Package: ABAData Version: 1.20.0 Depends: R (>= 3.2) Suggests: BiocStyle, knitr, ABAEnrichment License: GPL (>= 2) MD5sum: 1c23aaa7753793a26351e7b711c557d6 NeedsCompilation: no Title: Averaged gene expression in human brain regions from Allen Brain Atlas Description: Provides the data for the gene expression enrichment analysis conducted in the package 'ABAEnrichment'. The package includes three datasets which are derived from the Allen Brain Atlas: (1) Gene expression data from Human Brain (adults) averaged across donors, (2) Gene expression data from the Developing Human Brain pooled into five age categories and averaged across donors and (3) a developmental effect score based on the Developing Human Brain expression data. All datasets are restricted to protein coding genes. biocViews: ExpressionData, Homo_sapiens_Data, MicroarrayData, RNASeqData Author: Steffi Grote Maintainer: Steffi Grote VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ABAData git_branch: RELEASE_3_12 git_last_commit: c08a841 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ABAData_1.20.0.tar.gz vignettes: vignettes/ABAData/inst/doc/ABAData.html vignetteTitles: ABAData: gene expression data to use with enrichment analysis package ABAEnrichment hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ABAData/inst/doc/ABAData.R importsMe: ABAEnrichment dependencyCount: 0 Package: adductData Version: 1.6.0 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: 52755259db6664171723160f293276c3 NeedsCompilation: no Title: Data from untargeted MS of modifications to Cys34 of serum albumin Description: mzXML files from Grigoryan et al 2016 (Anal Chem). biocViews: ExperimentData,MassSpectrometryData,ExperimentHub Author: Josie Hayes Maintainer: Josie Hayes VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/adductData git_branch: RELEASE_3_12 git_last_commit: 24e2b4d git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/adductData_1.6.0.tar.gz vignettes: vignettes/adductData/inst/doc/adductData.html vignetteTitles: Raw mzXML data using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/adductData/inst/doc/adductData.R dependsOnMe: adductomicsR dependencyCount: 78 Package: affycompData Version: 1.28.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp License: GPL (>= 2) MD5sum: bbdbb831ee2ee7ce27c18b8d21ebd8b9 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: Harris Jaffee git_url: https://git.bioconductor.org/packages/affycompData git_branch: RELEASE_3_12 git_last_commit: eb50fbf git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/affycompData_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: affycomp dependencyCount: 8 Package: affydata Version: 1.38.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Imports: methods Suggests: hgu95av2cdf, hgu133acdf License: GPL (>= 2) MD5sum: b5f6d846e3a2ae09dc0bb9a1f0638042 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: Harris Jaffee git_url: https://git.bioconductor.org/packages/affydata git_branch: RELEASE_3_12 git_last_commit: b5e843b git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/affydata_1.38.0.tar.gz vignettes: vignettes/affydata/inst/doc/affydata.pdf vignetteTitles: affydata primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/affydata/inst/doc/affydata.R dependsOnMe: affyContam suggestsMe: affy, affycoretools, affyPara, affyPLM, affyQCReport, arrayMvout, ArrayTools, bgx, Biostrings, farms, gcrma, Harman, mimager, puma, pvac, RefPlus, RPA, sscore, TurboNorm, vsn, yaqcaffy, RobLoxBioC dependencyCount: 13 Package: Affyhgu133A2Expr Version: 1.26.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: ca43dcb47b19557465d897757ce2c4f7 NeedsCompilation: no Title: Affymetrix Human Genome U133A 2.0 Array (GPL571) Expression Data Package Description: Contains pre-built human (GPL571) databases of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133A2Expr git_branch: RELEASE_3_12 git_last_commit: 71b413a git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/Affyhgu133A2Expr_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: Affyhgu133aExpr Version: 1.28.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 712c088b0c7408eddf018a63b19dc065 NeedsCompilation: no Title: Affymetrix Human hgu133a Array (GPL96) Expression Data Package Description: Contains pre-built human (GPL96) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133aExpr git_branch: RELEASE_3_12 git_last_commit: 44cf3f3 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/Affyhgu133aExpr_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: Affyhgu133Plus2Expr Version: 1.24.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: a42161b83a4559f8b87af6e90ceb2874 NeedsCompilation: no Title: Affyhgu133Plus2Expr (GPL570) Expression Data Package Description: Contains pre-built human (GPL570) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133Plus2Expr git_branch: RELEASE_3_12 git_last_commit: 141936d git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/Affyhgu133Plus2Expr_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: AffymetrixDataTestFiles Version: 0.28.0 Depends: R (>= 2.5.0) License: LGPL-2.1 MD5sum: b4fdccca316dd7a98407c89f753e18d6 NeedsCompilation: no Title: Affymetrix data files (CEL, CDF, CHP, EXP, PGF, PSI) for testing Description: This package contains annotation data files and sample data files of Affymetrix file formats. The files originate from the Affymetrix' Fusion SDK distribution and other official sources. biocViews: ExperimentData, MicroarrayData Author: Henrik Bengtsson [aut, cre], James Bullard [aut], Kasper Daniel Hansen [aut] Maintainer: Henrik Bengtsson git_url: https://git.bioconductor.org/packages/AffymetrixDataTestFiles git_branch: RELEASE_3_12 git_last_commit: 0af6083 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/AffymetrixDataTestFiles_0.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: affxparser, affyILM, aroma.affymetrix dependencyCount: 0 Package: Affymoe4302Expr Version: 1.28.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 0d497a43b9b9d78f0f6c697c28f4b42c NeedsCompilation: no Title: Affymetrix Mouse Genome 430 2.0 Array (GPL1261) Expression Data Package Description: Contains pre-built mouse (GPL1261) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Mus_musculus_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affymoe4302Expr git_branch: RELEASE_3_12 git_last_commit: bb74007 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/Affymoe4302Expr_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: airway Version: 1.10.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: knitr, GEOquery License: LGPL MD5sum: 16f62759b25497b75645d3aab68ca9cd NeedsCompilation: no Title: RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014 Description: This package provides a RangedSummarizedExperiment object of read counts in genes for an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. Details on the gene model and read counting procedure are provided in the package vignette. The citation for the experiment is: Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri R Jr, Tantisira KG, Weiss ST, Lu Q. 'RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells.' PLoS One. 2014 Jun 13;9(6):e99625. PMID: 24926665. GEO: GSE52778. biocViews: ExperimentData, SequencingData, RNASeqData, GEO Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/airway git_branch: RELEASE_3_12 git_last_commit: dd99f8e git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/airway_1.10.0.tar.gz vignettes: vignettes/airway/inst/doc/airway.html vignetteTitles: Airway smooth muscle cells hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/airway/inst/doc/airway.R dependsOnMe: rnaseqGene importsMe: consensusDE suggestsMe: apeglm, biobroom, BioCor, BiocSet, CeTF, DelayedArray, DESeq2, EnhancedVolcano, EnrichmentBrowser, ideal, IHW, iSEEu, OPWeight, pathwayPCA, pcaExplorer, progeny, runibic, SummarizedExperiment, ToPASeq, TTMap, weitrix, IHWpaper, RegParallel, seqgendiff dependencyCount: 26 Package: ALL Version: 1.32.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Suggests: rpart License: Artistic-2.0 MD5sum: a7181423086d1ea752a3e417ff1063c0 NeedsCompilation: no Title: A data package Description: Data of T- and B-cell Acute Lymphocytic Leukemia from the Ritz Laboratory at the DFCI (includes Apr 2004 versions) biocViews: ExperimentData, CancerData, LeukemiaCancerData Author: Xiaochun Li Maintainer: Robert Gentleman git_url: https://git.bioconductor.org/packages/ALL git_branch: RELEASE_3_12 git_last_commit: 83327cf git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ALL_1.32.0.tar.gz vignettes: vignettes/ALL/inst/doc/ALLintro.pdf vignetteTitles: ALL data intro hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ALL/inst/doc/ALLintro.R importsMe: ConsensusClusterPlus, dGAselID, scRNAtools suggestsMe: a4, a4Base, a4Classif, a4Preproc, Biobase, BiocCaseStudies, BioNet, Category, CellMapper, ChromHeatMap, clipper, eisa, EnrichmentBrowser, esetVis, ExpressionView, genefilter, GeneSelectMMD, GOstats, graphite, GSAR, GSEAlm, mdgsa, MLInterfaces, npGSEA, pathRender, ReportingTools, rScudo, SNAGEE, topGO, SNAGEEdata, MMDvariance, nlcv, SourceSet dependencyCount: 7 Package: ALLMLL Version: 1.30.0 Depends: R (>= 2.10), affy (>= 1.23.4) License: GPL-2 MD5sum: 693726b515612095490f7526e650a45c NeedsCompilation: no Title: A subset of arrays from a large acute lymphoblastic leukemia (ALL) study Description: This package provides probe-level data for 20 HGU133A and 20 HGU133B arrays which are a subset of arrays from a large ALL study. The data is for the MLL arrays. This data was published in Mary E. Ross, Xiaodong Zhou, Guangchun Song, Sheila A. Shurtleff, Kevin Girtman, W. Kent Williams, Hsi-Che Liu, Rami Mahfouz, Susana C. Raimondi, Noel Lenny, Anami Patel, and James R. Downing (2003) Classification of pediatric acute lymphoblastic leukemia by gene expression profiling Blood 102: 2951-2959 biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData Author: B. M. Bolstad git_url: https://git.bioconductor.org/packages/ALLMLL git_branch: RELEASE_3_12 git_last_commit: 6a5347b git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ALLMLL_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQualityMetrics, pvac dependencyCount: 13 Package: alpineData Version: 1.16.0 Depends: ExperimentHub, GenomicAlignments Imports: utils, AnnotationHub Suggests: GenomicAlignments, knitr License: GPL (>=2) MD5sum: b8fb0e3c6e8cbe7b8b3415c8ad77302a NeedsCompilation: no Title: Data for the alpine package vignette Description: A small subset of paired-end RNA-seq reads from four samples of the GEUVADIS project. biocViews: SequencingData, RNASeqData, ExpressionData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/alpineData git_branch: RELEASE_3_12 git_last_commit: 379b61e git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/alpineData_1.16.0.tar.gz vignettes: vignettes/alpineData/inst/doc/alpineData.html vignetteTitles: tximport hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/alpineData/inst/doc/alpineData.R suggestsMe: alpine dependencyCount: 102 Package: AmpAffyExample Version: 1.30.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Suggests: hgu133acdf License: LGPL (>= 2) MD5sum: a140d828812d26cd8dd4ae56c5c650e5 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: Rafael A. Irizarry git_url: https://git.bioconductor.org/packages/AmpAffyExample git_branch: RELEASE_3_12 git_last_commit: 272695e git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/AmpAffyExample_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: AffyRNADegradation dependencyCount: 13 Package: AneuFinderData Version: 1.18.0 Depends: R (>= 3.3) License: file LICENSE MD5sum: 4511db22b073f9f363f01f80f149a0c9 NeedsCompilation: no Title: WGSCS Data for Demonstration Purposes Description: Whole-genome single cell sequencing data for demonstration purposes in the AneuFinder package. biocViews: CopyNumberVariationData, LungCancerData, Homo_sapiens_Data, SequencingData Author: Aaron Taudt Maintainer: Aaron Taudt git_url: https://git.bioconductor.org/packages/AneuFinderData git_branch: RELEASE_3_12 git_last_commit: 1bf1657 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/AneuFinderData_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: AneuFinder dependencyCount: 0 Package: antiProfilesData Version: 1.26.0 Depends: Biobase, Suggests: frma, GEOquery, GEOmetadb License: Artistic-2.0 MD5sum: 5081aa25de2620fe2b36889af6cbff6c NeedsCompilation: no Title: Normal colon and cancer preprocessed affy data for antiProfile building. Description: Colon normal tissue and cancer samples used in Corrada Bravo, et al. gene expression anti-profiles paper: BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272. Measurements are z-scores obtained from the GeneExpression Barcode in the 'frma' package biocViews: ExperimentData, MicroarrayData, Tissue, CancerData, ColonCancerData Author: Hector Corrada Bravo, Matthew McCall and Rafael A. Irizarry Maintainer: Hector Corrada Bravo git_url: https://git.bioconductor.org/packages/antiProfilesData git_branch: RELEASE_3_12 git_last_commit: 372e2ae git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/antiProfilesData_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: antiProfiles, epivizr, epivizrChart, messina dependencyCount: 7 Package: aracne.networks Version: 1.16.0 Depends: R (>= 3.3), viper License: file LICENSE MD5sum: ebb5c0e1389dbee4257a7c7152b7569b NeedsCompilation: no Title: ARACNe-inferred gene networks from TCGA tumor datasets Description: This package contains ARACNe-inferred networks from TCGA tumor datasets. It also contains a function to export them into plain-text format. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData Author: Federico M. Giorgi Maintainer: Federico M. Giorgi , Mariano Alvarez git_url: https://git.bioconductor.org/packages/aracne.networks git_branch: RELEASE_3_12 git_last_commit: 4b502d6 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/aracne.networks_1.16.0.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: 22 Package: ARRmData Version: 1.26.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: 505a7b4638390d6852c2fe5154ff222d NeedsCompilation: no Title: Example dataset for normalization of Illumina 450k Methylation data Description: Raw Beta values from 36 samples across 3 groups from Illumina 450k methylation arrays biocViews: ExperimentData, MethylationArrayData Author: Jean-Philippe Fortin, Celia M.T. Greenwood, Aurelie Labbe Maintainer: Jean-Philippe Fortin git_url: https://git.bioconductor.org/packages/ARRmData git_branch: RELEASE_3_12 git_last_commit: e0e4c3f git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ARRmData_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ARRmNormalization dependencyCount: 0 Package: AshkenazimSonChr21 Version: 1.20.0 Suggests: knitr, VariantAnnotation License: Artistic-2.0 MD5sum: 0bc7375e3ec8e03a8ded4204e3026a7f NeedsCompilation: no Title: Annotated variants on the chromosome 21, human genome 19, Ashkenazim Trio son sample Description: SonVariantsChr21 is a dataset of annotated genomic variants coming from Complete Genomics whole genome sequencing. Data comes from GIAB project, Ashkenazim Trio, sample HG002 run 1. Both vcf and annotated data frame are provided. biocViews: GenomicVariation, Sequencing, WholeGenome Author: Tomasz Stokowy Maintainer: Who to complain to VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/AshkenazimSonChr21 git_branch: RELEASE_3_12 git_last_commit: 66b710d git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/AshkenazimSonChr21_1.20.0.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: 1.10.0 Depends: R (>= 3.5) Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: b5ef1eab770a9884ab7c124c6358df67 NeedsCompilation: no Title: Example of 1D NMR spectra data for ASICS package Description: 1D NMR example spectra and additional data for use with the ASICS package. Raw 1D Bruker spectral data files were found in the MetaboLights database (https://www.ebi.ac.uk/metabolights/, study MTBLS1). biocViews: ExperimentData, Homo_sapiens_Data Author: Gaëlle Lefort [aut, cre], Rémi Servien [aut], Nathalie Villa-Vialaneix [aut] Maintainer: Gaëlle Lefort VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ASICSdata git_branch: RELEASE_3_12 git_last_commit: 7176761 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ASICSdata_1.10.0.tar.gz vignettes: vignettes/ASICSdata/inst/doc/ASICSdata.html vignetteTitles: ASICSdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ASICS dependencyCount: 0 Package: AssessORFData Version: 1.8.0 Depends: R (>= 3.5.0) Imports: DECIPHER, utils Suggests: AssessORF, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 292e80d30160a853bc7e4dbfae38f8e5 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, cre] Maintainer: Deepank Korandla VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/AssessORFData git_branch: RELEASE_3_12 git_last_commit: 8c560b1 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/AssessORFData_1.8.0.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: bcellViper Version: 1.26.0 Depends: R(>= 2.14.0), Biobase, methods License: GPL (>=2) MD5sum: 403524bec2d1d50787129570d3011366 NeedsCompilation: no Title: Human B-cell transcriptional interactome and normal human B-cell expression data Description: This package provides a human B-cell context-specific transcriptional regulatory network and a human normal B-cells dataset for the examples in package viper. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData Author: Mariano Javier Alvarez Maintainer: Mariano Javier Alvarez git_url: https://git.bioconductor.org/packages/bcellViper git_branch: RELEASE_3_12 git_last_commit: f82cb21 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/bcellViper_1.26.0.tar.gz vignettes: vignettes/bcellViper/inst/doc/bcellViper.pdf vignetteTitles: Using bcellViper hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bcellViper/inst/doc/bcellViper.R importsMe: dorothea suggestsMe: iterClust, pageRank, viper dependencyCount: 7 Package: beadarrayExampleData Version: 1.28.0 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>= 2.0.0) License: GPL-2 MD5sum: 5bda365319fbe079957deef1f35990fd 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: RELEASE_3_12 git_last_commit: a9d22f9 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/beadarrayExampleData_1.28.0.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, beadarrayFilter, RobLoxBioC dependencyCount: 76 Package: BeadArrayUseCases Version: 1.28.0 Imports: beadarray (>= 2.3.18), limma, GEOquery Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db License: GPL-2 MD5sum: 252c0c67c112d599ceaccc276ce3e087 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: RELEASE_3_12 git_last_commit: 5e935c0 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/BeadArrayUseCases_1.28.0.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: 92 Package: benchmarkfdrData2019 Version: 1.4.0 Depends: R (>= 3.6.0), SummarizedExperiment, ExperimentHub Imports: utils Suggests: knitr, BiocStyle, testthat, SummarizedBenchmark, dplyr, ggplot2, rlang License: MIT + file LICENSE MD5sum: 5b9ed222125247af1d761aa25d8707d2 NeedsCompilation: no Title: Data and Benchmarking Results from Korthauer and Kimes et al. (2019) Description: Benchmarking results for experimental and simulated data sets used in Korthauer and Kimes et al. (2019) to compare methods for controlling the false discovery rate. biocViews: SingleCellData, ExperimentData, RNASeqData, ExpressionData, ExperimentData, ExperimentHub Author: Stephanie Hicks [aut, cre] (), Keegan Korthauer [aut] (), Patrick Kimes [aut] () Maintainer: Stephanie Hicks VignetteBuilder: knitr BugReports: https://github.com/stephaniehicks/benchmarkfdrData2019/issues git_url: https://git.bioconductor.org/packages/benchmarkfdrData2019 git_branch: RELEASE_3_12 git_last_commit: 98823f5 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/benchmarkfdrData2019_1.4.0.tar.gz vignettes: vignettes/benchmarkfdrData2019/inst/doc/benchmarkfdrData2019.html vignetteTitles: Exploring and updating FDR benchmarking results hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/benchmarkfdrData2019/inst/doc/benchmarkfdrData2019.R dependencyCount: 91 Package: beta7 Version: 1.28.0 Depends: R (>= 2.4.0), marray License: LGPL MD5sum: 45af6b943d1a76f65d347a7a8656253c NeedsCompilation: no Title: Rodriguez et al. (2004) Differential Gene Expression by Memory/Effector T Helper Cells Bearing the Gut-Homing Receptor Integrin alpha4 beta7. Description: Data from 6 gpr files aims to identify differential expressed genes between the beta 7+ and beta 7- memory T helper cells. biocViews: ExperimentData, Homo_sapiens_Data, CGHData, MicroarrayData Author: Jean Yang Maintainer: Jean Yang git_url: https://git.bioconductor.org/packages/beta7 git_branch: RELEASE_3_12 git_last_commit: e89f68c git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/beta7_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: biotmleData Version: 1.14.0 Depends: R (>= 3.0) Suggests: Biobase, SummarizedExperiment License: file LICENSE MD5sum: 3c30d26ba76b9a2bc65e298988b627d8 NeedsCompilation: no Title: Example experimental microarray data set for the "biotmle" R package Description: Microarray data (from the Illumina Ref-8 BeadChips platform) and phenotype-level data from an epidemiological investigation of benzene exposure, packaged using "SummarizedExperiemnt", for use as an example with the "biotmle" R package. biocViews: GeneExpression, DifferentialExpression, Sequencing, Microarray, RNASeq Author: Nima Hejazi [aut, cre] Maintainer: Nima Hejazi git_url: https://git.bioconductor.org/packages/biotmleData git_branch: RELEASE_3_12 git_last_commit: b524e5e git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/biotmleData_1.14.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: biotmle dependencyCount: 0 Package: biscuiteerData Version: 1.4.0 Depends: R (>= 3.6.0), ExperimentHub Imports: AnnotationHub, utils, curl Suggests: knitr License: GPL-3 MD5sum: be43f39062eb86983c1938d2b7f395b2 NeedsCompilation: no Title: Data Package for Biscuiteer Description: Contains default datasets used by the Bioconductor package biscuiteer. biocViews: ExperimentHub, ExperimentData, Genome, Homo_sapiens_Data Author: Tim Triche, Jr. [aut, cre], Wanding Zhou [aut], Ben Johnson [aut], Jacob Morrison [aut], Lyong Heo [aut] Maintainer: "Jacob Morrison" VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/biscuiteerData git_branch: RELEASE_3_12 git_last_commit: c83cdb2 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/biscuiteerData_1.4.0.tar.gz vignettes: vignettes/biscuiteerData/inst/doc/biscuiteerData.html vignetteTitles: Biscuiteer User Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/biscuiteerData/inst/doc/biscuiteerData.R dependsOnMe: biscuiteer dependencyCount: 77 Package: bladderbatch Version: 1.28.0 Depends: Biobase License: Artistic-2.0 MD5sum: e1421ef1205eab02947a1dacd76b2b4c NeedsCompilation: no Title: Bladder gene expression data illustrating batch effects Description: This package contains microarray gene expression data on 57 bladder samples from 5 batches. The data are used as an illustrative example for the sva package. biocViews: ExperimentData, CancerData, MicroarrayData Author: Jeffrey T. Leek Maintainer: Jeffrey T. Leek git_url: https://git.bioconductor.org/packages/bladderbatch git_branch: RELEASE_3_12 git_last_commit: 5d604cb git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/bladderbatch_1.28.0.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, singleCellTK, sva dependencyCount: 7 Package: blimaTestingData Version: 1.10.0 Depends: R(>= 3.0.0) Suggests: blima, beadarray, illuminaHumanv4.db, BiocStyle License: GPL-3 MD5sum: b1a62eb143707a3f3cbcd48c98d56f17 NeedsCompilation: no Title: Data for testing of the package blima. Description: Experiment data package. The set were prepared using microarray images of human mesenchymal cells treated with various supplements. This package is intended to provide example data to test functionality provided by blima. biocViews: MicroarrayData, ExperimentData, GEO Author: Vojtech Kulvait Maintainer: Vojtech Kulvait URL: https://bitbucket.org/kulvait/blima git_url: https://git.bioconductor.org/packages/blimaTestingData git_branch: RELEASE_3_12 git_last_commit: ca61895 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/blimaTestingData_1.10.0.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: 1.10.0 Depends: R (>= 3.5.0) Imports: beeswarm, Biobase, DESeq2, devtools, dplyr, ggdendro, ggplot2, glmnet, graphics, grDevices, grid, gtable, ipflasso, methods, RColorBrewer, reshape2, scales, stats, SummarizedExperiment, survival, tibble Suggests: BiocStyle, knitr, rmarkdown, abind, AnnotationDbi, biomaRt, broom, colorspace, cowplot, dendsort, doParallel, foreach, forestplot, genefilter, ggbeeswarm, ggtern, gridExtra, hexbin, IHW, limma, magrittr, Matrix, maxstat, nat, org.Hs.eg.db, pheatmap, piano, readxl, Rtsne, tidyr, xtable License: LGPL (>= 3) MD5sum: f946cd2e702bbb48fcd3cfb37cdb3a5b NeedsCompilation: no Title: "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles 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, Oles M, Lu J et al., J. Clin. Invest. (2018) 128(1):427-445. doi:10.1172/JCI93801. biocViews: ExperimentData, ReproducibleResearch, CancerData, LeukemiaCancerData Author: Malgorzata Oles, Sascha Dietrich, Junyan Lu, Britta Velten, Andreas Mock, Vladislav Kim, Wolfgang Huber Maintainer: Malgorzata Oles VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/BloodCancerMultiOmics2017 git_branch: RELEASE_3_12 git_last_commit: 46a123d git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/BloodCancerMultiOmics2017_1.10.0.tar.gz vignettes: vignettes/BloodCancerMultiOmics2017/inst/doc/BloodCancerMultiOmics2017-dataOverview.html, vignettes/BloodCancerMultiOmics2017/inst/doc/BloodCancerMultiOmics2017.html vignetteTitles: BloodCancerMultiOmics2017 - data overview, BloodCancerMultiOmics2017 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BloodCancerMultiOmics2017/inst/doc/BloodCancerMultiOmics2017-dataOverview.R, vignettes/BloodCancerMultiOmics2017/inst/doc/BloodCancerMultiOmics2017.R dependencyCount: 148 Package: bodymapRat Version: 1.6.0 Depends: R (>= 3.6.0), SummarizedExperiment, ExperimentHub Imports: utils Suggests: knitr, BiocStyle, testthat License: CC BY 4.0 MD5sum: 60593e9c1b95d5e1363772f0b19d6fd7 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] (), Kwame Okrah [aut] Maintainer: Stephanie Hicks VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/bodymapRat git_branch: RELEASE_3_12 git_last_commit: da33656 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/bodymapRat_1.6.0.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: 91 Package: brainImageRdata Version: 1.8.0 Depends: ExperimentHub Suggests: knitr License: CC BY-SA 4.0 MD5sum: b1766a59e137f48555c150930ca9cdd9 NeedsCompilation: no Title: Image masks and expression data for use with BrainImageR Description: brainImageRdata contains image masks for the developing human and the adult human brain. These masks can be used in conjunction with the gene expression data to generate spatial gene set enrichment plots. It also contains the expression data for the 15 pcw human brain, the adult human brain, and the developing human brain. biocViews: OrganismData, Homo_sapiens_Data, ExpressionData Author: Sara Linker Maintainer: Sara Linker VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/brainImageRdata git_branch: RELEASE_3_12 git_last_commit: e4da301 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/brainImageRdata_1.8.0.tar.gz vignettes: vignettes/brainImageRdata/inst/doc/brainImageRdata.html vignetteTitles: brainImageRdata hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/brainImageRdata/inst/doc/brainImageRdata.R dependencyCount: 77 Package: breakpointRdata Version: 1.8.0 Depends: R (>= 3.5) Suggests: knitr, BiocStyle, License: file LICENSE MD5sum: cb4298e2ea31f8d0c6e21a3475c2cd51 NeedsCompilation: no Title: Strand-seq data for demonstration purposes Description: Strand-seq data to demonstrate functionalities of breakpointR package. biocViews: ExperimentData, Homo_sapiens_Data, SequencingData, DNASeqData, Genome, SingleCellData Author: David Porubsky, Aaron Taudt, Ashley Sanders Maintainer: David Porubsky URL: https://github.com/daewoooo/breakpointRdata VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/breakpointRdata git_branch: RELEASE_3_12 git_last_commit: e9f0df6 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/breakpointRdata_1.8.0.