sum: b8ef540dd1134b558236a291f116124f 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: devel git_last_commit: 87eda8b git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ALL_1.53.0.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 suggestsMe: a4, a4Base, a4Classif, a4Preproc, Biobase, BioNet, CellMapper, ChromHeatMap, clipper, esetVis, genefilter, GeneSelectMMD, graphite, GSAR, GSEAlm, MLInterfaces, npGSEA, pathRender, rScudo, SNAGEE, topGO, SNAGEEdata, MMDvariance, nlcv dependencyCount: 7 Package: ALLMLL Version: 1.51.0 Depends: R (>= 2.10), affy (>= 1.23.4) License: GPL-2 MD5sum: 6d85d644a1e97426c10d4d46e9db4acb 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: devel git_last_commit: 4ddcc9d git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ALLMLL_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQualityMetrics, pvac dependencyCount: 12 Package: AmpAffyExample Version: 1.51.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Suggests: hgu133acdf License: LGPL (>= 2) MD5sum: 0b15a82a18a74acbbf317720581a9a3c 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: devel git_last_commit: 3db8f88 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/AmpAffyExample_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: AffyRNADegradation dependencyCount: 12 Package: antiProfilesData Version: 1.47.0 Depends: Biobase, Suggests: frma, GEOquery, GEOmetadb License: Artistic-2.0 MD5sum: bf4934eee4bc5eef472966eb23d40135 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: devel git_last_commit: 8c5417e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/antiProfilesData_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: antiProfiles, epivizr, epivizrChart, messina dependencyCount: 7 Package: aracne.networks Version: 1.37.0 Depends: R (>= 3.3), viper License: file LICENSE MD5sum: 14af82ed9a26a24334c385464ff2b3ea 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: devel git_last_commit: a3120ba git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/aracne.networks_1.37.0.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: 1.47.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: 48cdb9856affcee892fe1b4d4ebe9859 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: devel git_last_commit: 49b67b9 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ARRmData_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ARRmNormalization dependencyCount: 0 Package: AshkenazimSonChr21 Version: 1.41.0 Suggests: knitr, VariantAnnotation License: Artistic-2.0 MD5sum: 2856b980fe57f0729a15fcf505410c07 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: devel git_last_commit: acd2e3e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/AshkenazimSonChr21_1.41.0.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: 1.31.0 Depends: R (>= 3.5) Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 1c7d8c0e56e59d85111a9bd4e0aefa20 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: devel git_last_commit: 49b46e5 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ASICSdata_1.31.0.tar.gz vignettes: vignettes/ASICSdata/inst/doc/ASICSdata.html vignetteTitles: ASICSdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: AssessORFData Version: 1.29.0 Depends: R (>= 3.5.0), RSQLite (>= 1.1) Imports: DECIPHER, utils Suggests: AssessORF, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 18ffb91af73b4075ba6d78c28c2c0300 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: devel git_last_commit: f19a398 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/AssessORFData_1.29.0.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: 31 Package: AWAggregatorData Version: 1.1.0 Depends: ExperimentHub Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 4dd59e80616ed5c29af879d476ee360f 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: devel git_last_commit: da6d936 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/AWAggregatorData_1.1.0.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: 64 Package: bcellViper Version: 1.47.0 Depends: R(>= 2.14.0), Biobase, methods License: GPL (>=2) MD5sum: b9748008dd72ac4ef65c63512a909761 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: devel git_last_commit: 2a25b56 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/bcellViper_1.47.0.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 suggestsMe: GenomicSuperSignature, pageRank, viper dependencyCount: 7 Package: beadarrayExampleData Version: 1.49.0 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>= 2.0.0) License: GPL-2 MD5sum: 561b5640640371644e71bfe1b8db6cda 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: 5a109c5 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/beadarrayExampleData_1.49.0.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: beadarray, MiRaGE dependencyCount: 66 Package: BeadArrayUseCases Version: 1.49.0 Imports: beadarray (>= 2.3.18), limma, GEOquery Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db License: GPL-2 MD5sum: c05e13f8492020f2a2dca9284b79291d 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: 121c013 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/BeadArrayUseCases_1.49.0.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: 100 Package: BeadSorted.Saliva.EPIC Version: 1.19.0 Depends: R (>= 4.1), minfi(>= 1.36.0), ExperimentHub Suggests: knitr, rmarkdown License: GPL-3 MD5sum: b245da68df6839184e2259290bb43888 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: devel git_last_commit: 56a3301 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/BeadSorted.Saliva.EPIC_1.19.0.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: 65 Package: beta7 Version: 1.49.0 Depends: R (>= 2.4.0), marray License: LGPL MD5sum: 1438b454768ec0fe4d0ecdadbaaa55f5 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: devel git_last_commit: ffae8e4 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/beta7_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 8 Package: BioImageDbs Version: 1.19.0 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: cdff0a48a286cb7ca9881715606b241c 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: devel git_last_commit: b483eaa git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/BioImageDbs_1.19.0.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: 101 Package: BioPlex Version: 1.17.1 Depends: R (>= 4.1.0), SummarizedExperiment Imports: BiocFileCache, GEOquery, graph, methods, utils Suggests: AnnotationDbi, AnnotationHub, BiocStyle, DEXSeq, ExperimentHub, depmap, knitr, rmarkdown License: Artistic-2.0 MD5sum: 663b20c7a205962adb7d529ddf22dbeb 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: 6576d48 git_last_commit_date: 2026-01-26 Date/Publication: 2026-04-21 source.ver: src/contrib/BioPlex_1.17.1.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: 85 Package: biotmleData Version: 1.35.0 Depends: R (>= 3.5.0) Suggests: Biobase, SummarizedExperiment License: file LICENSE MD5sum: fc3a7a717ca7a5ce2c94ffa3fde55af9 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: devel git_last_commit: 496cd46 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/biotmleData_1.35.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: biotmle dependencyCount: 0 Package: biscuiteerData Version: 1.25.0 Depends: R (>= 4.1.0), ExperimentHub Imports: AnnotationHub, utils, curl, GenomicRanges Suggests: knitr, rmarkdown, markdown License: GPL-3 MD5sum: 164f4fa41657ba6a30fcd8fcbb6ff297 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: devel git_last_commit: 88ae79b git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/biscuiteerData_1.25.0.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 dependencyCount: 65 Package: bladderbatch Version: 1.49.0 Depends: Biobase License: Artistic-2.0 MD5sum: a0a00c3f01b2b700889566eb1a2a7a06 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: devel git_last_commit: 70cd621 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/bladderbatch_1.49.0.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: Harman, sva dependencyCount: 7 Package: blimaTestingData Version: 1.31.0 Depends: R(>= 3.0.0) Suggests: blima, beadarray, illuminaHumanv4.db, BiocStyle License: GPL-3 MD5sum: bbfb01e50c590b7037ed090979a4ab77 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: devel git_last_commit: 2efea5a git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/blimaTestingData_1.31.0.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 suggestsMe: blima dependencyCount: 0 Package: BloodCancerMultiOmics2017 Version: 1.31.1 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: f09ed43700230c2b126f43eb26c820a1 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: devel git_last_commit: 2dfcb3d git_last_commit_date: 2026-03-01 Date/Publication: 2026-04-21 source.ver: src/contrib/BloodCancerMultiOmics2017_1.31.1.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: 1.27.0 Depends: R (>= 3.6.0), SummarizedExperiment, ExperimentHub Imports: utils Suggests: rmarkdown, knitr, BiocStyle, testthat License: CC BY 4.0 MD5sum: 9d1a64ac05ecd13655ac3625487f65e4 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: devel git_last_commit: e7e8778 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/bodymapRat_1.27.0.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: 75 Package: breakpointRdata Version: 1.29.0 Depends: R (>= 3.5) Suggests: knitr, BiocStyle, License: file LICENSE MD5sum: 3fa08a6576d5c4b56bb02754053e8f9e 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: devel git_last_commit: fdaa671 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/breakpointRdata_1.29.0.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: 1.49.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: b58435a28c2c51aeccdcfa6842f7eae3 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: devel git_last_commit: 3491d4d git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/breastCancerMAINZ_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: DART, genefu dependencyCount: 0 Package: breastCancerNKI Version: 1.49.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 94bcf9d588dbaf8309fe3d5343066cf4 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: devel git_last_commit: 8a0df9f git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/breastCancerNKI_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, SigCheck, seventyGeneData dependencyCount: 0 Package: breastCancerTRANSBIG Version: 1.49.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 7310b26aa25165ef7008e9268d00c001 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: devel git_last_commit: 4f21e28 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/breastCancerTRANSBIG_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, GSgalgoR dependencyCount: 0 Package: breastCancerUNT Version: 1.49.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: fb5c666c8ec2782622e82889b1538107 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: devel git_last_commit: 9c8e2bf git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/breastCancerUNT_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu dependencyCount: 0 Package: breastCancerUPP Version: 1.49.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 8995707b203c99e970d1399b77e34e91 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: devel git_last_commit: a0ecf38 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/breastCancerUPP_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, GSgalgoR dependencyCount: 0 Package: breastCancerVDX Version: 1.49.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 96b8fffb257b063c7da6a830f1ff1f67 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: devel git_last_commit: 656c9d5 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/breastCancerVDX_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: AIMS, DART, genefu dependencyCount: 0 Package: bronchialIL13 Version: 1.49.0 Depends: R(>= 2.10.0), affy (>= 1.23.4) License: GPL-2 MD5sum: f0df945d0984a4cceac2bdf86afd905f 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: devel git_last_commit: 0882d9b git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/bronchialIL13_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 12 Package: bsseqData Version: 0.49.0 Depends: R (>= 3.5.0), bsseq (>= 1.16.0) License: Artistic-2.0 MD5sum: 76608a949ba89821181c7d1f39129e04 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: devel git_last_commit: 8483790 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/bsseqData_0.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 1 Package: bugphyzz Version: 1.5.0 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: eda7ec66fea291b6270d6553982995cf 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: devel git_last_commit: b658011 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/bugphyzz_1.5.0.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: 46 Package: cancerdata Version: 1.49.0 Depends: R (>= 2.10.1), Biobase License: GPL (>= 2) MD5sum: 651beb42dc75a2dfbb270390e4fbdccd 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: devel git_last_commit: fe24762 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/cancerdata_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: cancerclass dependencyCount: 7 Package: CardinalWorkflows Version: 1.43.0 Depends: R (>= 2.10), Cardinal, methods Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: f78f5c5c4e2d4043193166b54fbc6fb7 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: devel git_last_commit: 366d98d git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/CardinalWorkflows_1.43.0.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: 66 Package: ccdata Version: 1.37.0 Depends: R (>= 3.3) License: MIT + file LICENSE MD5sum: 595baaca7636a18b1495d044f1372d50 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: devel git_last_commit: 0d2b81b git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ccdata_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: retriever dependencyCount: 0 Package: CCl4 Version: 1.49.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), limma License: Artistic-2.0 MD5sum: cb3344a73971bf6248966d898ff0a008 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: devel git_last_commit: 2cb7a96 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/CCl4_1.49.0.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 suggestsMe: arrayQualityMetrics dependencyCount: 10 Package: celarefData Version: 1.29.0 Depends: R (>= 3.5.0) Suggests: ExperimentHub, knitr, rmarkdown License: GPL-3 MD5sum: 54316f72157139d980dd1a4f49307fd2 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: devel git_last_commit: 9e8a11b git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/celarefData_1.29.0.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: 1.21.0 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: d4c0cf9365fc4cbafab403e734bd7ec9 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: devel git_last_commit: 18f38f4 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/celldex_1.21.0.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 suggestsMe: scDiagnostics, scGraphVerse, SingleR, tidySingleCellExperiment dependencyCount: 92 Package: CellMapperData Version: 1.37.0 Depends: ExperimentHub, CellMapper Suggests: BiocStyle License: Artistic-2.0 MD5sum: cb1ee5e8b518a67d1b1305959599614d 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: devel git_last_commit: 86abd0b git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/CellMapperData_1.37.0.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: 65 Package: cfToolsData Version: 1.9.0 Depends: R (>= 4.3.0) Imports: utils, ExperimentHub Suggests: BiocStyle, knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0) License: file LICENSE MD5sum: d5b3ba03df68569326b055a8359f848b 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: devel git_last_commit: 57c3cfe git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/cfToolsData_1.9.0.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 dependencyCount: 64 Package: ChAMPdata Version: 2.43.0 Depends: R (>= 3.5.0), GenomicRanges (>= 1.22.4), BiocGenerics (>= 0.16.1) License: GPL-3 MD5sum: 55ed637400d4b5f44675a53e4f8b46d8 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: devel git_last_commit: fa81053 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ChAMPdata_2.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: methyLImp2 dependencyCount: 11 Package: ChimpHumanBrainData Version: 1.49.0 Depends: affy,qvalue,limma,hexbin,statmod Suggests: hgu95av2cdf License: MIT MD5sum: 1edb30fedec12077a7a59a789b0a8420 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: devel git_last_commit: b120673 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ChimpHumanBrainData_1.49.0.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: 43 Package: ChIPDBData Version: 1.1.0 Imports: ExperimentHub Suggests: knitr, rmarkdown, BiocStyle, AnnotationHub, TFEA.ChIP, DESeq2, testthat (>= 3.0.0) License: GPL-3 MD5sum: 31281f87afebfacda853442bd86ed2fe 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: devel git_last_commit: d77edb2 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ChIPDBData_1.1.0.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: 64 Package: chipenrich.data Version: 2.35.0 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: e9fe3ca5da576c71bd4ab56194b19554 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: devel git_last_commit: ab7960d git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/chipenrich.data_2.35.0.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: 89 Package: ChIPexoQualExample Version: 1.35.0 Depends: R (>= 3.3) Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 72f7e681bbd7d4f80f3a0493a716bb1c 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: devel git_last_commit: b44ccfd git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ChIPexoQualExample_1.35.0.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: 1.27.0 Imports: AnnotationHub, ExperimentHub, Rsamtools, S4Vectors Suggests: knitr, BiocStyle, rmarkdown License: CC BY 4.0 MD5sum: 176f92de0629e13f6552fe5a06b33fbc 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: devel git_last_commit: a359f93 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/chipseqDBData_1.27.0.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: 77 Package: ChIPXpressData Version: 1.49.0 Depends: bigmemory License: GPL (>=2) MD5sum: acacd6db038400aed4ee1afb85e7bd7a 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: devel git_last_commit: c71f8b6 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ChIPXpressData_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ChIPXpress dependencyCount: 7 Package: CLL Version: 1.51.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: LGPL MD5sum: 1372bc266b212f7357bedfb6183f0b61 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: devel git_last_commit: 0211325 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/CLL_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 12 Package: CLLmethylation Version: 1.31.0 Depends: R (>= 3.5.0) Imports: SummarizedExperiment, ExperimentHub Suggests: BiocStyle, ggplot2, knitr, rmarkdown License: LGPL MD5sum: cfed538b3f6df8bb4f31931980cdb7d6 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: devel git_last_commit: 075775e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/CLLmethylation_1.31.0.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: 75 Package: CluMSIDdata Version: 1.27.0 Depends: R (>= 3.6) License: MIT + file LICENSE MD5sum: 51d472513f8029645a01b1861629fa07 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: devel git_last_commit: 4bbf0f7 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/CluMSIDdata_1.27.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: clustifyrdatahub Version: 1.21.0 Depends: R (>= 4.0), ExperimentHub Imports: utils Suggests: clustifyr, Seurat, usethis, rmarkdown, knitr, tidyr, BiocStyle License: MIT + file LICENSE MD5sum: 44cf06a2be5f979ac21eed5a0266cc96 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: devel git_last_commit: f92c1bd git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/clustifyrdatahub_1.21.0.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: 64 Package: cMap2data Version: 1.47.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 11600c14a6a272a07f2e6c94f65ae5f6 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: devel git_last_commit: 14e6577 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/cMap2data_1.47.0.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: 1.47.0 Depends: R (>= 2.10), cnvGSA License: LGPL MD5sum: fe02ff8150cf8dd4f79346b16654246d 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: devel git_last_commit: 3079a12 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/cnvGSAdata_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: cnvGSA dependencyCount: 21 Package: COHCAPanno Version: 1.47.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 219f6b0dc6c37f8b2de6bfcd841984f5 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: devel git_last_commit: dabb34b git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/COHCAPanno_1.47.0.