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: 1.28.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 20c0c500638dabd893af58ac27bba29e NeedsCompilation: no Title: Gene expression dataset published by Schmidt et al. [2008] (MAINZ). Description: Gene expression data from the breast cancer study published by Schmidt et al. in 2008, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerMAINZ git_branch: RELEASE_3_12 git_last_commit: 57c2a87 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/breastCancerMAINZ_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: DART, genefu, MIGSA, MineICA, STROMA4 dependencyCount: 0 Package: breastCancerNKI Version: 1.28.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 79e9b0a0836ac359f05bd7814e4d1766 NeedsCompilation: no Title: Genexpression dataset published by van't Veer et al. [2002] and van de Vijver et al. [2002] (NKI). Description: Genexpression data from a breast cancer study published by van't Veer et al. in 2002 and van de Vijver et al. in 2002, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, CGHData, MicroarrayData, OneChannelData, ChipOnChipData Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerNKI git_branch: RELEASE_3_12 git_last_commit: 3cc1834 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/breastCancerNKI_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, MIGSA, SigCheck, seventyGeneData dependencyCount: 0 Package: breastCancerTRANSBIG Version: 1.28.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 6fef4acd3bf1902f220787195b83d933 NeedsCompilation: no Title: Gene expression dataset published by Desmedt et al. [2007] (TRANSBIG). Description: Gene expression data from a breast cancer study published by Desmedt et al. in 2007, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerTRANSBIG git_branch: RELEASE_3_12 git_last_commit: e7de199 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/breastCancerTRANSBIG_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, GSgalgoR, MIGSA, MineICA dependencyCount: 0 Package: breastCancerUNT Version: 1.28.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 8b34ec4f5eb0d0d285e6d4a4fc871de8 NeedsCompilation: no Title: Gene expression dataset published by Sotiriou et al. [2007] (UNT). Description: Gene expression data from a breast cancer study published by Sotiriou et al. in 2007, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, TwoChannelData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerUNT git_branch: RELEASE_3_12 git_last_commit: 59fb821 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/breastCancerUNT_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, MIGSA dependencyCount: 0 Package: breastCancerUPP Version: 1.28.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: f174af97676727b7948d59c4ca575aa4 NeedsCompilation: no Title: Gene expression dataset published by Miller et al. [2005] (UPP). Description: Gene expression data from a breast cancer study published by Miller et al. in 2005, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerUPP git_branch: RELEASE_3_12 git_last_commit: 4d7fe07 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/breastCancerUPP_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, GSgalgoR, MIGSA, MineICA, safe dependencyCount: 0 Package: breastCancerVDX Version: 1.28.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 21bdffe570070496f61e7c8df1b38252 NeedsCompilation: no Title: Gene expression datasets published by Wang et al. [2005] and Minn et al. [2007] (VDX). Description: Gene expression data from a breast cancer study published by Wang et al. in 2005 and Minn et al. in 2007, provided as an eSet. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData, BreastCancerData, LungCancerData, MicroarrayData, OneChannelData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerVDX git_branch: RELEASE_3_12 git_last_commit: dfce14e git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/breastCancerVDX_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: BAGS suggestsMe: AIMS, DART, genefu, MIGSA, MineICA, ToPASeq dependencyCount: 0 Package: brgedata Version: 1.12.0 Depends: R (>= 3.4), Biobase Imports: SummarizedExperiment Suggests: minfi, MultiAssayExperiment, knitr, rexposome License: MIT + file LICENSE MD5sum: 4588d10ff9b8f5f4ceb3a6933d8d2c0f NeedsCompilation: no Title: Exposures, Gene Expression and Methylation data for ilustration purpouses Description: This package contains several sets of omics data including Gene Expression (ExpressionSet), Methylation (GenomicRatioSet), Proteome and Exposome (ExposomeSet). This data is used in vignettes and exaples at MEAL, MultiDataSet and omicRexposome. biocViews: ExperimentData,Homo_sapiens_Data,MicroarrayData,MethylationArrayData Author: Carlos Ruiz-Arenas [aut, cre], Carles Hernandez-Ferrer [aut], Juan R. Gonzalez [aut] Maintainer: Carlos Ruiz-Arenas VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/brgedata git_branch: RELEASE_3_12 git_last_commit: 6bbaafe git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/brgedata_1.12.0.tar.gz vignettes: vignettes/brgedata/inst/doc/general_description.html vignetteTitles: brgedata -- data R package with three omic data-set and exposome data-set from the same Spanish pupulation hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/brgedata/inst/doc/general_description.R suggestsMe: MEAL, MultiDataSet, omicRexposome dependencyCount: 26 Package: bronchialIL13 Version: 1.28.0 Depends: R(>= 2.10.0), affy (>= 1.23.4) License: GPL-2 MD5sum: b40ff627317375f01f7bbf21de872de3 NeedsCompilation: no Title: time course experiment involving il13 Description: derived from CNMC (pepr.cnmcresearch.org) http://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=95 Human Bronchial Cell line A549 biocViews: ExperimentData, MicroarrayData Author: Vince Carey Maintainer: Vince Carey URL: http://www.biostat.harvard.edu/~carey git_url: https://git.bioconductor.org/packages/bronchialIL13 git_branch: RELEASE_3_12 git_last_commit: b8d0db6 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/bronchialIL13_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 13 Package: bsseqData Version: 0.28.0 Depends: R (>= 2.15), bsseq (>= 1.16.0) License: Artistic-2.0 MD5sum: 180dede038973aa962c9c1ca417a3578 NeedsCompilation: no Title: Example whole genome bisulfite data for the bsseq package Description: Example whole genome bisulfite data for the bsseq package biocViews: Genome, CancerData, ColonCancerData, SequencingData Author: Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/bsseqData git_branch: RELEASE_3_12 git_last_commit: e83176a git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/bsseqData_0.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: bsseq, methylSig dependencyCount: 69 Package: cancerdata Version: 1.28.0 Depends: R (>= 2.10.1), Biobase License: GPL (>= 2) MD5sum: e2f87bfb6144bd25332a3acd963bb86b NeedsCompilation: no Title: Development and validation of diagnostic tests from high-dimensional molecular data: Datasets Description: Dataset for the R package cancerclass biocViews: CancerData, MicroarrayData Author: Jan Budczies, Daniel Kosztyla Maintainer: Daniel Kosztyla git_url: https://git.bioconductor.org/packages/cancerdata git_branch: RELEASE_3_12 git_last_commit: 0ac2fd4 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/cancerdata_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: cancerclass dependencyCount: 7 Package: CardinalWorkflows Version: 1.22.0 Depends: R (>= 2.10), Cardinal Suggests: BiocStyle, knitr License: Artistic-2.0 MD5sum: b361361e41a39a0a6d67a97dfccd233b NeedsCompilation: no Title: Datasets and workflows for the Cardinal mass spectrometry imaging package Description: Datasets and workflows for Cardinal: DESI and MALDI examples including pig fetus, cardinal painting, and human RCC. biocViews: ExperimentData, MassSpectrometryData, ImagingMassSpectrometryData Author: Kylie A. Bemis Maintainer: Kylie A. Bemis VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/CardinalWorkflows git_branch: RELEASE_3_12 git_last_commit: 0cef890 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/CardinalWorkflows_1.22.0.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: 65 Package: ccdata Version: 1.16.0 Depends: R (>= 3.3) License: MIT + file LICENSE MD5sum: dc31208e5291fa4f81d1b9842bad042d NeedsCompilation: no Title: Data for Combination Connectivity Mapping (ccmap) Package Description: This package contains microarray gene expression data generated from the Connectivity Map build 02 and LINCS l1000. The data are used by the ccmap package to find drugs and drug combinations to mimic or reverse a gene expression signature. biocViews: ExperimentData, MicroarrayData, ExpressionData Author: Alex Pickering Maintainer: Alex Pickering git_url: https://git.bioconductor.org/packages/ccdata git_branch: RELEASE_3_12 git_last_commit: 7cfa9c5 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ccdata_1.16.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE importsMe: ccmap dependencyCount: 0 Package: CCl4 Version: 1.28.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), limma License: Artistic-2.0 MD5sum: c8049af9173fdd949e25ca81bb2d1c29 NeedsCompilation: no Title: Carbon Tetrachloride (CCl4) treated hepatocytes Description: NChannelSet for rat hepatocytes treated with Carbon Tetrachloride (CCl4) data from LGC company. biocViews: ExperimentData, Genome, Rattus_norvegicus_Data, MicroarrayData Author: Audrey Kauffmann, Wolfgang Huber Maintainer: Audrey Kauffmann git_url: https://git.bioconductor.org/packages/CCl4 git_branch: RELEASE_3_12 git_last_commit: 452a2a5 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/CCl4_1.28.0.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, BiocCaseStudies dependencyCount: 9 Package: ccTutorial Version: 1.28.0 Depends: R (>= 2.10), Ringo(>= 1.9.8), affy(>= 1.23.4), topGO(>= 1.13.1) Imports: Biobase Suggests: biomaRt, Biobase(>= 2.5.5), xtable License: Artistic-2.0 MD5sum: a36b66e1fad77bd562e41ee01483a119 NeedsCompilation: no Title: Data package for ChIP-chip tutorial Description: This is a data package that accompanies a ChIP-chip tutorial, which has been published in PLoS Computational Biology. The data and source code in this package allow the reader to completely reproduce the steps in the tutorial. biocViews: ExperimentData, Mus_musculus_Data, MicroarrayData, ChipOnChipData Author: Joern Toedling, Wolfgang Huber Maintainer: Joern Toedling git_url: https://git.bioconductor.org/packages/ccTutorial git_branch: RELEASE_3_12 git_last_commit: a39d3f2 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ccTutorial_1.28.0.tar.gz vignettes: vignettes/ccTutorial/inst/doc/ccTutorial.pdf, vignettes/ccTutorial/inst/doc/ccTutorialSupplement.pdf vignetteTitles: A tutorial on how to analyze ChIP-chip readouts using Bioconductor, Supplement to A tutorial on how to analyze ChIP-chip readouts using Bioconductor hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ccTutorial/inst/doc/ccTutorial.R, vignettes/ccTutorial/inst/doc/ccTutorialSupplement.R dependencyCount: 81 Package: celarefData Version: 1.8.0 Depends: R (>= 3.5.0) Suggests: ExperimentHub, knitr, rmarkdown License: GPL-3 MD5sum: 339c1fdafb03680b9ef8e3df52f7e7fb NeedsCompilation: no Title: Processed scRNA data for celaref Vignette - cell labelling by reference Description: This experiment data contains some processed data used in the celaref package vignette. These are publically available datasets, that have been processed by celaref package, and can be manipulated further with it. biocViews: ExperimentData, SingleCellData, ExperimentHub Author: Sarah Williams [aut, cre] Maintainer: Sarah Williams VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/celarefData git_branch: RELEASE_3_12 git_last_commit: 1b2e482 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/celarefData_1.8.0.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: 1.0.0 Depends: SummarizedExperiment Imports: utils, ExperimentHub, AnnotationHub, AnnotationDbi, S4Vectors, DelayedArray, DelayedMatrixStats Suggests: testthat, knitr, rmarkdown, BiocStyle, DT License: GPL-3 MD5sum: fcbf9341066a8ece3a934a925a6b47f8 NeedsCompilation: no Title: Reference Index for Cell Types Description: Provides a collection of reference expression datasets with curated cell type labels, for use in procedures like automated annotation of single-cell data or deconvolution of bulk RNA-seq. biocViews: ExperimentHub, ExperimentData, ExpressionData, SequencingData, RNASeqData Author: Dvir Aran [aut], Aaron Lun [aut, cre, cph], Daniel Bunis [aut], Jared Andrews [aut], Friederike Dündar [aut] Maintainer: Aaron Lun URL: https://github.com/LTLA/celldex VignetteBuilder: knitr BugReports: https://support.bioconductor.org/ git_url: https://git.bioconductor.org/packages/celldex git_branch: RELEASE_3_12 git_last_commit: c398631 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/celldex_1.0.0.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 suggestsMe: ontoProc, SingleR, tidySingleCellExperiment dependencyCount: 104 Package: CellMapperData Version: 1.16.0 Depends: ExperimentHub, CellMapper Suggests: BiocStyle License: Artistic-2.0 MD5sum: 5c032fb20d4d96c52f622485848372b1 NeedsCompilation: no Title: Pre-processed data for use with the CellMapper package Description: Experiment data package. Contains microarray data from several large expression compendia that have been pre-processed for use with the CellMapper package. This pre-processed data is recommended for routine searches using the CellMapper package. biocViews: ExperimentData, MicroarrayData, ExpressionData Author: Brad Nelms Maintainer: Brad Nelms git_url: https://git.bioconductor.org/packages/CellMapperData git_branch: RELEASE_3_12 git_last_commit: d6d5b69 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/CellMapperData_1.16.0.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: 78 Package: ceu1kg Version: 0.28.0 Depends: R (>= 2.12.0), GGBase (>= 3.9.0), GGtools, Biobase Suggests: SNPlocs.Hsapiens.dbSNP.20101109 License: Artistic-2.0 MD5sum: a52f1dac8b569a939c9967d101b63049 NeedsCompilation: no Title: CEU (N=60) genotypes from 1000 genomes pilot phase I Description: CEU genotypes from 1000 genomes "low coverage" pilot phase I (approx 8 million SNP calls released July 2010); includes Wellcome trust GENEVAR expression for 43 indiv biocViews: SNPData, HapMap, Project1000genomes Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/ceu1kg git_branch: RELEASE_3_12 git_last_commit: baecf9f git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ceu1kg_0.28.0.tar.gz vignettes: vignettes/ceu1kg/inst/doc/ceu1kg.pdf vignetteTitles: ceu1kg overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ceu1kg/inst/doc/ceu1kg.R dependencyCount: 164 Package: ceu1kgv Version: 0.32.0 Depends: R (>= 3.0), GGBase Imports: Biobase License: Artistic-2.0 MD5sum: 06142b0a3776177b425b42c5c4a089fe NeedsCompilation: no Title: expression + genotype on 79 unrelated CEU individuals Description: expression + genotype on 79 unrelated CEU individuals biocViews: ArrayExpress Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/ceu1kgv git_branch: RELEASE_3_12 git_last_commit: 99148cd git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ceu1kgv_0.32.0.tar.gz vignettes: vignettes/ceu1kgv/inst/doc/ceu1kgv.pdf vignetteTitles: ceu1kgv -- genotype plus expression for HapMap CEU hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ceu1kgv/inst/doc/ceu1kgv.R dependencyCount: 60 Package: ceuhm3 Version: 0.28.0 Depends: R (>= 2.12.0), GGBase, Biobase Imports: GGtools License: Artistic-2.0 MD5sum: ee18605d8a8288b06d888fdfabb36838 NeedsCompilation: no Title: ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort Description: ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort biocViews: SNPData, HapMap Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/ceuhm3 git_branch: RELEASE_3_12 git_last_commit: 1b2abea git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ceuhm3_0.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 164 Package: cgdv17 Version: 0.28.0 Depends: R (>= 2.15), methods, VariantAnnotation (>= 1.15.15) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biobase Suggests: parallel, GGtools, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, illuminaHumanv1.db License: Artistic-2.0 MD5sum: 37f5ae3d4f5ff05dbecf18340991ad74 NeedsCompilation: no Title: Complete Genomics Diversity Panel, chr17 on 46 individuals Description: Complete Genomics Diversity Panel, chr17 on 46 individuals biocViews: SequencingData, SNPData, BiocViews Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/cgdv17 git_branch: RELEASE_3_12 git_last_commit: 60af2c9 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/cgdv17_0.28.0.tar.gz vignettes: vignettes/cgdv17/inst/doc/cgdv.pdf vignetteTitles: cgdv17: extract from Complete Genomics diversity panel hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cgdv17/inst/doc/cgdv.R dependsOnMe: variants dependencyCount: 90 Package: ChAMPdata Version: 2.22.0 Depends: GenomicRanges (>= 1.22.4),BiocGenerics(>= 0.16.1),R (>= 3.3) License: GPL-3 MD5sum: 3da92daf51d2d0079b5f68da32f8199b NeedsCompilation: no Title: Data Packages for ChAMP package Description: Provides datasets needed for ChAMP including a test dataset and blood controls for CNA analysis. biocViews: ExperimentData Author: Yuan Tian [ctb,aut], Tiffany Morris [cre,aut], Lee Stirling [ctb] and Andrew Teschendorff [ctb] Maintainer: Yuan Tian git_url: https://git.bioconductor.org/packages/ChAMPdata git_branch: RELEASE_3_12 git_last_commit: eeedd4c git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ChAMPdata_2.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ChAMP dependencyCount: 17 Package: ChIC.data Version: 1.10.0 Depends: R (>= 3.5) Imports: caret (>= 6.0-78) License: GPL-2 MD5sum: 88e93f1ec65b7f668f67f7452d7b3674 NeedsCompilation: no Title: ChIC package data Description: This package contains annotation and metagene profile data for the ChIC package. biocViews: ExperimentData, ENCODE Author: Carmen Maria Livi [aut, cre, dtc], Endre Sebestyen [aut] Maintainer: Carmen Maria Livi git_url: https://git.bioconductor.org/packages/ChIC.data git_branch: RELEASE_3_12 git_last_commit: 1ceb1d5 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ChIC.data_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: ChIC dependencyCount: 72 Package: ChimpHumanBrainData Version: 1.28.0 Depends: affy,qvalue,limma,hexbin,statmod License: MIT MD5sum: dc42f1fe38088b10e3065652f29cc516 NeedsCompilation: no Title: Chimp and human brain data package Description: This data package contains chimp and human brain data extracted from the ArrayExpress accession E-AFMX-2. Both human and chimp RNAs were run on human hgu95av2 Affymetrix arrays. It is a useful dataset for tutorials. biocViews: Tissue, Homo_sapiens_Data, Pan_troglodytes_Data, MicroarrayData, TissueMicroarrayData, GEO Author: Roman Jaksik, Naomi Altman, and Sean Davis Maintainer: Sean Davis git_url: https://git.bioconductor.org/packages/ChimpHumanBrainData git_branch: RELEASE_3_12 git_last_commit: e5fcb42 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ChimpHumanBrainData_1.28.0.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: 56 Package: chipenrich.data Version: 2.14.0 Depends: R (>= 3.4.0) 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: fec4b10f3d4395558fcfc7ad3624a533 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, cre], Laura J. Scott [ths], Maureen A. Sartor [ths] Maintainer: Raymond G. Cavalcante VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/chipenrich.data git_branch: RELEASE_3_12 git_last_commit: 15d78e9 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/chipenrich.data_2.14.0.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: 68 Package: ChIPexoQualExample Version: 1.14.0 Depends: R (>= 3.3) License: GPL (>= 2) MD5sum: 5b280808c6b8294eedad2b9d63dc21f7 NeedsCompilation: no Title: Example data for the ChIPexoQual package, which implements a quality control pipeline for ChIP-exo data Description: Data for the ChIPexoQual package, consisting of (3) chromosome 1 aligned reads from a ChIP-exo experiment for FoxA1 in mouse liver cell lines aligned to the mm9 genome. biocViews: ExperimentData, Genome Author: Rene Welch, Dongjun Chung, Sunduz Keles Maintainer: Rene Welch URL: http://www.github.com/keleslab/ChIPexoQualExample VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ChIPexoQualExample git_branch: RELEASE_3_12 git_last_commit: 8fc9b51 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ChIPexoQualExample_1.14.0.tar.gz vignettes: vignettes/ChIPexoQualExample/inst/doc/vignette.html vignetteTitles: Vignette Title hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ChIPexoQualExample/inst/doc/vignette.R suggestsMe: ChIPexoQual dependencyCount: 0 Package: chipseqDBData Version: 1.6.0 Imports: AnnotationHub, ExperimentHub, Rsamtools, S4Vectors Suggests: knitr, BiocStyle License: CC BY 4.0 MD5sum: d2e9b600e63871f7e6de934928eeb909 NeedsCompilation: no Title: Data for the chipseqDB Workflow Description: Sorted and indexed BAM files for ChIP-seq libraries, for use in the chipseqDB workflow. BAM indices are also included. biocViews: SequencingData, ChIPSeqData, ExperimentHub Author: Aaron Lun [aut, cre] Maintainer: Aaron Lun VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/chipseqDBData git_branch: RELEASE_3_12 git_last_commit: ffdf891 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/chipseqDBData_1.6.0.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 suggestsMe: chipseqDB, csawUsersGuide dependencyCount: 94 Package: ChIPXpressData Version: 1.28.0 Depends: bigmemory License: GPL (>=2) MD5sum: ba7ef6f12e2580e8e5d614275834cf85 NeedsCompilation: no Title: ChIPXpress Pre-built Databases Description: Contains pre-built mouse (GPL1261) and human (GPL570) database of gene expression profiles to be used for ChIPXpress ranking. biocViews: Homo_sapiens_Data, Mus_musculus_Data, GEO Author: George Wu Maintainer: George Wu git_url: https://git.bioconductor.org/packages/ChIPXpressData git_branch: RELEASE_3_12 git_last_commit: 2c31561 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ChIPXpressData_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ChIPXpress dependencyCount: 6 Package: chromstaRData Version: 1.16.0 Depends: R (>= 3.3) License: GPL-3 MD5sum: a8695bc238dd3712c532f301bd19a824 NeedsCompilation: no Title: ChIP-seq data for Demonstration Purposes Description: ChIP-seq data for demonstration purposes in the chromstaR package. biocViews: Mus_musculus_Data, StemCell, ChIPSeqData Author: Aaron Taudt Maintainer: Aaron Taudt git_url: https://git.bioconductor.org/packages/chromstaRData git_branch: RELEASE_3_12 git_last_commit: de21cd8 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/chromstaRData_1.16.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: chromstaR dependencyCount: 0 Package: CLL Version: 1.30.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: LGPL MD5sum: e9732351c00670d6708201866f150119 NeedsCompilation: no Title: A Package for CLL Gene Expression Data Description: The CLL package contains the chronic lymphocytic leukemia (CLL) gene expression data. The CLL data had 24 samples that were either classified as progressive or stable in regards to disease progression. The data came from Dr. Sabina Chiaretti at Division of Hematology, Department of Cellular Biotechnologies and Hematology, University La Sapienza, Rome, Italy and Dr. Jerome Ritz at Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts. biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData Author: Elizabeth Whalen Maintainer: Robert Gentleman git_url: https://git.bioconductor.org/packages/CLL git_branch: RELEASE_3_12 git_last_commit: e2e2507 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/CLL_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: BiocCaseStudies dependencyCount: 13 Package: CLLmethylation Version: 1.10.0 Depends: R (>= 3.5.0) Imports: SummarizedExperiment, ExperimentHub Suggests: BiocStyle, ggplot2, knitr, rmarkdown License: LGPL MD5sum: a204c3eb034492961b1e3a4352f58b59 NeedsCompilation: no Title: Methylation data of primary CLL samples in PACE project Description: The package includes DNA methylation data for the primary Chronic Lymphocytic Leukemia samples included in the Primary Blood Cancer Encyclopedia (PACE) project. Raw data from the 450k DNA methylation arrays is stored in the European Genome-Phenome Archive (EGA) under accession number EGAS0000100174. For more information concerning the project please refer to the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) and R/Bioconductor package BloodCancerMultiOmics2017. biocViews: ExperimentData, DiseaseModel, CancerData, LeukemiaCancerData Author: Malgorzata Oles, Andreas Mock Maintainer: Malgorzata Oles , Andreas Mock VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/CLLmethylation git_branch: RELEASE_3_12 git_last_commit: 731aab4 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/CLLmethylation_1.10.0.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: 91 Package: CluMSIDdata Version: 1.6.0 Depends: R (>= 3.6) License: MIT + file LICENSE MD5sum: 1471f858ae85a021e8173acc74ad4d3f NeedsCompilation: no Title: Data for the CluMSID package Description: This package contains various LC-MS/MS and GC-MS data that is used in vignettes and examples in the CluMSID package. biocViews: ExperimentData, MassSpectrometryData Author: Tobias Depke [aut, cre] Maintainer: Tobias Depke git_url: https://git.bioconductor.org/packages/CluMSIDdata git_branch: RELEASE_3_12 git_last_commit: df11685 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/CluMSIDdata_1.6.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: CluMSID dependencyCount: 0 Package: clustifyrdatahub Version: 1.0.0 Depends: R (>= 4.0), ExperimentHub Imports: utils Suggests: clustifyr, Seurat, usethis, rmarkdown, knitr, tidyr, BiocStyle License: MIT + file LICENSE MD5sum: fa00df701fefb222dce66346414395c8 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, cre] (), Kent Riemondy [aut] (), RNA Bioscience Initiative [fnd], Austin Gillen [ctb] (), Jay Hesselberth [ctb] (), Sidhant Puntambekar [ctb] Maintainer: Rui Fu URL: https://rnabioco.github.io/clustifyrdatahub VignetteBuilder: knitr BugReports: https://github.com/rnabioco/clustifyrdatahub/issues git_url: https://git.bioconductor.org/packages/clustifyrdatahub git_branch: RELEASE_3_12 git_last_commit: cbd5308 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/clustifyrdatahub_1.0.0.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: 77 Package: cMap2data Version: 1.26.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 3eee624936f9f324ef7a5f337a158734 NeedsCompilation: no Title: Connectivity Map (version 2) Data Description: Data package which provides default drug profiles for the DrugVsDisease package as well as associated gene lists and data clusters used by the DrugVsDisease package. biocViews: Homo_sapiens_Data, MicroarrayData, GEO Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/cMap2data git_branch: RELEASE_3_12 git_last_commit: 8ac71dd git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/cMap2data_1.26.0.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: 1.26.0 Depends: R (>= 2.10), cnvGSA License: LGPL MD5sum: e3c8db1abea6b0ba8a43d98d462de475 NeedsCompilation: no Title: Data used in the vignette of the cnvGSA package Description: This package contains the data used in the vignette of the cnvGSA package. biocViews: ExperimentData, Genome, CopyNumberVariationData Author: Joseph Lugo Maintainer: Joseph Lugo git_url: https://git.bioconductor.org/packages/cnvGSAdata git_branch: RELEASE_3_12 git_last_commit: b699546 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/cnvGSAdata_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: cnvGSA dependencyCount: 26 Package: COHCAPanno Version: 1.26.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 298ff9d979750c2247bbbcb21fd9065f NeedsCompilation: no Title: Annotations for City of Hope CpG Island Analysis Pipeline Description: Provides genomic location, nearby CpG island and nearby gene information for common Illumina methylation array platforms biocViews: Homo_sapiens_Data, MicroarrayData, MethylationArrayData, CpGIslandData, GEO, ArrayExpress Author: Charles Warden Maintainer: Charles Warden git_url: https://git.bioconductor.org/packages/COHCAPanno git_branch: RELEASE_3_12 git_last_commit: a896171 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/COHCAPanno_1.26.0.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 dependsOnMe: COHCAP dependencyCount: 0 Package: colonCA Version: 1.32.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: cd267cda8d61b65fb0df3d7c1aa0b734 NeedsCompilation: no Title: exprSet for Alon et al. (1999) colon cancer data Description: exprSet for Alon et al. (1999) colon cancer data biocViews: ExperimentData, Tissue, CancerData, ColonCancerData, MicroarrayData, TissueMicroarrayData Author: Sylvia Merk Maintainer: W Sylvia Merk git_url: https://git.bioconductor.org/packages/colonCA git_branch: RELEASE_3_12 git_last_commit: 001877f git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/colonCA_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: clustComp, copa dependencyCount: 7 Package: CONFESSdata Version: 1.18.0 Depends: R (>= 3.3) License: GPL-2 MD5sum: dda8f172ecf21ba0b00e963d6231cb37 NeedsCompilation: no Title: Example dataset for CONFESS package Description: Example text-converted C01 image files for use in the CONFESS Bioconductor package. biocViews: HighThroughputImagingData,CellCulture,Homo_sapiens_Data,ExpressionData Author: Diana LOW and Efthimios MOTAKIS Maintainer: Diana LOW git_url: https://git.bioconductor.org/packages/CONFESSdata git_branch: RELEASE_3_12 git_last_commit: 26bb1fc git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/CONFESSdata_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CONFESS dependencyCount: 0 Package: ConnectivityMap Version: 1.26.0 Depends: R (>= 2.15.1) Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 5c08dc220e174734ca74fd589aec189a NeedsCompilation: no Title: Functional connections between drugs, genes and diseases as revealed by common gene-expression changes Description: The Broad Institute's Connectivity Map (cmap02) is a "large reference catalogue of gene-expression data from cultured human cells perturbed with many chemicals and genetic reagents", containing more than 7000 gene expression profiles and 1300 small molecules. biocViews: ExperimentData, CancerData, MicroarrayData Author: Paul Shannon Maintainer: Paul Shannon git_url: https://git.bioconductor.org/packages/ConnectivityMap git_branch: RELEASE_3_12 git_last_commit: a724faa git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ConnectivityMap_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: COPDSexualDimorphism.data Version: 1.26.0 License: LGPL-2.1 MD5sum: 7247454744e4b193f56e990e2feb18ac NeedsCompilation: no Title: Data to support sexually dimorphic and COPD differential analysis for gene expression and methylation. Description: Datasets to support COPDSexaulDimorphism Package. biocViews: ExperimentData, Tissue, COPDData Author: J Fah Sathirapongsasuti Maintainer: J Fah Sathirapongsasuti git_url: https://git.bioconductor.org/packages/COPDSexualDimorphism.data git_branch: RELEASE_3_12 git_last_commit: c093858 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/COPDSexualDimorphism.data_1.26.0.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: 1.22.0 Depends: R(>= 2.10) Suggests: BiocStyle License: GPL-2 MD5sum: fb29dbd790ca5fc2325534c31b0ed02f NeedsCompilation: no Title: Helper files for CopywriteR Description: This package contains the helper files that are required to run the Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content and mappability files for the reference genomes hg18, hg19, hg38, mm9 and mm10. In addition, it contains a blacklist filter to remove regions that display CNV. Files are stored as GRanges objects from the GenomicRanges Bioconductor package. biocViews: Homo_sapiens, GenomicSequence Author: Thomas Kuilman Maintainer: Oscar Krijgsman git_url: https://git.bioconductor.org/packages/CopyhelpeR git_branch: RELEASE_3_12 git_last_commit: 205e1ab git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/CopyhelpeR_1.22.0.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 importsMe: CopywriteR dependencyCount: 0 Package: CopyNeutralIMA Version: 1.8.0 Depends: R (>= 3.5.0) Imports: ExperimentHub,Rdpack (>= 0.8) Suggests: BiocStyle,knitr,rmarkdown,minfi,conumee,minfiData License: Artistic-2.0 MD5sum: 71821baad71fd44f7ae150de964cb906 NeedsCompilation: no Title: Copy Neutral Illumina Methylation Arrays Description: Provides a set of genomic copy neutral samples hybridized using Illumina Methylation arrays (450k and EPIC). biocViews: ExperimentData,Homo_sapiens_Data,MicroarrayData,TwoChannelData,MethylationArrayData,GEO Author: Xavier Pastor Hostench [aut, cre], Moritz Przybilla [aut] Maintainer: Xavier Pastor Hostench VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/CopyNeutralIMA git_branch: RELEASE_3_12 git_last_commit: 2f77b25 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/CopyNeutralIMA_1.8.0.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: 79 Package: COSMIC.67 Version: 1.26.0 Depends: R (>= 3.0.2) Imports: GenomicRanges, SummarizedExperiment, VariantAnnotation Suggests: testthat, BiocStyle, knitr License: GPL-3 MD5sum: fffff2f348c0206f432ddcb35ad2ba19 NeedsCompilation: no Title: COSMIC.67 Description: COSMIC: Catalogue Of Somatic Mutations In Cancer, version 67 (2013-10-24) biocViews: ExperimentData, Genome, CancerData Author: Julian Gehring Maintainer: Julian Gehring VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/COSMIC.67 git_branch: RELEASE_3_12 git_last_commit: ae9f5cb git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/COSMIC.67_1.26.0.tar.gz vignettes: vignettes/COSMIC.67/inst/doc/COSMIC.67.pdf vignetteTitles: COSMIC.67 - PDF hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/COSMIC.67/inst/doc/COSMIC.67.R importsMe: appreci8R dependencyCount: 90 Package: CRCL18 Version: 1.10.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 331bd8ee85f2e873748545e4a992ec6d NeedsCompilation: no Title: CRC cell line dataset Description: colorectal cancer mRNA and miRNA on 18 cell lines biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/CRCL18 git_branch: RELEASE_3_12 git_last_commit: 401b60e git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/CRCL18_1.10.0.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: curatedAdipoArray Version: 1.2.0 Depends: R (>= 4.0) Suggests: knitr, rmarkdown, ExperimentHub, SummarizedExperiment License: GPL-3 + file LICENSE MD5sum: 81026f9ca27d857e8fe4831d9c63859b 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] () Maintainer: Mahmoud Ahmed URL: https://github.com/MahShaaban/curatedAdipoArray VignetteBuilder: knitr BugReports: https://github.com/MahShaaban/curatedAdipoArray/issues git_url: https://git.bioconductor.org/packages/curatedAdipoArray git_branch: RELEASE_3_12 git_last_commit: 1c38c92 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/curatedAdipoArray_1.2.0.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: 1.6.0 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: 9bd98da195821d9c0a53c0e3f5acae60 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] () Maintainer: Mahmoud Ahmed URL: https://github.com/MahShaaban/curatedAdipoChIP VignetteBuilder: knitr BugReports: https://github.com/MahShaaban/curatedAdipoChIP/issues git_url: https://git.bioconductor.org/packages/curatedAdipoChIP git_branch: RELEASE_3_12 git_last_commit: 8d022c7 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/curatedAdipoChIP_1.6.0.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: 91 Package: curatedAdipoRNA Version: 1.6.0 Depends: R (>= 3.6), SummarizedExperiment Suggests: knitr, rmarkdown, DESeq2, fastqcr, devtools, testthat, readr, dplyr, tidyr, ggplot2, S4Vectors License: GPL-3 MD5sum: 443349a9adfb56bfea59313f48586108 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] () Maintainer: Mahmoud Ahmed URL: https://github.com/MahShaaban/curatedAdipoRNA VignetteBuilder: knitr BugReports: https://github.com/MahShaaban/curatedAdipoRNA/issues git_url: https://git.bioconductor.org/packages/curatedAdipoRNA git_branch: RELEASE_3_12 git_last_commit: 0f10b2d git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/curatedAdipoRNA_1.6.0.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: 26 Package: curatedBladderData Version: 1.26.0 Depends: R (>= 2.10.0), affy Suggests: BiocStyle, survival, xtable, sva, genefilter, logging License: Artistic-2.0 MD5sum: 41e26d27e586d73abca624091e1012cc NeedsCompilation: no Title: Bladder Cancer Gene Expression Analysis Description: The curatedBladderData package provides relevant functions and data for gene expression analysis in patients with bladder cancer. biocViews: ExperimentData, CancerData, OvarianCancerData, MicroarrayData, ExpressionData Author: Markus Riester Maintainer: Markus Riester URL: https://github.com/lima1/curatedBladderData git_url: https://git.bioconductor.org/packages/curatedBladderData git_branch: RELEASE_3_12 git_last_commit: 10c26cc git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/curatedBladderData_1.26.0.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: 13 Package: curatedBreastData Version: 2.18.0 Depends: R (>= 3.0.0), XML, ggplot2, impute, Biobase, BiocStyle Imports: methods, stats License: GPL (>= 2) MD5sum: a7d4a16107607aac279cf9408454189a NeedsCompilation: no Title: Curated breast cancer gene expression data with survival and treatment information Description: Curated human breast cancer tissue S4 ExpresionSet datasets from over 16 clinical trials comprising over 2,000 patients. All datasets contain at least one type of outcomes variable and treatment information (minimum level: whether they had chemotherapy and whether they had hormonal therapy). Includes code to post-process these datasets. biocViews: ExperimentData, ExpressionData, CancerData, Tissue, BreastCancerData, qPCRData, MicroarrayData, TissueMicroarrayData, GEO Author: Katie Planey Maintainer: Katie Planey git_url: https://git.bioconductor.org/packages/curatedBreastData git_branch: RELEASE_3_12 git_last_commit: 464335b git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/curatedBreastData_2.18.0.tar.gz vignettes: vignettes/curatedBreastData/inst/doc/curatedBreastData-manual.pdf vignetteTitles: Manual hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedBreastData/inst/doc/curatedBreastData-manual.R dependencyCount: 61 Package: curatedCRCData Version: 2.22.0 Depends: R (>= 2.10.0), nlme Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle License: Artistic-2.0 MD5sum: a6979b1f911ecb7321e2ccdac26962cb 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: Colorectal, Cancer, TCGA, ExperimentData, RNAExpressionData Author: Princy Parsana, Markus Riester, Curtis Huttenhower, Levi Waldron Maintainer: Princy Parsana URL: https://bitbucket.org/biobakery/curatedcrcdata git_url: https://git.bioconductor.org/packages/curatedCRCData git_branch: RELEASE_3_12 git_last_commit: fe88edd git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/curatedCRCData_2.22.0.tar.gz vignettes: vignettes/curatedCRCData/inst/doc/curatedCRCData_vignette.pdf vignetteTitles: curatedCRCData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedCRCData/inst/doc/curatedCRCData_vignette.R dependencyCount: 10 Package: curatedMetagenomicData Version: 1.20.0 Depends: R (>= 4.0.0), AnnotationHub (>= 2.9.0), Biobase (>= 2.37.0), dplyr (>= 0.5.0), ExperimentHub (>= 1.3.0) Imports: magrittr, methods, S4Vectors, tidyr, utils Suggests: ape, covr, BiocCheck, BiocManager, BiocParallel, BiocStyle, devtools, ggplot2, knitr, metagenomeSeq, phyloseq, readr, RISmed, rmarkdown, roxygen2, testthat License: Artistic-2.0 MD5sum: 2d9208076ddeb06ee8c52e46521f6fb7 NeedsCompilation: no Title: Curated Metagenomic Data of the Human Microbiome Description: The curatedMetagenomicData package provides microbial taxonomic, functional, and gene marker abundance for samples collected from different bodysites. biocViews: Homo_sapiens_Data, ReproducibleResearch, MicrobiomeData, ExperimentHub Author: Lucas Schiffer , Edoardo Pasolli , Levi Waldron , Faizan Malik , Nicola Segata , Valerie Obenchain , Morgan Martin 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: RELEASE_3_12 git_last_commit: 0af9806 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/curatedMetagenomicData_1.20.0.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: lefser, metavizr, MMUPHin, HMP16SData dependencyCount: 79 Package: curatedOvarianData Version: 1.28.0 Depends: R (>= 2.10.0), affy Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle License: Artistic-2.0 MD5sum: a85ad4d6258a7a78a000c185e7b17e3d 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 F. Ganzfried, Markus Riester, Steve Skates, Victoria Wang, Thomas Risch, Benjamin Haibe-Kains, Svitlana Tyekucheva, Jie Ding, Ina Jazic, Michael Birrer, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron Maintainer: Levi Waldron URL: http://bcb.dfci.harvard.edu/ovariancancer git_url: https://git.bioconductor.org/packages/curatedOvarianData git_branch: RELEASE_3_12 git_last_commit: 27fa1d5 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/curatedOvarianData_1.28.0.tar.gz vignettes: vignettes/curatedOvarianData/inst/doc/curatedOvarianData_vignette.pdf vignetteTitles: curatedOvarianData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedOvarianData/inst/doc/curatedOvarianData_vignette.R suggestsMe: doppelgangR, simulatorZ dependencyCount: 13 Package: curatedTCGAData Version: 1.12.1 Depends: R (>= 3.5.0), MultiAssayExperiment Imports: AnnotationHub, ExperimentHub, HDF5Array, methods, S4Vectors, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, RaggedExperiment, readr, rmarkdown, TCGAutils, testthat License: Artistic-2.0 MD5sum: 31afbe438f83a01613291454d930d0d5 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], Levi Waldron [ctb], Lucas Schiffer [ctb], Ludwig Geistlinger [ctb], Valerie Obenchain [ctb], Martin Morgan [ctb] Maintainer: Marcel Ramos VignetteBuilder: knitr BugReports: https://github.com/waldronlab/curatedTCGAData/issues git_url: https://git.bioconductor.org/packages/curatedTCGAData git_branch: RELEASE_3_12 git_last_commit: 967b951 git_last_commit_date: 2021-04-23 Date/Publication: 2021-04-26 source.ver: src/contrib/curatedTCGAData_1.12.1.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, BiocOncoTK suggestsMe: CNVRanger, deco, glmSparseNet, netDx, TCGAutils dependencyCount: 98 Package: DAPARdata Version: 1.20.1 Depends: R (>= 4.0.3) Imports: utils, knitr, MSnbase Suggests: DAPAR, Prostar License: GPL-2 MD5sum: f91728791d6d45d5e50eca764af4a499 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 Author: Samuel Wieczorek and Florence Combes Maintainer: Samuel Wieczorek URL: http://www.prostar-proteomics.org/ BugReports: https://github.com/samWieczorek/DAPARdata/issues git_url: https://git.bioconductor.org/packages/DAPARdata git_branch: RELEASE_3_12 git_last_commit: 65d3947 git_last_commit_date: 2020-11-16 Date/Publication: 2020-11-16 source.ver: src/contrib/DAPARdata_1.20.1.tar.gz vignettes: vignettes/DAPARdata/inst/doc/Exp1_R2_pept.pdf, vignettes/DAPARdata/inst/doc/Exp1_R2_prot.pdf, vignettes/DAPARdata/inst/doc/Exp1_R25_pept.pdf, vignettes/DAPARdata/inst/doc/Exp1_R25_prot.pdf, vignettes/DAPARdata/inst/doc/Exp2_R10_pept.pdf, vignettes/DAPARdata/inst/doc/Exp2_R10_prot.pdf, vignettes/DAPARdata/inst/doc/Exp2_R100_pept.pdf, vignettes/DAPARdata/inst/doc/Exp2_R100_prot.pdf, vignettes/DAPARdata/inst/doc/Exp2_R2_pept.pdf, vignettes/DAPARdata/inst/doc/Exp2_R2_prot.pdf vignetteTitles: Exp1_R2_pept.pdf, Exp1_R2_prot.pdf, Exp1_R25_pept.pdf, Exp1_R25_prot.pdf, Exp2_R10_pept.pdf, Exp2_R10_prot.pdf, Exp2_R100_pept.pdf, Exp2_R100_prot.pdf, Exp2_R2_pept.pdf, Exp2_R2_prot.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: davidTiling Version: 1.30.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db License: LGPL MD5sum: 020cdac17c49a10583970d2c4ef2c238 NeedsCompilation: no Title: Data and analysis scripts for David, Huber et al. yeast tiling array paper Description: This package contains the data for the paper by L. David et al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix genechips, an ExpressionSet object with the raw feature data, a probe annotation data structure for the chip and the yeast genome annotation (GFF file) that was used. In addition, some custom-written analysis functions are provided, as well as R scripts in the scripts directory. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, MicroarrayData, ReproducibleResearch Author: Wolfgang Huber , Joern Toedling Maintainer: Wolfgang Huber URL: http://www.ebi.ac.uk/huber git_url: https://git.bioconductor.org/packages/davidTiling git_branch: RELEASE_3_12 git_last_commit: d086898 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/davidTiling_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 81 Package: depmap Version: 1.4.0 Depends: R (>= 3.6), methods, dplyr Imports: utils, ExperimentHub, AnnotationHub Suggests: knitr, rmarkdown, BiocStyle, viridis, gridExtra, ggplot2, readr, tibble, stringr, tidyr License: Artistic-2.0 MD5sum: acf3810b6d2120cdee9354ac32418f64 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], Theo Killian [aut] Maintainer: Laurent Gatto VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/depmap git_branch: RELEASE_3_12 git_last_commit: 8f31da1 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/depmap_1.4.0.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 dependencyCount: 77 Package: derfinderData Version: 2.8.1 Depends: R(>= 3.1.1) Suggests: sessioninfo, knitr (>= 1.6), RefManageR, rmarkdown (>= 0.3.3), BiocStyle License: Artistic-2.0 MD5sum: f869a002a5f352d038887b03e85e6ece 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] (), Andrew Jaffe [aut] (), Jeffrey Leek [aut, ths] () Maintainer: Leonardo Collado-Torres URL: https://github.com/leekgroup/derfinderData VignetteBuilder: knitr BugReports: https://github.com/leekgroup/derfinderData/issues git_url: https://git.bioconductor.org/packages/derfinderData git_branch: RELEASE_3_12 git_last_commit: 4f572dd git_last_commit_date: 2020-12-17 Date/Publication: 2020-12-21 source.ver: src/contrib/derfinderData_2.8.1.tar.gz vignettes: vignettes/derfinderData/inst/doc/derfinderData.html vignetteTitles: Introduction to derfinderData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/derfinderData/inst/doc/derfinderData.R suggestsMe: derfinder, derfinderPlot dependencyCount: 0 Package: DeSousa2013 Version: 1.26.0 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: de6791649f9c7eb0ee52e07ac94081d1 NeedsCompilation: no Title: Poor prognosis colon cancer is defined by a molecularly distinct subtype and precursor lesion Description: This package reproduces the main pipeline to analyze the AMC-AJCCII-90 microarray data set in De Sousa et al. accepted by Nature Medicine in 2013. biocViews: CancerData, ColonCancerData, MicroarrayData Author: Xin Wang Maintainer: Xin Wang git_url: https://git.bioconductor.org/packages/DeSousa2013 git_branch: RELEASE_3_12 git_last_commit: 46e8cec git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/DeSousa2013_1.26.0.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: 135 Package: diffloopdata Version: 1.18.0 Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: c4846251bd0310376e6e2bd684230f34 NeedsCompilation: no Title: Example ChIA-PET Datasets for the diffloop Package Description: ChIA-PET example datasets and additional data for use with the diffloop package. biocViews: ExperimentData, SequencingData Author: Caleb Lareau [aut], Martin Aryee [aut, cre] Maintainer: Caleb Lareau VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/diffloopdata git_branch: RELEASE_3_12 git_last_commit: 02b0f89 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/diffloopdata_1.18.0.tar.gz vignettes: vignettes/diffloopdata/inst/doc/diffloopdata.html vignetteTitles: diffloopdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: diffloop dependencyCount: 0 Package: diggitdata Version: 1.22.0 Depends: R(>= 2.14.0), Biobase, methods Imports: viper License: GPL (>=2) MD5sum: 76cecf55162d30e82871e14710f3cfa7 NeedsCompilation: no Title: Example data for the diggit package Description: This package provides expression profile and CNV data for glioblastoma from TCGA, and transcriptional and post-translational regulatory networks assembled with the ARACNe and MINDy algorithms, respectively. biocViews: ExperimentData, Cancer Author: Mariano Javier Alvarez Maintainer: Mariano Javier Alvarez git_url: https://git.bioconductor.org/packages/diggitdata git_branch: RELEASE_3_12 git_last_commit: d913c35 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/diggitdata_1.22.0.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: 22 Package: DLBCL Version: 1.30.0 Depends: R(>= 2.11.0), Biobase License: GPL (>=2) MD5sum: 07852b15eed41ac0e616691d984b3eaa NeedsCompilation: no Title: Diffuse large B-cell lymphoma expression data Description: This package provides additional expression data on diffuse large B-cell lymphomas for the BioNet package. biocViews: ExperimentData, CancerData, MicroarrayData, ChipOnChipData Author: Marcus Dittrich and Daniela Beisser Maintainer: Marcus Dittrich URL: http://bionet.bioapps.biozentrum.uni-wuerzburg.de/ git_url: https://git.bioconductor.org/packages/DLBCL git_branch: RELEASE_3_12 git_last_commit: b7a34f3 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/DLBCL_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: BioNet dependencyCount: 7 Package: DmelSGI Version: 1.22.1 Depends: R (>= 3.0) Imports: grid, TSP, limma, rhdf5, knitr, abind, gplots, igraph, grDevices, graphics, stats Suggests: BiocStyle, EBImage, RColorBrewer, RNAinteractMAPK, RSVGTipsDevice, cgdsr, hwriter, xtable, beeswarm License: Artistic-2.0 MD5sum: 9a0cfcec3136b07bf23d1b10a89dea36 NeedsCompilation: no Title: Experimental data and documented source code for the paper "A Map of Directional Genetic Interactions in a Metazoan Cell" Description: The package contains the experimental data and documented source code of the manuscript "Fischer et al., A Map of Directional Genetic Interactions in a Metazoan Cell, eLife, 2015, in Press.". The vignette code generates all figures in the paper. biocViews: MicrotitrePlateAssayData, CellCulture, HighthroughputImagingData, Drosophila_melanogaster_Data, ExperimentData, HighThroughputImagingData, ReproducibleResearch Author: Bernd Fischer [aut], Wolfgang Huber [ctb], Mike Smith [cre] Maintainer: Mike Smith VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DmelSGI git_branch: RELEASE_3_12 git_last_commit: 32f1478 git_last_commit_date: 2020-12-17 Date/Publication: 2020-12-21 source.ver: src/contrib/DmelSGI_1.22.1.tar.gz vignettes: vignettes/DmelSGI/inst/doc/DmelSGI.pdf vignetteTitles: DmelSGI hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DmelSGI/inst/doc/DmelSGI.R dependencyCount: 36 Package: DMRcatedata Version: 2.8.2 Depends: R (>= 3.6), ExperimentHub Imports: GenomicFeatures, Gviz, readxl, plyr, rtracklayer, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr License: GPL-3 MD5sum: 2749d251c87be574964588508b110ab5 NeedsCompilation: no Title: Data Package for DMRcate Description: This package contains 9 data objects supporting functionality and examples of the Bioconductor package DMRcate. biocViews: ExperimentHub, ExperimentData, SNPData, Homo_sapiens_Data, Mus_musculus_Data, SequencingData, MicroarrayData, Genome Author: Tim Peters Maintainer: Tim Peters VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DMRcatedata git_branch: RELEASE_3_12 git_last_commit: 65779e8 git_last_commit_date: 2021-02-08 Date/Publication: 2021-02-11 source.ver: src/contrib/DMRcatedata_2.8.2.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: 195 Package: DonaPLLP2013 Version: 1.28.0 Depends: EBImage, parallel License: Artistic-2.0 MD5sum: a712142d0ef20154b977ac84881d4761 NeedsCompilation: no Title: Supplementary data package for Dona et al. (2013) containing example images and tables Description: An experiment data package associated with the publication Dona et al. (2013). Package contains runnable vignettes showing an example image segmentation for one posterior lateral line primordium, and also the data table and code used to analyze tissue-scale lifetime-ratio statistics. biocViews: ExperimentData, Tissue Author: Erika Dona, Joseph D. Barry, Guillaume Valentin, Charlotte Quirin, Anton Khmelinskii, Andreas Kunze, Sevi Durdu, Lionel R. Newton, Ana Fernandez-Minan, Wolfgang Huber, Michael Knop, Darren Gilmour Maintainer: Joseph D. Barry git_url: https://git.bioconductor.org/packages/DonaPLLP2013 git_branch: RELEASE_3_12 git_last_commit: da3f5ed git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/DonaPLLP2013_1.28.0.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: 25 Package: dorothea Version: 1.2.2 Depends: R (>= 4.0) Imports: dplyr, magrittr, bcellViper, viper Suggests: Biobase, BiocStyle, knitr, pheatmap, pkgdown, rmarkdown, Seurat, SingleCellExperiment, SummarizedExperiment, testthat (>= 2.1.0), tibble, tidyr, utils License: GPL-3 + file LICENSE MD5sum: 3b1e90fe8e55a5579ba83fb59933f856 NeedsCompilation: no Title: Collection Of Human And Mouse TF Regulons Description: This package contains human and mouse TF regulons. The human regulons were curated and collected from different types of evidence such as literature curated resources, ChIP-seq peaks, TF binding site motifs and interactions inferred directly from gene expression. The mouse regulons were constructed by mapping the human gene symbols to their orthologs in mice. Those regulons can be coupled with any statistical method that aims to analyse gene sets to infer TF activity from gene expression data. Preferably the statistical method viper is used. biocViews: ExperimentData, Homo_sapiens_Data, Mus_musculus_Data Author: Christian H. Holland [cre, aut] (), Luz Garcia-Alonso [aut], Alberto Valdeolivas [ctb], Minoo Ashtiani [ctb], Attila Gabor [ctb] Maintainer: Christian H. Holland URL: https://saezlab.github.io/dorothea/, https://github.com/saezlab/dorothea VignetteBuilder: knitr BugReports: https://github.com/saezlab/dorothea/issues git_url: https://git.bioconductor.org/packages/dorothea git_branch: RELEASE_3_12 git_last_commit: 88a7812 git_last_commit_date: 2021-04-18 Date/Publication: 2021-04-19 source.ver: src/contrib/dorothea_1.2.2.tar.gz vignettes: vignettes/dorothea/inst/doc/bulk_vignette.html, vignettes/dorothea/inst/doc/single_cell_vignette.html vignetteTitles: TF activity inference from bulk transcriptomic data with DoRothEA as regulon resource., TF activity inference from scRNA-seq data with DoRothEA as regulon resource. hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/dorothea/inst/doc/bulk_vignette.R, vignettes/dorothea/inst/doc/single_cell_vignette.R suggestsMe: MethReg dependencyCount: 41 Package: DREAM4 Version: 1.26.0 Depends: R (>= 2.15.1), SummarizedExperiment Suggests: RUnit, networkBMA License: GPL MD5sum: 7c586716529100136738a81ff4091df1 NeedsCompilation: no Title: Synthetic Expression Data for Gene Regulatory Network Inference from the 2009 DREAM4 challenge Description: Simulated expression data for five 10-node, and five 100-node networks, with associated data (including solutions) from the 2009 DREAM4 challenge. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, SequencingData Author: Paul Shannon Maintainer: Paul Shannon git_url: https://git.bioconductor.org/packages/DREAM4 git_branch: RELEASE_3_12 git_last_commit: 6ae07c0 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/DREAM4_1.26.0.tar.gz vignettes: vignettes/DREAM4/inst/doc/DREAM4_InSilico_Description.pdf, vignettes/DREAM4/inst/doc/DREAM4.pdf vignetteTitles: DREAM4_InSilico_Description.pdf, DREAM4 Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DREAM4/inst/doc/DREAM4.R dependencyCount: 26 Package: dressCheck Version: 0.28.0 Depends: R (>= 2.10.1), methods, Biobase (>= 2.5.5) Suggests: survival, chron License: Artistic-2.0 MD5sum: a97ead2bc0d2455642ce4649245e2f2b NeedsCompilation: no Title: data and software for checking Dressman JCO 25(5) 2007 Description: data and software for checking Dressman JCO 25(5) 2007 biocViews: ExperimentData, Genome Author: Vincent Carey Maintainer: Vincent Carey git_url: https://git.bioconductor.org/packages/dressCheck git_branch: RELEASE_3_12 git_last_commit: 1551865 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/dressCheck_0.28.0.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: 1.0.0 Imports: utils, ExperimentHub, AnnotationHub, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, testthat, DropletUtils License: GPL-3 MD5sum: 1ece96b688674c1001b7adb4dd816433 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: RELEASE_3_12 git_last_commit: 47f2429 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/DropletTestFiles_1.0.0.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 suggestsMe: DropletUtils dependencyCount: 77 Package: DrugVsDiseasedata Version: 1.26.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 8171e917de9d7c39412b4cd440204237 NeedsCompilation: no Title: Drug versus Disease Data Description: Data package which provides default disease expression profiles, clusters and annotation information for use with the DrugVsDisease package. biocViews: Homo_sapiens_Data, MicroarrayData Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/DrugVsDiseasedata git_branch: RELEASE_3_12 git_last_commit: 343ffe5 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/DrugVsDiseasedata_1.26.0.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: dsQTL Version: 0.28.0 Depends: R (>= 2.15.0), utils, Biobase, SummarizedExperiment, GGBase (>= 3.31.1) Suggests: GGtools, rtracklayer License: Artistic-2.0 MD5sum: fbfe32fb1a198d0d3b2af1d521b83828 NeedsCompilation: no Title: dsQTL, data excerpt from Degner et al. 2012 Nature letter Description: dsQTL, excerpt from Degner et al. 2012 Nature letter on DNA variants associated with DnaseI hypersensitivity biocViews: ExperimentData, Genome, SequencingData, DNASeqData, NCI, Project1000genomes, BiocViews Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/dsQTL git_branch: RELEASE_3_12 git_last_commit: 7026e53 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/dsQTL_0.28.0.tar.gz vignettes: vignettes/dsQTL/inst/doc/dsq.pdf vignetteTitles: dsQTL,, data excerpt from Degner et al. 2012 Nature letter hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/dsQTL/inst/doc/dsq.R importsMe: yriMulti dependencyCount: 60 Package: DuoClustering2018 Version: 1.8.0 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: 6b5e862d99d00d4af5238bc26bf4de6e 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: RELEASE_3_12 git_last_commit: 6cdb6ba git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/DuoClustering2018_1.8.0.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: 104 Package: DvDdata Version: 1.26.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: a2c804758996296c68585304ba76ea26 NeedsCompilation: no Title: Drug versus Disease Data Description: Data package which provides default drug and disease expression profiles for the DvD package. biocViews: GEO Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/DvDdata git_branch: RELEASE_3_12 git_last_commit: 11bae02 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/DvDdata_1.26.0.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: 1.30.0 Depends: R (>= 1.4.1), marray, GEOquery Suggests: dyebias, convert, Biobase License: GPL-3 MD5sum: 9c09e15dec9d1ef74135df21905a20a3 NeedsCompilation: no Title: Example data for the dyebias package, which implements the GASSCO method. Description: Data for the dyebias package, consisting of 4 self-self hybrizations of self-spotted yeast slides, as well as data from Array Express accession E-MTAB-32 biocViews: ExperimentData, SAGEData, CGHData, MicroarrayData, TwoChannelData, ArrayExpress Author: Philip Lijnzaad and Thanasis Margaritis Maintainer: Philip Lijnzaad URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad git_url: https://git.bioconductor.org/packages/dyebiasexamples git_branch: RELEASE_3_12 git_last_commit: bd3863c git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/dyebiasexamples_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: dyebias dependencyCount: 44 Package: EatonEtAlChIPseq Version: 0.28.0 Depends: GenomicRanges (>= 1.5.42), ShortRead, rtracklayer License: Artistic 2.0 MD5sum: 9ed0412eab89b316b17c190c6d2c167c NeedsCompilation: no Title: ChIP-seq data of ORC-binding sites in Yeast excerpted from Eaton et al. 2010 Description: ChIP-seq analysis subset from "Conserved nucleosome positioning defines replication origins" (PMID 20351051) biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, ChIPSeqData, GEO Author: Patrick Aboyoun Maintainer: Patrick Aboyoun git_url: https://git.bioconductor.org/packages/EatonEtAlChIPseq git_branch: RELEASE_3_12 git_last_commit: 2fdb80c git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/EatonEtAlChIPseq_0.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 46 Package: ecoliLeucine Version: 1.30.0 Depends: R (>= 1.9.0), affy (>= 1.23.4), ecolicdf License: GPL (>= 2) MD5sum: da5ba90ef198c3bf7f4b5f1090e37cdb NeedsCompilation: no Title: Experimental data with Affymetrix E. coli chips Description: Experimental data with Affymetrix E. coli chips, as reported in She-pin Hung, Pierre Baldi, and G. Wesley Hatfield, J. Biol. Chem., Vol. 277, Issue 43, 40309-40323, October 25, 2002 biocViews: ExperimentData, MicroarrayData Author: Laurent Gautier Maintainer: Laurent Gautier git_url: https://git.bioconductor.org/packages/ecoliLeucine git_branch: RELEASE_3_12 git_last_commit: 17c3f26 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ecoliLeucine_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ecolitk dependencyCount: 33 Package: EGSEAdata Version: 1.18.0 Depends: R (>= 3.4) Suggests: EGSEA License: file LICENSE MD5sum: 0f3e2631bed49e54122484c3fb141790 NeedsCompilation: no Title: Gene set collections for the EGSEA package Description: This package includes gene set collections that are used for the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. It includes Human and Mouse versions of the MSidDB (Subramanian, et al. (2005) PNAS, 102(43):15545-15550) and GeneSetDB (Araki, et al. (2012) FEBS Open Bio, 2:76-82) collections. biocViews: ExperimentData, Homo_sapiens_Data, Mus_musculus_Data, Rattus_norvegicus_Data Author: Monther Alhamdoosh, Yifang Hu and Gordon K. Smyth Maintainer: Monther Alhamdoosh git_url: https://git.bioconductor.org/packages/EGSEAdata git_branch: RELEASE_3_12 git_last_commit: dee7183 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/EGSEAdata_1.18.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE importsMe: EGSEA dependencyCount: 0 Package: ELMER.data Version: 2.14.0 Depends: R (>= 3.5.0) Imports: GenomicRanges Suggests: BiocStyle, knitr, dplyr, devtools, DT License: GPL-3 MD5sum: 731029db8af9f972705aac37cf4a30de NeedsCompilation: no Title: Data for the ELMER package Description: Supporting data for the ELMER package. It includes: - elmer.data.example.promoter: mae.promoter - elmer.data.example: data - EPIC.hg38.manifest - EPIC.hg19.manifest - hm450.hg38.manifest - hm450.hg19.manifest - hocomoco.table - human.TF - LUSC_meth_refined: Meth - LUSC_RNA_refined: GeneExp - Probes.motif.hg19.450K - Probes.motif.hg19.EPIC - Probes.motif.hg38.450K - Probes.motif.hg38.EPIC - TF.family - TF.subfamily - Human_genes__GRCh37_p13 - Human_genes__GRCh38_p12 - Human_genes__GRCh37_p13__tss - Human_genes__GRCh38_p12__tss biocViews: AssayDomainData, TechnologyData, OrganismData Author: Tiago Chedraoui Silva, Lijing Yao Simon Coetzee, Benjamin P. Berman Maintainer: Tiago Chedraoui Silva VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ELMER.data git_branch: RELEASE_3_12 git_last_commit: f9d6121 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ELMER.data_2.14.0.tar.gz vignettes: vignettes/ELMER.data/inst/doc/vignettes.html vignetteTitles: ELMER.data: Supporting data for the ELMER package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ELMER.data/inst/doc/vignettes.R dependsOnMe: ELMER dependencyCount: 17 Package: estrogen Version: 1.36.0 Suggests: affy, hgu95av2, hgu95av2cdf, vsn, knitr License: LGPL MD5sum: 2d2db0089775e2269a83d091e43f8e69 NeedsCompilation: no Title: Microarray dataset that can be used as example for 2x2 factorial designs Description: Data from 8 Affymetrix genechips, looking at a 2x2 factorial design (with 2 repeats per level). biocViews: ExperimentData, MicroarrayData Author: Wolfgang Huber, Robert Gentleman Maintainer: Wolfgang Huber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/estrogen git_branch: RELEASE_3_12 git_last_commit: bc62605 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/estrogen_1.36.0.tar.gz vignettes: vignettes/estrogen/inst/doc/estrogen.pdf vignetteTitles: estrogen hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/estrogen/inst/doc/estrogen.R suggestsMe: AffyExpress, categoryCompare dependencyCount: 0 Package: etec16s Version: 1.18.0 Depends: R (>= 3.3), Biobase, metagenomeSeq(>= 1.12.0) License: Artistic-2.0 MD5sum: b21ca05bc6c54f26c97d6253524906c4 NeedsCompilation: no Title: Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment Description: 16S rRNA gene sequencing data to study changes in the faecal microbiota of 12 volunteers during a human challenge study with ETEC (H10407) and subsequent treatment with ciprofloxacin. biocViews: ExperimentData, SequencingData, MicrobiomeData Author: Joseph N. Paulson Maintainer: Joseph N. Paulson git_url: https://git.bioconductor.org/packages/etec16s git_branch: RELEASE_3_12 git_last_commit: 5c229f4 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/etec16s_1.18.0.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 suggestsMe: metavizr dependencyCount: 29 Package: faahKO Version: 1.30.0 Depends: R (>= 2.10), xcms (>= 3.4.0) License: LGPL MD5sum: 79b9f4f1ee9df24f65b0c9437b273f85 NeedsCompilation: no Title: Saghatelian et al. (2004) FAAH knockout LC/MS data Description: Positive ionization mode data in NetCDF file format. Centroided subset from 200-600 m/z and 2500-4500 seconds. Data originally reported in "Assignment of Endogenous Substrates to Enzymes by Global Metabolite Profiling" Biochemistry; 2004; 43(45). Also includes detected peaks in an xcmsSet. biocViews: ExperimentData, MassSpectrometryData Author: Colin A. Smith Maintainer: Steffen Neumann URL: http://dx.doi.org/10.1021/bi0480335 git_url: https://git.bioconductor.org/packages/faahKO git_branch: RELEASE_3_12 git_last_commit: 08e8a3d git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/faahKO_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: cosmiq suggestsMe: CAMERA, IPO, MAIT, peakPantheR, Risa, xcms dependencyCount: 92 Package: fabiaData Version: 1.28.0 Depends: R (>= 2.10.0), Biobase Imports: utils Suggests: fabia License: LGPL (>= 2.1) MD5sum: ca293edfe8825ec23d92e687e6aaa7c3 NeedsCompilation: no Title: Data sets for FABIA (Factor Analysis for Bicluster Acquisition) Description: Supplying gene expression data sets for the demos of the biclustering method "Factor Analysis for Bicluster Acquisition" (FABIA). The following three data sets are provided: A) breast cancer (van't Veer, Nature, 2002), B) multiple tissues (Su, PNAS, 2002), and C) diffuse large-B-cell lymphoma (Rosenwald, N Engl J Med, 2002). biocViews: CancerData, BreastCancerData, MicroarrayData Author: Sepp Hochreiter Maintainer: Sepp Hochreiter URL: http://www.bioinf.jku.at/software/fabia/fabia.html git_url: https://git.bioconductor.org/packages/fabiaData git_branch: RELEASE_3_12 git_last_commit: 303b9fa git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/fabiaData_1.28.0.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: facsDorit Version: 1.32.0 Depends: R (>= 1.9.1), prada (>= 1.0.5) License: GPL-2 MD5sum: 47ebdabaa1996948fc860b0ec7746549 NeedsCompilation: no Title: DKFZ FACS example data Description: FACS example data for cell-based assays. This data is used in the examples and vignettes of the package prada. biocViews: ExperimentData, MicrotitrePlateAssayData Author: Florian Hahne Maintainer: Florian Hahne URL: http://www.dkfz.de/mga git_url: https://git.bioconductor.org/packages/facsDorit git_branch: RELEASE_3_12 git_last_commit: b2236cc git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/facsDorit_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 1 Package: FANTOM3and4CAGE Version: 1.26.0 Depends: R (>= 2.15.0) License: GPL-3 MD5sum: 391989302c9e5c4648880e437621846a NeedsCompilation: no Title: CAGE data from FANTOM3 and FANTOM4 projects Description: CAGE (Cap Analysis Gene Expression) data from FANTOM3 and FANTOM4 projects produced by RIKEN Omics Science Center. biocViews: ExperimentData, Tissue Author: Vanja Haberle, Department of Biology, University of Bergen, Norway Maintainer: Vanja Haberle git_url: https://git.bioconductor.org/packages/FANTOM3and4CAGE git_branch: RELEASE_3_12 git_last_commit: 5d4f3b9 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/FANTOM3and4CAGE_1.26.0.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: 1.28.0 Depends: R (>= 2.10.0), lumi Suggests: genefilter, affy License: GPL (>2) MD5sum: 358082994186101e379ebd587203fd02 NeedsCompilation: no Title: Illumina DASL example microarray data Description: A subset of GSE17565 (April et al. 2009) containing 32 FFPE samples of Burkitts Lymphoma and Breast Adenocarcinoma, with a dilution series in technical duplicate. biocViews: Tissue, Genome, MicroarrayData, TissueMicroarrayData, GEO Author: Levi Waldron Maintainer: Levi Waldron git_url: https://git.bioconductor.org/packages/ffpeExampleData git_branch: RELEASE_3_12 git_last_commit: 6c21a7b git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ffpeExampleData_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ffpe dependencyCount: 151 Package: fibroEset Version: 1.32.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: 8904c2a4b2860cfb07e0aa68f8958344 NeedsCompilation: no Title: exprSet for Karaman et al. (2003) fibroblasts data Description: exprSet for Karaman et al. (2003) human, bonobo and gorilla fibroblasts data biocViews: ExperimentData, Genome, Homo_sapiens_Data, MicroarrayData, ChipOnChipData Author: Sylvia Merk Maintainer: Sylvia Merk git_url: https://git.bioconductor.org/packages/fibroEset git_branch: RELEASE_3_12 git_last_commit: 63d4a9b git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/fibroEset_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: biocGraph, clusterStab, geneplotter dependencyCount: 7 Package: FieldEffectCrc Version: 1.0.0 Depends: utils Imports: BiocStyle, RUnit, SummarizedExperiment, ExperimentHub (>= 0.99.6), AnnotationHub, DESeq2 Suggests: knitr, rmarkdown, BiocGenerics, sva, BiocManager License: Artistic-2.0 MD5sum: 0839850a87335d4073f74c6281bf3b91 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] (), 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: RELEASE_3_12 git_last_commit: 5d85803 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/FieldEffectCrc_1.0.0.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: 132 Package: FIs Version: 1.18.0 Depends: R (>= 3.3) License: GPL-3 MD5sum: 4ee01349e2693325aeb5d791c0477c8e NeedsCompilation: no Title: Human Functional Interactions (FIs) for splineTimeR package Description: Data set containing two complete lists of identified functional interaction partners in Human. Data are derived from Reactome and BioGRID databases. biocViews: PathwayInteractionDatabase, Homo_sapiens_Data Author: Agata Michna Maintainer: Herbert Braselmann , Martin Selmansberger git_url: https://git.bioconductor.org/packages/FIs git_branch: RELEASE_3_12 git_last_commit: 3ec7700 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/FIs_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: splineTimeR dependencyCount: 0 Package: fission Version: 1.10.0 Depends: R (>= 2.10), SummarizedExperiment Suggests: knitr License: LGPL MD5sum: f7cfcd0f5b86b9ed1028c9719e451271 NeedsCompilation: no Title: RangedSummarizedExperiment for time course RNA-Seq of fission yeast in response to stress, by Leong et al., Nat Commun 2014. Description: This package provides a RangedSummarizedExperiment object of read counts in genes for a time course RNA-Seq experiment of fission yeast (Schizosaccharomyces pombe) in response to oxidative stress (1M sorbitol treatment) at 0, 15, 30, 60, 120 and 180 mins. The samples are further divided between a wild-type group and a group with deletion of atf21. The read count matrix was prepared and provided by the author of the study: Leong HS, Dawson K, Wirth C, Li Y, Connolly Y, Smith DL, Wilkinson CR, Miller CJ. "A global non-coding RNA system modulates fission yeast protein levels in response to stress". Nat Commun 2014 May 23;5:3947. PMID: 24853205. GEO: GSE56761. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData, GEO Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/fission git_branch: RELEASE_3_12 git_last_commit: ce9c694 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/fission_1.10.0.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: 26 Package: Fletcher2013a Version: 1.26.0 Depends: R (>= 2.15), limma Imports: Biobase ,VennDiagram, gplots,grid License: GPL (>= 2) MD5sum: db06990ebb49a4761bd8d77760c825a4 NeedsCompilation: no Title: Gene expression data from breast cancer cells under FGFR2 signalling perturbation Description: The package Fletcher2013a contains time-course gene expression data from MCF-7 cells treated under different experimental systems in order to perturb FGFR2 signalling. The data comes from Fletcher et al. (Nature Comms 4:2464, 2013) where further details about the background and the experimental design of the study can be found. biocViews: ExperimentData, ExpressionData, CancerData, BreastCancerData, MicroarrayData Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin Meyer. Maintainer: Mauro Castro URL: http://dx.doi.org/10.1038/ncomms3464 git_url: https://git.bioconductor.org/packages/Fletcher2013a git_branch: RELEASE_3_12 git_last_commit: dfcc5cf git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/Fletcher2013a_1.26.0.tar.gz vignettes: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.pdf vignetteTitles: Main vignette:Fletcher2013a hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.R dependsOnMe: Fletcher2013b dependencyCount: 20 Package: Fletcher2013b Version: 1.26.0 Depends: R (>= 2.15), Fletcher2013a, RTN (>= 1.1.2), RedeR (>= 1.8.1), igraph Imports: RColorBrewer License: GPL (>= 2) MD5sum: 5c265a7b8870cc699a2bf2dee3d08621 NeedsCompilation: no Title: Master regulators of FGFR2 signalling and breast cancer risk Description: This package reproduces the systems biology analysis for the data in package Fletcher2013a using RTN. biocViews: ExperimentData, ChIPSeqData, CancerData, BreastCancerData, SNPData Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin Meyer. Maintainer: Mauro Castro URL: http://dx.doi.org/10.1038/ncomms3464 git_url: https://git.bioconductor.org/packages/Fletcher2013b git_branch: RELEASE_3_12 git_last_commit: 99bb143 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/Fletcher2013b_1.26.0.tar.gz vignettes: vignettes/Fletcher2013b/inst/doc/Fletcher2013b.pdf vignetteTitles: Main vignette:Fletcher2013b hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Fletcher2013b/inst/doc/Fletcher2013b.R suggestsMe: geneplast, RTNsurvival dependencyCount: 133 Package: flowFitExampleData Version: 1.26.0 Depends: R (>= 2.12.2), flowCore Imports: methods License: Artistic-2.0 MD5sum: f84c6a4199827c4f31921d363c24e383 NeedsCompilation: no Title: Example data for the flowFit package Description: Two dataset that can be used to run examples from the flowFit vignette and examples biocViews: FlowCytometryData Author: davide Rambaldi Maintainer: Davide Rambaldi PackageStatus: Deprecated git_url: https://git.bioconductor.org/packages/flowFitExampleData git_branch: RELEASE_3_12 git_last_commit: dd51ba5 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/flowFitExampleData_1.26.0.tar.gz vignettes: vignettes/flowFitExampleData/inst/doc/flowFitExampleData.pdf vignetteTitles: flowFitExampleData: example data for the beadarray package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowFitExampleData/inst/doc/flowFitExampleData.R dependencyCount: 19 Package: flowPloidyData Version: 1.16.0 Suggests: knitr, rmarkdown, flowCore License: GPL-3 MD5sum: 65ae27ef08ec3633dbe2f25ab5574adc NeedsCompilation: no Title: Example Flow Cytometry Data Description: A collection of raw flow cytometry data for use in vignettes for the flowPloidy package. biocViews: FlowCytometryData Author: Tyler Smith Maintainer: Tyler Smith VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/flowPloidyData git_branch: RELEASE_3_12 git_last_commit: f1cc4d8 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/flowPloidyData_1.16.0.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: 1.28.0 Depends: R (>= 2.13.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: d2e60244abf62d37defcd2a8d00956ba NeedsCompilation: no Title: Illumina HumanMethylation data on sorted blood cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays, and an object depicting which CpGs on the array are associated with cell type. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Andrew E Jaffe Maintainer: Andrew E Jaffe git_url: https://git.bioconductor.org/packages/FlowSorted.Blood.450k git_branch: RELEASE_3_12 git_last_commit: e784ed9 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/FlowSorted.Blood.450k_1.28.0.tar.gz vignettes: vignettes/FlowSorted.Blood.450k/inst/doc/FlowSorted.Blood.450k.pdf vignetteTitles: FlowSorted Blood 450k Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.Blood.450k/inst/doc/FlowSorted.Blood.450k.R dependsOnMe: methylCC, methylationArrayAnalysis suggestsMe: mCSEA, minfi, sesame, FlowSorted.Blood.EPIC dependencyCount: 130 Package: FlowSorted.Blood.EPIC Version: 1.8.0 Depends: R (>= 3.5), minfi (>= 1.21.2), SummarizedExperiment, genefilter, quadprog, nlme, S4Vectors, graphics, stats, utils, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, ExperimentHub Suggests: knitr, rmarkdown, EpiDISH, FlowSorted.CordBloodCombined.450k, FlowSorted.Blood.450k(>= 1.0.1), FlowSorted.CordBlood.450k, FlowSorted.CordBloodNorway.450k, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: GPL-3 MD5sum: 9105fa404dee763cb23fefe5ef0626c8 NeedsCompilation: no Title: Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells Description: Raw data objects to be used for blood cell proportion estimation in minfi and similar packages. The FlowSorted.Blood.EPIC object is based in samples assayed by Brock Christensen and colleagues; for details see Salas et al. 2018. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, Genome, TissueMicroarrayData, MethylationArrayData Author: Lucas A. Salas [cre, aut], Devin C. Koestler [aut], Rondi A. Butler [ctb], Helen M. Hansen [ctb], John K. Wiencke [ctb], Karl T. Kelsey [ctb], Brock C. Christensen [ctb], Kasper Daniel Hansen [ctb] (author and maintainer of the original minfi estimateCellCounts and internal functions), Jean-Philippe Fortin [ctb] (contributor in the original minfi estimateCellCounts and internal functions), Shan V. Andrews [ctb] (contributor in the original minfi estimateCellCounts and internal functions), E. Andres Houseman [ctb] (author of the original quadratic programming function used for cell projection), Andrew E Jaffe [ctb] (author of the original estimateCellCounts and internal functions within minfi) Maintainer: Lucas A. Salas URL: https://github.com/immunomethylomics/FlowSorted.Blood.EPIC VignetteBuilder: knitr BugReports: https://github.com/immunomethylomics/FlowSorted.Blood.EPIC/issues. git_url: https://git.bioconductor.org/packages/FlowSorted.Blood.EPIC git_branch: RELEASE_3_12 git_last_commit: ffc8bf0 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/FlowSorted.Blood.EPIC_1.8.0.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 dependsOnMe: FlowSorted.CordBloodCombined.450k dependencyCount: 153 Package: FlowSorted.CordBlood.450k Version: 1.18.0 Depends: R (>= 3.2.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 53bad1f7dc311b5a652a9920b5fd1247 NeedsCompilation: no Title: Illumina 450k data on sorted cord blood cells Description: Raw data objects to be used for cord blood cell proportion estimation in minfi. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Shan V. Andrews [cre, aut], Kelly M. Bakulski [aut] Maintainer: Shan V. Andrews git_url: https://git.bioconductor.org/packages/FlowSorted.CordBlood.450k git_branch: RELEASE_3_12 git_last_commit: edd3525 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/FlowSorted.CordBlood.450k_1.18.0.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: 130 Package: FlowSorted.CordBloodCombined.450k Version: 1.6.0 Depends: R (>= 3.6), minfi (>= 1.21.2), SummarizedExperiment, IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b4.hg19, ExperimentHub(>= 1.9.1), FlowSorted.Blood.EPIC, utils Suggests: knitr, rmarkdown, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: GPL-3 MD5sum: 00526756acad9a09c7cd4d5a7411415a NeedsCompilation: no Title: Illumina 450k/EPIC data on FACS and MACS umbilical blood cells Description: Raw data objects to be used for umbilical cord blood cell proportion estimation in minfi and similar packages. The FlowSorted.CordBloodCombined.450k object is based in samples assayed by Bakulski et al, Gervin et al., de Goede et al., and Lin et al. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, Genome, TissueMicroarrayData, MethylationArrayData, ExperimentHub Author: Lucas A. Salas [cre, aut], Kristina Gervin [aut], Meaghan C. Jones [aut], Kelly M. Bakulski [ctb], Devin C. Koestler [ctb], John K. Wiencke [ctb], Karl T. Kelsey [ctb], Robert Lyle [ctb], Brock C. Christensen [ctb], Janine Felix [ctb] Maintainer: Lucas A. Salas URL: https://github.com/immunomethylomics/FlowSorted.CordBloodCombined.450k VignetteBuilder: knitr BugReports: https://github.com/immunomethylomics/FlowSorted.CordBloodCombined.450k/issues. git_url: https://git.bioconductor.org/packages/FlowSorted.CordBloodCombined.450k git_branch: RELEASE_3_12 git_last_commit: 6b7dc43 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/FlowSorted.CordBloodCombined.450k_1.6.0.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 suggestsMe: FlowSorted.Blood.EPIC dependencyCount: 155 Package: FlowSorted.CordBloodNorway.450k Version: 1.16.0 Depends: R (>= 3.2.