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: 1.53.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: fe79e91fa303e268dd5cbe00d53e9352 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: devel git_last_commit: 7a4b56b git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/colonCA_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: clustComp, copa dependencyCount: 7 Package: CONFESSdata Version: 1.39.0 Depends: R (>= 3.3) License: GPL-2 MD5sum: 8c18d3cd436deda795749d0a57a0cf07 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: devel git_last_commit: 39c1b31 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/CONFESSdata_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CONFESS dependencyCount: 0 Package: ConnectivityMap Version: 1.47.0 Depends: R (>= 2.15.1) Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 1b0959ae83165ea64c3ec5eea3a3b681 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: devel git_last_commit: 831c695 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ConnectivityMap_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: COPDSexualDimorphism.data Version: 1.47.0 License: LGPL-2.1 MD5sum: 35193ff4af894ae98ae6d73586dd1a0f 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: devel git_last_commit: e28beeb git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/COPDSexualDimorphism.data_1.47.0.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: 1.43.0 Depends: R (>= 3.5.0) Suggests: BiocStyle License: GPL-2 MD5sum: fd2f70764a5d89558723de4107eacde9 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: devel git_last_commit: c73ec6a git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/CopyhelpeR_1.43.0.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: 1.29.0 Depends: R (>= 3.5.0) Imports: ExperimentHub,Rdpack (>= 0.8) Suggests: BiocStyle,knitr,rmarkdown,minfi,conumee,minfiData License: Artistic-2.0 MD5sum: 7b15f4b4a2ad96f98d23dfe2eee43cb7 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: devel git_last_commit: 2a0c1c8 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/CopyNeutralIMA_1.29.0.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: 66 Package: CoSIAdata Version: 1.11.0 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: 3f6b6cf11f6b88a46f5407d3742a5a92 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: devel git_last_commit: 1933a6f git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/CoSIAdata_1.11.0.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: 64 Package: COSMIC.67 Version: 1.47.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, SummarizedExperiment, VariantAnnotation Suggests: testthat, BiocStyle, knitr License: GPL-3 MD5sum: 47f300fa7431293b167dfcf917d11b5d 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: devel git_last_commit: d2199ba git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/COSMIC.67_1.47.0.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 dependencyCount: 77 Package: CRCL18 Version: 1.31.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: c22587bf51764a4392385ac5a8127dfd 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: devel git_last_commit: b007204 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/CRCL18_1.31.0.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: 1.15.0 Depends: ExperimentHub Imports: AnnotationHub, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: af4c40000704da27b0db5c7790269bd6 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: devel git_last_commit: c1ddb7e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/crisprScoreData_1.15.0.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 dependencyCount: 64 Package: curatedAdipoArray Version: 1.23.0 Depends: R (>= 4.0) Suggests: knitr, rmarkdown, ExperimentHub, SummarizedExperiment License: GPL-3 + file LICENSE MD5sum: 300ed1abad3b7aff62a4c49b33fb5895 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: devel git_last_commit: a9c5b14 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/curatedAdipoArray_1.23.0.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: 1.27.0 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: 0cf2eeb7b4b3d7e4991f6b55f7e27d87 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: devel git_last_commit: df61fac git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/curatedAdipoChIP_1.27.0.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: 75 Package: curatedAdipoRNA Version: 1.27.0 Depends: R (>= 3.6), SummarizedExperiment Suggests: knitr, rmarkdown, DESeq2, fastqcr, devtools, testthat, readr, dplyr, tidyr, ggplot2, S4Vectors License: GPL-3 MD5sum: f4557744902781a19f3b27d17f8fa7a7 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: devel git_last_commit: 3a5ad7f git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/curatedAdipoRNA_1.27.0.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: 1.47.0 Depends: R (>= 2.10.0), affy Suggests: BiocStyle, survival, xtable, sva, genefilter, logging License: Artistic-2.0 MD5sum: 52cc6ad9bc3cd98e013c83b7b1e9a0cf 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: devel git_last_commit: 5332db8 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/curatedBladderData_1.47.0.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: curatedCRCData Version: 2.43.1 Depends: R (>= 4.0.0), Biobase Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 6a6fba6b238014fcd3c375de68fff116 NeedsCompilation: no 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: ExperimentData, CancerData, ExpressionData Author: Princy Parsana [aut], Markus Riester [aut], Curtis Huttenhower [aut], Levi Waldron [aut, cre] (ORCID: ), National Cancer Institute [fnd] (5U24CA180996) Maintainer: Levi Waldron URL: https://github.com/waldronlab/curatedCRCData VignetteBuilder: knitr BugReports: https://github.com/waldronlab/curatedCRCData/issues git_url: https://git.bioconductor.org/packages/curatedCRCData git_branch: devel git_last_commit: 6961479 git_last_commit_date: 2026-04-10 Date/Publication: 2026-04-21 source.ver: src/contrib/curatedCRCData_2.43.1.tar.gz vignettes: vignettes/curatedCRCData/inst/doc/curatedCRCData_vignette.html vignetteTitles: curatedCRCData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedCRCData/inst/doc/curatedCRCData_vignette.R dependencyCount: 7 Package: curatedMetagenomicData Version: 3.19.0 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: 50d012cc0eb61e3ca29ea26d5b70a6a7 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: 5cacdd9 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/curatedMetagenomicData_3.19.0.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: CrcBiomeScreen, lefser, MMUPHin dependencyCount: 154 Package: curatedOvarianData Version: 1.49.0 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: 3fd1f41b43456353f678b62b46f51f32 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: devel git_last_commit: 793fa91 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/curatedOvarianData_1.49.0.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: 1.7.0 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: c4a63f0deb9239928669916761f67efc 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: 29ec7b9 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/curatedPCaData_1.7.0.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: 80 Package: curatedTBData Version: 2.7.0 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: ee9ba83ae79f317e88c41e06355ad1c3 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: acf1650 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/curatedTBData_2.7.0.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 dependencyCount: 76 Package: curatedTCGAData Version: 1.33.2 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: c9218ed1b68458064a89d6141e6d3e72 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], NCI [fnd] (GrantNo.: U24CA289073) 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: 18525bc git_last_commit_date: 2026-03-26 Date/Publication: 2026-04-21 source.ver: src/contrib/curatedTCGAData_1.33.2.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: 77 Package: CytoMethIC Version: 1.7.0 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: 2c8bb2d69deeb889eb36fd747114d2bb 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: b4ad7c0 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/CytoMethIC_1.7.0.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: 109 Package: DAPARdata Version: 1.41.0 Depends: R (>= 4.4.0), MSnbase Imports: utils Suggests: knitr, DAPAR, BiocStyle License: GPL-2 MD5sum: d53e5c68fb0c3d5ceef55483ce290bcf 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: devel git_last_commit: 1733867 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/DAPARdata_1.41.0.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 dependencyCount: 2 Package: davidTiling Version: 1.51.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db License: LGPL MD5sum: deec3b75736f4ea8d1ddfc2eb805fc24 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: devel git_last_commit: e0e8ddc git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/davidTiling_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 76 Package: depmap Version: 1.25.0 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: dd1ea01d02f9f6e396164d72f13261f4 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: a389e6e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/depmap_1.25.0.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: CRISPRball, mastR, BioPlex dependencyCount: 64 Package: derfinderData Version: 2.29.0 Depends: R (>= 3.5.0) Suggests: sessioninfo, knitr (>= 1.6), RefManageR, rmarkdown (>= 0.3.3), BiocStyle License: Artistic-2.0 MD5sum: df671e1e9261b484e4d9c7364c3ac513 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: devel git_last_commit: 9cfcdf7 git_last_commit_date: 2026-03-31 Date/Publication: 2026-04-21 source.ver: src/contrib/derfinderData_2.29.0.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 dependencyCount: 0 Package: DeSousa2013 Version: 1.47.0 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: b3aaf82515101e0c294f29c31c539e1b 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: devel git_last_commit: da2a9e4 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/DeSousa2013_1.47.0.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: 123 Package: DExMAdata Version: 1.19.0 Depends: R (>= 4.1) Imports: Biobase Suggests: BiocStyle License: GPL-2 MD5sum: ae456be110df8a57fc93ebfd3a068724 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: devel git_last_commit: aa10ee3 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/DExMAdata_1.19.0.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: 1.39.0 Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 81b67ee29987147431825f28f3074001 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: devel git_last_commit: 87201a4 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/diffloopdata_1.39.0.tar.gz vignettes: vignettes/diffloopdata/inst/doc/diffloopdata.html vignetteTitles: diffloopdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: diggitdata Version: 1.43.0 Depends: R(>= 2.14.0), Biobase, methods Imports: viper License: GPL (>=2) MD5sum: 5d9fa061ada43120a7aabc7a8dde76d6 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: devel git_last_commit: a541bb7 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/diggitdata_1.43.0.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: 1.51.0 Depends: R(>= 2.11.0), Biobase, graph License: GPL (>=2) MD5sum: 6757b6f2b6b06a66263a7140702d7568 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: devel git_last_commit: f638520 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/DLBCL_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: BioNet, mwcsr dependencyCount: 9 Package: DMRcatedata Version: 2.29.0 Depends: R (>= 4.0), ExperimentHub Imports: GenomicFeatures, Gviz, readxl, plyr, rtracklayer, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr License: GPL-3 MD5sum: 122ab785d9393e7a59355c8ca55c9943 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: devel git_last_commit: 35e67c4 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/DMRcatedata_2.29.0.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 dependencyCount: 163 Package: DMRsegaldata Version: 0.99.7 Depends: R (>= 4.5.0), ExperimentHub Suggests: knitr, rmarkdown, BiocStyle, ExperimentHubData License: GPL (>= 2) MD5sum: 407bdd318aa2ebff0faa47140b2c6ac7 NeedsCompilation: no Title: Example DNAm Data for DMRsegal Description: Data package providing example DNA methylation files used in the DMRsegal vignette and examples. Includes a sorted beta matrix as a tab-delimited, bgzip-compressed file and a matching phenotype table. The data contains 10 healthy and 10 cancer samples, and preprocessing has already been performed on the beta values. biocViews: ExperimentHub, ExperimentData, SNPData, SequencingData, MicroarrayData, Genome Author: Vasileios Lemonidis [aut, cre, cph] (ORCID: ), Center for Oncological Research, University of Antwerp [cph, fnd], Stichting Tegen Kanker [fnd] Maintainer: Vasileios Lemonidis URL: https://github.com/CMG-UA/DMRsegal VignetteBuilder: knitr BugReports: https://github.com/CMG-UA/DMRsegal/issues git_url: https://git.bioconductor.org/packages/DMRsegaldata git_branch: devel git_last_commit: 3907489 git_last_commit_date: 2026-04-02 Date/Publication: 2026-04-21 source.ver: src/contrib/DMRsegaldata_0.99.7.tar.gz vignettes: vignettes/DMRsegaldata/inst/doc/DMRsegaldata.html vignetteTitles: Introduction to DMRsegaldata hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DMRsegaldata/inst/doc/DMRsegaldata.R dependencyCount: 64 Package: DNAZooData Version: 1.11.0 Depends: R (>= 4.2), HiCExperiment Imports: BiocFileCache, S4Vectors, rjson, utils, tools Suggests: dplyr, testthat, methods, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 07c1b0d10d95ce7a37456aa7aaf8ec48 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: devel git_last_commit: 0ff405e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/DNAZooData_1.11.0.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: 87 Package: dominatRData Version: 0.99.1 Depends: R (>= 4.5.0) Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 4bd0986dddf85bbaa864cae3fc463901 NeedsCompilation: no Title: Datasets for R Package dominatR Description: dominatRData is a data package useful for showcasing dominatR examples. dominatR is an R package for quantifying and visualizing feature dominance in datasets. dominatR makes use of entropy-based triangular projections and compositional comparison metrics. biocViews: ExperimentData, ChIPSeqData, Tissue, PackageTypeData Author: Simon Lizarazo [aut, cre] (ORCID: ), Ethan Chen [ctb], Rajendra K C [ctb], Kevin Van Bortle [ctb] Maintainer: Simon Lizarazo URL: https://github.com/VanBortleLab/dominatRData VignetteBuilder: knitr BugReports: https://github.com/VanBortleLab/dominatRData/issues git_url: https://git.bioconductor.org/packages/dominatRData git_branch: devel git_last_commit: eca9c4c git_last_commit_date: 2025-10-22 Date/Publication: 2026-04-21 source.ver: src/contrib/dominatRData_0.99.1.tar.gz vignettes: vignettes/dominatRData/inst/doc/dominatRData.html vignetteTitles: Introduction to dominatR hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/dominatRData/inst/doc/dominatRData.R suggestsMe: dominatR dependencyCount: 0 Package: DonaPLLP2013 Version: 1.49.0 Depends: EBImage, parallel License: Artistic-2.0 MD5sum: 1b5f289ae21d3e5ffdedba8f21e95126 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: devel git_last_commit: 47912a6 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/DonaPLLP2013_1.49.0.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: 46 Package: DoReMiTra Version: 1.1.2 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: eb1a9c9793961da92b223999a44d5572 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: devel git_last_commit: 794f30a git_last_commit_date: 2026-03-04 Date/Publication: 2026-04-21 source.ver: src/contrib/DoReMiTra_1.1.2.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: 127 Package: dressCheck Version: 0.49.0 Depends: R (>= 2.10.1), methods, Biobase (>= 2.5.5) Suggests: survival, chron License: Artistic-2.0 MD5sum: 09c8ba25f92d316badb635d9df51842b 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: devel git_last_commit: 8d71ec2 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/dressCheck_0.49.0.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: 1.21.0 Imports: utils, ExperimentHub, AnnotationHub, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, testthat, DropletUtils License: GPL-3 MD5sum: de55a54c5586941c0bb228367beda2dd 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: e5a7c45 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/DropletTestFiles_1.21.0.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.intro, OSCA.workflows, scrapbook dependencyCount: 64 Package: DrugVsDiseasedata Version: 1.47.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 467cb3007c7f77d6805f7af68758e220 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: devel git_last_commit: f197524 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/DrugVsDiseasedata_1.47.0.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: 1.29.0 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: addf2b95fd8111d73627f810ebd4238a 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: 0334a08 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/DuoClustering2018_1.29.0.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: 81 Package: DvDdata Version: 1.47.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 0281c680fe63c905887bd2255050f484 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: devel git_last_commit: 3a2de12 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/DvDdata_1.47.0.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: 1.51.0 Depends: R (>= 1.4.1), marray, GEOquery Suggests: dyebias, convert, Biobase License: GPL-3 MD5sum: b7dd08574cf065537cd304ca5ee6d6ab 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: devel git_last_commit: dd7d2fd git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/dyebiasexamples_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: dyebias dependencyCount: 76 Package: easierData Version: 1.17.0 Depends: R (>= 4.1.0) Imports: ExperimentHub, AnnotationHub, utils, SummarizedExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 30ca977014e9c7d44ceea45df8b138ca 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: devel git_last_commit: f034d6f git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/easierData_1.17.0.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 dependencyCount: 75 Package: EatonEtAlChIPseq Version: 0.49.0 Depends: GenomicRanges (>= 1.5.42), ShortRead, rtracklayer License: Artistic 2.0 MD5sum: 66e57785e0d7735dd3b7bbb6412dff0e 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: devel git_last_commit: d8e55dd git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/EatonEtAlChIPseq_0.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 69 Package: ecoliLeucine Version: 1.51.0 Depends: R (>= 1.9.0), affy (>= 1.23.4), ecolicdf License: GPL (>= 2) MD5sum: c22ea4fe1734ebf3c4bafb6907e46a7e 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: devel git_last_commit: 69fb3bc git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ecoliLeucine_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ecolitk dependencyCount: 47 Package: EGSEAdata Version: 1.39.0 Depends: R (>= 3.4) Suggests: EGSEA License: file LICENSE MD5sum: 76eed189f4e06d54825de4928e288235 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: devel git_last_commit: 6546cdb git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/EGSEAdata_1.39.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: ELMER.data Version: 2.35.0 Depends: R (>= 3.5.0) Imports: GenomicRanges Suggests: BiocStyle, knitr, dplyr, devtools, DT, rmarkdown License: GPL-3 MD5sum: 1ae2204240c96c7f7ed36a7ee2c51b10 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: devel git_last_commit: 5e9c212 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ELMER.data_2.35.0.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 dependencyCount: 11 Package: emtdata Version: 1.19.0 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: aea3adb003a40ef532677b0a68b29cf8 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: dd35ae5 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/emtdata_1.19.0.