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 7fa6b88f0996ddbd3ba2b59bf7d713da NeedsCompilation: no Title: Illumina HumanMethylation data on sorted cord blood cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays, for cell type composition estimation. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: kristina gervin [cre, aut], Kasper Daniel Hansen [aut] Maintainer: kristina gervin URL: https://bitbucket.com/kasperdanielhansen/Illumina_CordBlood git_url: https://git.bioconductor.org/packages/FlowSorted.CordBloodNorway.450k git_branch: RELEASE_3_12 git_last_commit: 00dc1f1 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/FlowSorted.CordBloodNorway.450k_1.16.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: sesame, FlowSorted.Blood.EPIC dependencyCount: 130 Package: FlowSorted.DLPFC.450k Version: 1.26.0 Depends: R (>= 2.13.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: a2d4c816e10735c38c9301ae1fd99024 NeedsCompilation: no Title: Illumina HumanMethylation data on sorted frontal cortex cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Andrew E Jaffe, Zachary A. Kaminsky Maintainer: Andrew E Jaffe git_url: https://git.bioconductor.org/packages/FlowSorted.DLPFC.450k git_branch: RELEASE_3_12 git_last_commit: 7cdd758 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/FlowSorted.DLPFC.450k_1.26.0.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 dependencyCount: 130 Package: flowWorkspaceData Version: 3.2.0 License: GPL-2 MD5sum: cc6c73d1be535a7ff684560b18691d18 NeedsCompilation: no Title: A data package containing two flowJo, one diva xml workspace and the associated fcs files as well as three GatingSets for testing the flowWorkspace, openCyto and CytoML packages. Description: The necessary external data to run the flowWorkspace and openCyto vignette is found in this package. biocViews: ExperimentData, FlowCytometryData Author: Greg Finak Maintainer: Mike Jiang git_url: https://git.bioconductor.org/packages/flowWorkspaceData git_branch: RELEASE_3_12 git_last_commit: 1722110 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/flowWorkspaceData_3.2.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: COMPASS, CytoML, flowClust, flowCore, flowWorkspace, ggcyto, openCyto dependencyCount: 0 Package: frmaExampleData Version: 1.26.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: fa9b975e279a2c6dcee3b77f7a623ed9 NeedsCompilation: no Title: Frma Example Data Description: Data files used by the examples in frma and frmaTools packages biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/frmaExampleData git_branch: RELEASE_3_12 git_last_commit: 319cc8b git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/frmaExampleData_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: frma, frmaTools dependencyCount: 0 Package: furrowSeg Version: 1.18.0 Depends: R (>= 3.3), EBImage Imports: abind, dplyr, locfit, tiff Suggests: BiocStyle, ggplot2, knitr License: Artistic-2.0 MD5sum: 908a1933c02e1b4c0976366fb71a2657 NeedsCompilation: no Title: Furrow Segmentation Description: Image feature data and analysis codes for the Guglielmi, Barry et al. paper describing the application of an optogenetics tools to disrupt Drosophila embryo furrowing. biocViews: ExperimentData, Drosophila_melanogaster_Data, Tissue, ReproducibleResearch Author: Joseph Barry Maintainer: Joseph Barry VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/furrowSeg git_branch: RELEASE_3_12 git_last_commit: 772b9de git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/furrowSeg_1.18.0.tar.gz vignettes: vignettes/furrowSeg/inst/doc/exampleFurrowSegmentation.pdf, vignettes/furrowSeg/inst/doc/genPaperFigures.pdf vignetteTitles: Supplementary Methods - Example furrow segmentation, Supplementary Methods - Automatic generation of paper figures hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/furrowSeg/inst/doc/exampleFurrowSegmentation.R, vignettes/furrowSeg/inst/doc/genPaperFigures.R dependencyCount: 42 Package: gageData Version: 2.28.0 Depends: R (>= 2.10) Suggests: gage, pathview, genefilter License: GPL (>=2.0) MD5sum: 9b35f4982ee08e306f85da97748094f3 NeedsCompilation: no Title: Auxillary data for gage package Description: This is a supportive data package for the software package, gage. However, the data supplied here are also useful for gene set or pathway analysis or microarray data analysis in general. In this package, we provide two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and BMP6 (originally published as an demo dataset for GAGE, also registered as GSE13604 in GEO). This package also includes commonly used gene set data based on KEGG pathways and GO terms for major research species, including human, mouse, rat and budding yeast. Mapping data between common gene IDs for budding yeast are also included. biocViews: ExperimentData, StemCell, CancerData, BreastCancerData, MicroarrayData, GEO Author: Weijun Luo Maintainer: Weijun Luo git_url: https://git.bioconductor.org/packages/gageData git_branch: RELEASE_3_12 git_last_commit: 364cde7 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/gageData_2.28.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: gage dependencyCount: 0 Package: gaschYHS Version: 1.28.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: f5d6cb2475a29d034c2e8c2b960a908c NeedsCompilation: no Title: ExpressionSet for response of yeast to heat shock and other environmental stresses Description: Data from PMID 11102521 biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data Author: Audrey Gasch and colleagues Maintainer: Vince Carey URL: http://genome-www.stanford.edu/yeast_stress/data/rawdata/complete_dataset.txt git_url: https://git.bioconductor.org/packages/gaschYHS git_branch: RELEASE_3_12 git_last_commit: ee18d6a git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/gaschYHS_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: gatingMLData Version: 2.30.0 Depends: R (>= 1.9.0) Suggests: flowUtils License: GPL MD5sum: c59b4ff5a1101584c69d6793b80b256e NeedsCompilation: no Title: Data and XML files for Gating-ML Test suite Description: Test data and XML files for testing compliance of the flowUtils/flowCore packages with Gating-ML (1.5 and 2.0) standards. biocViews: ExperimentData, FlowCytometryData Author: J. Spidlen, N. Gopalakrishnan Maintainer: J. Spidlen git_url: https://git.bioconductor.org/packages/gatingMLData git_branch: RELEASE_3_12 git_last_commit: 6f9614e git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/gatingMLData_2.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: flowUtils dependencyCount: 0 Package: gcspikelite Version: 1.28.0 Depends: R (>= 2.5.0) License: LGPL MD5sum: ed0730bb47a0fc586c8169f55523b261 NeedsCompilation: no Title: Spike-in data for GC/MS data and methods within flagme Description: Spike-in data for GC/MS data and methods within flagme biocViews: MassSpectrometryData Author: Mark Robinson Maintainer: Mark Robinson git_url: https://git.bioconductor.org/packages/gcspikelite git_branch: RELEASE_3_12 git_last_commit: 8ac5bc6 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/gcspikelite_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: flagme dependencyCount: 0 Package: geneLenDataBase Version: 1.26.0 Depends: R (>= 2.11.0) Imports: utils, rtracklayer, GenomicFeatures (>= 1.3.15) License: LGPL (>= 2) MD5sum: 789e5613f0ed33e31fd475154322e25f 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 biocViews: ExperimentData, Genome Author: Matthew Young Maintainer: Matthew Young , Nadia Davidson git_url: https://git.bioconductor.org/packages/geneLenDataBase git_branch: RELEASE_3_12 git_last_commit: 2724715 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/geneLenDataBase_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: goseq importsMe: SMITE dependencyCount: 88 Package: genomationData Version: 1.22.0 Suggests: knitr License: GPL-3 MD5sum: 9ed5ae9ce1c67be0d933d10e6b6ad7f2 NeedsCompilation: no Title: Experimental data for showing functionalities of the genomation package Description: The package contains Chip Seq, Methylation and Cage data, downloaded from Encode biocViews: ExperimentData, Genome, StemCell, SequencingData, ChIPSeqData, ChipOnChipData, ENCODE Author: Altuna Akalin, Vedran Franke Maintainer: Vedran Franke VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/genomationData git_branch: RELEASE_3_12 git_last_commit: e1d4810 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/genomationData_1.22.0.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: GeuvadisTranscriptExpr Version: 1.18.0 Depends: R (>= 3.3.0) Suggests: limma, rtracklayer, GenomicRanges, Rsamtools, VariantAnnotation, tools, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: d07a57af5638d89a643169cd8755ecf0 NeedsCompilation: no Title: Data package with transcript expression and bi-allelic genotypes from the GEUVADIS project Description: Provides transcript expression and bi-allelic genotypes corresponding to the chromosome 19 for CEU individuals from the GEUVADIS project, Lappalainen et al. biocViews: Homo_sapiens_Data, SNPData, Genome, RNASeqData, SequencingData, ExpressionData Author: Malgorzata Nowicka [aut, cre] Maintainer: Malgorzata Nowicka VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GeuvadisTranscriptExpr git_branch: RELEASE_3_12 git_last_commit: 21a70c6 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/GeuvadisTranscriptExpr_1.18.0.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: geuvPack Version: 1.22.0 Depends: R (>= 2.10), SummarizedExperiment License: Artistic-2.0 MD5sum: 9038fcfaa7b4ea265043b050ee096c3e NeedsCompilation: no Title: summarized experiment with expression data from GEUVADIS Description: FPKM from GEUVADIS, annotated to gencode regions biocViews: ExperimentData, Genome, SequencingData, MicroarrayData, ArrayExpress Author: VJ Carey Maintainer: VJ Carey PackageStatus: Deprecated git_url: https://git.bioconductor.org/packages/geuvPack git_branch: RELEASE_3_12 git_last_commit: c24735f git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/geuvPack_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: yriMulti suggestsMe: gQTLBase, gQTLstats, yriMulti dependencyCount: 26 Package: geuvStore2 Version: 1.19.0 Depends: BatchJobs, GenomicRanges Imports: methods, gQTLBase Suggests: Homo.sapiens, knitr (>= 1.7), rmarkdown License: Artistic-2.0 MD5sum: 2ace13e6f654dceeeed0bc902218de48 NeedsCompilation: no Title: demonstrate storage discipline for eQTL enumerations, revised Description: demonstrate storage discipline for eQTL enumerations and analyses based on a selection of GEUVADIS results biocViews: ExperimentData, SequencingData, MicroarrayData Author: VJ Carey Maintainer: VJ Carey VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/geuvStore2 git_branch: master git_last_commit: 4630bcf git_last_commit_date: 2020-04-27 Date/Publication: 2020-04-30 source.ver: src/contrib/geuvStore2_1.19.0.tar.gz vignettes: vignettes/geuvStore2/inst/doc/geuvStore2.pdf vignetteTitles: geuvStore: sharded storage for cis-association statistics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/geuvStore2/inst/doc/geuvStore2.R suggestsMe: gQTLBase, gQTLstats dependencyCount: 108 Package: GGdata Version: 1.28.0 Depends: R (>= 2.12.0), methods, Biobase (>= 2.5.5), GGBase, snpStats, illuminaHumanv1.db, AnnotationDbi Enhances: GGtools License: LGPL MD5sum: 9239aa844a4a5856a2c2387c221080f2 NeedsCompilation: no Title: all 90 hapmap CEU samples, 47K expression, 4mm SNP Description: data exemplars dealing with hapmap SNP reports, GWAS, etc. biocViews: ExperimentData, HapMap, Genome, SequencingData, MicroarrayData, SNPData Author: VJ Carey Maintainer: VJ Carey PackageStatus: Deprecated git_url: https://git.bioconductor.org/packages/GGdata git_branch: RELEASE_3_12 git_last_commit: c3d63d9 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/GGdata_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: eQTL suggestsMe: crlmm, GGtools dependencyCount: 62 Package: GIGSEAdata Version: 1.8.0 Depends: R (>= 3.5) Suggests: GIGSEA, knitr, rmarkdown License: LGPL-3 MD5sum: 6b43dae5cef85628ef86ebd96619c016 NeedsCompilation: no Title: Gene set collections for the GIGSEA package Description: The gene set collection used for the GIGSEA package. biocViews: ExperimentData, Homo_sapiens_Data Author: Shijia Zhu Maintainer: Shijia Zhu VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GIGSEAdata git_branch: RELEASE_3_12 git_last_commit: ca487c4 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/GIGSEAdata_1.8.0.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: 1.32.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: LGPL MD5sum: 66c2f633c545a1965990fd7ababfb895 NeedsCompilation: no Title: exprSets for golub leukemia data Description: representation of public golub data with some covariate data of provenance unknown to the maintainer at present; now employs ExpressionSet format biocViews: ExperimentData, Genome, CancerData, LeukemiaCancerData Author: Todd Golub Maintainer: Vince Carey git_url: https://git.bioconductor.org/packages/golubEsets git_branch: RELEASE_3_12 git_last_commit: 1745916 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/golubEsets_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: adSplit, Biobase, biosigner, GlobalAncova, globaltest, idiogram, MLInterfaces, pvca, RDRToolbox, twilight, rknn dependencyCount: 7 Package: gpaExample Version: 1.2.0 Depends: R (>= 4.0.0) License: GPL (>= 2) MD5sum: 6ff1aa08699bf83b1d88bbe5908494f9 NeedsCompilation: no Title: Example data for the GPA package (Genetic analysis incorporating Pleiotropy and Annotation) Description: Example data for the GPA package, consisting of the p-values of 1,219,805 SNPs for five psychiatric disorder GWAS from the psychiatric GWAS consortium (PGC), with the annotation data using genes preferentially expressed in the central nervous system (CNS). biocViews: ExperimentData, Homo_sapiens_Data, SNPData Author: Dongjun Chung, Carter Allen Maintainer: Dongjun Chung URL: http://dongjunchung.github.io/GPA/ git_url: https://git.bioconductor.org/packages/gpaExample git_branch: RELEASE_3_12 git_last_commit: 96a535e git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/gpaExample_1.2.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GPA dependencyCount: 0 Package: grndata Version: 1.22.0 Depends: R (>= 2.10) Suggests: RUnit, BiocGenerics, knitr License: GPL-3 MD5sum: 6a5f370e2c824477b216ef9ffa584121 NeedsCompilation: no Title: Synthetic Expression Data for Gene Regulatory Network Inference Description: Simulated expression data for five large Gene Regulatory Networks from different simulators biocViews: ExperimentData, NetworkInference, GeneExpression, Microarray, GeneRegulation, Network Author: Pau Bellot, Catharina Olsen, Patrick E Meyer Maintainer: Pau Bellot VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/grndata git_branch: RELEASE_3_12 git_last_commit: 29acc96 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/grndata_1.22.0.tar.gz vignettes: vignettes/grndata/inst/doc/grndata.html vignetteTitles: GRNdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: GSBenchMark Version: 1.10.0 Depends: R (>= 2.13.1) License: GPL-2 MD5sum: 04dcb99485ebff382e0eeddc413bf105 NeedsCompilation: no Title: Gene Set Benchmark Description: Benchmarks for Machine Learning Analysis of the Gene Sets. The package contains a list of pathways and gene expression data sets used in "Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)" (2010) by Eddy et al. biocViews: MicroarrayData Author: Bahman Afsari , Elana J. Fertig Maintainer: Bahman Afsari git_url: https://git.bioconductor.org/packages/GSBenchMark git_branch: RELEASE_3_12 git_last_commit: c532dc3 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/GSBenchMark_1.10.0.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: GSE62944 Version: 1.18.0 Depends: Biobase, GEOquery Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle License: Artistic-2.0 MD5sum: baaa6cf7c3a975a4016bdb1759490957 NeedsCompilation: no Title: GEO accession data GSE62944 as a SummarizedExperiment Description: TCGA processed RNA-Seq data for 9264 tumor and 741 normal samples across 24 cancer types and made them available as GEO accession [GSE62944](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944). GSE62944 data have been parsed into a SummarizedExperiment object available in ExperimentHub. biocViews: ExperimentData, Genome, DNASeqData, RNASeqData Author: Sonali Arora Maintainer: Bioconductor Package Maintainer URL: http://bioconductor.org/packages/release/bioc/html/GSE62944.html VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GSE62944 git_branch: RELEASE_3_12 git_last_commit: 9d577f4 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/GSE62944_1.18.0.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: 43 Package: gskb Version: 1.22.0 Depends: R (>= 3.2.0) Suggests: PGSEA License: Artistic-2.0 MD5sum: fb695e1ed9f8cba8467751048f385ceb NeedsCompilation: no Title: Gene Set data for pathway analysis in mouse Description: Gene Set Knowledgebase (GSKB) is a comprehensive knowledgebase for pathway analysis in mouse. Interpretation of high-throughput genomics data based on biological pathways constitutes a constant challenge, partly because of the lack of supporting pathway database. We created a functional genomics knowledgebase in mouse, which includes 33,261 pathways and gene sets compiled from 40 sources such as Gene Ontology, KEGG, GeneSetDB, PANTHER, microRNA and transcription factor target genes, etc. In addition, we also manually collected and curated 8,747 lists of differentially expressed genes from 2,526 published gene expression studies to enable the detection of similarity to previously reported gene expression signatures. These two types of data constitute a comprehensive Gene Set Knowledgebase (GSKB), which can be readily used by various pathway analysis software such as gene set enrichment analysis (GSEA). As a first step, we gathered annotation information from 40 existing databases for mouse-related gene sets. These gene sets are divided into 7 categories, namely, Gene Ontology, Curated pathways, Metabolic Pathways, Transcription Factor (TF) and microRNA target genes, location (cytogenetics band), and others. We used information in GeneSetDB for some of the databases. Detailed information on these 40 sources and the citations is available http://ge-lab.org/gskb/Table%201-sources.pdf . The gene lists from literature were retrieved manually from individual gene expression studies through a process similar to the one used to create AraPath, a similar resource for Arabidopsis[12]. As most expression studies upload raw data to repositories like GEO and ArrayExpress, we used the meta-data in these databases to search for publications. We scanned all datasets we can found and retrieved 4,313 potentially useful papers reporting gene expression studies in mouse. These papers were individually read by curators to identify lists of differentially expressed genes in various conditions. We compiled a total of 8,747 lists of differently expressed genes from 2,518 of papers. Each gene list was annotated with a unique name, brief description, and publication information, similar to the protocol used in MSigDB and Arapath. These gene lists constitute a large collection of published gene expression signatures that form a foundation for interpret new gene lists and expression profiles. More information about this data is available here http://ge-lab.org/gskb/. There is also a paper describing these data are currently in revision by Database: The Journal of Biological Databases and Curation. biocViews: ExperimentData, Mus_musculus Author: Valerie Bares, Xijin Ge Maintainer: Valerie Bares git_url: https://git.bioconductor.org/packages/gskb git_branch: RELEASE_3_12 git_last_commit: b9c0097 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/gskb_1.22.0.tar.gz vignettes: vignettes/gskb/inst/doc/gskb.pdf vignetteTitles: gskb: mouse data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/gskb/inst/doc/gskb.R dependencyCount: 0 Package: GSVAdata Version: 1.26.0 Depends: R (>= 2.10), Biobase, GSEABase, hgu95a.db License: GPL (>= 2) MD5sum: 157b93098a0771a5550ca042c6da00ed NeedsCompilation: no Title: Data employed in the vignette of the GSVA package Description: This package stores the data employed in the vignette of the GSVA package. These data belong to the following publications: Armstrong et al. Nat Genet 30:41-47, 2002; Cahoy et al. J Neurosci 28:264-278, 2008; Carrel and Willard, Nature, 434:400-404, 2005; Huang et al. PNAS, 104:9758-9763, 2007; Pickrell et al. Nature, 464:768-722, 2010; Skaletsky et al. Nature, 423:825-837; Verhaak et al. Cancer Cell 17:98-110, 2010 biocViews: ExperimentData, RNASeqData, Homo_sapiens_Data, CancerData, LeukemiaCancerData Author: Robert Castelo Maintainer: Robert Castelo git_url: https://git.bioconductor.org/packages/GSVAdata git_branch: RELEASE_3_12 git_last_commit: 189f22e git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/GSVAdata_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: singleCellTK, RVA suggestsMe: GSAR, GSVA dependencyCount: 42 Package: GWASdata Version: 1.28.0 Depends: GWASTools License: Artistic-2.0 MD5sum: cd1491b4eb1ad786e3b18b94ea3f24c8 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 , Adrienne Stilp git_url: https://git.bioconductor.org/packages/GWASdata git_branch: RELEASE_3_12 git_last_commit: 3989318 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/GWASdata_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GENESIS, GWASTools dependencyCount: 69 Package: h5vcData Version: 2.10.0 Suggests: h5vc License: GPL (>= 3) MD5sum: dfca68c2d5ee8c8f166cef2bff832e47 NeedsCompilation: no Title: Example data for the h5vc package Description: This package contains the data used in the vignettes and examples of the 'h5vc' package biocViews: CancerData Author: Paul Theodor Pyl Maintainer: Paul Theodor Pyl git_url: https://git.bioconductor.org/packages/h5vcData git_branch: RELEASE_3_12 git_last_commit: d6eb85a git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/h5vcData_2.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: h5vc suggestsMe: HDF5Array, Rariant dependencyCount: 0 Package: hapmap100khind Version: 1.32.0 Suggests: oligo License: GPL MD5sum: 0ab398d99116dd6832dbf56d3a7f76b7 NeedsCompilation: no Title: Sample data - Hapmap 100K HIND Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap100khind git_branch: RELEASE_3_12 git_last_commit: dc1968d git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/hapmap100khind_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmap100kxba Version: 1.32.0 Suggests: oligo License: GPL MD5sum: f7b98d38a58342bcb18e77bece6b073a NeedsCompilation: no Title: Sample data - Hapmap 100K XBA Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap100kxba git_branch: RELEASE_3_12 git_last_commit: 12e7208 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/hapmap100kxba_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligo dependencyCount: 0 Package: hapmap500knsp Version: 1.32.0 Suggests: oligo License: GPL MD5sum: 588ebf9ce5514ac872e150a5f6dd617c NeedsCompilation: no Title: Sample data - Hapmap 500K NSP Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap500knsp git_branch: RELEASE_3_12 git_last_commit: 4d99b4c git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/hapmap500knsp_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmap500ksty Version: 1.32.0 Suggests: oligo License: GPL MD5sum: 803cc8d481cc44920d3fc729a56c29b5 NeedsCompilation: no Title: Sample data - Hapmap 500K STY Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap500ksty git_branch: RELEASE_3_12 git_last_commit: 5d2f1ff git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/hapmap500ksty_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmapsnp5 Version: 1.32.0 Suggests: oligo License: GPL MD5sum: e0430312a90a36f0509c98a9056adb31 NeedsCompilation: no Title: Sample data - Hapmap SNP 5.0 Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData, SNPData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmapsnp5 git_branch: RELEASE_3_12 git_last_commit: e9007d4 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/hapmapsnp5_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligoClasses dependencyCount: 0 Package: hapmapsnp6 Version: 1.32.0 Depends: R (>= 2.15) Suggests: oligo, oligoClasses License: GPL MD5sum: 11f85eea7363a487738610586e622ecf NeedsCompilation: no Title: Sample data - Hapmap SNP 6.0 Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, SNPData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmapsnp6 git_branch: RELEASE_3_12 git_last_commit: 4d80cd5 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/hapmapsnp6_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: crlmm, oligoClasses dependencyCount: 0 Package: harbChIP Version: 1.28.0 Depends: R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5), Biostrings Imports: methods, stats License: Artistic-2.0 MD5sum: 652671ee0af64c10801b632aca8eee42 NeedsCompilation: no Title: Experimental Data Package: harbChIP Description: data from a yeast ChIP-chip experiment biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/harbChIP git_branch: RELEASE_3_12 git_last_commit: 413ca21 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/harbChIP_1.28.0.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: 1.18.0 Depends: R (>= 3.2.3) Suggests: BiocGenerics, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 53b21f1bf6c29d31a1621dc63be5adee NeedsCompilation: no Title: Data for the Harman package Description: Datasets of accompany Harman, a PCA and constrained optimisation based technique. Contains three 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. biocViews: ExpressionData, MicroarrayData, ExperimentData, Homo_sapiens_Data, Mus_musculus_Data Author: Josh Bowden [aut], Jason Ross [aut, cre], Yalchin Oytam [aut] Maintainer: Jason Ross URL: http://www.bioinformatics.csiro.au/harman/ VignetteBuilder: knitr BugReports: https://github.com/JasonR055/Harman/issues git_url: https://git.bioconductor.org/packages/HarmanData git_branch: RELEASE_3_12 git_last_commit: 1f1b6bd git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/HarmanData_1.18.0.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: 1.12.0 Depends: R (>= 3.4.0) Imports: ExperimentHub Suggests: AnnotationHub, knitr, rmarkdown, igraph, survival, ANF, stats, testthat License: GPL-3 MD5sum: b68539f8e4298cfec21d84f29269d0c4 NeedsCompilation: no Title: Processed Harmonized TCGA Data of Five Selected Cancer Types Description: This package contains the processed harmonized TCGA data of five cancer types used in "Tianle Ma and Aidong Zhang, Integrate Multi-omic Data Using Affinity Network Fusion (ANF) for Cancer Patient Clustering". biocViews: CancerData, ReproducibleResearch Author: Tianle Ma Maintainer: Tianle Ma VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/HarmonizedTCGAData git_branch: RELEASE_3_12 git_last_commit: 88f70a3 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/HarmonizedTCGAData_1.12.0.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: 77 Package: HCAData Version: 1.6.0 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: a5d900fef0e4bea286d2d765f03c5908 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] () Maintainer: Federico Marini URL: https://github.com/federicomarini/HCAData VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/HCAData git_branch: RELEASE_3_12 git_last_commit: 37094ca git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/HCAData_1.6.0.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 dependencyCount: 96 Package: HD2013SGI Version: 1.30.0 Depends: R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots, limma, vcd, LSD,EBImage Suggests: BiocStyle License: Artistic-2.0 MD5sum: 586411d5b3526cba04977b060e6f26d4 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: Bernd Fischer SystemRequirements: GNU make git_url: https://git.bioconductor.org/packages/HD2013SGI git_branch: RELEASE_3_12 git_last_commit: 119ea3a git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/HD2013SGI_1.30.0.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 dependencyCount: 69 Package: HDCytoData Version: 1.10.0 Depends: ExperimentHub, SummarizedExperiment, flowCore Imports: utils, methods Suggests: BiocStyle, knitr, rmarkdown, Rtsne, umap, ggplot2, FlowSOM, mclust, diffcyt License: MIT + file LICENSE MD5sum: 522b735486293bf2517e1b684b7526ea NeedsCompilation: no Title: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats Description: Data package containing a set of publicly available high-dimensional cytometry benchmark datasets, formatted into SummarizedExperiment and flowSet Bioconductor object formats, including all required metadata. Row metadata includes sample IDs, group IDs, patient IDs, reference cell population or cluster labels (where available), and labels identifying 'spiked in' cells (where available). Column metadata includes channel names, protein marker names, and protein marker classes (cell type or cell state). biocViews: ExperimentHub, ExperimentData, ExpressionData, FlowCytometryData, SingleCellData, Homo_sapiens_Data, ImmunoOncologyData Author: Lukas M. Weber [aut, cre], Charlotte Soneson [aut] Maintainer: Lukas M. Weber URL: https://github.com/lmweber/HDCytoData VignetteBuilder: knitr BugReports: https://github.com/lmweber/HDCytoData/issues git_url: https://git.bioconductor.org/packages/HDCytoData git_branch: RELEASE_3_12 git_last_commit: bc12c72 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/HDCytoData_1.10.0.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: diffcyt dependencyCount: 98 Package: healthyFlowData Version: 1.28.0 Depends: R (>= 2.15.0), flowCore Imports: methods License: Artistic-2.0 MD5sum: 79038935238c2ead511362971872c265 NeedsCompilation: no Title: Healthy dataset used by the flowMatch package Description: A healthy dataset with 20 flow cytometry samples used by the flowMatch package. biocViews: FlowCytometryData Author: Ariful Azad Maintainer: Ariful Azad git_url: https://git.bioconductor.org/packages/healthyFlowData git_branch: RELEASE_3_12 git_last_commit: 6fbfb52 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/healthyFlowData_1.28.0.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: 19 Package: HEEBOdata Version: 1.28.0 License: LGPL MD5sum: 583bbe64e660308f14490fabf12ab408 NeedsCompilation: no Title: HEEBO set and HEEBO controls. Description: R objects describing the HEEBO oligo set. biocViews: ExperimentData Author: Agnes Paquet Maintainer: Agnes Paquet URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/ git_url: https://git.bioconductor.org/packages/HEEBOdata git_branch: RELEASE_3_12 git_last_commit: 8c7fa51 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/HEEBOdata_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQuality dependencyCount: 0 Package: HelloRangesData Version: 1.16.0 Suggests: BiocStyle License: GPL (>= 2) MD5sum: 71a2163d60ece098698e7d3d81364bef NeedsCompilation: no Title: Data for the HelloRanges tutorial vignette Description: Provides the data that were used in the bedtools tutorial by Aaron Quinlan (http://quinlanlab.org/tutorials/bedtools/bedtools.html). Includes a subset of the DnaseI hypersensitivity data from "Maurano et al. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA. Science. 2012. Vol. 337 no. 6099 pp. 1190-1195." The rest of the tracks were originally downloaded from the UCSC table browser. See the HelloRanges vignette for a port of the bedtools tutorial to R. biocViews: ExperimentData, SequencingData Author: Michael Lawrence Maintainer: Michael Lawrence git_url: https://git.bioconductor.org/packages/HelloRangesData git_branch: RELEASE_3_12 git_last_commit: 56bb56b git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/HelloRangesData_1.16.0.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: 1.28.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 820ce265759752b2ab31cabb1d03408a NeedsCompilation: no Title: hgu133a data for barcode Description: Data used by the barcode package for microarrays of type hgu133a. biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/hgu133abarcodevecs git_branch: RELEASE_3_12 git_last_commit: 9bbca38 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/hgu133abarcodevecs_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hgu133plus2barcodevecs Version: 1.28.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: fe94ce7b665890693dd9bb2aa9d7aa6a NeedsCompilation: no Title: hgu133plus2 data for barcode Description: Data used by the barcode package for microarrays of type hgu133plus2. biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/hgu133plus2barcodevecs git_branch: RELEASE_3_12 git_last_commit: 1cdf74e git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/hgu133plus2barcodevecs_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hgu133plus2CellScore Version: 1.10.0 Depends: R (>= 3.5.0) Imports: Biobase (>= 2.39.1) Suggests: knitr License: GPL-3 MD5sum: c408d29a5ffa009519acf74fa97a746a NeedsCompilation: no Title: CellScore Standard Cell Types Expression Dataset [hgu133plus2] Description: The CellScore Standard Dataset contains expression data from a wide variety of human cells and tissues, which should be used as standard cell types in the calculation of the CellScore. All data was curated from public databases such as Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) or ArrayExpress (https://www.ebi.ac.uk/arrayexpress/). This standard dataset only contains data from the Affymetrix GeneChip Human Genome U133 Plus 2.0 microarrays. Samples were manually annotated using the database information or consulting the publications in which the datasets originated. The sample annotations are stored in the phenoData slot of the expressionSet object. Raw data (CEL files) were processed with the affy package to generate present/absent calls (mas5calls) and background-subtracted values, which were then normalized by the R-package yugene to yield the final expression values for the standard expression matrix. The annotation table for the microarray was retrieved from the BioC annotation package hgu133plus2. All data are stored in an expressionSet object. biocViews: ExpressionData, MicroarrayData, GEO, ExperimentData, Homo_sapiens_Data, Genome, ArrayExpress Author: Nancy Mah, Katerina Taskova Maintainer: Nancy Mah VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/hgu133plus2CellScore git_branch: RELEASE_3_12 git_last_commit: 8d8ce81 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/hgu133plus2CellScore_1.10.0.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 suggestsMe: CellScore dependencyCount: 7 Package: hgu2beta7 Version: 1.30.0 Depends: R (>= 2.0.0) License: Artistic-2.0 MD5sum: c28d584be6b16b136982e999ac3936a5 NeedsCompilation: no Title: A data package containing annotation data for hgu2beta7 Description: Annotation data file for hgu2beta7 assembled using data from public data repositories biocViews: Genome Author: Chenwei Lin Maintainer: Bioconductor Package Maintainer git_url: https://git.bioconductor.org/packages/hgu2beta7 git_branch: RELEASE_3_12 git_last_commit: 72cec45 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/hgu2beta7_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: HiCDataHumanIMR90 Version: 1.10.0 Depends: R (>= 2.10) Suggests: HiTC License: GPL-3 MD5sum: 0b7a7227889105ee709e2dc0d5a09016 NeedsCompilation: no Title: Human IMR90 Fibroblast HiC data from Dixon et al. 2012 Description: The HiC data from Human Fibroblast IMR90 cell line (HindIII restriction) was retrieved from the GEO website, accession number GSE35156 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35156). The raw reads were processed as explained in Dixon et al. (Nature 2012). biocViews: ExperimentData, Genome, Homo_sapiens_Data, GEO Author: Nicolas Servant Maintainer: Nicolas Servant git_url: https://git.bioconductor.org/packages/HiCDataHumanIMR90 git_branch: RELEASE_3_12 git_last_commit: c14938a git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/HiCDataHumanIMR90_1.10.0.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: 1.26.0 Suggests: ShortRead License: GPL-3 MD5sum: 09b2af74a0e55d9be7b56af34c0e3714 NeedsCompilation: no Title: Human lymphoblastoid HiC data from Lieberman-Aiden et al. 2009 Description: The HiC data from human lymphoblastoid cell line (HindIII restriction) was retrieved from the sequence read archive and two ends of the paired reads were aligned separately with bowtie. biocViews: ExperimentData, Homo_sapiens_Data Author: Borbala Mifsud Maintainer: Borbala Mifsud git_url: https://git.bioconductor.org/packages/HiCDataLymphoblast git_branch: RELEASE_3_12 git_last_commit: b52f792 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/HiCDataLymphoblast_1.26.0.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: HighlyReplicatedRNASeq Version: 1.2.0 Depends: SummarizedExperiment, ExperimentHub Imports: S4Vectors Suggests: BiocStyle, BiocFileCache, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 963bfa9341ba5ac9aae0d5c183fe2b52 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] () Maintainer: Constantin Ahlmann-Eltze URL: https://github.com/const-ae/HighlyReplicatedRNASeq VignetteBuilder: knitr BugReports: https://github.com/const-ae/HighlyReplicatedRNASeq/issues git_url: https://git.bioconductor.org/packages/HighlyReplicatedRNASeq git_branch: RELEASE_3_12 git_last_commit: 8de508b git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/HighlyReplicatedRNASeq_1.2.0.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: 91 Package: Hiiragi2013 Version: 1.26.0 Depends: R (>= 3.0.0), affy, Biobase, boot, clue, cluster, genefilter, geneplotter, gplots, gtools, KEGGREST, MASS, mouse4302.db, RColorBrewer, xtable Imports: grid, lattice, latticeExtra Suggests: ArrayExpress, BiocStyle License: Artistic-2.0 MD5sum: 9967bfd582d79ce18e4ecdd84fba2bb3 NeedsCompilation: no Title: Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages Description: This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881." biocViews: ExperimentData, MicroarrayData, qPCRData, ReproducibleResearch Author: Andrzej Oles, Wolfgang Huber Maintainer: Andrzej Oles git_url: https://git.bioconductor.org/packages/Hiiragi2013 git_branch: RELEASE_3_12 git_last_commit: a962879 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/Hiiragi2013_1.26.0.tar.gz vignettes: vignettes/Hiiragi2013/inst/doc/Hiiragi2013.pdf vignetteTitles: Hiiragi2013 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Hiiragi2013/inst/doc/Hiiragi2013.R dependencyCount: 70 Package: HIVcDNAvantWout03 Version: 1.30.0 License: GPL (>= 2) MD5sum: 8c942d197ca060dacca8a6770dc8e023 NeedsCompilation: no Title: T cell line infections with HIV-1 LAI (BRU) Description: The expression levels of approximately 4600 cellular RNA transcripts were assessed in CD4+ T cell lines at different times after infection with HIV-1BRU using DNA microarrays. This data corresponds to the first block of a 12 block array image (001030_08_1.GEL) in the first data set (2000095918 A) in the first experiment (CEM LAI vs HI-LAI 24hr). There are two data sets, which are part of a dye-swap experiment with replicates, representing the Cy3 (green) absorption intensities for channel 1 (hiv1raw) and the Cy5 (red) absorption intensities for channel 2 (hiv2raw). biocViews: ExperimentData, MicroarrayData, TwoChannelData, HIVData Author: Dr. Angelique van't Wout, Department of Microbiology, University of Washington Maintainer: Chris Fraley URL: http://expression.microslu.washington.edu/expression/vantwoutjvi2002.html git_url: https://git.bioconductor.org/packages/HIVcDNAvantWout03 git_branch: RELEASE_3_12 git_last_commit: a5ec5d8 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/HIVcDNAvantWout03_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: HMP16SData Version: 1.10.0 Depends: R (>= 4.0.0), SummarizedExperiment Imports: AnnotationHub, assertthat, dplyr, ExperimentHub, kableExtra, knitr, magrittr, methods, readr, S4Vectors, stringr, tibble, utils Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, circlize, covr, cowplot, curatedMetagenomicData, dendextend, devtools, ggplot2, gridExtra, haven, phyloseq, rmarkdown, roxygen2, stats, testthat License: Artistic-2.0 MD5sum: 8c013975de58a3833513e7756d747ac2 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 , Rimsha Azhar , Marcel Ramos , Ludwig Geistlinger , Levi Waldron Maintainer: Lucas Schiffer URL: https://github.com/waldronlab/HMP16SData VignetteBuilder: knitr BugReports: https://github.com/waldronlab/HMP16SData/issues git_url: https://git.bioconductor.org/packages/HMP16SData git_branch: RELEASE_3_12 git_last_commit: c37993e git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/HMP16SData_1.10.0.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: 123 Package: HMP2Data Version: 1.4.0 Depends: R (>= 3.6.0) Imports: AnnotationHub, assertthat, dplyr, ExperimentHub, kableExtra, knitr, magrittr, methods, readr, S4Vectors, SummarizedExperiment, phyloseq, MultiAssayExperiment, data.table Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, cowplot, devtools, ggplot2, gridExtra, haven, rmarkdown, roxygen2, stats, testthat, tibble, UpSetR License: Artistic-2.0 MD5sum: c264c2f8f4ae972dca65c1dc169f827a NeedsCompilation: no Title: 16s rRNA sequencing data from the Human Microbiome Project 2 Description: HMP2Data is a Bioconductor package of the Human Microbiome Project 2 (HMP2) 16S rRNA sequencing data. Processed data is provided as phyloseq, SummarizedExperiment, and MultiAssayExperiment class objects. Individual matrices and data.frames used for building these S4 class objects are also provided in the package. biocViews: ExperimentData, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch, SequencingData Author: John Stansfield , Ekaterina Smirnova , Ni Zhao , Jennifer Fettweis , Levi Waldron , Mikhail Dozmorov Maintainer: John Stansfield , Ekaterina Smirnova URL: https://github.com/jstansfield0/HMP2Data VignetteBuilder: knitr BugReports: https://github.com/jstansfield0/HMP2Data/issues git_url: https://git.bioconductor.org/packages/HMP2Data git_branch: RELEASE_3_12 git_last_commit: b9ed5eb git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/HMP2Data_1.4.0.tar.gz vignettes: vignettes/HMP2Data/inst/doc/hmp2data.html vignetteTitles: HMP2Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HMP2Data/inst/doc/hmp2data.R dependencyCount: 156 Package: hmyriB36 Version: 1.26.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.5.5), GGBase Suggests: GGtools, illuminaHumanv1.db License: Artistic-2.0 MD5sum: 299c4cc1c567d4e22dd574ba84dbae48 NeedsCompilation: no Title: YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes Description: YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes biocViews: ExperimentData, Genome, SNPData, HapMap Author: Vincent Carey Maintainer: Vincent Carey git_url: https://git.bioconductor.org/packages/hmyriB36 git_branch: RELEASE_3_12 git_last_commit: 6a9b11e git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/hmyriB36_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 60 Package: HSMMSingleCell Version: 1.10.0 Depends: R (>= 2.10) License: Artistic-2.0 MD5sum: 216744f2773a0c0cc7b11a1e27619055 NeedsCompilation: no Title: Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM) Description: Skeletal myoblasts undergo a well-characterized sequence of morphological and transcriptional changes during differentiation. In this experiment, primary human skeletal muscle myoblasts (HSMM) were expanded under high mitogen conditions (GM) and then differentiated by switching to low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several hundred cells taken over a time-course of serum-induced differentiation. Between 49 and 77 cells were captured at each of four time points (0, 24, 48, 72 hours) following serum switch using the Fluidigm C1 microfluidic system. RNA from each cell was isolated and used to construct mRNA-Seq libraries, which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell. biocViews: ExperimentData, RNASeqData Author: Cole Trapnell Maintainer: Cole Trapnell git_url: https://git.bioconductor.org/packages/HSMMSingleCell git_branch: RELEASE_3_12 git_last_commit: e872b6b git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/HSMMSingleCell_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: ctgGEM, monocle suggestsMe: cellTree dependencyCount: 0 Package: HumanAffyData Version: 1.16.0 Depends: ExperimentHub, Biobase, R (>= 3.3) Suggests: BiocStyle License: Artistic-2.0 MD5sum: 684682dd1a2ef50adf237d3869b682a6 NeedsCompilation: no Title: GEO accession GSE64985 and ArrayExpress accession E-MTAB-62 as ExpressionSet objects Description: Re-analysis of human gene expression data generated on the Affymetrix HG_U133PlusV2 (EH176) and Affymetrix HG_U133A (EH177) platforms. The original data were normalized using robust multiarray averaging (RMA) to obtain an integrated gene expression atlas across diverse biological sample types and conditions. The entire compendia comprisee 9395 arrays for EH176 and 5372 arrays for EH177. biocViews: ExperimentData, GEO, ArrayExpress, Homo_sapiens_Data, MicroarrayData, ExpressionData Author: Brad Nelms Maintainer: Brad Nelms git_url: https://git.bioconductor.org/packages/HumanAffyData git_branch: RELEASE_3_12 git_last_commit: 93e2c3c git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/HumanAffyData_1.16.0.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: 77 Package: humanStemCell Version: 0.30.0 Depends: Biobase (>= 2.5.5), hgu133plus2.db License: Artistic-2.0 MD5sum: cc6ab0bf3f1afc723ac82ab5f928fe09 NeedsCompilation: no Title: Human Stem Cells time course experiment Description: Affymetrix time course experiment on human stem cells (two time points: undifferentiated and differentiated). biocViews: ExperimentData, Homo_sapiens_Data Author: R. Gentleman, N. Le Meur, M. Tewari Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/humanStemCell git_branch: RELEASE_3_12 git_last_commit: 29e0718 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/humanStemCell_0.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MiRaGE, rtracklayer dependencyCount: 28 Package: IHWpaper Version: 1.18.0 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, pasilla, DESeq, locfdr, tidyr, ggbio, latex2exp License: Artistic-2.0 MD5sum: cd9648189ae94a6dac79695bbc29483a 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 latest arXiv preprint available under http://arxiv.org/abs/1701.05179. Thus it is a companion package to the Bioconductor IHW package. biocViews: ReproducibleResearch, ExperimentData, RNASeqData, ExpressionData Author: Nikos Ignatiadis [aut, cre] Maintainer: Nikos Ignatiadis VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/IHWpaper git_branch: RELEASE_3_12 git_last_commit: 8bdf566 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/IHWpaper_1.18.0.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: 104 Package: Illumina450ProbeVariants.db Version: 1.26.0 Depends: R (>= 3.0.1) License: GPL-3 MD5sum: c9df1737e02bed11c152d3f5e89c3db4 NeedsCompilation: no Title: Annotation Package combining variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes Description: Includes details on variants for each probe on the 450k bead chip for each of the four populations (Asian, American, African and European) biocViews: Homo_sapiens_Data, CancerData, ChipOnChipData, SNPData Author: Lee Butcher Maintainer: Tiffany Morris git_url: https://git.bioconductor.org/packages/Illumina450ProbeVariants.db git_branch: RELEASE_3_12 git_last_commit: fffe603 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/Illumina450ProbeVariants.db_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: IlluminaDataTestFiles Version: 1.28.0 License: Artistic-2.0 MD5sum: 28569835232e68198dec50650f437dfa NeedsCompilation: no Title: Illumina microarray files (IDAT) for testing Description: Example data for Illumina microarray output files, for testing purposes biocViews: MicroarrayData Author: Kasper Daniel Hansen, Mike L. Smith Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/IlluminaDataTestFiles git_branch: RELEASE_3_12 git_last_commit: 55e39d8 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/IlluminaDataTestFiles_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: illuminaio dependencyCount: 0 Package: ITALICSData Version: 2.28.0 Depends: R (>= 2.0.0) License: GPL MD5sum: 230ef6bf192cffe58db43e808181b46c NeedsCompilation: no Title: ITALICSData Description: Data needed to use the ITALICS package biocViews: ExperimentData, HapMap Author: Guillem Rigaill Maintainer: Guillem Rigaill URL: http://bioinfo.curie.fr git_url: https://git.bioconductor.org/packages/ITALICSData git_branch: RELEASE_3_12 git_last_commit: 9ec1919 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ITALICSData_2.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ITALICS dependencyCount: 0 Package: Iyer517 Version: 1.32.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 51d87a8341cb9c69243aa156ba0ad39e NeedsCompilation: no Title: exprSets for Iyer, Eisen et all 1999 Science paper Description: representation of public Iyer data from http://genome-www.stanford.edu/serum/clusters.html biocViews: ExperimentData Author: Vishy Iyer Maintainer: Vince Carey git_url: https://git.bioconductor.org/packages/Iyer517 git_branch: RELEASE_3_12 git_last_commit: cdc6191 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/Iyer517_1.32.0.tar.gz vignettes: vignettes/Iyer517/inst/doc/Iyer517.pdf vignetteTitles: Iyer517 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Iyer517/inst/doc/Iyer517.R dependencyCount: 7 Package: JASPAR2014 Version: 1.26.0 Depends: R (>= 3.0.1), methods, Biostrings (>= 2.29.19) License: GPL-2 MD5sum: 04bec9056564f8ace769c30b929d475c NeedsCompilation: no Title: Data package for JASPAR Description: Data package for JASPAR 2014. To search this databases, please use the package TFBSTools. biocViews: ExperimentData, SequencingData Author: Ge Tan Maintainer: Ge Tan URL: http://jaspar.genereg.net/ git_url: https://git.bioconductor.org/packages/JASPAR2014 git_branch: RELEASE_3_12 git_last_commit: 90d06a2 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/JASPAR2014_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MatrixRider, TFBSTools dependencyCount: 15 Package: JASPAR2016 Version: 1.18.0 Depends: R (>= 3.2.2), methods License: GPL-2 MD5sum: 1f255af7e1fd7e5f87cd11d48b1279dc NeedsCompilation: no Title: Data package for JASPAR 2016 Description: Data package for JASPAR 2016. To search this databases, please use the package TFBSTools (>= 1.8.1). biocViews: ExperimentData, MotifAnnotation, GeneRegulation Author: Ge Tan Maintainer: Ge Tan URL: http://jaspar.genereg.net/ git_url: https://git.bioconductor.org/packages/JASPAR2016 git_branch: RELEASE_3_12 git_last_commit: 5334d72 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/JASPAR2016_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: chromVAR, TFBSTools, CAGEWorkflow dependencyCount: 1 Package: JctSeqData Version: 1.20.0 Depends: R (>= 3.3) Suggests: knitr, BiocStyle, DESeq2, DEXSeq, edgeR, JunctionSeq License: file LICENSE MD5sum: dcf4c571e87ec6f9df7f949bb7f77d35 NeedsCompilation: no Title: Example Junction Count data for use with JunctionSeq Description: Junction count data from an example dataset taken from a subset of the RNA-seq reads from six samples. Data was subsampled and modified to provide edge cases for testing and to reduce file sizes. biocViews: Rattus_norvegicus_Data, ExperimentData, Genome, RNASeqData, RepositoryData, GEO Author: Stephen Hartley [aut, cre] (PhD) Maintainer: Stephen Hartley URL: http://hartleys.github.io/JunctionSeq/ VignetteBuilder: knitr BugReports: http://github.com/hartleys/JunctionSeq/issues git_url: https://git.bioconductor.org/packages/JctSeqData git_branch: RELEASE_3_12 git_last_commit: b5ac061 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/JctSeqData_1.20.0.tar.gz vignettes: vignettes/JctSeqData/inst/doc/JunctionSeqExampleData.pdf vignetteTitles: Example Walkthrough hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: KEGGandMetacoreDzPathwaysGEO Version: 1.10.0 Depends: R (>= 2.15.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: 6e9b54de535554f7c7c769e526ffa779 NeedsCompilation: no Title: Disease Datasets from GEO Description: This is a collection of 18 data sets for which the phenotype is a disease with a corresponding pathway in either KEGG or metacore database.This collection of datasets were used as gold standard in comparing gene set analysis methods. biocViews: ExperimentData, GEO Author: Gaurav Bhatti Maintainer: Gaurav Bhatti git_url: https://git.bioconductor.org/packages/KEGGandMetacoreDzPathwaysGEO git_branch: RELEASE_3_12 git_last_commit: af35edc git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/KEGGandMetacoreDzPathwaysGEO_1.10.0.tar.gz vignettes: vignettes/KEGGandMetacoreDzPathwaysGEO/inst/doc/KEGGandMetacoreDzPathwaysGEO.pdf vignetteTitles: KEGGandMetacoreDzPathwaysGEO Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/KEGGandMetacoreDzPathwaysGEO/inst/doc/KEGGandMetacoreDzPathwaysGEO.R importsMe: GSEABenchmarkeR dependencyCount: 7 Package: KEGGdzPathwaysGEO Version: 1.28.0 Depends: R (>= 2.13.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: 77aa90c670c3ca5d46d6e2ead3580268 NeedsCompilation: no Title: KEGG Disease Datasets from GEO Description: This is a collection of 24 data sets for which the phenotype is a disease with a corresponding pathway in the KEGG database.This collection of datasets were used as gold standard in comparing gene set analysis methods by the PADOG package. biocViews: MicroarrayData, GEO, ExperimentData Author: Gaurav Bhatti, Adi L. Tarca Maintainer: Gaurav Bhatti git_url: https://git.bioconductor.org/packages/KEGGdzPathwaysGEO git_branch: RELEASE_3_12 git_last_commit: 28546ca git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/KEGGdzPathwaysGEO_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: PADOG importsMe: GSEABenchmarkeR dependencyCount: 7 Package: kidpack Version: 1.32.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5) License: GPL-2 MD5sum: 09e1c525df259e35f78bdf691a987a2b NeedsCompilation: no Title: DKFZ kidney package Description: kidney microarray data biocViews: ExperimentData, CancerData, KidneyCancerData, MicroarrayData, ArrayExpress Author: Wolfgang Huber Maintainer: Wolfgang Huber URL: http://www.dkfz.de/mga git_url: https://git.bioconductor.org/packages/kidpack git_branch: RELEASE_3_12 git_last_commit: d6074d5 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/kidpack_1.32.0.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: 1.16.0 Depends: R (>= 3.3.0) License: MIT + file LICENSE MD5sum: 5d1c07ed4acf32ba0899aec0aa2be9cb NeedsCompilation: no Title: LINCS Knock-Out Data Package Description: Contains consensus genomic signatures (CGS) for experimental cell-line specific gene knock-outs as well as baseline gene expression data for a subset of experimental cell-lines. Intended for use with package KEGGlincs. biocViews: ExpressionData, CancerData, Homo_sapiens_Data Author: Shana White Maintainer: Shana White git_url: https://git.bioconductor.org/packages/KOdata git_branch: RELEASE_3_12 git_last_commit: dbf7a3d git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/KOdata_1.16.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: KEGGlincs dependencyCount: 0 Package: leeBamViews Version: 1.26.0 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: 01010069b76c4784842b27dbda169adf NeedsCompilation: no Title: leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009 Description: data from PMID 19096707; prototype for managing multiple NGS samples biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData, SNPData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/leeBamViews git_branch: RELEASE_3_12 git_last_commit: e8f0e19 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/leeBamViews_1.26.0.