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: 79 Package: EMTscoreData Version: 0.99.10 Imports: SummarizedExperiment, Seurat, SingleCellExperiment, AnnotationHub, ExperimentHub, ggplot2 Suggests: BiocFileCache, SeuratObject, knitr, rmarkdown, googledrive, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: 53417351939dff53e189b6d6f390794c NeedsCompilation: no Title: Single-cell RNA-seq datasets of EMT responses from Cook et al. (2020) Description: Provides 12 single-cell RNA-seq datasets profiling epithelial–mesenchymal transition (EMT) in human cancer cell lines (MCF7, OVCA420, DU145, and A549) under TGF-beta stimulation, kinase inhibition, and time-course conditions, as reported by Cook DP and Vanderhyden BC (2020). The datasets are distributed via ExperimentHub as SingleCellExperiment objects. biocViews: ExperimentHub, SingleCellData, ExpressionData, CancerData, RNASeqData Author: Haimei Wen [aut, cre] (ORCID: ), Tian Hong [fnd] Maintainer: Haimei Wen URL: https://github.com/wenmm/EMTscoreData VignetteBuilder: knitr BugReports: https://github.com/wenmm/EMTscoreData/issues git_url: https://git.bioconductor.org/packages/EMTscoreData git_branch: devel git_last_commit: 7c82f51 git_last_commit_date: 2026-01-23 Date/Publication: 2026-04-21 source.ver: src/contrib/EMTscoreData_0.99.10.tar.gz vignettes: vignettes/EMTscoreData/inst/doc/EMTscoreData.html vignetteTitles: EMTscoreData Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/EMTscoreData/inst/doc/EMTscoreData.R dependencyCount: 183 Package: eoPredData Version: 1.5.0 Depends: ExperimentHub Suggests: BiocStyle, knitr, rmarkdown, RefManageR, planet, mixOmics License: MIT + file LICENSE MD5sum: 09035d8aa3a9b28fb0b848b21bf7f2fa 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: devel git_last_commit: 5854957 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/eoPredData_1.5.0.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: 64 Package: EpiMix.data Version: 1.13.0 Depends: R (>= 4.2.0), ExperimentHub (>= 0.99.6) Suggests: rmarkdown, knitr License: GPL-3 MD5sum: f4cc31ce35b34c2437b28fd679602859 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: devel git_last_commit: cbd428f git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/EpiMix.data_1.13.0.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 dependencyCount: 64 Package: epimutacionsData Version: 1.15.0 Depends: R (>= 4.2.0) Suggests: rmarkdown, BiocStyle, knitr, ExperimentHub, minfi License: MIT + file LICENSE MD5sum: 7728419df41268cdd27ee019e36e272f 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: a9114cc git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/epimutacionsData_1.15.0.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 dependencyCount: 0 Package: EpipwR.data Version: 1.5.0 Imports: ExperimentHub Suggests: knitr, rmarkdown, sessioninfo License: Artistic-2.0 MD5sum: 23907a9cc5e49531b87e456224d14f48 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: devel git_last_commit: dba6b48 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/EpipwR.data_1.5.0.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: 64 Package: estrogen Version: 1.57.0 Suggests: affy, hgu95av2.db, hgu95av2cdf, vsn, knitr, genefilter License: LGPL MD5sum: c735275ffab3793d9dacd9f3e4890901 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: devel git_last_commit: 83848e7 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/estrogen_1.57.0.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 dependencyCount: 0 Package: etec16s Version: 1.39.0 Depends: R (>= 3.3), Biobase, metagenomeSeq(>= 1.12.0) License: Artistic-2.0 MD5sum: 85c96d68775f4938d2281e57ff6de040 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: devel git_last_commit: 7a9789d git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/etec16s_1.39.0.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: 1.19.0 Depends: R (>= 4.1), ExperimentHub Suggests: knitr, BiocStyle, ggplot2, cowplot, rmarkdown, markdown, rbibutils, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 8a6fec82538dc6b0df66cdd1a274d42a 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 [aut] (ORCID: ), Hiranyamaya Dash [cre] (ORCID: ), Nathan Skene [aut] (ORCID: ) Maintainer: Hiranyamaya Dash URL: https://github.com/neurogenomics/ewceData VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ewceData git_branch: devel git_last_commit: d337c62 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ewceData_1.19.0.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: 64 Package: faahKO Version: 1.51.0 Depends: R (>= 3.5) Imports: xcms (>= 4.5.4) Suggests: MSnbase (>= 2.33.3) License: LGPL MD5sum: 19e1b431906633ee8076961bcb5a5939 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: devel git_last_commit: 620ca15 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/faahKO_1.51.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 1 Package: fabiaData Version: 1.49.0 Depends: R (>= 2.10.0), Biobase Imports: utils Suggests: fabia License: LGPL (>= 2.1) MD5sum: ea04ba948c7d78ecb43f3f5773513de4 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: devel git_last_commit: 24c7ef6 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/fabiaData_1.49.0.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: 1.47.0 Depends: R (>= 2.15.0) License: GPL-3 MD5sum: 3ff0a6492c54251d4d242bace2d24534 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: devel git_last_commit: 549d299 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/FANTOM3and4CAGE_1.47.0.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: 1.49.0 Depends: R (>= 2.10.0), lumi Suggests: genefilter, affy License: GPL (>2) MD5sum: ae6ec202ee4eb2c85f91ffa84403851f 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: devel git_last_commit: eba216e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ffpeExampleData_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 1 Package: fibroEset Version: 1.53.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: b752787bebad30f9c6303f2368f46e0e 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: devel git_last_commit: 03efe2f git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/fibroEset_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: biocGraph, clusterStab, geneplotter dependencyCount: 7 Package: FieldEffectCrc Version: 1.21.0 Depends: utils Imports: BiocStyle, RUnit, SummarizedExperiment, ExperimentHub (>= 0.99.6), AnnotationHub, DESeq2 Suggests: knitr, rmarkdown, BiocGenerics, sva, BiocManager License: Artistic-2.0 MD5sum: 6dcc73dda27bd8753157a5dc098980b2 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: 9cafadd git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/FieldEffectCrc_1.21.0.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: 114 Package: FIs Version: 1.39.0 Depends: R (>= 3.3) License: GPL-3 MD5sum: 6156b79320d1d28039ade635352588e0 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: devel git_last_commit: 9345c69 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/FIs_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: splineTimeR dependencyCount: 0 Package: fission Version: 1.31.0 Depends: R (>= 2.10), SummarizedExperiment Suggests: knitr, markdown License: LGPL MD5sum: d6626f2a246557bd5565a4dbbf9a8a98 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: devel git_last_commit: 475d7c5 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/fission_1.31.0.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: 1.47.0 Depends: R (>= 2.15), limma Imports: Biobase ,VennDiagram, gplots,grid License: GPL (>= 2) MD5sum: 40093e96a4c16dbdeaa6ffce09a2ec77 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: devel git_last_commit: 08e2b20 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/Fletcher2013a_1.47.0.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 suggestsMe: NetActivity dependencyCount: 21 Package: flowPloidyData Version: 1.37.0 Suggests: knitr, rmarkdown, flowCore License: GPL-3 MD5sum: 2f4f4554530d07614fc5f9921b88809c 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: devel git_last_commit: 85c7d5c git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/flowPloidyData_1.37.0.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: 1.49.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: aeda627db1a9a8feade34abef1a9b268 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: devel git_last_commit: 0bb1304 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/FlowSorted.Blood.450k_1.49.0.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: methylationArrayAnalysis suggestsMe: FlowSorted.Blood.EPIC dependencyCount: 1 Package: FlowSorted.Blood.EPIC Version: 2.15.0 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: da6117c959f83641fc5672c573061325 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: devel git_last_commit: ce5e87e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/FlowSorted.Blood.EPIC_2.15.0.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: FlowSorted.CordBloodCombined.450k dependencyCount: 84 Package: FlowSorted.CordBlood.450k Version: 1.39.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 9358c9ee7d886349c791a6800c4dfe8f 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: devel git_last_commit: 7defe7f git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/FlowSorted.CordBlood.450k_1.39.0.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: 1 Package: FlowSorted.CordBloodCombined.450k Version: 1.27.0 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: 9a029f3a9d287a91e0a821d1f32ba108 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: devel git_last_commit: 0cbf411 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/FlowSorted.CordBloodCombined.450k_1.27.0.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: 78 Package: FlowSorted.CordBloodNorway.450k Version: 1.37.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: c8f746e092b2829de98b1de6634254a6 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: devel git_last_commit: 7c2cdc6 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/FlowSorted.CordBloodNorway.450k_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 1 Package: FlowSorted.DLPFC.450k Version: 1.47.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: f20beefd5b82f022b910a9aa4ce6efdb 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: devel git_last_commit: e1bdb4b git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/FlowSorted.DLPFC.450k_1.47.0.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: 1 Package: flowWorkspaceData Version: 3.23.0 License: GPL-2 MD5sum: b109b2ff870b4fc7f462e42758fedbeb 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: devel git_last_commit: 839dc56 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/flowWorkspaceData_3.23.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CytoML, flowClust, flowCore, flowWorkspace, ggcyto, openCyto dependencyCount: 0 Package: fourDNData Version: 1.11.0 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: add31ec4e248d9037411348ec352c0ed 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: devel git_last_commit: 4072966 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/fourDNData_1.11.0.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: 86 Package: frmaExampleData Version: 1.47.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 2df420c8a99fb06c6648e267af439050 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: devel git_last_commit: 0774595 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/frmaExampleData_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: frma, frmaTools dependencyCount: 0 Package: gageData Version: 2.49.0 Depends: R (>= 2.10) Suggests: gage, pathview, genefilter License: GPL (>=2.0) MD5sum: c2b22ecad0e011a2b57b91e3d9685f71 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: devel git_last_commit: ccb2858 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/gageData_2.49.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: gage dependencyCount: 0 Package: gaschYHS Version: 1.49.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 21448b6f473f7a234679cf08531381d7 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: devel git_last_commit: 8eb7191 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/gaschYHS_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: gcspikelite Version: 1.49.0 Depends: R (>= 2.5.0) License: LGPL MD5sum: d97d1be98dc5046ac40ebb1d762d2238 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: devel git_last_commit: 7f8bef9 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/gcspikelite_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: erah dependencyCount: 0 Package: gDNAinRNAseqData Version: 1.11.0 Depends: R (>= 4.3) Imports: RCurl, XML, ExperimentHub, BiocGenerics, Rsamtools Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 0e423804b21de15baceea909cb9442d0 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: devel git_last_commit: f627492 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/gDNAinRNAseqData_1.11.0.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: 79 Package: gDRtestData Version: 1.9.2 Depends: R (>= 4.2) Imports: checkmate, data.table Suggests: BiocStyle, gDRstyle (>= 1.7.1), knitr, qs2, reshape2, rmarkdown, SummarizedExperiment, testthat, yaml License: Artistic-2.0 MD5sum: 1eaa2a6711d03235d5ada6d8ce10f2d0 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 qs2 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: devel git_last_commit: 5b60e65 git_last_commit_date: 2026-04-19 Date/Publication: 2026-04-21 source.ver: src/contrib/gDRtestData_1.9.2.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: gDRimport, gDRutils dependencyCount: 5 Package: geneLenDataBase Version: 1.47.0 Depends: R (>= 2.11.0) Imports: utils, rtracklayer, GenomicFeatures, txdbmaker License: LGPL (>= 2) MD5sum: 6967edd08c772584ea7d027c09f32d17 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: devel git_last_commit: 8b3da6c git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/geneLenDataBase_1.47.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: goseq importsMe: SMITE dependencyCount: 76 Package: genomationData Version: 1.43.0 Suggests: knitr License: GPL-3 MD5sum: 91bfe6f419b0e18aa621960b1ab0e8a7 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: devel git_last_commit: 3b87aeb git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/genomationData_1.43.0.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: 1.19.0 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: 3d279f95efc294ae03bcb4acacb42670 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: devel git_last_commit: fd79329 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/GenomicDistributionsData_1.19.0.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: 104 Package: GeuvadisTranscriptExpr Version: 1.39.0 Depends: R (>= 3.5.0) Suggests: limma, rtracklayer, GenomicRanges, Rsamtools, VariantAnnotation, tools, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: b2ed94256e833411f3e967bc0ccd2efc 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: devel git_last_commit: 092c368 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/GeuvadisTranscriptExpr_1.39.0.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: 1.29.0 Depends: R (>= 3.5) Suggests: GIGSEA, knitr, rmarkdown License: LGPL-3 MD5sum: 234d706417d49b8900358286689ba172 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: devel git_last_commit: 0f84c05 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/GIGSEAdata_1.29.0.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: 1.53.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: LGPL MD5sum: 9fb8aefae17075d9cb52ffa5253d1bdd 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: devel git_last_commit: 3236968 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/golubEsets_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: adSplit, Biobase, GlobalAncova, globaltest, idiogram, MLInterfaces, pvca, RDRToolbox, twilight dependencyCount: 7 Package: gpaExample Version: 1.23.0 Depends: R (>= 4.0.0) License: GPL (>= 2) MD5sum: ce3d4e69126ab5ded674bafc334964af 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: devel git_last_commit: a830843 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/gpaExample_1.23.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GPA dependencyCount: 0 Package: grndata Version: 1.43.0 Depends: R (>= 2.10) Suggests: RUnit, BiocGenerics, knitr License: GPL-3 MD5sum: 741d2fe47fc27e1aa25a4fef66c9c883 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: devel git_last_commit: b3d66cb git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/grndata_1.43.0.tar.gz vignettes: vignettes/grndata/inst/doc/grndata.html vignetteTitles: GRNdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: GSBenchMark Version: 1.31.0 Depends: R (>= 2.13.1) License: GPL-2 MD5sum: 68c8b5c5bc0e0a4953c73000601fb2b4 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: devel git_last_commit: e235e22 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/GSBenchMark_1.31.0.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: 1.17.0 Depends: Biobase, GEOquery Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown, SummarizedExperiment, SingleCellExperiment License: Artistic-2.0 MD5sum: 3488ba5f6256b8a42c27b8298d3c6103 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: devel git_last_commit: ecedb6c git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/GSE103322_1.17.0.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: 1.19.0 Depends: Biobase, GEOquery Imports: preprocessCore, SummarizedExperiment, GEOquery, Biobase Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown License: MIT License MD5sum: fb803f2197096df673e663b9562280bd 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: devel git_last_commit: b09ee23 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/GSE13015_1.19.0.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: 1.17.0 Suggests: ExperimentHub, BiocStyle, RefManageR, knitr, rmarkdown, testthat, minfi, tibble, sessioninfo License: MIT + file LICENSE MD5sum: 9e3b37e9842c87a7b38f82bc17b86e7d 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: devel git_last_commit: fc248ee git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/GSE159526_1.17.0.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: 1.39.0 Depends: Biobase, GEOquery Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown, DESeq2 License: Artistic-2.0 MD5sum: 796615d07a651b3a3080937d9ad1801a 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: devel git_last_commit: 18be338 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/GSE62944_1.39.0.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 dependencyCount: 75 Package: GSVAdata Version: 1.47.3 Depends: R (>= 4.0), Biobase, GSEABase, SummarizedExperiment Imports: methods, utils, Matrix, SpatialExperiment License: Artistic-2.0 MD5sum: 49f7e67c30e67583a5563bfe402204b8 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: 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, ExpressionData, SequencingData, Homo_sapiens_Data, CancerData, Tissue Author: Robert Castelo Maintainer: Robert Castelo git_url: https://git.bioconductor.org/packages/GSVAdata git_branch: devel git_last_commit: 40ba477 git_last_commit_date: 2026-04-17 Date/Publication: 2026-04-21 source.ver: src/contrib/GSVAdata_1.47.3.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSAR dependencyCount: 79 Package: GWASdata Version: 1.49.0 Depends: GWASTools Suggests: ncdf4 License: Artistic-2.0 MD5sum: 71eba9aacfe87a619cdd6fd76b324f33 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: devel git_last_commit: e6e0413 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/GWASdata_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GENESIS, GWASTools dependencyCount: 95 Package: h5vcData Version: 2.31.0 Suggests: h5vc License: GPL (>= 3) MD5sum: b8440eb5ef1d8a215ac630fe0fafea0e 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: devel git_last_commit: 6e2c7e2 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/h5vcData_2.31.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: h5vc dependencyCount: 0 Package: hapmap100khind Version: 1.53.0 Suggests: oligo License: GPL MD5sum: 48b0773fe8c2a5beeaa598701db0c4aa 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: devel git_last_commit: 45e32ee git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/hapmap100khind_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmap100kxba Version: 1.53.0 Suggests: oligo License: GPL MD5sum: 2ed467bdf7d4664c2fcfcba5536c63ea 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: devel git_last_commit: 2549fab git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/hapmap100kxba_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligo dependencyCount: 0 Package: hapmap500knsp Version: 1.53.0 Suggests: oligo License: GPL MD5sum: 0d6f5ba49fc640da45355783d652fd1e 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: devel git_last_commit: 65fe4f0 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/hapmap500knsp_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmap500ksty Version: 1.53.0 Suggests: oligo License: GPL MD5sum: c63d33f38aa3774b0d13e7c1aa2d1970 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: devel git_last_commit: b6467fc git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/hapmap500ksty_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmapsnp5 Version: 1.53.0 Suggests: oligo License: GPL MD5sum: 6f6014ccf38e06aad2fca81566ab4492 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: devel git_last_commit: 924b003 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/hapmapsnp5_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligoClasses dependencyCount: 0 Package: hapmapsnp6 Version: 1.53.0 Depends: R (>= 2.15) Suggests: oligo, oligoClasses License: GPL MD5sum: f79c74e77d802d120a59a68735d27512 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: devel git_last_commit: 3be1258 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/hapmapsnp6_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: crlmm, oligoClasses dependencyCount: 0 Package: harbChIP Version: 1.49.0 Depends: R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5), Biostrings Imports: methods, stats License: Artistic-2.0 MD5sum: b182b428d39e675d877a716f3f83a9a1 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: devel git_last_commit: 90701ae git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/harbChIP_1.49.0.