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: 41 Package: leukemiasEset Version: 1.26.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: f9018f85f407e29c30409596f6e5797f NeedsCompilation: no Title: Leukemia's microarray gene expression data (expressionSet). Description: Expressionset containing gene expresion data from 60 bone marrow samples of patients with one of the four main types of leukemia (ALL, AML, CLL, CML) or non-leukemia. biocViews: Tissue, Genome, Homo_sapiens_Data, CancerData, LeukemiaCancerData, MicroarrayData, ChipOnChipData, TissueMicroarrayData, GEO Author: Sara Aibar, Celia Fontanillo and Javier De Las Rivas. Bioinformatics and Functional Genomics Group. Cancer Research Center (CiC-IBMCC, CSIC/USAL). Salamanca. Spain. Maintainer: Sara Aibar git_url: https://git.bioconductor.org/packages/leukemiasEset git_branch: RELEASE_3_12 git_last_commit: 2f260f7 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/leukemiasEset_1.26.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: geNetClassifier, mCSEA, multiclassPairs dependencyCount: 7 Package: LiebermanAidenHiC2009 Version: 0.28.0 Depends: KernSmooth, IRanges License: LGPL MD5sum: 2ec616658f92b93df6b438223e2c22f3 NeedsCompilation: no Title: Selected data from the HiC paper of E. Lieberman-Aiden et al. in Science (2009) Description: This package provides data that were presented in the article "Comprehensive mapping of long-range interactions reveals folding principles of the human genome", Science 2009 Oct 9;326(5950):289-93. PMID: 19815776 biocViews: ExperimentData, Genome, SequencingData, DNASeqData, ChIPSeqData, miRNAData, SmallRNAData, ChipOnChipData, GEO, NCI, ENCODE Author: Wolfgang Huber, Felix Klein Maintainer: Felix Klein git_url: https://git.bioconductor.org/packages/LiebermanAidenHiC2009 git_branch: RELEASE_3_12 git_last_commit: 78285a4 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/LiebermanAidenHiC2009_0.28.0.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: 1.22.0 Depends: R (>= 3.1.1), methylPipe Suggests: BSgenome.Hsapiens.UCSC.hg18 License: Artistic 2.0 MD5sum: 9c9f16800c12a49e9113c3df3ac54375 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: Kamal Kishore Maintainer: Kamal Kishore git_url: https://git.bioconductor.org/packages/ListerEtAlBSseq git_branch: RELEASE_3_12 git_last_commit: 91cb664 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ListerEtAlBSseq_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 145 Package: lumiBarnes Version: 1.30.0 Depends: R (>= 2.0), Biobase (>= 2.5.5), lumi (>= 1.1.0) License: LGPL MD5sum: a8149ecc6362cb36b1a8e8b1ba89faaa NeedsCompilation: no Title: Barnes Benchmark Illumina Tissues Titration Data Description: The Barnes benchmark dataset can be used to evaluate the algorithms for Illumina microarrays. It measured a titration series of two human tissues, blood and placenta, and includes six samples with the titration ratio of blood and placenta as 100:0, 95:5, 75:25, 50:50, 25:75 and 0:100. The samples were hybridized on HumanRef-8 BeadChip (Illumina, Inc) in duplicate. The data is loaded as an LumiBatch Object (see documents in the lumi package). biocViews: ExperimentData, Tissue, MicroarrayData, ChipOnChipData Author: Pan Du Maintainer: Pan Du git_url: https://git.bioconductor.org/packages/lumiBarnes git_branch: RELEASE_3_12 git_last_commit: d2d3571 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/lumiBarnes_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayMvout, lumi dependencyCount: 151 Package: LungCancerACvsSCCGEO Version: 1.26.0 Depends: R (>= 2.15.0) License: GPL-2 MD5sum: 560c2e1111179119384c321a3dfbdca9 NeedsCompilation: no Title: A lung cancer dataset that can be used with maPredictDSC package for developing outcome prediction models from Affymetrix CEL files. Description: This package contains 30 Affymetrix CEL files for 7 Adenocarcinoma (AC) and 8 Squamous cell carcinoma (SCC) lung cancer samples taken at random from 3 GEO datasets (GSE10245, GSE18842 and GSE2109) and other 15 samples from a dataset produced by the organizers of the IMPROVER Diagnostic Signature Challenge available from GEO (GSE43580). biocViews: CancerData, LungCancerData, MicroarrayData, GEO Author: Adi Laurentiu Tarca Maintainer: Adi Laurentiu Tarca URL: http://bioinformaticsprb.med.wayne.edu/ git_url: https://git.bioconductor.org/packages/LungCancerACvsSCCGEO git_branch: RELEASE_3_12 git_last_commit: 0bfc3ac git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/LungCancerACvsSCCGEO_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: LungCancerLines Version: 0.28.0 Imports: Rsamtools License: Artistic-2.0 MD5sum: 0de328eb92537fed4220d7f6fc4b1f3c 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: Cory Barr git_url: https://git.bioconductor.org/packages/LungCancerLines git_branch: RELEASE_3_12 git_last_commit: cd224d9 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/LungCancerLines_0.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: gmapR, HTSeqGenie, VariantTools dependencyCount: 29 Package: lungExpression Version: 0.28.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 0e1d7fc7f5eff698d3802bbed86f1a35 NeedsCompilation: no Title: ExpressionSets for Parmigiani et al., 2004 Clinical Cancer Research paper Description: Data from three large lung cancer studies provided as ExpressionSets biocViews: ExperimentData, CancerData, LungCancerData Author: Robert Scharpf , Simens Zhong , Giovanni Parmigiani Maintainer: Robert Scharpf git_url: https://git.bioconductor.org/packages/lungExpression git_branch: RELEASE_3_12 git_last_commit: 3c5334d git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/lungExpression_0.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: globaltest dependencyCount: 7 Package: lydata Version: 1.16.0 License: MIT + file LICENSE MD5sum: ecbed576f18fc74f0fb4ccb17fb4a1ea NeedsCompilation: no Title: Example Dataset for crossmeta Package Description: Raw data downloaded from GEO for the compound LY294002. Raw data is from multiple platforms from Affymetrix and Illumina. This data is used to illustrate the cross-platform meta-analysis of microarray data using the crossmeta package. biocViews: ExperimentData, MicroarrayData Author: Alex Pickering Maintainer: Alex Pickering git_url: https://git.bioconductor.org/packages/lydata git_branch: RELEASE_3_12 git_last_commit: 1a232ae git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/lydata_1.16.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: ccmap, crossmeta dependencyCount: 0 Package: M3DExampleData Version: 1.16.0 Depends: R (>= 3.3) License: GPL (>=2) MD5sum: e9dc468595bb9005f391c7ed92090e26 NeedsCompilation: no Title: M3Drop Example Data Description: Example data for M3Drop package. biocViews: Mus_musculus_Data, RNASeqData, ExpressionData, GEO, Tissue, ExperimentData Author: Tallulah Andrews Maintainer: Tallulah Andrews git_url: https://git.bioconductor.org/packages/M3DExampleData git_branch: RELEASE_3_12 git_last_commit: 6f0dcd8 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/M3DExampleData_1.16.0.tar.gz hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: celda, M3Drop dependencyCount: 0 Package: macrophage Version: 1.6.0 Depends: R (>= 3.5.0) Suggests: knitr License: GPL (>= 2) MD5sum: 749f419e5c6ef325bb6f742af9e02fa4 NeedsCompilation: no Title: Human macrophage immune response Description: This package provides the output of running Salmon on a set of 24 RNA-seq samples from Alasoo, et al. "Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response", published in Nature Genetics, January 2018. For details on version numbers and how the samples were processed see the package vignette. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/macrophage git_branch: RELEASE_3_12 git_last_commit: 770b471 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/macrophage_1.6.0.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: fishpond, GeneTonic, fluentGenomics dependencyCount: 0 Package: mammaPrintData Version: 1.26.0 Depends: R (>= 2.13.0) Suggests: Biobase, gdata, limma License: Artistic-2.0 MD5sum: 3da2eda420dea0af88854d580e43ea56 NeedsCompilation: no Title: RGLists from the Glas and Buyse breast cancer studies Description: Gene expression data for the two breast cancer cohorts published by Glas and Buyse in 2006. This cohorts were used to implement and validate the mammaPrint breast cancer test. biocViews: ExperimentData, ExpressionData, CancerData, BreastCancerData, MicroarrayData, TwoChannelData Author: Luigi Marchionni Maintainer: Luigi Marchionni URL: http://luigimarchionni.org/breastTSP.html git_url: https://git.bioconductor.org/packages/mammaPrintData git_branch: RELEASE_3_12 git_last_commit: 835ea9d git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/mammaPrintData_1.26.0.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: mAPKLData Version: 1.22.0 Depends: R (>= 3.2.0) Suggests: Biobase License: Artistic-2.0 MD5sum: fae437ec8d2ef7f1752cd2f8b8a3a0c9 NeedsCompilation: no Title: Gene expression data for testing of the package mAPKL. Description: Gene expression data from a breast cancer study published by Turashvili et al. in 2007, provided as an eSet. biocViews: ExperimentData, ExpressionData, Cancer, Breast Author: Argiris Sakellariou Maintainer: Argiris Sakellariou git_url: https://git.bioconductor.org/packages/mAPKLData git_branch: RELEASE_3_12 git_last_commit: d71db97 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/mAPKLData_1.22.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: mAPKL dependencyCount: 0 Package: maqcExpression4plex Version: 1.34.0 Suggests: oligo, pdInfoBuilder License: GPL MD5sum: 27afa66e5943a7e91b05572fd07aaafa NeedsCompilation: no Title: Sample Expression Data - MAQC / HG18 - NimbleGen Description: Data from human (HG18) 4plex NimbleGen array. It has 24k genes with 3 60mer probes per gene. biocViews: ExperimentData, CancerData Author: NimbleGen Systems Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/maqcExpression4plex git_branch: RELEASE_3_12 git_last_commit: 8be1875 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/maqcExpression4plex_1.34.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligo dependencyCount: 0 Package: MAQCsubset Version: 1.28.0 Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), lumi, methods Suggests: genefilter, codelink License: Artistic-2.0 MD5sum: ad0c877da467036705cecfa4ea055805 NeedsCompilation: no Title: Experimental Data Package: MAQCsubset Description: Data Package automatically created on Sun Nov 19 15:59:29 2006. biocViews: ExperimentData, MicroarrayData, GEO Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/MAQCsubset git_branch: RELEASE_3_12 git_last_commit: 87827b5 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/MAQCsubset_1.28.0.tar.gz vignettes: vignettes/MAQCsubset/inst/doc/maqcNotes.pdf vignetteTitles: MAQC notes hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MAQCsubset/inst/doc/maqcNotes.R suggestsMe: arrayMvout dependencyCount: 151 Package: MAQCsubsetAFX Version: 1.28.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: aead14b87a16b6b7ebd6a6c718f1e3ca NeedsCompilation: no Title: MAQC data subset for the Affymetrix platform Description: MAQC data subset for the Affymetrix platform biocViews: ExperimentData, Genome, Homo_sapiens_Data, MicroarrayData Author: Laurent Gatto Maintainer: Laurent Gatto git_url: https://git.bioconductor.org/packages/MAQCsubsetAFX git_branch: RELEASE_3_12 git_last_commit: fee1a3d git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/MAQCsubsetAFX_1.28.0.tar.gz vignettes: vignettes/MAQCsubsetAFX/inst/doc/MAQCsubsetAFX.pdf vignetteTitles: MAQCsubsetAFX: MAQC data subset for the Affymetrix platform hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MAQCsubsetAFX/inst/doc/MAQCsubsetAFX.R suggestsMe: qcmetrics, yaqcaffy dependencyCount: 13 Package: MAQCsubsetILM Version: 1.28.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), lumi License: Artistic-2.0 MD5sum: ad9a3d88df5fcb0990f0ea2cb8f03d58 NeedsCompilation: no Title: MAQC data subset for the Illumina platform Description: MAQC data subset for the Illumina platform biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData Author: Laurent Gatto Maintainer: Laurent Gatto git_url: https://git.bioconductor.org/packages/MAQCsubsetILM git_branch: RELEASE_3_12 git_last_commit: fb4a3d8 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/MAQCsubsetILM_1.28.0.tar.gz vignettes: vignettes/MAQCsubsetILM/inst/doc/MAQCsubsetILM.pdf vignetteTitles: MAQCsubsetILM: MAQC data subset for the Illumina platform hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MAQCsubsetILM/inst/doc/MAQCsubsetILM.R dependencyCount: 151 Package: mCSEAdata Version: 1.10.1 Depends: R (>= 3.5) Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 755233b7db7210f225e63f9358a011e6 NeedsCompilation: no Title: Data package for mCSEA package Description: Data objects necessary to some mCSEA package functions. There are also example data objects to illustrate mCSEA package functionality. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData, ExperimentData Author: Jordi Martorell Marugán Maintainer: Jordi Martorell Marugán VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mCSEAdata git_branch: RELEASE_3_12 git_last_commit: 25099f6 git_last_commit_date: 2020-12-09 Date/Publication: 2020-12-10 source.ver: src/contrib/mCSEAdata_1.10.1.tar.gz vignettes: vignettes/mCSEAdata/inst/doc/mCSEAdata.pdf vignetteTitles: Data for mCSEA package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mCSEAdata/inst/doc/mCSEAdata.R dependsOnMe: mCSEA dependencyCount: 0 Package: mcsurvdata Version: 1.8.0 Depends: R (>= 3.5), ExperimentHub Imports: AnnotationHub, Biobase Suggests: knitr License: GPL (>=2) MD5sum: 737e83fe1c9a1ad9a2e47747d04b64c4 NeedsCompilation: no Title: Meta cohort survival data Description: This package stores two merged expressionSet objects that contain the gene expression profile and clinical information of -a- six breast cancer cohorts and -b- four colorectal cancer cohorts. Breast cancer data are employed in the vignette of the hrunbiased package for survival analysis of gene signatures. biocViews: ExperimentData, Homo_sapiens_Data, GEO, MicroarrayData Author: Adria Caballe Mestres [aut, cre], Antoni Berenguer Llergo [aut], Camille Stephan-Otto Attolini [aut] Maintainer: Adria Caballe Mestres URL: https://github.com/adricaba/mcsurvdata VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mcsurvdata git_branch: RELEASE_3_12 git_last_commit: a143a94 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/mcsurvdata_1.8.0.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: 77 Package: MEDIPSData Version: 1.26.0 Depends: R (>= 2.15.0) License: GPL (>= 2) MD5sum: 93de288633bb0d94c381d4d4fc960c7a NeedsCompilation: no Title: Example data for MEDIPS and QSEA packages Description: Example data for MEDIPS and QSEA packages, consisting of chromosome 22 MeDIP and control/Input sample data. Additionally, the package contains MeDIP seq data from 3 NSCLC samples and adjacent normal tissue (chr 20-22). All data has been aligned to human genome hg19. biocViews: ExperimentData, Genome, SequencingData Author: Lukas Chavez Maintainer: Lukas Chavez git_url: https://git.bioconductor.org/packages/MEDIPSData git_branch: RELEASE_3_12 git_last_commit: 11ae33d git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/MEDIPSData_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MEDIPS, qsea dependencyCount: 0 Package: MEEBOdata Version: 1.28.0 License: LGPL MD5sum: c2ce1628a9d24cbec64a61756333643c NeedsCompilation: no Title: MEEBO set and MEEBO controls. Description: R objects describing the MEEBO set. biocViews: ExperimentData Author: Agnes Paquet Maintainer: Agnes Paquet URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/ git_url: https://git.bioconductor.org/packages/MEEBOdata git_branch: RELEASE_3_12 git_last_commit: a0bca3b git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/MEEBOdata_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQuality dependencyCount: 0 Package: MetaGxBreast Version: 1.10.1 Depends: R (>= 3.6.0), Biobase, AnnotationHub, ExperimentHub Imports: stats, lattice, impute, SummarizedExperiment Suggests: testthat, xtable, tinytex License: Apache License (>= 2) MD5sum: b2f597f3abfade9d0fcc58dbcac0ceac NeedsCompilation: no Title: Transcriptomic Breast Cancer Datasets Description: A collection of Breast Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium. biocViews: ExpressionData, ExperimentHub, CancerData, Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData, ExperimentData Author: Michael Zon [aut], Deena M.A. Gendoo [aut], Christopher Eeles [ctb], Benjamin Haibe-Kains [aut, cre] Maintainer: Benjamin Haibe-Kains git_url: https://git.bioconductor.org/packages/MetaGxBreast git_branch: RELEASE_3_12 git_last_commit: b3b15a6 git_last_commit_date: 2021-04-23 Date/Publication: 2021-04-26 source.ver: src/contrib/MetaGxBreast_1.10.1.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: 92 Package: MetaGxOvarian Version: 1.10.0 Depends: Biobase, stats, lattice, impute, AnnotationHub, ExperimentHub, SummarizedExperiment, R (>= 3.6.0) Suggests: testthat, xtable License: Artistic-2.0 MD5sum: f70f0daf06d6bdd45b499ddabb6dc22d 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 , Deena M.A. Gendoo , Benjamin Haibe-Kains Maintainer: Michael Zon git_url: https://git.bioconductor.org/packages/MetaGxOvarian git_branch: RELEASE_3_12 git_last_commit: f7fa049 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/MetaGxOvarian_1.10.0.tar.gz vignettes: vignettes/MetaGxOvarian/inst/doc/MetaGxOvarian.pdf 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: 92 Package: MetaGxPancreas Version: 1.10.0 Depends: SummarizedExperiment, ExperimentHub, R (>= 3.6.0) Imports: stats, impute, S4Vectors, AnnotationHub Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: f46a2c0a046236934312283551267921 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, cre], Vandana Sandhu [aut], Benjamin Haibe-Kains [aut] Maintainer: Michael Zon VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MetaGxPancreas git_branch: RELEASE_3_12 git_last_commit: 6525a6c git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/MetaGxPancreas_1.10.0.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: 92 Package: metaMSdata Version: 1.26.0 License: GPL (>= 2) MD5sum: 9f8ac3fb6158ed9235f678f8cb77cb05 NeedsCompilation: no Title: Example CDF data for the metaMS package Description: Example CDF data for the metaMS package biocViews: ExperimentData, MassSpectrometryData Author: Ron Wehrens [aut, cre], Pietro Franceschi [aut], Georg Weingart [ctb] Maintainer: Yann Guitton git_url: https://git.bioconductor.org/packages/metaMSdata git_branch: RELEASE_3_12 git_last_commit: 69e6aa1 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/metaMSdata_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CluMSID, metaMS dependencyCount: 0 Package: MethylAidData Version: 1.22.0 Depends: MethylAid, R (>= 3.2) Suggests: BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC License: GPL (>= 2) MD5sum: 5c52c3d758757ac600cc230cb3390c9d NeedsCompilation: no Title: MethylAid-summarized data for 2800 Illumina 450k array samples and 2620 EPIC array samples Description: A data package containing summarized Illumina 450k array data on 2800 samples and summarized EPIC data for 2620 samples. The data can be use as a background data set in the interactive application. biocViews: ExperimentData, TechnologyData, MicroarrayData, MethylationArrayData Author: Davy Cats, Tyler J. Gorrie-Stone, Bastiaan T. Heijmans, John W. Holloway, BIOS Consortium, Maarten van Iterson, Faisal I. Rezwam, Leonard Schalkwyk Maintainer: M. van Iterson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MethylAidData git_branch: RELEASE_3_12 git_last_commit: d71d35f git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/MethylAidData_1.22.0.tar.gz vignettes: vignettes/MethylAidData/inst/doc/MethylAidData.pdf vignetteTitles: MethylAid-summarized data on 2800 Illumina 450k array samples hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MethylAidData/inst/doc/MethylAidData.R suggestsMe: MethylAid dependencyCount: 155 Package: MethylSeqData Version: 1.0.0 Depends: SummarizedExperiment Imports: ExperimentHub, HDF5Array, rhdf5, GenomeInfoDb, S4Vectors, GenomicRanges, stats, IRanges, utils Suggests: BiocFileCache, BiocStyle, data.table, knitr, rmarkdown License: CC0 MD5sum: 2af02a8bed3a2b754209964afdef1239 NeedsCompilation: no Title: Collection of Public DNA Methylation Sequencing Datasets Description: Base-level (i.e. cytosine-level) counts for a collection of public bisulfite-seq datasets (e.g., WGBS and RRBS), provided as SummarizedExperiment objects with sample- and base-level metadata. biocViews: ExperimentHub, ExperimentData, SequencingData, Homo_sapiens_Data, Mus_musculus_Data, MethylSeqData Author: Peter Hickey [aut, cre] Maintainer: Peter Hickey VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MethylSeqData git_branch: RELEASE_3_12 git_last_commit: f8abcd3 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/MethylSeqData_1.0.0.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: 95 Package: methyvimData Version: 1.12.0 Depends: R (>= 3.4.0), minfi Suggests: Biobase, BiocStyle, SummarizedExperiment, knitr, rmarkdown License: file LICENSE MD5sum: 6d6ed82ae238729bf17d77c80bff1b50 NeedsCompilation: no Title: Example experimental data for use with the methyvim package Description: Contains a reduced set of simulated data inspired by data produced by the Infinium EPIC BeadChip assays by Illumina. The example data set is made available to highlight many of the key procedures that are available within the core functions of the methyvim package. biocViews: Clustering, DNAMethylation, DifferentialMethylation, MethylationArray, MethylSeq Author: Nima Hejazi [aut, cre] Maintainer: Nima Hejazi VignetteBuilder: knitr PackageStatus: Deprecated git_url: https://git.bioconductor.org/packages/methyvimData git_branch: RELEASE_3_12 git_last_commit: 58262df git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/methyvimData_1.12.0.tar.gz vignettes: vignettes/methyvimData/inst/doc/data_methyvim.html vignetteTitles: Anatomy of the `methyvimData` package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/methyvimData/inst/doc/data_methyvim.R suggestsMe: methyvim dependencyCount: 130 Package: microRNAome Version: 1.12.0 Depends: R (>= 3.4), SummarizedExperiment Suggests: BiocGenerics, RUnit License: GPL (>= 2) MD5sum: 7fa776a9f0adeb0bc6a3d47baa7a7ad8 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 Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/microRNAome git_branch: RELEASE_3_12 git_last_commit: d63146a git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/microRNAome_1.12.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 26 Package: MIGSAdata Version: 1.14.0 Depends: R (>= 3.4) Suggests: BiocGenerics License: GPL (>= 2) MD5sum: b07b7a6f0ac2a4d561441a7efb88eef1 NeedsCompilation: no Title: MIGSA vignette data Description: MIGSA vignette data. The MIGSAdata package provides several data objects needed by MIGSA package to correctly generate its vignette, and follow it step by step. biocViews: ExperimentData, RepositoryData, ReproducibleResearch, CancerData, BreastCancerData, MicroarrayData Author: Juan C. Rodriguez, Cristobal Fresno, Andrea S. Llera and Elmer A. Fernandez Maintainer: Juan C. Rodriguez URL: http://www.bdmg.com.ar/ git_url: https://git.bioconductor.org/packages/MIGSAdata git_branch: RELEASE_3_12 git_last_commit: 77a1c75 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/MIGSAdata_1.14.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MIGSA dependencyCount: 0 Package: minfiData Version: 0.36.0 Depends: R (>= 3.3.0), minfi (>= 1.21.2), IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 License: Artistic-2.0 MD5sum: 7be8e0f0c797c9e01af0d16b6109aef3 NeedsCompilation: no Title: Example data for the Illumina Methylation 450k array Description: Data from 6 samples across 2 groups from 450k methylation arrays. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData Author: Kasper Daniel Hansen, Martin Aryee, Winston Timp Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/minfiData git_branch: RELEASE_3_12 git_last_commit: fa2879d git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/minfiData_0.36.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: methylationArrayAnalysis suggestsMe: bigmelon, conumee, ENmix, funtooNorm, Harman, mCSEA, MEAL, MethylAid, methyvim, minfi, missMethyl, MultiDataSet, shinyMethyl, skewr, MethylAidData dependencyCount: 132 Package: minfiDataEPIC Version: 1.16.0 Depends: R (>= 3.3), minfi (>= 1.21.2), IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: Artistic-2.0 MD5sum: 1b73837c3ba0c2cbc4501da54dda4855 NeedsCompilation: no Title: Example data for the Illumina Methylation EPIC array Description: Data from 3 technical replicates of the cell line GM12878 from the EPIC methylation array. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData Author: Jean-Philippe Fortin, Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/minfiDataEPIC git_branch: RELEASE_3_12 git_last_commit: 30645f1 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/minfiDataEPIC_1.16.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MethylAid, minfi, REMP, MethylAidData dependencyCount: 132 Package: minionSummaryData Version: 1.20.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 1f92bd6f0175e8073465fad0e37ddbba NeedsCompilation: no Title: Summarised MinION sequencing data published by Ashton et al. 2015 Description: Summarised MinION sequencing data for Salmonella Typhi published by Ashton et al. in 2015. Three replicate runs are each provided as Fast5Summary objects. biocViews: ExperimentData, SequencingData Author: Mike Smith [aut, cre] Maintainer: Mike Smith VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/minionSummaryData git_branch: RELEASE_3_12 git_last_commit: 6053d53 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/minionSummaryData_1.20.0.tar.gz vignettes: vignettes/minionSummaryData/inst/doc/creating-Styphi-Dataset.html vignetteTitles: Creating example MinION summary dataset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/minionSummaryData/inst/doc/creating-Styphi-Dataset.R suggestsMe: IONiseR dependencyCount: 0 Package: miRcompData Version: 1.20.0 Depends: R (>= 3.2), Imports: utils License: GPL-3 | file LICENSE MD5sum: 53d2b44cd41d26e3c4fb2fdbc4c38b6b NeedsCompilation: no Title: Data used in the miRcomp package Description: Raw amplification data from a large microRNA mixture / dilution study. These data are used by the miRcomp package to assess the performance of methods that estimate expression from the amplification curves. biocViews: ExperimentData, ExpressionData, qPCRData, Homo_sapiens_Data Author: Matthew N. McCall Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/miRcompData git_branch: RELEASE_3_12 git_last_commit: 949ec31 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/miRcompData_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: miRcomp dependencyCount: 1 Package: miRNATarget Version: 1.28.0 Depends: R (>= 2.10), Biobase License: GPL MD5sum: dbb8088782dff5d7c43c48a62bac3ee8 NeedsCompilation: no Title: gene target tabale of miRNA for human/mouse used for MiRaGE package Description: gene target tabale of miRNA for human/mouse used for MiRaGE package biocViews: ExperimentData, Homo_sapiens_Data Author: Y-h. Taguchi Maintainer: Y-h. Taguchi git_url: https://git.bioconductor.org/packages/miRNATarget git_branch: RELEASE_3_12 git_last_commit: b7ba873 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/miRNATarget_1.28.0.