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: 1.39.0 Depends: R (>= 3.5.0) Suggests: BiocGenerics, BiocStyle, knitr, rmarkdown, Harman (>= 1.23.3) License: GPL-3 MD5sum: 3ce56a33437b8a04b3b1e0bec78fa09f 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: devel git_last_commit: bf87e60 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/HarmanData_1.39.0.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: 1.33.0 Depends: R (>= 3.4.0) Imports: ExperimentHub Suggests: AnnotationHub, knitr, rmarkdown, igraph, survival, ANF, stats, testthat License: GPL-3 MD5sum: c36a26c3435153ca4cf6963a6fc7aae6 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: devel git_last_commit: a85f517 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/HarmonizedTCGAData_1.33.0.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: 64 Package: HCAData Version: 1.27.0 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: 1a161105663fc6ea90830651cda69245 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: devel git_last_commit: 2a738d3 git_last_commit_date: 2025-12-01 Date/Publication: 2026-04-21 source.ver: src/contrib/HCAData_1.27.0.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: 77 Package: HCATonsilData Version: 1.9.0 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: a31c0e8092b6b41b14733f46d7a46804 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: devel git_last_commit: 3cdd05d git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/HCATonsilData_1.9.0.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: 95 Package: HD2013SGI Version: 1.51.0 Depends: R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots, limma, vcd, LSD,EBImage Suggests: BiocStyle License: Artistic-2.0 MD5sum: 9d6f8774fbfc689642774de68fb368c8 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: devel git_last_commit: cf6aec3 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/HD2013SGI_1.51.0.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: 87 Package: HDCytoData Version: 1.31.0 Depends: ExperimentHub, SummarizedExperiment, flowCore Imports: utils, methods Suggests: BiocStyle, knitr, rmarkdown, Rtsne, umap, ggplot2, FlowSOM, mclust License: MIT + file LICENSE MD5sum: ec1c27c99b1a8261eac224cb35ecec8a 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: devel git_last_commit: 7007c4a git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/HDCytoData_1.31.0.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, MDSvis, tidyFlowCore dependencyCount: 83 Package: healthyControlsPresenceChecker Version: 1.15.0 Depends: R (>= 4.0.0) Imports: xml2, GEOquery, geneExpressionFromGEO, magrittr Suggests: RUnit, BiocGenerics, markdown, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 76cdaf3ebaa77ac6a1bf9601f1654b6d 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: 2d17613 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/healthyControlsPresenceChecker_1.15.0.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: 88 Package: healthyFlowData Version: 1.49.0 Depends: R (>= 2.15.0), flowCore Imports: methods License: Artistic-2.0 MD5sum: 3dae5eaa0440f31604086f6a0aa69198 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: devel git_last_commit: c6fcc5d git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/healthyFlowData_1.49.0.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: 22 Package: HEEBOdata Version: 1.49.0 License: LGPL MD5sum: 8e383d901c708f399e1e40bcc734e5b9 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: devel git_last_commit: c9299c3 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/HEEBOdata_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQuality dependencyCount: 0 Package: HelloRangesData Version: 1.37.0 Suggests: BiocStyle License: GPL (>= 2) MD5sum: a2c16cadeeb3bf6b21f1fdf11a6175a1 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: devel git_last_commit: 7fad08b git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/HelloRangesData_1.37.0.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: 1.49.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 608d44be01d3a1c9ff95e33aa931e6c2 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: devel git_last_commit: 697af76 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/hgu133abarcodevecs_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hgu133plus2barcodevecs Version: 1.49.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 0584cdff37dca33f9438d7223d4c037f 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: devel git_last_commit: 36aaeb6 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/hgu133plus2barcodevecs_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hgu133plus2CellScore Version: 1.31.0 Depends: R (>= 3.5.0) Imports: Biobase (>= 2.39.1) Suggests: knitr License: GPL-3 MD5sum: 2051b6bfa2989f552445ceee8624e1cc 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: devel git_last_commit: dc96491 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/hgu133plus2CellScore_1.31.0.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: 1.51.0 Depends: R (>= 2.0.0) License: Artistic-2.0 MD5sum: 790f018fb6bf0416da07fcb836195c36 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: devel git_last_commit: c9cd1f5 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/hgu2beta7_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: HiBED Version: 1.9.0 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: ffb3ca08c6eaa56b3b22a8e9c8d1ebc7 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: devel git_last_commit: 07e667d git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/HiBED_1.9.0.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: 86 Package: HiCDataHumanIMR90 Version: 1.31.0 Depends: R (>= 3.5.0) Suggests: HiTC, BiocStyle License: GPL-3 MD5sum: 375aac778b01301b592dcb58af54e800 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: devel git_last_commit: b03f8a8 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/HiCDataHumanIMR90_1.31.0.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: 1.47.0 Suggests: ShortRead License: GPL-3 MD5sum: da09abdba8f9266f0fccd0826657623e 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: devel git_last_commit: 9eba266 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/HiCDataLymphoblast_1.47.0.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: 1.13.0 Depends: ExperimentHub Imports: BiocFileCache, AnnotationHub Suggests: testthat, methods, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: a906001e80d4662980cdade81afbd2a2 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: devel git_last_commit: 300b55b git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/HiContactsData_1.13.0.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, HiSpaR, plyinteractions dependencyCount: 64 Package: HighlyReplicatedRNASeq Version: 1.23.0 Depends: SummarizedExperiment, ExperimentHub Imports: S4Vectors Suggests: BiocStyle, BiocFileCache, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 76f5cf574f18934da060c19e075bf42c 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: devel git_last_commit: cc0c8b9 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/HighlyReplicatedRNASeq_1.23.0.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: 75 Package: HIVcDNAvantWout03 Version: 1.51.0 License: GPL (>= 2) MD5sum: 14cb88902ab47675cb65218f4ba6194c 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: devel git_last_commit: 2a1feff git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/HIVcDNAvantWout03_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: HMP16SData Version: 1.31.0 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: 42a3069e16b16053cb7c721018ddd45d 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: devel git_last_commit: dbabb16 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/HMP16SData_1.31.0.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: 108 Package: HSMMSingleCell Version: 1.31.0 Depends: R (>= 2.10) License: Artistic-2.0 MD5sum: 8824113cdb473b65d1ffa3cd531aa1d1 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: devel git_last_commit: 53600e2 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/HSMMSingleCell_1.31.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: monocle dependencyCount: 0 Package: HumanAffyData Version: 1.37.0 Depends: ExperimentHub, Biobase, R (>= 3.3) Suggests: BiocStyle License: Artistic-2.0 MD5sum: 5ce6fda2956ed92bb6525d105f76f2d3 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: devel git_last_commit: 1dc982b git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/HumanAffyData_1.37.0.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: 64 Package: humanHippocampus2024 Version: 1.3.0 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: f48b1bf3d0b295c8116b56ab9ea65f5d 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: devel git_last_commit: 25483ec git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/humanHippocampus2024_1.3.0.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: 80 Package: HumanRetinaLRSData Version: 0.99.5 Depends: R (>= 4.6.0), SummarizedExperiment Imports: osfr, BiocFileCache Suggests: testthat, knitr, rmarkdown, ggplot2, ggrepel License: MIT + file LICENSE MD5sum: dcb6aa769085c9c6c40a64067d036c37 NeedsCompilation: no Title: Long-read RNA-seq gene count data from human retinal organoids Description: Dataset package containing gene and isoform count matrices, and sample metadata for long-read direct cDNA sequencing of human retinal organoids, 2D retinal ganglion cell (RGC) cultures, and flowthrough fractions from H9 and EP1 iPSC cell lines. Data were generated using Oxford Nanopore Technology (ONT) direct cDNA sequencing and mapped to the GRCh38 reference genome (GENCODE v46 annotation). The package provides accessor functions returning SummarizedExperiment objects for gene-level counts, isoform-level counts, and a matrix of allele-specific expression (ASE) gene counts. Data files are stored in flat CSV format in an Open Science Framework (OSF) repository and cached locally via BiocFileCache. biocViews: ExperimentData, RNASeqData, ExpressionData, Homo_sapiens_Data, CellCulture Author: Sowmya Parthiban [aut, cre] Maintainer: Sowmya Parthiban URL: https://github.com/sparthib/HumanRetinaLrsData VignetteBuilder: knitr BugReports: https://github.com/sparthib/HumanRetinaLrsData/issues git_url: https://git.bioconductor.org/packages/HumanRetinaLRSData git_branch: devel git_last_commit: e3942cd git_last_commit_date: 2026-03-31 Date/Publication: 2026-04-21 source.ver: src/contrib/HumanRetinaLRSData_0.99.5.tar.gz vignettes: vignettes/HumanRetinaLRSData/inst/doc/example_analysis.html vignetteTitles: Retinal Organoids counts data: Gene and Isoform Level Exploration hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HumanRetinaLRSData/inst/doc/example_analysis.R dependencyCount: 71 Package: humanStemCell Version: 0.51.0 Depends: Biobase (>= 2.5.5), hgu133plus2.db License: Artistic-2.0 MD5sum: 1cfa175a5e02cb0841d78ab1ea4a172d 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: devel git_last_commit: 0464958 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/humanStemCell_0.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MiRaGE, rtracklayer dependencyCount: 44 Package: IHWpaper Version: 1.39.0 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: 4fdbd27d8417fe2be0402c7a055cd8e7 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: devel git_last_commit: 947f36c git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/IHWpaper_1.39.0.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: 98 Package: Illumina450ProbeVariants.db Version: 1.47.0 Depends: R (>= 3.0.1) License: GPL-3 MD5sum: ee0c8430b5b7f5e77a5322071de1bc36 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: devel git_last_commit: d58d0d2 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/Illumina450ProbeVariants.db_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: IlluminaDataTestFiles Version: 1.49.0 License: Artistic-2.0 MD5sum: c765cce97afaa44ee8e497bed3186d4a 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: devel git_last_commit: 82be2b6 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/IlluminaDataTestFiles_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: illuminaio dependencyCount: 0 Package: imcdatasets Version: 1.19.0 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: b2afd23b0e346b44e4bb6172594d60e8 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: devel git_last_commit: 67f1ac9 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/imcdatasets_1.19.0.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: 82 Package: iModMixData Version: 1.1.0 Imports: ExperimentHub Suggests: knitr, testthat License: GPL-3 MD5sum: 824d7bbd894c6fc0b24fba6cca9c2ac5 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: devel git_last_commit: 7f21dc6 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/iModMixData_1.1.0.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: 64 Package: ITALICSData Version: 2.49.0 Depends: R (>= 2.0.0) License: GPL MD5sum: 66e7094f3f80b8936203f94beb685e59 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: devel git_last_commit: fc81046 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ITALICSData_2.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ITALICS dependencyCount: 0 Package: Iyer517 Version: 1.53.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: f545f5e6e434618d086cc140802e39a5 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: devel git_last_commit: aa66305 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/Iyer517_1.53.0.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 suggestsMe: DendSer dependencyCount: 7 Package: JASPAR2014 Version: 1.47.0 Depends: R (>= 3.0.1), methods, Biostrings (>= 2.29.19) License: GPL-2 MD5sum: 880662f867ef8c3b8c7f04ea3d6887c5 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: devel git_last_commit: d27e6eb git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/JASPAR2014_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MatrixRider, TFBSTools dependencyCount: 15 Package: JASPAR2016 Version: 1.39.0 Depends: R (>= 3.2.2), methods License: GPL-2 MD5sum: 1bb2f54076e2ab05c98609ca10be6e09 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: devel git_last_commit: 3f35e9b git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/JASPAR2016_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: TFBSTools, CAGEWorkflow dependencyCount: 1 Package: JohnsonKinaseData Version: 1.7.0 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: d76cc6226493270c9a7966e3164d2965 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: devel git_last_commit: cd968b0 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/JohnsonKinaseData_1.7.0.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: 75 Package: KEGGandMetacoreDzPathwaysGEO Version: 1.31.0 Depends: R (>= 2.15.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: a05201ec152d04364b4fd3bea29bc726 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: devel git_last_commit: 2339475 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/KEGGandMetacoreDzPathwaysGEO_1.31.0.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 dependencyCount: 7 Package: KEGGdzPathwaysGEO Version: 1.49.0 Depends: R (>= 2.13.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: 40ebe60691ece2d6f2fabf7753fd269a 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: devel git_last_commit: 19d5122 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/KEGGdzPathwaysGEO_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: PADOG dependencyCount: 7 Package: kidpack Version: 1.53.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5) License: GPL-2 MD5sum: f440e37916ca9590621a9dc7eaec0e2b 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: devel git_last_commit: 3a850d1 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/kidpack_1.53.0.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: 1.37.0 Depends: R (>= 3.3.0) License: MIT + file LICENSE MD5sum: c6b6582ed982eee505c48ab1dd372585 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: devel git_last_commit: 42652c7 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/KOdata_1.37.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: KEGGlincs dependencyCount: 0 Package: leeBamViews Version: 1.47.0 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: 202e0daa62348c99a3a46a4d75af51ef 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: devel git_last_commit: 8820778 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/leeBamViews_1.47.0.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: 1.5.0 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: f3f89cd86a96c31765558eab926bb2ea 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: devel git_last_commit: e6be75b git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/LegATo_1.5.0.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: 190 Package: leukemiasEset Version: 1.47.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: de02f827e63eec31e363e1bc4102da76 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: devel git_last_commit: 5ac319a git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/leukemiasEset_1.47.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: geNetClassifier, multiclassPairs dependencyCount: 7 Package: LiebermanAidenHiC2009 Version: 0.49.0 Depends: KernSmooth, IRanges License: LGPL MD5sum: 070870d4200262848eb289ec4c40a273 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: devel git_last_commit: 7144525 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/LiebermanAidenHiC2009_0.49.0.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: 1.43.0 Depends: R (>= 3.1.1), methylPipe Suggests: BSgenome.Hsapiens.UCSC.hg18 License: Artistic 2.0 MD5sum: 2745ca5cd093342c285fb3f23b8fcb14 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: devel git_last_commit: 2f0c547 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ListerEtAlBSseq_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 159 Package: LRcellTypeMarkers Version: 1.19.0 Depends: R (>= 4.1) Imports: ExperimentHub Suggests: LRcell, BiocStyle, knitr, rmarkdown, roxygen2, testthat License: MIT + file LICENSE MD5sum: a1edafafa7866ace0915cb77dfab105c 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: devel git_last_commit: f891879 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/LRcellTypeMarkers_1.19.0.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: 64 Package: lumiBarnes Version: 1.51.0 Depends: R (>= 2.0), Biobase (>= 2.5.5), lumi (>= 1.1.0) License: LGPL MD5sum: 7a5d3af8886752d7c33d6c78247a34ab 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: devel git_last_commit: 5dc920e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/lumiBarnes_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 8 Package: LungCancerACvsSCCGEO Version: 1.47.0 Depends: R (>= 2.15.0) License: GPL-2 MD5sum: b9d1c83d3d44df47ccab6c0c413dea13 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: devel git_last_commit: f43d276 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/LungCancerACvsSCCGEO_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: LungCancerLines Version: 0.49.2 Imports: Rsamtools License: Artistic-2.0 MD5sum: 7fdbb419da4edd0ecad15fcb11f6e453 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: devel git_last_commit: 15622ad git_last_commit_date: 2026-02-14 Date/Publication: 2026-04-21 source.ver: src/contrib/LungCancerLines_0.49.2.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: gmapR, VariantTools dependencyCount: 29 Package: lungExpression Version: 0.49.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 56acb93fd9e9146fc67d3e62a0a07343 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: devel git_last_commit: a782b57 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/lungExpression_0.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: globaltest dependencyCount: 7 Package: lydata Version: 1.37.0 License: MIT + file LICENSE MD5sum: 53e07baeaaf0fcc7bc43ee69318056a6 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: devel git_last_commit: 70e0424 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/lydata_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: M3DExampleData Version: 1.37.0 Depends: R (>= 3.3) License: GPL (>=2) MD5sum: 0f07a2eec74ad9a0794e5a430635791a 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: devel git_last_commit: ccbc7fe git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/M3DExampleData_1.37.0.tar.gz hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: celda, M3Drop dependencyCount: 0 Package: macrophage Version: 1.27.0 Depends: R (>= 3.5.0) Suggests: knitr, markdown License: GPL (>= 2) MD5sum: a4f817b90f674ee352b86d977f539896 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: devel git_last_commit: c9296a1 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/macrophage_1.27.0.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, fluentGenomics dependencyCount: 0 Package: MACSdata Version: 1.19.0 License: file LICENSE MD5sum: 2ae1886a0209828a8af0792091cd2183 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: devel git_last_commit: 771d018 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/MACSdata_1.19.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: mammaPrintData Version: 1.47.0 Depends: R (>= 2.13.0) Suggests: Biobase, readxl, limma License: Artistic-2.0 MD5sum: 18249496686e4bcacdd8df9811de8fc0 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: devel git_last_commit: ec4044a git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/mammaPrintData_1.47.0.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: 1.55.0 Suggests: oligo, pdInfoBuilder License: GPL MD5sum: d2e871d81ce13b522f54f50d031fdefe 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: devel git_last_commit: 022851d git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/maqcExpression4plex_1.55.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligo dependencyCount: 0 Package: MAQCsubset Version: 1.49.0 Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), lumi, methods Suggests: genefilter, codelink License: Artistic-2.0 MD5sum: b879cd401eccb63d967e930fe6bd6773 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: devel git_last_commit: e617b52 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/MAQCsubset_1.49.0.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 dependencyCount: 13 Package: marinerData Version: 1.11.0 Imports: utils, ExperimentHub Suggests: knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0) License: GPL-3 MD5sum: 7d48d122c3d7299064869bf5d9bf99d2 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: devel git_last_commit: 81431b4 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/marinerData_1.11.0.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 dependencyCount: 64 Package: mCSEAdata Version: 1.31.1 Depends: R (>= 3.5) Imports: GenomicRanges Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 22c8a83a4b122a813bbef0fb45ecd77c 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: devel git_last_commit: 679fb79 git_last_commit_date: 2025-11-07 Date/Publication: 2026-04-21 source.ver: src/contrib/mCSEAdata_1.31.1.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: 1.29.0 Depends: R (>= 3.5), ExperimentHub Imports: AnnotationHub, Biobase Suggests: BiocStyle, knitr License: GPL (>=2) MD5sum: d827db805673e08afae8cece3e508e4f 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: devel git_last_commit: 6a39a6d git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/mcsurvdata_1.29.0.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: 64 Package: MEDIPSData Version: 1.47.0 Depends: R (>= 3.5) Suggests: MEDIPS, GenomicRanges, qsea License: GPL (>= 2) MD5sum: 9e1145a31a52d7511a4310e90ca59675 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: devel git_last_commit: 5388692 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/MEDIPSData_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MEDIPS, qsea dependencyCount: 0 Package: MEEBOdata Version: 1.49.0 License: LGPL MD5sum: af29d6d92879124ac2d63ed0983d745f 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: devel git_last_commit: 5664775 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/MEEBOdata_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQuality dependencyCount: 0 Package: MetaGxBreast Version: 1.31.0 Depends: R (>= 3.6.0), Biobase, AnnotationHub, ExperimentHub Imports: stats, lattice, impute, SummarizedExperiment Suggests: testthat, xtable, tinytex License: Apache License (>= 2) MD5sum: a9122d2229070bffd84c997975361c27 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: devel git_last_commit: e909c99 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/MetaGxBreast_1.31.0.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: 76 Package: MetaGxOvarian Version: 1.31.0 Depends: Biobase, AnnotationHub, ExperimentHub, SummarizedExperiment, R (>= 3.6.0) Imports: stats, lattice, impute Suggests: testthat, xtable, rmarkdown, knitr, BiocStyle, markdown License: Artistic-2.0 MD5sum: 71a84f510741089e51ac3c3b78d544bf 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 git_url: https://git.bioconductor.org/packages/MetaGxOvarian git_branch: devel git_last_commit: f7961b3 git_last_commit_date: 2026-04-01 Date/Publication: 2026-04-21 source.ver: src/contrib/MetaGxOvarian_1.31.0.tar.gz vignettes: vignettes/MetaGxOvarian/inst/doc/MetaGxOvarian.html vignetteTitles: MetaGxOvarian: A Package for Ovarian Cancer Gene Expression Analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MetaGxOvarian/inst/doc/MetaGxOvarian.R dependencyCount: 76 Package: MetaGxPancreas Version: 1.31.0 Depends: SummarizedExperiment, ExperimentHub, R (>= 3.6.0) Imports: stats, impute, S4Vectors, AnnotationHub Suggests: testthat, knitr, BiocStyle, rmarkdown, markdown License: Artistic-2.0 MD5sum: 0e9386ca902897e21fe820a3d3802303 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: devel git_last_commit: c90980a git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/MetaGxPancreas_1.31.0.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: 76 Package: metaMSdata Version: 1.47.0 License: GPL (>= 2) MD5sum: 0387565e4e0576cc9babac372f83fa5f 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: devel git_last_commit: 8953db0 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/metaMSdata_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: MetaScope Version: 1.99.10 Depends: R (>= 4.2.0) Imports: BiocFileCache, Biostrings, data.table (>= 1.16.2), dplyr, ggplot2, magrittr, Matrix, MultiAssayExperiment, purrr, 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: 7c3fe8a1f56d8e45da756a1f1c2dc8ec 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: d49e047 git_last_commit_date: 2025-11-07 Date/Publication: 2026-04-21 source.ver: src/contrib/MetaScope_1.99.10.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: 99 Package: MethylAidData Version: 1.43.0 Depends: MethylAid, R (>= 3.2) Suggests: BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC License: GPL (>= 2) MD5sum: 93366c9176fa3e0d22d7046e1b9ba0a6 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: devel git_last_commit: 1bf3996 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/MethylAidData_1.43.0.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 dependencyCount: 1 Package: methylclockData Version: 1.19.0 Imports: ExperimentHubData, ExperimentHub, utils Suggests: knitr, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: 62c2a47b97d1379f21cc07e16fd5cd57 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: devel git_last_commit: 4ef1a25 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/methylclockData_1.19.0.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 dependencyCount: 119 Package: MethylSeqData Version: 1.21.0 Depends: SummarizedExperiment Imports: ExperimentHub, HDF5Array, rhdf5, GenomeInfoDb, S4Vectors, GenomicRanges, stats, IRanges, utils Suggests: BiocFileCache, BiocStyle, data.table, knitr, rmarkdown License: CC0 MD5sum: eb3ae61f4a6c2f71c59cb1eb971f3457 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: devel git_last_commit: 7f8e7ed git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/MethylSeqData_1.21.0.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: 1.13.0 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: 0577c37b235843846aa6adf613a279be 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: devel git_last_commit: f616b77 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/MicrobiomeBenchmarkData_1.13.0.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: 84 Package: microbiomeDataSets Version: 1.19.0 Depends: R (>= 4.1), SummarizedExperiment, TreeSummarizedExperiment, MultiAssayExperiment Imports: methods, utils, BiocGenerics, ExperimentHub, Biostrings, ape Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, testthat License: CC0 MD5sum: 9e937e2ee88b642af027eee3dedb1cd8 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: devel git_last_commit: 192159c git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/microbiomeDataSets_1.19.0.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: 96 Package: microRNAome Version: 1.33.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: BiocGenerics, RUnit License: GPL (>= 2) MD5sum: 1f3b64238b97207cfa236e302ff08a80 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: devel git_last_commit: de18465 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/microRNAome_1.33.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 25 Package: minfiData Version: 0.57.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2), IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 License: Artistic-2.0 MD5sum: 9892bab1d187260ea05111c1e95b9c48 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: devel git_last_commit: 537d2da git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/minfiData_0.57.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: methylationArrayAnalysis suggestsMe: Harman, MultiDataSet, regionalpcs, MethylAidData dependencyCount: 3 Package: minfiDataEPIC Version: 1.37.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2), IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: Artistic-2.0 MD5sum: 8501eba899f11a09ed33f507173c5766 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: devel git_last_commit: b3b48f5 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/minfiDataEPIC_1.37.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MethylAidData dependencyCount: 3 Package: minionSummaryData Version: 1.41.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 9ba0d99ab176bea38e50d5449ac8991d 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: devel git_last_commit: 9ecdff9 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/minionSummaryData_1.41.0.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 dependencyCount: 0 Package: miRcompData Version: 1.41.0 Depends: R (>= 3.2), Imports: utils License: GPL-3 | file LICENSE MD5sum: 8826f6c6ab9fa6f7d9f89ff0a4cb0cc1 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: devel git_last_commit: d087ded git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/miRcompData_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: miRcomp dependencyCount: 1 Package: miRNATarget Version: 1.49.0 Depends: R (>= 2.10), Biobase License: GPL MD5sum: f91a928c38c685e6be1dda8d139972bf 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: devel git_last_commit: 8e138de git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/miRNATarget_1.49.0.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: 1.47.0 Suggests: MMDiff2 License: LGPL MD5sum: d6493d00af7683cd16c94a27cc64bb45 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: devel git_last_commit: 0b7e95a git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/MMDiffBamSubset_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MMDiff2 dependencyCount: 0 Package: MOFAdata Version: 1.27.0 Depends: R (>= 3.5) Suggests: knitr, MultiAssayExperiment, rmarkdown, BiocStyle License: LGPL-3 MD5sum: d40b3980005c299f6aa705c5ba334622 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: devel git_last_commit: f1a188a git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/MOFAdata_1.27.0.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: SUMO dependencyCount: 0 Package: mosaicsExample Version: 1.49.0 Depends: R (>= 2.11.1) License: GPL (>= 2) MD5sum: e48275cd066b7c4c6e2be7bc5ad40564 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: devel git_last_commit: 1f3e0a1 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/mosaicsExample_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: mosaics dependencyCount: 0 Package: mouse4302barcodevecs Version: 1.49.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 1ec3fc01865cd0de573f7e12db7f7fb0 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: devel git_last_commit: 0280de3 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/mouse4302barcodevecs_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: MouseAgingData Version: 1.7.1 Depends: R (>= 4.4.0), SingleCellExperiment Imports: AnnotationHub, ExperimentHub Suggests: BiocStyle, knitr, rmarkdown, scater License: Artistic-2.0 MD5sum: 1bb98f11234d8ea852b47d4ef2a94d84 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: devel git_last_commit: 667daf0 git_last_commit_date: 2026-04-07 Date/Publication: 2026-04-21 source.ver: src/contrib/MouseAgingData_1.7.1.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: 76 Package: MouseGastrulationData Version: 1.25.0 Depends: R (>= 4.1), SingleCellExperiment, SummarizedExperiment, SpatialExperiment Imports: methods, ExperimentHub, BiocGenerics, S4Vectors, BumpyMatrix Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 97cb89b5e8e16dcf0d72eec666518754 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: devel git_last_commit: eba42d3 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/MouseGastrulationData_1.25.0.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: 81 Package: MouseThymusAgeing Version: 1.19.0 Depends: SingleCellExperiment, SummarizedExperiment Imports: ExperimentHub, methods, BiocGenerics, S4Vectors Suggests: knitr, scuttle, rmarkdown, BiocStyle License: GPL-3 MD5sum: 25adcc857aa0fd79c51ae3bcadb49254 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: devel git_last_commit: 7a75646 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/MouseThymusAgeing_1.19.0.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: 76 Package: msd16s Version: 1.31.0 Depends: R (>= 2.10), Biobase, metagenomeSeq, License: Artistic-2.0 MD5sum: b3b608ad1226e0fffa3bc551cd3f3237 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: devel git_last_commit: 8e42a58 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/msd16s_1.31.0.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: 0.51.2 Depends: R (>= 3.5.0) Suggests: xcms, mzR, MSnbase License: GPL (>= 2) MD5sum: 89891c42748da5f0278b7565d057dad7 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: devel git_last_commit: 04043a9 git_last_commit_date: 2026-04-16 Date/Publication: 2026-04-21 source.ver: src/contrib/msdata_0.51.2.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: Chromatograms, QFeatures, TargetDecoy, RforProteomics dependencyCount: 0 Package: msigdb Version: 1.19.0 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: e9bd47191695ab6aa32c05965971ee44 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: devel git_last_commit: 5e3257e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/msigdb_1.19.0.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, postNet, vissE suggestsMe: epiregulon.extra, escape dependencyCount: 71 Package: MSMB Version: 1.29.0 Depends: R (>= 3.5), tibble Suggests: knitr, BiocStyle License: LGPL MD5sum: 9d9fea01a1211b0843a6748e372e3f6a 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: devel git_last_commit: 838367e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/MSMB_1.29.0.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: 1.39.1 Suggests: knitr License: GPL (>= 2) MD5sum: 2674dad5befd360c5cc458027fe02aa2 NeedsCompilation: no Title: Data to test the msPurity package Description: 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: devel git_last_commit: babdf58 git_last_commit_date: 2026-02-19 Date/Publication: 2026-04-21 source.ver: src/contrib/msPurityData_1.39.1.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: msPurity dependencyCount: 0 Package: msqc1 Version: 1.39.0 Depends: R (>= 3.6), lattice, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, specL (>= 1.2) License: GPL MD5sum: 38485d642f93fe9ef1316578f1823c32 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: devel git_last_commit: ecf7b45 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/msqc1_1.39.0.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: 1.41.0 Depends: R (>= 2.10) Suggests: MSnbase, xcms (>= 3.13.8), CAMERA, knitr, Heatplus, pcaMethods, sp, rmarkdown, Biobase License: CC0 MD5sum: 271bc5e349656e100009c2183ded2161 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: devel git_last_commit: 7de31ee git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/mtbls2_1.41.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: yamss dependencyCount: 0 Package: MUGAExampleData Version: 1.31.0 Depends: R (>= 2.10.0) License: GPL-3 MD5sum: 0ea738fb8dad85c4f02f4f782a5e5af9 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: devel git_last_commit: 4ad6682 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/MUGAExampleData_1.31.0.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: 1.7.0 Suggests: knitr, rmarkdown, ExperimentHub, dplyr License: MIT + file LICENSE MD5sum: a19341b7a1ef724dd29e795c41daa1d1 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: devel git_last_commit: 6aa879e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/muleaData_1.7.0.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: 1.9.0 Depends: ExperimentHub Imports: utils Suggests: BiocStyle, knitr, multiWGCNA, rmarkdown, SummarizedExperiment License: Artistic-2.0 MD5sum: fff121b8188bf865d517e03b7ac4d0f3 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: devel git_last_commit: 1e66c88 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/multiWGCNAdata_1.9.0.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: 64 Package: muscData Version: 1.25.0 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: d66504f9debb52275165b81e11403c2c 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: devel git_last_commit: 15308ed git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/muscData_1.25.0.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 dependencyCount: 76 Package: muSpaData Version: 1.3.0 Depends: R (>= 4.5.0), ExperimentHub Suggests: SpatialExperiment, ggplot2, BiocStyle, knitr, rmarkdown, R.utils License: MIT + file LICENSE MD5sum: fd98f20c362480e83be8893665aa8db7 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: devel git_last_commit: cfc96e3 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/muSpaData_1.3.0.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: 64 Package: MutSeqRData Version: 0.99.4 Depends: R (>= 3.5.0) Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 3261729fed31a01186b15bf44633d937 NeedsCompilation: no Title: Experimental Data for MutSeqR Examples Description: Experimental data for use with the MutSeqR vignette and examples. This dataset is taken from LeBlanc et al., 2022. 24 MutaMouse animals were exposed to one of three doses of benzo[a]pyrene or a vehicle control for 28 days by oral gavage. 28 days after the end of the exposure, bone marrow of the femurs was harvested from euthanized animals. DNA extraction was conducted via DNeasy Blood and Tissue kit. DNA samples were sequenced using TwinStrand's Duplex Sequencing on the Mouse Mutagenesis Panel at > 10,000 depth. The Mouse Mutagenesis Panel comprises 20 2.4kb genomic targets with one located on each mouse autosome (two on chromosome 1). Pre-processing of sequence reads was redone since publication using an updated version of TwinStrand's Mutagenesis App (v. 3.20.1) which produced tabular mutation data files for each sample. Data contained herein are only those required for running MutSeqR examples and vignette. biocViews: ExperimentHub, Mus_musculus_Data, Genome, Somatic, SequencingData Author: Annette E. Dodge [aut] (ORCID: ), Andrew Williams [aut] (ORCID: ), Danielle P.M. LeBlanc [aut] (ORCID: ), David M. Schuster [aut] (ORCID: ), Elena Esina [aut] (ORCID: ), Clint C. Valentine [aut], Jesse J. Salk [aut], Alexander Y. Maslov [aut], Christopher Bradley [aut], Carole L. Yauk [aut] (ORCID: ), Francesco Marchetti [aut] (ORCID: ), Matthew J. Meier [aut, cre] (ORCID: ), Geronimo Matteo [ctb] (ORCID: ) Maintainer: Matthew J. Meier URL: https://github.com/EHSRB-BSRSE-Bioinformatics/MutSeqRData/ VignetteBuilder: knitr BugReports: https://github.com/EHSRB-BSRSE-Bioinformatics/MutSeqRData/issues git_url: https://git.bioconductor.org/packages/MutSeqRData git_branch: devel git_last_commit: 121dd0f git_last_commit_date: 2025-12-09 Date/Publication: 2026-04-21 source.ver: src/contrib/MutSeqRData_0.99.4.tar.gz vignettes: vignettes/MutSeqRData/inst/doc/Supporting_data_for_MutSeqR.html vignetteTitles: SUpporting data for the MutSeqR package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/MutSeqRData/inst/doc/Supporting_data_for_MutSeqR.R suggestsMe: MutSeqR dependencyCount: 0 Package: mvoutData Version: 1.47.0 Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4), lumi License: Artistic-2.0 MD5sum: d7340ed9ab72472f8971fdbed4d7abe4 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: devel git_last_commit: a19777a git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/mvoutData_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 13 Package: NanoporeRNASeq Version: 1.21.0 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: 7199530e34c011f66b5f5fd130dda7a4 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: devel git_last_commit: 6c1af5c git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/NanoporeRNASeq_1.21.0.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: 64 Package: nanotubes Version: 1.27.0 Depends: R (>= 3.6) Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, rtracklayer, CAGEfightR License: GPL-3 MD5sum: 9ba980c30a29566f661954bcfb19d9c3 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: devel git_last_commit: b1ab539 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/nanotubes_1.27.0.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: 1.47.0 Depends: R (>= 2.10.0) Suggests: Rgraphviz License: GPL-3 MD5sum: 192837fe033410320bfce36c25ff0eac 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: devel git_last_commit: 791af8f git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/NCIgraphData_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: NestLink Version: 1.27.0 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: dbc3ed2140f1a4977ebb06d060ff4108 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: devel git_last_commit: e814733 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/NestLink_1.27.0.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: 105 Package: NetActivityData Version: 1.13.0 Depends: R (>= 4.2.0) Suggests: BiocStyle, knitr License: MIT + file LICENSE MD5sum: ee92681dc862adc272462c32ee9c1eed 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: devel git_last_commit: 28d1a6e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/NetActivityData_1.13.0.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: 0.49.0 Depends: R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0), hgu133a.db, annotate License: Artistic-2.0 MD5sum: 57f6fe0fdd9cec7bb5987fd6a5ac3e0e 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: devel git_last_commit: 1ce99ca git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/Neve2006_0.49.0.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: 47 Package: NGScopyData Version: 1.31.0 License: GPL (>=2) MD5sum: 4b81f01178538ea1cb09711cd3de8449 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: devel git_last_commit: c1a07b3 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/NGScopyData_1.31.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: nmrdata Version: 1.1.0 Imports: ExperimentHub, Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 91c055089ba6633c10060abb1d5b0d18 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: devel git_last_commit: 17a3827 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/nmrdata_1.1.0.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: 64 Package: nullrangesData Version: 1.17.0 Depends: R (>= 4.1.0), ExperimentHub, GenomicRanges, InteractionSet Imports: utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 2de664f774bfed2bd70a2f6d387843e0 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: devel git_last_commit: 00b15eb git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/nullrangesData_1.17.0.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: 77 Package: NxtIRFdata Version: 1.17.0 Imports: ExperimentHub, BiocFileCache, rtracklayer, R.utils Suggests: testthat (>= 3.0.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: 81c7a16c62e81ef87bc3634f8b54de87 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: devel git_last_commit: 5da9a2a git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/NxtIRFdata_1.17.0.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 dependencyCount: 98 Package: ObMiTi Version: 1.19.0 Depends: R (>= 4.1), SummarizedExperiment, ExperimentHub Suggests: knitr, rmarkdown, BiocManager, GenomicFeatures, S4Vectors, devtools, testthat License: GPL-3 MD5sum: 53dbfb890761032210b55fae7ef65a96 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: devel git_last_commit: 97a959e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ObMiTi_1.19.0.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: 75 Package: oct4 Version: 1.27.0 Suggests: knitr, markdown License: GPL (>= 2) MD5sum: c04c809e41868aa5e75fc3ea9d57590e 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: devel git_last_commit: c904f57 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/oct4_1.27.0.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: 1.13.0 Depends: R (>= 4.2.0), ExperimentHub Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 997b756ccb1a93960020025b1fc030d2 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: devel git_last_commit: 55a36e8 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/octad.db_1.13.0.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 dependencyCount: 64 Package: OMICsPCAdata Version: 1.29.0 Depends: R (>= 3.5.0), MultiAssayExperiment Suggests: knitr, kableExtra, rmarkdown License: GPL-3 MD5sum: 9120ec9585c33ecec2a45e916c544890 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: devel git_last_commit: d48d813 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/OMICsPCAdata_1.29.0.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: 1.33.0 Depends: R (>= 3.4) Imports: rJava Suggests: BiocStyle, rmarkdown, knitr License: GPL-2 MD5sum: e155092d0c82c862fdfc255415203429 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: devel git_last_commit: 1dfe39a git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/OnassisJavaLibs_1.33.0.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: 1.23.0 Depends: R (>= 4.0) Suggests: knitr, BiocStyle, rmarkdown, magick License: Artistic-2.0 MD5sum: 9acf885d42b29024c8ab862d554b8df4 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: devel git_last_commit: af24258 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/optimalFlowData_1.23.0.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: 1.9.0 Imports: AnnotationHub, BiocFileCache, ExperimentHub, HDF5Array, stringr, SummarizedExperiment Suggests: BiocStyle, ggplot2, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 0d85d153b756e7d67dea69eff220be58 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: devel git_last_commit: ab47470 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/orthosData_1.9.0.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 dependencyCount: 76 Package: pasilla Version: 1.39.0 Depends: R (>= 3.5.0), DEXSeq Suggests: rmarkdown, BiocStyle, knitr, roxygen2 License: LGPL MD5sum: eadeaf6244664ff3c4618dfe088f3dc7 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: devel git_last_commit: 876d078 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/pasilla_1.39.0.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, EnhancedVolcano, gsean, regionReport, tidybulk, tidyprint, pasillaBamSubset dependencyCount: 109 Package: pasillaBamSubset Version: 0.49.0 Suggests: pasilla License: LGPL MD5sum: dbb906571efd4bb19e640e9670c13fba 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: devel git_last_commit: a8954ab git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/pasillaBamSubset_0.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: DEXSeq, GenomicAlignments, GenomicFeatures, GenomicRanges, gmoviz, IRanges, plyranges dependencyCount: 0 Package: PasillaTranscriptExpr Version: 1.39.0 Depends: R (>= 3.3.0) Suggests: rtracklayer, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: f176f91b5bc47f248bbb50c78e0f35f9 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: devel git_last_commit: 55e1912 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/PasillaTranscriptExpr_1.39.0.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: 1.47.0 Depends: R (>= 1.14.0) License: GPL-3 MD5sum: 23880d54d6908d8144163aa1d22a08a2 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: devel git_last_commit: 8187cdb git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/PathNetData_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PathNet dependencyCount: 0 Package: PCHiCdata Version: 1.39.0 Depends: R (>= 3.2), Chicago Suggests: testthat, BiocStyle, knitr License: Artistic-2.0 MD5sum: 42f26262233322e50ce510e54f51ead3 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: devel git_last_commit: 32f8cec git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/PCHiCdata_1.39.0.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: 67 Package: pd.atdschip.tiling Version: 0.49.0 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: 85b3151c1006af7fe05e28faa9d55fa5 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: devel git_last_commit: 32acb73 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/pd.atdschip.tiling_0.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 53 Package: pepDat Version: 1.31.0 Depends: R (>= 3.5.0) Imports: GenomicRanges Suggests: knitr License: Artistic-2.0 MD5sum: c736f504f9bbfa274a1c7a478024c3fe 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: devel git_last_commit: 73e9ec1 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/pepDat_1.31.0.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: 1.29.0 Depends: R (>= 3.5) Suggests: knitr, markdown, rmarkdown, BiocStyle License: GPL-2 | file LICENSE MD5sum: 75dc28ce6643e73a552f6e0dd9389fd2 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: devel git_last_commit: 0fd124e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/PepsNMRData_1.29.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: PepsNMR dependencyCount: 0 Package: PhyloProfileData Version: 1.25.0 Depends: R (>= 4.5.0) Imports: ExperimentHub, Biostrings, BiocStyle Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: ee0a104f415974bffb857c53fae0142b 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: devel git_last_commit: a0cd0b5 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/PhyloProfileData_1.25.0.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: 80 Package: plotgardenerData Version: 1.17.0 Depends: R (>= 4.1.0) Suggests: rmarkdown, knitr License: MIT + file LICENSE MD5sum: cb4fbcc6cb0fcd34847bffa23a003315 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: devel git_last_commit: e34744d git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/plotgardenerData_1.17.0.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: 1.47.0 Depends: R (>= 2.14.0) License: Artistic-2.0 MD5sum: 1885fab1064cb173be6f6c82b2cb76e8 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: devel git_last_commit: 9a01d9e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/prebsdata_1.47.0.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: 1.19.0 Depends: R (>= 4.1) Imports: ExperimentHub Suggests: knitr, rmarkdown, markdown, BiocStyle, preciseTAD License: MIT + file LICENSE MD5sum: ce2b9d68828dc8c54b65607e3db89436 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: devel git_last_commit: 8f46731 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/preciseTADhub_1.19.0.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: 64 Package: PREDAsampledata Version: 0.51.0 Depends: R (>= 2.10.0), methods, PREDA, Biobase, affy, annotate Suggests: hgu133plus2.db, hgu133plus2cdf License: Artistic-2.0 MD5sum: 32a409fcfd850d91a5272c9f3f1c92e2 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: devel git_last_commit: dd68e55 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/PREDAsampledata_0.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PREDA dependencyCount: 59 Package: ProData Version: 1.49.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL MD5sum: 1b73774983585bce99b272359e4189f1 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: devel git_last_commit: 71f554d git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ProData_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CorrectedFDR dependencyCount: 7 Package: pRolocdata Version: 1.49.0 Depends: R (>= 3.6.3), MSnbase Imports: Biobase, utils Suggests: pRoloc (>= 1.13.8), testthat, SummarizedExperiment License: GPL-2 MD5sum: a13debfb13492951cad6c2a4c2ff5ec1 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: devel git_last_commit: ffa71ae git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/pRolocdata_1.49.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics dependencyCount: 8 Package: prostateCancerCamcap Version: 1.39.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 5b02428b7adfb06b675834355a510b49 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: devel git_last_commit: 0f9a8b4 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/prostateCancerCamcap_1.39.0.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: 1.39.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 6fabf805b5c1d5af09c068ac599a6102 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: devel git_last_commit: 1455e0a git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/prostateCancerGrasso_1.39.0.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: 1.39.0 Depends: Biobase , R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 45a584163ef587dca2d24a809086be35 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: devel git_last_commit: 55b3527 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/prostateCancerStockholm_1.39.0.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: 1.39.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery, org.Hs.eg.db License: Artistic-2.0 MD5sum: 0362115107dbed30f3ece0821e16f6a6 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: devel git_last_commit: b7b0d5d git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/prostateCancerTaylor_1.39.0.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: 1.39.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 25a7bd4a03d28815c267a16fbb3b36d5 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: devel git_last_commit: 4a226a3 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/prostateCancerVarambally_1.39.0.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: 1.5.1 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: 0e107ba8dfdc0b5c66da23c2a597f301 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: devel git_last_commit: f4c9a24 git_last_commit_date: 2026-04-07 Date/Publication: 2026-04-21 source.ver: src/contrib/ProteinGymR_1.5.1.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: 71 Package: ptairData Version: 1.19.0 Imports: rhdf5, signal, stats, graphics Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 584fd9aed25a471de040c5b471644485 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: devel git_last_commit: 634124c git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ptairData_1.19.0.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 dependencyCount: 14 Package: PtH2O2lipids Version: 1.37.0 Depends: R (>= 3.3), xcms, CAMERA, LOBSTAHS, methods, utils Suggests: gplots, RColorBrewer, cluster, vegan License: MIT + file LICENSE MD5sum: 775230e20538eab19bb3a9a057ac16b7 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: devel git_last_commit: 2258fc0 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/PtH2O2lipids_1.37.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 5 Package: pumadata Version: 2.47.0 Depends: R (>= 3.2.0), Biobase (>= 2.5.5),puma, oligo(>= 1.32.0) License: LGPL MD5sum: db3f0edeb3bdb42cbff8acdf6fb31882 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: devel git_last_commit: beb5433 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/pumadata_2.47.0.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: 56 Package: PWMEnrich.Dmelanogaster.background Version: 4.45.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: b0fc9d25482fec778a1902a30e784406 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: devel git_last_commit: 13405a2 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/PWMEnrich.Dmelanogaster.background_4.45.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 21 Package: PWMEnrich.Hsapiens.background Version: 4.45.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: 4eae1478539ed8d5476c98bd073ac299 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: devel git_last_commit: af8619b git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/PWMEnrich.Hsapiens.background_4.45.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 21 Package: PWMEnrich.Mmusculus.background Version: 4.45.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: 670352a4ad0ccce8f7e49cdd7ac4e5bc 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: devel git_last_commit: 2cfc905 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/PWMEnrich.Mmusculus.background_4.45.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 21 Package: QDNAseq.hg19 Version: 1.41.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: 99acdac56a256d0ed30b96b1eac08803 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: devel git_last_commit: 1edda98 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/QDNAseq.hg19_1.41.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: QDNAseq dependencyCount: 49 Package: QDNAseq.mm10 Version: 1.41.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: ed3a17e416a0f5a48cc058f1c6986cd6 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: devel git_last_commit: 7ea13fa git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/QDNAseq.mm10_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: QDNAseq dependencyCount: 49 Package: QUBICdata Version: 1.39.0 Depends: R (>= 3.1) Suggests: knitr, rmarkdown License: Unlimited | file LICENSE MD5sum: 8a6a45fb276897bcdfbe60d82fee0b82 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: devel git_last_commit: 27c963f git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/QUBICdata_1.39.0.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: 1.9.0 Imports: ExperimentHub, Rsamtools, BiocGenerics, rtracklayer, SingleCellExperiment Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 7fc626d320d5593cb5e9fa78ba7fff09 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: devel git_last_commit: 49e691c git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/raerdata_1.9.0.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: 96 Package: rcellminerData Version: 2.33.0 Depends: R (>= 3.5.0), Biobase Suggests: knitr, testthat, BiocStyle, rcellminer, rmarkdown License: LGPL-3 + file LICENSE MD5sum: 754158a27b38235d12851472a0ac57bc 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: devel git_last_commit: bd87310 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/rcellminerData_2.33.0.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: 1.31.0 Depends: R (>= 3.3) Imports: data.table License: GPL-3 MD5sum: d83e2c84c32d3fa9196dcca29b576947 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: devel git_last_commit: 767f18d git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.31.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 2 Package: ReactomeGSA.data Version: 1.25.0 Depends: R (>= 3.6), limma, edgeR, ReactomeGSA, Seurat License: Artistic-2.0 MD5sum: 832e084299756d9ed07ab97c1113f54a 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: devel git_last_commit: a2a3132 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ReactomeGSA.data_1.25.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 156 Package: RegParallel Version: 1.29.0 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: 8b00daf09663f91142449f476f759884 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: devel git_last_commit: 151111c git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RegParallel_1.29.0.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: 1.49.0 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: 8fb20d910f7e31b285981ded7e9413ff 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: devel git_last_commit: bd10592 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RforProteomics_1.49.0.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 dependencyCount: 22 Package: rheumaticConditionWOLLBOLD Version: 1.49.0 Depends: R (>= 2.10.0) Suggests: genefilter, Biobase, hgu133plus2.db License: Artistic-2.0 MD5sum: 1b3c834e0fd10fbc7790d228fe60b97c 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: devel git_last_commit: c9232dc git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/rheumaticConditionWOLLBOLD_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: RITANdata Version: 1.35.0 Depends: R (>= 4.2) Suggests: knitr License: file LICENSE MD5sum: a61348d429a887ed14f61fb5db8a1dfd 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: devel git_last_commit: b5ac6ab git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RITANdata_1.35.0.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 dependencyCount: 0 Package: RMassBankData Version: 1.49.0 Suggests: RMassBank License: Artistic-2.0 MD5sum: 6faef4d4ced3733eb3f2d5656994a40d 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: devel git_last_commit: 1ca6e13 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RMassBankData_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: RNAmodR.Data Version: 1.25.0 Depends: R (>= 3.6), ExperimentHub, ExperimentHubData (>= 1.9.2) Imports: utils Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, sessioninfo, testthat License: Artistic-2.0 MD5sum: 0c704c12157189174f881a0d35690200 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: devel git_last_commit: dea0139 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RNAmodR.Data_1.25.0.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 dependencyCount: 119 Package: RNAseqData.HNRNPC.bam.chr14 Version: 0.49.0 Suggests: GenomicAlignments, BiocManager License: LGPL MD5sum: 9bd7f70e3a8042d261acf1ffc4314431 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: devel git_last_commit: 6917b74 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RNAseqData.HNRNPC.bam.chr14_0.49.0.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: 1.43.0 Depends: edgeR,R (>= 2.10) Suggests: BiocStyle, knitr License: GPL (>= 2) MD5sum: b686fb90b1b76e0bf97e42cb3726a3e1 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: devel git_last_commit: 6fd1997 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RnaSeqSampleSizeData_1.43.0.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 dependencyCount: 11 Package: RnBeads.hg19 Version: 1.43.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 1c1681954227f81ac28ccc09191be669 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: devel git_last_commit: 19b8914 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RnBeads.hg19_1.43.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 11 Package: RnBeads.hg38 Version: 1.43.1 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: f16e64625941cdd67df61f3e9ccb1b8c 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: devel git_last_commit: 1d05e90 git_last_commit_date: 2026-04-09 Date/Publication: 2026-04-21 source.ver: src/contrib/RnBeads.hg38_1.43.1.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 11 Package: RnBeads.mm10 Version: 2.19.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 24df09af8f6bfb00ab94b388f2ebfecd 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: devel git_last_commit: bb99da6 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RnBeads.mm10_2.19.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 11 Package: RnBeads.mm9 Version: 1.43.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 4928b6a26b49d7c46f13eb20a945ee1e 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: devel git_last_commit: 1bef9ef git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RnBeads.mm9_1.43.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 11 Package: RnBeads.rn5 Version: 1.43.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: e8e196c348486dbb9ad6a68b59d29465 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: devel git_last_commit: 3b42c86 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RnBeads.rn5_1.43.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 11 Package: RRBSdata Version: 1.31.0 Depends: R (>= 3.5.0), BiSeq (>= 1.9.2) License: LGPL-3 MD5sum: 1fd78820329fb2930642189542b4de8f 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: devel git_last_commit: 0a02ab6 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RRBSdata_1.31.0.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: 90 Package: RTCGA.clinical Version: 20151101.41.0 Depends: R (>= 3.2.0), RTCGA Suggests: rmarkdown, knitr License: GPL-2 MD5sum: ad0d32fde347f3265e1c1a03a424c76c 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: devel git_last_commit: 7ac7064 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RTCGA.clinical_20151101.41.0.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 dependencyCount: 1 Package: RTCGA.CNV Version: 1.39.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 7551107ea56e862c1ef544149cf9777c 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: devel git_last_commit: d752a3d git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RTCGA.CNV_1.39.0.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 dependencyCount: 1 Package: RTCGA.methylation Version: 1.39.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: b75414700dec955e14302ab4a5485a20 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: devel git_last_commit: cf22483 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RTCGA.methylation_1.39.0.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 dependencyCount: 1 Package: RTCGA.miRNASeq Version: 1.39.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: c2f4b49d77180666e634140654639c34 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: devel git_last_commit: 355ad51 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RTCGA.miRNASeq_1.39.0.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 dependencyCount: 1 Package: RTCGA.mRNA Version: 1.39.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 582bb53c2ed34cc47ae10b245b191c79 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: devel git_last_commit: b385193 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RTCGA.mRNA_1.39.0.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 dependencyCount: 1 Package: RTCGA.mutations Version: 20151101.41.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 76c36831488105114e9ac38793cabca5 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: devel git_last_commit: 437eb1f git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RTCGA.mutations_20151101.41.0.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 dependencyCount: 1 Package: RTCGA.PANCAN12 Version: 1.39.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 5b142683b33f62ff2088e5853cc9b0b6 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: devel git_last_commit: 4526368 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RTCGA.PANCAN12_1.39.0.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: 1 Package: RTCGA.rnaseq Version: 20151101.41.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 26aae8bbbbff1401fb95d2d6dca310b6 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: devel git_last_commit: 80f3b23 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RTCGA.rnaseq_20151101.41.0.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: FSelectorRcpp dependencyCount: 1 Package: RTCGA.RPPA Version: 1.39.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 444f4df85662b6e96d752abe9ff0c3a7 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: devel git_last_commit: 165c154 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RTCGA.RPPA_1.39.0.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 dependencyCount: 1 Package: RUVnormalizeData Version: 1.31.0 Depends: R (>= 2.10.0), Biobase License: GPL-3 MD5sum: d4cdb90a8bad4d70aafcb8169c5a5729 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: devel git_last_commit: 9e78531 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RUVnormalizeData_1.31.0.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: 1.35.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: BiocStyle License: Artistic-2.0 MD5sum: 500f9729fa03a53d7efe73c51fb7e5f3 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: devel git_last_commit: d26958c git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/sampleClassifierData_1.35.0.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: 1.25.0 Depends: R (>= 3.6) Imports: knitr, rmarkdown, bookdown Suggests: SummarizedExperiment License: AGPL-3 MD5sum: 832483b7aacc3e6f86529a6e72b40a6e 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: devel git_last_commit: 0821fde git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/SBGNview.data_1.25.0.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: 31 Package: scaeData Version: 1.7.0 Depends: R (>= 4.4.0) Imports: ExperimentHub Suggests: knitr, rmarkdown, markdown, SingleCellAlleleExperiment, Matrix, BiocStyle License: MIT + file LICENSE MD5sum: 578fe964dee0ac55cefbfdcae34b7864 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: devel git_last_commit: 4c50bf7 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/scaeData_1.7.0.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: 64 Package: scanMiRData Version: 1.17.0 Depends: R (>= 4.0) Imports: scanMiR, utils Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 271975d312bddf50e26759298593412c 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: devel git_last_commit: 3730fa2 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/scanMiRData_1.17.0.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 dependencyCount: 49 Package: scATAC.Explorer Version: 1.17.0 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: 7028e9ddb0862ba81e21746f09a0dc99 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: devel git_last_commit: 295a297 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/scATAC.Explorer_1.17.0.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: 64 Package: SCLCBam Version: 1.43.0 Depends: R(>= 2.10) Suggests: BiocStyle License: GPL-2 MD5sum: 767867c879ef9cf7def39c049af43b8f 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: devel git_last_commit: 538ae18 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/SCLCBam_1.43.0.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: 1.11.0 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: c34d8acd8feb327367f8452b884dc9de 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: devel git_last_commit: 943f023 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/scMultiome_1.11.0.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: 94 Package: scRNAseq Version: 2.25.0 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: 8a0d2c2e8ad5653dcca85bf4dbcc2614 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: devel git_last_commit: 2fad4dd git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/scRNAseq_2.25.0.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.basic, OSCA.intro, OSCA.workflows, scrapbook, SingleRBook importsMe: OSTA suggestsMe: APL, BASiCS, batchelor, bluster, ccImpute, CellMentor, ClusterFoldSimilarity, Coralysis, CSOA, destiny, dittoSeq, hammers, iSEE, iSEEfier, iSEEhex, iSEEindex, iSEEu, looking4clusters, miloR, miQC, mumosa, scAnnotatR, scater, scDblFinder, scDiagnostics, scDotPlot, scECODA, scFeatureFilter, scLang, scone, scran, scrapper, scTreeViz, scuttle, SingleCellExperiment, SingleR, SplineDV, UCell, zinbwave, LISTO, scStability, speakeasyR dependencyCount: 117 Package: scTHI.data Version: 1.23.0 Depends: R (>= 4.0) License: GPL-2 MD5sum: 0d00a7b20d9b48bc5aa65ad127a0a56f 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: devel git_last_commit: 463aeca git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/scTHI.data_1.23.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: scTHI dependencyCount: 0 Package: seq2pathway.data Version: 1.43.0 Depends: R (>= 3.6.2) License: GPL (>= 2) MD5sum: a30a5ad13e35ae65e0d827d7f5f4e23d 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: devel git_last_commit: 297df96 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/seq2pathway.data_1.43.0.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 importsMe: seq2pathway dependencyCount: 0 Package: seqc Version: 1.45.0 Depends: R (>= 2.10) Imports: utils, Biobase License: GPL-3 MD5sum: 4bc561a0201c5711e44fab68a470da33 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: devel git_last_commit: 08452f4 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/seqc_1.45.0.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: 1.47.0 Depends: R (>= 2.10) License: GPL (>= 2) MD5sum: 5f7b1281d6518cf394cc9bb9d3d4c595 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: devel git_last_commit: f367b6d git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/serumStimulation_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: sesameData Version: 1.29.10 Depends: R (>= 4.3.0), 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: 6e00232ee0673920b9422c257b692784 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. Currently 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, fnd] (ORCID: ), Hui Shen [aut, fnd], Timothy Triche [ctb] Maintainer: Wanding Zhou URL: https://github.com/zwdzwd/sesame VignetteBuilder: knitr BugReports: https://github.com/zwdzwd/sesame/issues git_url: https://git.bioconductor.org/packages/sesameData git_branch: devel git_last_commit: 55bde28 git_last_commit_date: 2026-02-06 Date/Publication: 2026-04-21 source.ver: src/contrib/sesameData_1.29.10.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, TENET, CytoMethIC dependencyCount: 72 Package: seventyGeneData Version: 1.47.0 Depends: R (>= 2.13.0) Suggests: Biobase, limma, breastCancerNKI, knitr, rmarkdown, readxl, BiocStyle License: Artistic-2.0 MD5sum: 8c52f94a9946a9269dee5e8d3c3a64f7 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: devel git_last_commit: e1754b9 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/seventyGeneData_1.47.0.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: 1.13.0 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: 04cd9864d8a2f56f5e9f08a65fdd6778 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: devel git_last_commit: 46b7ae7 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/SFEData_1.13.0.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: concordexR, jazzPanda dependencyCount: 64 Package: shinyMethylData Version: 1.31.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: 8452e5c4b1608da98e8dd280cbea2591 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: devel git_last_commit: 9d2733d git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/shinyMethylData_1.31.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: signatureSearchData Version: 1.25.0 Depends: R (>= 3.6) Imports: ExperimentHub, utils, affy, limma, Biobase, magrittr, dplyr, R.utils, stats, rhdf5 Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 170adf84d5003aea1f8a73a80136d6da 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: devel git_last_commit: ee7e356 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/signatureSearchData_1.25.0.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 suggestsMe: DFD dependencyCount: 77 Package: SimBenchData Version: 1.19.0 Depends: ExperimentHub Imports: S4Vectors, utils Suggests: BiocStyle, knitr, rmarkdown, Seurat License: GPL-3 MD5sum: 924b9008e97716745be75eb14b1b758d 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: devel git_last_commit: e762a0f git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/SimBenchData_1.19.0.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: 64 Package: simpIntLists Version: 1.47.0 License: GPL (>= 2) MD5sum: 595e167dbef20526c4b28c7fa146d6c5 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: devel git_last_commit: 14b0aaa git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/simpIntLists_1.47.0.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: 1.39.0 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: 424d7cbf8e2789a9711348842634e013 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: devel git_last_commit: 6831d50 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/Single.mTEC.Transcriptomes_1.39.0.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: 1.23.0 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: 0bb2bf694de714c8f4aaba56404cc948 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: devel git_last_commit: 2a345af git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/SingleCellMultiModal_1.23.0.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: 82 Package: SingleMoleculeFootprintingData Version: 1.19.0 Imports: ExperimentHub, utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 4868086fc816664374b2d7a162cd8104 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: devel git_last_commit: 49980e9 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/SingleMoleculeFootprintingData_1.19.0.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 dependencyCount: 64 Package: smokingMouse Version: 1.9.0 Suggests: AnnotationHubData, BiocStyle, ExperimentHub, ExperimentHubData, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 1bf778419c534a33d76e0169b15f701e 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: devel git_last_commit: 22c6710 git_last_commit_date: 2026-03-31 Date/Publication: 2026-04-21 source.ver: src/contrib/smokingMouse_1.9.0.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: 1.57.0 Depends: R (>= 2.4.0), graph Suggests: Rgraphviz License: LGPL MD5sum: 5a3750464fed1fcb1c6c635d1e701d7c 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: devel git_last_commit: e884b1c git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/SNAData_1.57.0.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: 1.47.0 Depends: R (>= 2.6.0) Suggests: ALL, hgu95av2.db, SNAGEE License: Artistic-2.0 MD5sum: 7419d0da78bfea9b289b0117ad8f5d3e 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: devel git_last_commit: 95d529e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/SNAGEEdata_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: SNAGEE dependencyCount: 0 Package: SNPhoodData Version: 1.41.0 Depends: R (>= 3.2) Suggests: BiocStyle,knitr,rmarkdown License: LGPL (>= 3) MD5sum: 1d5582285b65aac35861981105f81bfa 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: devel git_last_commit: 0a680bd git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/SNPhoodData_1.41.0.tar.gz vignettes: vignettes/SNPhoodData/inst/doc/SNPhoodData.html vignetteTitles: The *SNPhoodData* package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: SomatiCAData Version: 1.49.0 Depends: R (>= 2.14) License: Artistic-2.0 MD5sum: 0ad621371289ebf22a447c67663b0124 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: devel git_last_commit: ae5f18c git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/SomatiCAData_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: SomaticCancerAlterations Version: 1.47.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, IRanges, S4Vectors Suggests: testthat, ggbio, ggplot2, knitr License: GPL-3 MD5sum: 340eb8c793ff5c8b3505e26e9c9c6c6b 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: devel git_last_commit: b8d87a7 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/SomaticCancerAlterations_1.47.0.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 dependencyCount: 11 Package: SpatialDatasets Version: 1.9.0 Depends: ExperimentHub, SpatialExperiment, Imports: utils Suggests: BiocStyle, knitr, rmarkdown, cytomapper License: GPL-3 MD5sum: f7192b9832c743605be609e35cdfee5e 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: devel git_last_commit: 971469e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/SpatialDatasets_1.9.0.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 dependencyCount: 80 Package: spatialDmelxsim Version: 1.17.0 Depends: R (>= 4.1), ExperimentHub, SummarizedExperiment Imports: utils Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: b80c44e63e42b0807906e43ac7200ec5 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: devel git_last_commit: dcbc1d5 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/spatialDmelxsim_1.17.0.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: 75 Package: spatialLIBD Version: 1.23.2 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: 66b831426fc84b98e39356034eb0a295 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: devel git_last_commit: e4921b4 git_last_commit_date: 2026-03-26 Date/Publication: 2026-04-21 source.ver: src/contrib/spatialLIBD_1.23.2.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, OSTA suggestsMe: Banksy, BatchSVG, BayesSpace, DESpace dependencyCount: 197 Package: SpikeIn Version: 1.53.0 Depends: R (>= 2.10), affy (>= 1.23.4) License: Artistic-2.0 MD5sum: 8959541a01eef0b484c02ca5f951a40d 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: devel git_last_commit: c8a5cb8 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/SpikeIn_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PECA dependencyCount: 12 Package: SpikeInSubset Version: 1.51.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5), affy (>= 1.23.4) License: LGPL MD5sum: 9cf4175f0f39ec9dc2c2d259b11cccea 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: devel git_last_commit: f815c90 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/SpikeInSubset_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 12 Package: spqnData Version: 1.23.0 Depends: R (>= 4.0), SummarizedExperiment License: Artistic-2.0 MD5sum: b71c688ddac3d8ee3f1f05695c6bc4b1 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: devel git_last_commit: 0223aed git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/spqnData_1.23.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: spqn dependencyCount: 25 Package: stemHypoxia Version: 1.47.0 Depends: R (>= 2.14.1) License: GPL (>=2) MD5sum: 164c47165bfad1f933bdbf6b274ae3a2 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: devel git_last_commit: 8a6a2bc git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/stemHypoxia_1.47.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: lmdme dependencyCount: 0 Package: STexampleData Version: 1.19.0 Depends: ExperimentHub, SingleCellExperiment, SpatialExperiment Imports: utils Suggests: BiocStyle, knitr, rmarkdown, BumpyMatrix, HDF5Array License: MIT + file LICENSE MD5sum: c44ddde348cb0c3a175347d6a1e5e89d 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: devel git_last_commit: 0745bbd git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/STexampleData_1.19.0.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: Battlefield, BulkSignalR, escheR, ggsc, ggspavis, nnSVG, poem, smoothclust, spatialSimGP, spoon, SpotSweeper, SVP, tpSVG dependencyCount: 80 Package: SubcellularSpatialData Version: 1.7.0 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: eb96c364589e78381db419da8c868a88 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: devel git_last_commit: 7a88847 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/SubcellularSpatialData_1.7.0.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: 67 Package: SVM2CRMdata Version: 1.43.0 Depends: R(>= 3.2.0) License: LGPL (>= 2) MD5sum: 9fb871778894ca82d042082c062fd42b 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: devel git_last_commit: 4dcfb73 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/SVM2CRMdata_1.43.0.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: 2.15.6 Depends: R (>= 3.6.0) Imports: methods, Biostrings, BiocGenerics, jsonlite, remotes Suggests: GenomicFeatures, DT, txdbmaker, GenomicRanges, IRanges, Rsamtools, ShortRead, rtracklayer, RUnit, BiocStyle, knitr, rmarkdown, systemPipeR, kableExtra, magrittr, dplyr, gert License: Artistic-2.0 MD5sum: 5f238dde75888920252abf77cb6a1aca 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: devel git_last_commit: f961db0 git_last_commit_date: 2026-03-05 Date/Publication: 2026-04-21 source.ver: src/contrib/systemPipeRdata_2.15.6.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: 1.29.0 Depends: R (>= 3.5) Imports: ExperimentHub, utils Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran, scater, iSEE, testthat License: MIT + file LICENSE MD5sum: d203a45c3c85c0866ebe09c7cd990c47 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: devel git_last_commit: 7e20152 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/TabulaMurisData_1.29.0.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: 64 Package: TabulaMurisSenisData Version: 1.17.0 Imports: ExperimentHub, SingleCellExperiment, HDF5Array, SummarizedExperiment, gdata, AnnotationHub Suggests: ggplot2, testthat, knitr, rmarkdown, iSEE, BiocStyle License: MIT + file LICENSE MD5sum: 604dcf6c1b35c201120e3a043d3c40fe 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: devel git_last_commit: 94ed110 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/TabulaMurisSenisData_1.17.0.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: 79 Package: TargetScoreData Version: 1.47.0 Suggests: TargetScore, gplots License: GPL-2 MD5sum: 6c7c1e4f45650170acaa735f2a503cab 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: devel git_last_commit: 34207eb git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/TargetScoreData_1.47.0.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: 1.49.0 License: GPL (>= 2) MD5sum: 752ce0e5fdad55d463ff663db4b090d5 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: devel git_last_commit: 66dd545 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/TargetSearchData_1.49.0.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: 1.25.0 Depends: R (>= 4.1), AnnotationHub (>= 2.16), ExperimentHub (>= 1.0) Imports: utils Suggests: BiocStyle, knitr, rmarkdown, testthat, tools License: GPL-3 MD5sum: c0bde5b16b9adcae1104438d55cb7310 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: devel git_last_commit: c5a3b3e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/tartare_1.25.0.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: 64 Package: TBX20BamSubset Version: 1.47.0 Depends: Rsamtools (>= 1.9.8) Imports: xtable License: LGPL MD5sum: 4d20e0c7ae5e3988dc399fc3962d2f99 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: devel git_last_commit: f81cffd git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/TBX20BamSubset_1.47.0.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: 1.31.0 Depends: R (>= 3.5.0) Suggests: BiocStyle, knitr, rmarkdown, readr, DT License: GPL-3 MD5sum: 6f4b079e48847467fb26745b0c95c074 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: devel git_last_commit: e7aa3af git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/TCGAbiolinksGUI.data_1.31.0.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: 1.31.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 9d1d4fea70a0174947faf59e8c7725cc 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: devel git_last_commit: 3583f06 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/TCGAcrcmiRNA_1.31.0.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: 1.31.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: dba53a3798b238566b64e07eb2d88652 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: devel git_last_commit: 2892141 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/TCGAcrcmRNA_1.31.0.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: 1.47.0 License: GPL-2 MD5sum: af8b4202334789c87621a523e965c1a4 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: devel git_last_commit: 284c80f git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/TCGAMethylation450k_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: TCGAWorkflowData Version: 1.35.0 Depends: R (>= 3.5.0) Imports: SummarizedExperiment Suggests: knitr, rmarkdown, pander, testthat, BiocStyle License: GPL-3 MD5sum: 6be74b3a6deb2e4525bc4b895b10803c 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: devel git_last_commit: 3c83ff0 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/TCGAWorkflowData_1.35.0.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: 1.3.0 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: 329146ccbf652f09d24260475103fcbf 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: devel git_last_commit: a829d1f git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/TENET.ExperimentHub_1.3.0.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: 85 Package: TENxBrainData Version: 1.31.0 Depends: SingleCellExperiment, HDF5Array Imports: AnnotationHub (>= 2.9.22), ExperimentHub Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel, data.table, rmarkdown License: CC BY 4.0 MD5sum: 48b82fa99d930638e9087140e8288801 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: devel git_last_commit: dde9968 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/TENxBrainData_1.31.0.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 suggestsMe: h5mread dependencyCount: 77 Package: TENxBUSData Version: 1.25.0 Imports: ExperimentHub, AnnotationHub, utils, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle License: BSD_2_clause + file LICENSE MD5sum: 42bb6abe6dfef15455743e870beffdb7 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: devel git_last_commit: caa7ff1 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/TENxBUSData_1.25.0.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: 64 Package: TENxPBMCData Version: 1.29.0 Depends: SingleCellExperiment, HDF5Array Imports: AnnotationHub, ExperimentHub Suggests: rmarkdown, knitr, BiocStyle, snow, BiocFileCache, BiocParallel License: CC BY 4.0 MD5sum: 0e74979e612a9911da097a60ab31d7f6 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: devel git_last_commit: fdc8ce4 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/TENxPBMCData_1.29.0.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, scrapbook, SingleRBook suggestsMe: adverSCarial, ASURAT, celda, concordexR, decontX, ExperimentSubset, iSEE, mbkmeans, scGraphVerse, schex, scone, scry, Seqtometry dependencyCount: 77 Package: TENxVisiumData Version: 1.19.0 Depends: ExperimentHub, SpatialExperiment Imports: utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 68260393a43da1f6f098614a27bc8eaf 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: devel git_last_commit: 7e13cec git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/TENxVisiumData_1.19.0.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: 80 Package: TENxXeniumData Version: 1.7.0 Depends: ExperimentHub Imports: SpatialExperiment, SpatialFeatureExperiment, BumpyMatrix, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: f39bc0d420d243ce3928b2accc763c22 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: devel git_last_commit: c9f5f11 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/TENxXeniumData_1.7.0.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: 82 Package: timecoursedata Version: 1.21.0 Depends: R (>= 4.0), SummarizedExperiment Suggests: testthat (>= 1.0.0), knitr, rmarkdown, markdown, covr, BiocStyle License: BSD 3-clause License + file LICENSE MD5sum: 62e0a9a1ba4e446ed4e733785933e86d 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: devel git_last_commit: 6d9c28b git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/timecoursedata_1.21.0.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 dependencyCount: 25 Package: tinesath1cdf Version: 1.49.0 License: Artistic-2.0 MD5sum: 5508477d29eb335f2cc90bcd899ee406 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: devel git_last_commit: 0294a8b git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/tinesath1cdf_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: XhybCasneuf dependencyCount: 0 Package: tinesath1probe Version: 1.49.0 Depends: R (>= 1.6), AnnotationDbi (>= 1.11.9) License: LGPL MD5sum: c3c5dbdd09508c4971e51988406e2e86 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: devel git_last_commit: 4cc0c14 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/tinesath1probe_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 42 Package: tissueTreg Version: 1.31.0 Depends: R (>= 3.5) Suggests: BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq, SummarizedExperiment, ggplot2, reshape2 License: GPL (>= 2) MD5sum: b1901a631440e2336ba973e341d04153 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: devel git_last_commit: 86ffe39 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/tissueTreg_1.31.0.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 dependencyCount: 0 Package: TMExplorer Version: 1.21.0 Depends: R (>= 4.1), SingleCellExperiment, BiocFileCache Imports: methods, Matrix Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 6ea0bd0a3917f377edcbd06f4a377939 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: devel git_last_commit: 717f86a git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/TMExplorer_1.21.0.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: 62 Package: tofsimsData Version: 1.39.0 Depends: R (>= 3.2.0) Suggests: knitr, rmarkdown, tools License: GPL-3 MD5sum: 433b8e335c8ea2d3517b0ff669a65beb 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: devel git_last_commit: fb2161c git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/tofsimsData_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: topdownrdata Version: 1.33.0 Depends: topdownr License: GPL (>= 3) MD5sum: 13a5cbeb88df2418ef7c9db76a4ee76d 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: devel git_last_commit: 062bb26 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/topdownrdata_1.33.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 1 Package: TransOmicsData Version: 1.7.0 Imports: S4Vectors, utils Suggests: BiocStyle, knitr, rmarkdown, RefManageR, sessioninfo, testthat, ExperimentHub License: GPL-3 + file LICENSE MD5sum: 3996173476a088042b1557c7a3f17276 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: devel git_last_commit: cd83c45 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/TransOmicsData_1.7.0.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: 1.17.0 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: 9fcc263b48ee2cbca0ef7de97a2df74c 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: devel git_last_commit: dcbbafb git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/tuberculosis_1.17.0.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: 75 Package: tweeDEseqCountData Version: 1.49.0 Depends: Biobase, R (>= 4.3.0) Suggests: knitr, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: c9d22116a603d1773cd6d7336e8620cf 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: devel git_last_commit: 97ea89e git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/tweeDEseqCountData_1.49.0.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, tweeDEseq dependencyCount: 7 Package: tximportData Version: 1.39.0 Suggests: knitr, markdown License: GPL (>= 2) MD5sum: 336fdddd4de5964c2aa29ecdad18829e 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: devel git_last_commit: 311444a git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/tximportData_1.39.0.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, tximport dependencyCount: 0 Package: VariantToolsData Version: 1.35.2 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: c58889acbee3521977310f845044a789 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: devel git_last_commit: 43d4925 git_last_commit_date: 2026-03-16 Date/Publication: 2026-04-21 source.ver: src/contrib/VariantToolsData_1.35.2.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: 77 Package: VectraPolarisData Version: 1.15.0 Depends: ExperimentHub, SpatialExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, dplyr License: Artistic-2.0 MD5sum: 1ef7aa6b7a7d7648fcf0448efb3f4434 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: devel git_last_commit: 5ad67c7 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/VectraPolarisData_1.15.0.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: 80 Package: vulcandata Version: 1.33.0 Imports: utils Suggests: viper License: LGPL-3 MD5sum: 90f83da03119d84bc94ea1a0e3525517 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: devel git_last_commit: 583091f git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/vulcandata_1.33.0.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 dependencyCount: 1 Package: WeberDivechaLCdata Version: 1.13.0 Depends: ExperimentHub, SpatialExperiment, SingleCellExperiment Imports: utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 84ca3ac68743a0f979df824ea77da051 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: devel git_last_commit: 04200a2 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/WeberDivechaLCdata_1.13.0.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: 80 Package: WES.1KG.WUGSC Version: 1.43.0 License: GPL-2 MD5sum: 7a8e8ba266827d760bc7788e42cb726f 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: devel git_last_commit: 16dd402 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/WES.1KG.WUGSC_1.43.0.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: 1.23.0 Depends: R (>= 3.6.0), GenomicRanges License: GPL-2 MD5sum: a3323637afeb1d56a28665168b71c57d 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: devel git_last_commit: 7dcf161 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/WGSmapp_1.23.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: SCOPE dependencyCount: 11 Package: xcoredata Version: 1.15.0 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: ee0f795abc7bdb3dec1d4d378e1e9428 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: devel git_last_commit: b8c7f61 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/xcoredata_1.15.0.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: 64 Package: XhybCasneuf Version: 1.49.0 Depends: R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf , RColorBrewer , methods, grid License: Artistic-2.0 MD5sum: a5148dd8b4f52c1ea94dd069853449e4 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: devel git_last_commit: 9b1dfb0 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/XhybCasneuf_1.49.0.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: 50 Package: yeastCC Version: 1.51.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: dcb4dc92eb0954176cf2db6fe1a17f79 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: devel git_last_commit: 9491a18 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/yeastCC_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: LiquidAssociation suggestsMe: fastLiquidAssociation, ibh dependencyCount: 7 Package: yeastExpData Version: 0.57.0 Depends: R (>= 2.4), graph (>= 1.9.26) Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db License: GPL MD5sum: 0b62a943f80fc253a09fe1db71cb94fa 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: devel git_last_commit: abc7928 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/yeastExpData_0.57.0.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: 0.49.0 License: Artistic-2.0 MD5sum: e1b565ad94ff4fae749498189ab24e81 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: devel git_last_commit: 3b0a4d9 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/yeastGSData_0.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: yeastNagalakshmi Version: 1.47.0 License: Artistic-2.0 MD5sum: d09d02624eb7598a035e87aa53b642b2 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: devel git_last_commit: b51e9a6 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/yeastNagalakshmi_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ShortRead dependencyCount: 0 Package: yeastRNASeq Version: 0.49.0 Depends: R (>= 2.4) Suggests: Biobase, ShortRead, IRanges License: GPL MD5sum: 6054bb961f113ccbb50d825acc88b17a 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: devel git_last_commit: c4feb7b git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/yeastRNASeq_0.49.0.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: 1.31.0 Depends: R (>= 2.10) Suggests: BiocStyle, knitr License: GPL MD5sum: f507956723883c56e201e1a845a4caa3 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: devel git_last_commit: b4c2621 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/zebrafishRNASeq_1.31.0.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: Hiiragi2013 Version: 1.47.1 Depends: R (>= 4.0.0), Biobase Imports: MASS, RColorBrewer, cluster, gplots, grid, lattice, latticeExtra, genefilter Suggests: affy, BiocStyle, boot, clue, geneplotter, gtools, KEGGREST, mouse4302.db, xtable License: Artistic-2.0 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 [aut], Wolfgang Huber [aut, cre] Maintainer: Wolfgang Huber Package: TimerQuant Version: 1.41.0 Depends: shiny Imports: ggplot2, grid, gridExtra, deSolve, dplyr, locfit Suggests: BiocStyle, reshape2, knitr, shinyBS License: Artistic-2.0 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 Package: furrowSeg Version: 1.39.0 Depends: R (>= 3.3), EBImage Imports: abind, dplyr, locfit, tiff Suggests: BiocStyle, ggplot2, knitr License: Artistic-2.0 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 Package: qPLEXdata Version: 1.29.0 Depends: R (>= 3.5), qPLEXanalyzer Imports: utils, knitr, MSnbase, dplyr Suggests: statmod License: GPL-2 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 Package: HMP2Data Version: 1.25.0 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 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 Package: dorothea Version: 1.23.0 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 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 Package: scpdata Version: 1.19.1 Depends: R (>= 4.2.0), QFeatures, ExperimentHub Imports: utils, AnnotationHub, SingleCellExperiment, S4Vectors Suggests: scp, magrittr, dplyr, knitr, BiocStyle, BiocCheck, rmarkdown, testthat License: GPL-2 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 Package: brgedata Version: 1.33.0 Depends: R (>= 3.4), Biobase Imports: SummarizedExperiment Suggests: minfi, MultiAssayExperiment, knitr, rmarkdown, rexposome, BiocStyle License: MIT + file LICENSE 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 Package: MerfishData Version: 1.13.0 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 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 Package: TumourMethData Version: 1.9.0 Depends: R (>= 4.2), SummarizedExperiment Imports: base, BSgenome.Hsapiens.UCSC.hg19, dplyr, ExperimentHub, ExperimentHubData, GenomicRanges, HDF5Array, knitr, methodical, methrix, openxlsx, R.utils, readr, rhdf5, rmarkdown, stringr, TCGAutils, tibble, usethis, xlsx Suggests: ggplot2 License: Artistic-2.0 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 Package: homosapienDEE2CellScore Version: 1.7.0 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) 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 Package: CENTREprecomputed Version: 1.1.0 Depends: R (>= 4.5.0) Imports: ExperimentHub, RSQLite, DBI, BiocGenerics, methods Suggests: knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 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