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: mitoODEdata Version: 1.26.0 Depends: R (>= 2.14.0) Imports: methods, graphics License: LGPL MD5sum: e5b78fa55840c36c08a6ae09a887d71e NeedsCompilation: no Title: Experimental data associated to the paper "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay" Description: This package contains the experimental data (assay annotation, siRNA annotation, time-lapse cell counts) associated to the paper "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay". The data ultimately come from the Mitocheck assay reported in "Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes" (Neumann, Walter et al, Nature 2010). biocViews: ExperimentData, Genome Author: Gregoire Pau Maintainer: Gregoire Pau SystemRequirements: PackageStatus: Deprecated git_url: https://git.bioconductor.org/packages/mitoODEdata git_branch: RELEASE_3_12 git_last_commit: cb91b09 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/mitoODEdata_1.26.0.tar.gz vignettes: vignettes/mitoODEdata/inst/doc/mitoODEdata-introduction.pdf vignetteTitles: Mitoode data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mitoODEdata/inst/doc/mitoODEdata-introduction.R dependencyCount: 2 Package: MMAPPR2data Version: 1.4.0 Depends: R (>= 3.6.0) Imports: Rsamtools Suggests: knitr, rmarkdown, BiocStyle, roxygen2, seqinr, readr Enhances: MMAPPR2 License: GPL-3 MD5sum: 799f3d5d7ef8f9393ee54fdccfaf69f8 NeedsCompilation: no Title: Sample Data for MMAPPR2 Description: Contains data for illustration purposes in the MMAPPR2 package, namely simulated BAM files containing RNA-Seq data for a mutation in the slc24a5 gene, taken from the GRCz11 genome. Also contains reference sequence and annotation files for the region. biocViews: RNASeqData, Danio_rerio_Data, SequencingData, Genome Author: Kyle Johnsen [aut], Jonathon Hill [cre] Maintainer: Jonathon Hill URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3613585/, https://github.com/kjohnsen/MMAPPR2 VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MMAPPR2data git_branch: RELEASE_3_12 git_last_commit: f0ff55d git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/MMAPPR2data_1.4.0.tar.gz vignettes: vignettes/MMAPPR2data/inst/doc/MMAPPR2data.html vignetteTitles: Using MMAPPR2data Resources hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MMAPPR2data/inst/doc/MMAPPR2data.R suggestsMe: MMAPPR2 dependencyCount: 29 Package: MMDiffBamSubset Version: 1.26.0 Suggests: MMDiff2 License: LGPL MD5sum: 7331050e61076bdba1a2914d7062743a NeedsCompilation: no Title: Example ChIP-Seq data for the MMDiff package Description: Subset of BAM files, including WT_2.bam, Null_2.bam, Resc_2.bam, Input.bam from the "Cfp1" experiment (see Clouaire et al., Genes Dev. 2012). Data is available under ArrayExpress accession numbers E-ERAD-79. Additionally, corresponding subset of peaks called by MACS biocViews: ExperimentData, Genome, StemCell, Mus_musculus_Data, DNASeqData, ChIPSeqData, ArrayExpress Author: Gabriele Schweikert Maintainer: Gabriele Schweikert git_url: https://git.bioconductor.org/packages/MMDiffBamSubset git_branch: RELEASE_3_12 git_last_commit: 20f772f git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/MMDiffBamSubset_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MMDiff2 dependencyCount: 0 Package: MOFAdata Version: 1.6.0 Depends: R (>= 3.5) Suggests: knitr, MultiAssayExperiment License: LGPL-3 MD5sum: c18255b015dd3ab41e1d935c9c859b17 NeedsCompilation: yes Title: Data package for Multi-Omics Factor Analysis (MOFA) Description: A collection of datasets to accompany the R package MOFA and illustrate running and analysing MOFA models. biocViews: ReproducibleResearch Author: Ricard Argelaguet, Britta Velten, Damien Arnol, Florian Buettner, Wolfgang Huber, Oliver Stegle Maintainer: Britta Velten VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MOFAdata git_branch: RELEASE_3_12 git_last_commit: 1bcd0ae git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/MOFAdata_1.6.0.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 suggestsMe: MOFA dependencyCount: 0 Package: mosaicsExample Version: 1.28.0 Depends: R (>= 2.11.1) License: GPL (>= 2) MD5sum: e34adaddcf317e2d2bb62387adee5665 NeedsCompilation: no Title: Example data for the mosaics package, which implements MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data for transcription factor binding and histone modification Description: Data for the mosaics package, consisting of (1) chromosome 22 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding and H3K4me3 modification in MCF7 cell line from ENCODE database (HG19) and (2) chromosome 21 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding, with mappability, GC content, and sequence ambiguity scores of human genome HG18. biocViews: ExperimentData, ChIPseqData, Homo_sapiens Author: Dongjun Chung, Pei Fen Kuan, Rene Welch, Sunduz Keles Maintainer: Dongjun Chung URL: http://groups.google.com/group/mosaics_user_group git_url: https://git.bioconductor.org/packages/mosaicsExample git_branch: RELEASE_3_12 git_last_commit: 0c24f1d git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/mosaicsExample_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: mosaics dependencyCount: 0 Package: mouse4302barcodevecs Version: 1.28.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: c2af8d2969541e5f77da51e42f992f0b NeedsCompilation: no Title: mouse4302 data for barcode Description: Data used by the barcode package for microarrays of type mouse4302. biocViews: Mus_musculus_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/mouse4302barcodevecs git_branch: RELEASE_3_12 git_last_commit: e939425 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/mouse4302barcodevecs_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: MouseGastrulationData Version: 1.4.0 Depends: R (>= 4.0), SingleCellExperiment, SummarizedExperiment Imports: methods, ExperimentHub, BiocGenerics, S4Vectors Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 55b3d08082a5acfc85e1c4d02cacc25e NeedsCompilation: no Title: Single-Cell Transcriptomics Data across Mouse Gastrulation and Early Organogenesis Description: Provides processed and raw count matrices for single-cell RNA sequencing data from a timecourse of mouse gastrulation and early organogenesis. biocViews: ExperimentData, ExpressionData, SequencingData, RNASeqData, SingleCellData, ExperimentHub Author: Jonathan Griffiths [aut, cre], Aaron Lun [aut] Maintainer: Jonathan Griffiths URL: https://github.com/MarioniLab/MouseGastrulationData VignetteBuilder: knitr BugReports: https://github.com/MarioniLab/MouseGastrulationData/issues git_url: https://git.bioconductor.org/packages/MouseGastrulationData git_branch: RELEASE_3_12 git_last_commit: 0440a1c git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/MouseGastrulationData_1.4.0.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 dependencyCount: 92 Package: msd16s Version: 1.10.0 Depends: R (>= 2.10), Biobase, metagenomeSeq, License: Artistic-2.0 MD5sum: 4ecc50918504769e729a9e8857446712 NeedsCompilation: no Title: Healthy and moderate to severe diarrhea 16S expression data Description: Gut 16S sequencing expression data from 992 healthy and moderate-to-severe diarrhetic samples used in 'Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition'. biocViews: ExperimentData, SequencingData, MicrobiomeData Author: Joseph N. Paulson, Hector Corrada Bravo, Mihai Pop Maintainer: Joseph N. Paulson URL: http://www.cbcb.umd.edu/research/projects/GEMS-pathogen-discovery git_url: https://git.bioconductor.org/packages/msd16s git_branch: RELEASE_3_12 git_last_commit: 270ed4c git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/msd16s_1.10.0.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: metavizr dependencyCount: 29 Package: msdata Version: 0.30.0 Depends: R (>= 2.10) Suggests: xcms, mzR, MSnbase License: GPL (>= 2) MD5sum: 03723043fc93835c6615b11e823a9f0b NeedsCompilation: no Title: Various Mass Spectrometry raw data example files Description: Ion Trap positive ionization mode data in mzData 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 mzData, mzML and mz5. LC-MSMS and MRM files from proteomics experiments. PSI mzIdentML example files for various search engines. biocViews: ExperimentData, MassSpectrometryData Author: Steffen Neumann , Laurent Gatto with contriutions from Johannes Rainer Maintainer: Steffen Neumann , Laurent Gatto git_url: https://git.bioconductor.org/packages/msdata git_branch: RELEASE_3_12 git_last_commit: 821821a git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/msdata_0.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: IPO, MSnbase, mzR, peakPantheR, QFeatures, Spectra, xcms, RforProteomics dependencyCount: 0 Package: MSMB Version: 1.8.0 Depends: R (>= 2.10) Suggests: knitr, BiocStyle License: LGPL MD5sum: 261e60bf66142bf66bcb7011c0d3a47c 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, ReproducibleResearch Author: Wolfgang Huber, Andrzej Oles, Mike Smith Maintainer: Wolfgang Huber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MSMB git_branch: RELEASE_3_12 git_last_commit: 5ce6b52 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/MSMB_1.8.0.tar.gz vignettes: vignettes/MSMB/inst/doc/MSMB.pdf vignetteTitles: Modern Statistics for Modern Biology hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MSMB/inst/doc/MSMB.R dependencyCount: 0 Package: msPurityData Version: 1.18.0 Suggests: knitr License: GPL (>= 2) MD5sum: 4fd99010fb927b81c3d37bdcf088a3ba NeedsCompilation: no Title: Fragmentation spectral libraries and data to test the msPurity package Description: Fragmentation spectral libraries and data to test the msPurity package biocViews: ExperimentData, MassSpectrometryData Author: Thomas N. Lawson Maintainer: Thomas N. Lawson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/msPurityData git_branch: RELEASE_3_12 git_last_commit: d886117 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/msPurityData_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: msPurity dependencyCount: 0 Package: msqc1 Version: 1.18.0 Depends: R (>= 3.6), lattice, stats, utils Suggests: BiocStyle, knitr, testthat, specL (>= 1.2) License: GPL MD5sum: 9834d58363b4027a188fb06d9f0d5e7d 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] (), Christian Trachsel [aut], Christian Panse [aut, cre] () Maintainer: Christian Panse URL: https://panoramaweb.org/labkey/MSQC1.url, http://fgcz-bfabric.uzh.ch/bfabric/project.html?projectId=1959 VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/msqc1 git_branch: RELEASE_3_12 git_last_commit: be38dc3 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/msqc1_1.18.0.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 dependencyCount: 6 Package: MSstatsBioData Version: 1.12.0 Depends: R (>= 3.4) Suggests: BiocStyle, knitr, MSstats License: Artistic-2.0 MD5sum: 936e940e8a9511585b4708862b3d718d NeedsCompilation: no Title: Datasets of published biological studies with DDA or SRM experiments Description: Provides the peak intensity data for detecting differentially abundant proteins in seven published biological investigations. biocViews: ExperimentData, MassSpectrometryData, Proteome Author: Meena Choi Maintainer: Meena Choi VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MSstatsBioData git_branch: RELEASE_3_12 git_last_commit: e2631a8 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/MSstatsBioData_1.12.0.tar.gz vignettes: vignettes/MSstatsBioData/inst/doc/MSstatsBioData.html vignetteTitles: MSstatsBioData: Datasets of published biological studies with DDA or SRM experiments hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MSstatsBioData/inst/doc/MSstatsBioData.R suggestsMe: MSstats dependencyCount: 0 Package: mtbls2 Version: 1.20.1 Depends: R (>= 2.10) Suggests: xcms (>= 3.11.8), CAMERA, Risa (>= 1.0.0), knitr, Heatplus, pcaMethods, sp License: CC0 MD5sum: c212b7abdca4cf3309219a7479b251ca NeedsCompilation: no Title: MetaboLights MTBLS2: Comparative LC/MS-based profiling of silver nitrate-treated Arabidopsis thaliana leaves of wild-type and cyp79B2 cyp79B3 double knockout plants. Böttcher et al. (2004) Description: Indole-3-acetaldoxime (IAOx) represents an early intermediate of the biosynthesis of a variety of indolic secondary metabolites including the phytoanticipin indol-3-ylmethyl glucosinolate and the phytoalexin camalexin (3-thiazol-2'-yl-indole). Arabidopsis thaliana cyp79B2 cyp79B3 double knockout plants are completely impaired in the conversion of tryptophan to indole-3-acetaldoxime and do not accumulate IAOx-derived metabolites any longer. Consequently, comparative analysis of wild-type and cyp79B2 cyp79B3 plant lines has the potential to explore the complete range of IAOx-derived indolic secondary metabolites. biocViews: MassSpectrometryData, RepositoryData Author: Steffen Neumann Maintainer: Steffen Neumann URL: http://www.ebi.ac.uk/metabolights/MTBLS2, https://github.com/sneumann/mtbls2 VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mtbls2 git_branch: RELEASE_3_12 git_last_commit: 01210c4 git_last_commit_date: 2020-11-28 Date/Publication: 2020-11-30 source.ver: src/contrib/mtbls2_1.20.1.tar.gz vignettes: vignettes/mtbls2/inst/doc/MTBLS2-xcms3.html, vignettes/mtbls2/inst/doc/MTBLS2.html vignetteTitles: MTBLS2 Processing and Analysis with xcms3,, CAMERA and export to MetaboLights, MTBLS2 Processing and Analysis with xcms,, CAMERA and export to MetaboLights hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mtbls2/inst/doc/MTBLS2-xcms3.R, vignettes/mtbls2/inst/doc/MTBLS2.R suggestsMe: Autotuner, IPO, yamss dependencyCount: 0 Package: MUGAExampleData Version: 1.10.0 Depends: R (>= 2.10.0) License: GPL-3 MD5sum: b76917129371e6dfeac211201cd9f90e NeedsCompilation: no Title: Example {M}ouse {U}niversal {G}enotyping {A}rray data for genome reconstruction and quantitative trait locus mapping. Description: This package contains example data for the MUGA array that is used by the R package DOQTL. biocViews: ExperimentData, Mus_musculus_Data Author: Daniel Gatti Maintainer: Daniel Gatti git_url: https://git.bioconductor.org/packages/MUGAExampleData git_branch: RELEASE_3_12 git_last_commit: 418b1ed git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/MUGAExampleData_1.10.0.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: muscData Version: 1.4.0 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: ce6d68f9bd537bf18be48652b017f48a NeedsCompilation: no Title: Multi-sample multi-group scRNA-seq data Description: Data package containing a collection of multi-sample multi-group scRNA-seq datasets in SingleCellExperiment Bioconductor object format. biocViews: ExperimentHub, ExperimentData, ExpressionData, GEO, Homo_sapiens_Data, ImmunoOncologyData, SingleCellData Author: Helena L. Crowell [aut, cre] Maintainer: Helena L. Crowell URL: https://github.com/HelenaLC/muscData VignetteBuilder: knitr BugReports: https://github.com/HelenaLC/muscData/issues git_url: https://git.bioconductor.org/packages/muscData git_branch: RELEASE_3_12 git_last_commit: 3a3a116 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/muscData_1.4.0.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: 92 Package: mvoutData Version: 1.26.0 Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4), lumi License: Artistic-2.0 MD5sum: 199cfe2ca4029544b91b148909877bf5 NeedsCompilation: no Title: affy and illumina raw data for assessing outlier detector performance Description: affy and illumina raw data for assessing outlier detector performance biocViews: ExperimentData, MicroarrayData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/mvoutData git_branch: RELEASE_3_12 git_last_commit: e29ed31 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/mvoutData_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayMvout dependencyCount: 151 Package: NanoporeRNASeq Version: 1.0.0 Depends: R(>= 4.0.0), ExperimentHub (>= 1.15.3) Suggests: knitr, bambu, ggbio, BSgenome.Hsapiens.NCBI.GRCh38, circlize, ComplexHeatmap, apeglm, rlang, GenomicAlignments, Rsamtools Enhances: parallel License: GPL-3 + file LICENSE MD5sum: aea2d0400b2f9b2ff2c315642d520d59 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 Developer [aut], Ying Chen Developer [cre], Yuk Kei Wan Developer [aut] Maintainer: Ying Chen Developer URL: https://github.com/GoekeLab/NanoporeRNASeq VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/NanoporeRNASeq git_branch: RELEASE_3_12 git_last_commit: f06482d git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/NanoporeRNASeq_1.0.0.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: 77 Package: nanotubes Version: 1.6.0 Depends: R (>= 3.6) Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, rtracklayer, CAGEfightR License: GPL-3 MD5sum: c6eaa509f7d4968675a872cfd72549cd NeedsCompilation: no Title: Mouse nanotube CAGE data Description: Cap Analysis of Gene Expression (CAGE) data from "Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo" by Bornholdt et al. supplied as CAGE Transcription Start Sites (CTSSs). biocViews: ExperimentData, SequencingData, ExpressionData Author: Malte Thodberg Maintainer: Malte Thodberg URL: https://github.com/MalteThodberg/nanotubes VignetteBuilder: knitr BugReports: https://github.com/MalteThodberg/nanotubes/issues git_url: https://git.bioconductor.org/packages/nanotubes git_branch: RELEASE_3_12 git_last_commit: 70746bd git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/nanotubes_1.6.0.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: 1.26.0 Depends: R (>= 2.10.0) Suggests: Rgraphviz License: GPL-3 MD5sum: 39845152e5fedba7a016dafec26e8fb9 NeedsCompilation: no Title: Data for the NCIgraph software package Description: Provides pathways from the NCI Pathways Database as R graph objects biocViews: NCI Author: Laurent Jacob Maintainer: Laurent Jacob git_url: https://git.bioconductor.org/packages/NCIgraphData git_branch: RELEASE_3_12 git_last_commit: 2dc6fca git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/NCIgraphData_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: NestLink Version: 1.6.0 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: 7c828fec20fe1af6e303d688801d787f 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] (), Iwan Zimmermann [ctb] (), Fabian M. Arnold [ctb], Cedric A.J. Hutter [ctb] (), Lennart Opitz [aut, cre] (), Lucy Poveda [ctb] (), Hans-Anton Keserue [ctb], Christian Panse [aut, ctb] (), Bernd Roschitzki [aut] (), Markus Seeger [aut] () Maintainer: Lennart Opitz VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/NestLink git_branch: RELEASE_3_12 git_last_commit: 02d40a4 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/NestLink_1.6.0.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: 113 Package: Neve2006 Version: 0.28.0 Depends: R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0), hgu133a.db, annotate License: Artistic-2.0 MD5sum: d382b1d36d68afe7c08a41fd23833786 NeedsCompilation: no Title: expression and CGH data on breast cancer cell lines Description: Experimental organization of combined expression and CGH data biocViews: ExperimentData, CancerData, BreastCancerData Author: M. Neve et al. in Gray Lab at LBL Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/Neve2006 git_branch: RELEASE_3_12 git_last_commit: 1fa3869 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/Neve2006_0.28.0.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: 40 Package: NGScopyData Version: 1.10.0 License: GPL (>=2) MD5sum: 1269189e1a0ce421247335d808f88368 NeedsCompilation: no Title: Subset of BAM files of human tumor and pooled normal sequencing data (Zhao et al. 2014) for the NGScopy package Description: Subset of BAM files of human lung tumor and pooled normal samples by targeted panel sequencing. [Zhao et al 2014. Targeted Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using the University of North Carolina (UNC) Sequencing Assay Captures Most Previously Described Genetic Aberrations in NSCLC. In preparation.] Each sample is a 10 percent random subsample drawn from the original sequencing data. The pooled normal sample has been rescaled accroding to the total number of normal samples in the "pool". Here provided is the subsampled data on chr6 (hg19). biocViews: ExperimentData, CancerData, LungCancerData, SequencingData Author: Xiaobei Zhao [aut, cre, cph] Maintainer: Xiaobei Zhao URL: http://www.bioconductor.org/packages/release/data/experiment/html/NGScopyData.html git_url: https://git.bioconductor.org/packages/NGScopyData git_branch: RELEASE_3_12 git_last_commit: 1be2f08 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/NGScopyData_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: oct4 Version: 1.6.0 Suggests: knitr License: GPL (>= 2) MD5sum: 1649199754337c520da0409e3d9c5b29 NeedsCompilation: no Title: Conditional knockdown of OCT4 in mouse ESCs Description: This package provides the output of running Salmon on a set of 12 RNA-seq samples from King & Klose, "The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells", published in eLIFE, March 2017. For details on version numbers and how the samples were processed see the package vignette. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/oct4 git_branch: RELEASE_3_12 git_last_commit: 875d1fa git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/oct4_1.6.0.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: OMICsPCAdata Version: 1.8.0 Depends: R (>= 3.5.0), MultiAssayExperiment Suggests: knitr, kableExtra, rmarkdown License: GPL-3 MD5sum: bf2d969591668d8217c27e90b31fee3d NeedsCompilation: no Title: Supporting data for package OMICsPCA Description: Supporting data for package OMICsPCA biocViews: RepositoryData, TechnologyData, ChIPSeqData, SequencingData, ExpressionData, ENCODE Author: Author: Subhadeep Das Maintainer: Subhadeep Das VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/OMICsPCAdata git_branch: RELEASE_3_12 git_last_commit: f114162 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/OMICsPCAdata_1.8.0.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: 47 Package: OnassisJavaLibs Version: 1.12.0 Depends: R (>= 3.4) Imports: rJava Suggests: BiocStyle, rmarkdown, knitr License: GPL-2 MD5sum: dcad3f01f013848ce70ca4a7852dc100 NeedsCompilation: no Title: OnassisJavaLibs, java libraries to run conceptmapper and semantic similarity Description: A package that contains java libraries to call conceptmapper and compute semnatic similarity from R biocViews: ExperimentData Author: Eugenia Galeota Maintainer: Eugenia Galeota SystemRequirements: Java (>= 1.8) VignetteBuilder: rmarkdown, knitr git_url: https://git.bioconductor.org/packages/OnassisJavaLibs git_branch: RELEASE_3_12 git_last_commit: e053621 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/OnassisJavaLibs_1.12.0.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 dependsOnMe: Onassis dependencyCount: 2 Package: optimalFlowData Version: 1.2.0 Depends: R (>= 4.0) Suggests: knitr, BiocStyle, rmarkdown, magick License: Artistic-2.0 MD5sum: 1a38124fe2886e193b38e0f8e24e7fda NeedsCompilation: no Title: optimalFlowData Description: Data files used as examples and for testing of the software provided in the optimalFlow package. biocViews: ExperimentData, PackageTypeData, ImmunoOncologyData, FlowCytometryData Author: Hristo Inouzhe Maintainer: Hristo Inouzhe VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/optimalFlowData git_branch: RELEASE_3_12 git_last_commit: 930e8b9 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/optimalFlowData_1.2.0.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: parathyroidSE Version: 1.28.0 Depends: SummarizedExperiment, R (>= 2.10) Suggests: Rsamtools, GenomicAlignments, GEOquery, SRAdb, GenomicFeatures, BiocStyle License: LGPL MD5sum: 120a4b8889f5c1783dbbcd436764c9a7 NeedsCompilation: no Title: RangedSummarizedExperiment for RNA-Seq of primary cultures of parathyroid tumors by Haglund et al., J Clin Endocrinol Metab 2012. Description: This package provides RangedSummarizedExperiment objects of read counts in genes and exonic parts for paired-end RNA-Seq data from experiments on primary cultures of parathyroid tumors. The data were presented in the article "Evidence of a Functional Estrogen Receptor in Parathyroid Adenomas" by Haglund F, Ma R, Huss M, Sulaiman L, Lu M, Nilsson IL, Hoog A, Juhlin CC, Hartman J, Larsson C, J Clin Endocrinol Metab. jc.2012-2484, Epub 2012 Sep 28, PMID: 23024189. The sequencing was performed on tumor cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control). One control sample was omitted by the paper authors due to low quality. The package vignette describes the creation of the object from raw sequencing data provided by NCBI Gene Expression Omnibus under accession number GSE37211. The gene and exon features are the GRCh37 Ensembl annotations. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love git_url: https://git.bioconductor.org/packages/parathyroidSE git_branch: RELEASE_3_12 git_last_commit: 3608789 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/parathyroidSE_1.28.0.tar.gz vignettes: vignettes/parathyroidSE/inst/doc/parathyroidSE.pdf vignetteTitles: parathyroidGenesSE hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/parathyroidSE/inst/doc/parathyroidSE.R suggestsMe: ClassifyR, DEXSeq, simulatorZ dependencyCount: 26 Package: pasilla Version: 1.18.1 Depends: R (>= 3.3.0) Suggests: DEXSeq, rmarkdown, BiocStyle, knitr License: LGPL MD5sum: 29c5ffe2e8a95525d33cda768bfbb8b4 NeedsCompilation: no Title: Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011. Description: This package provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in the article "Conservation of an RNA regulatory map between Drosophila and mammals" by Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR, Genome Res. 2011 Feb;21(2):193-202, Epub 2010 Oct 4, PMID: 20921232. The experiment studied the effect of RNAi knockdown of Pasilla, the Drosophila melanogaster ortholog of mammalian NOVA1 and NOVA2, on the transcriptome. The package vignette describes how the data provided here were derived from the RNA-Seq read sequence data that are provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. biocViews: ExperimentData, Genome, Drosophila_melanogaster_Data, RNASeqData Author: Wolfgang Huber, Alejandro Reyes Maintainer: Alejandro Reyes VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/pasilla git_branch: RELEASE_3_12 git_last_commit: 1889939 git_last_commit_date: 2020-12-23 Date/Publication: 2020-12-24 source.ver: src/contrib/pasilla_1.18.1.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, DESeq2, DEXSeq, EnhancedVolcano, regionReport, ReportingTools, tidybulk, IHWpaper, pasillaBamSubset dependencyCount: 0 Package: pasillaBamSubset Version: 0.28.0 Suggests: pasilla License: LGPL MD5sum: 050cd33be3e9af1da31a1576b530284b NeedsCompilation: no Title: Subset of BAM files from "Pasilla" experiment Description: Subset of BAM files untreated1.bam (single-end reads) and untreated3.bam (paired-end reads) from "Pasilla" experiment (Pasilla knock-down by Brooks et al., Genome Research 2011). See the vignette in the pasilla data package for how BAM files untreated1.bam and untreated3.bam were obtained from the RNA-Seq read sequence data that is provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. Also contains the DNA sequence for fly chromosome 4 to which the reads can be mapped. biocViews: ExperimentData, Genome, DNASeqData, RNASeqData Author: Hervé Pagès Maintainer: Hervé Pagès git_url: https://git.bioconductor.org/packages/pasillaBamSubset git_branch: RELEASE_3_12 git_last_commit: 6e5cec4 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/pasillaBamSubset_0.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GenomicAlignments, GenomicFeatures, GenomicRanges, gmoviz, IRanges, karyoploteR, plyranges, TransView dependencyCount: 0 Package: PasillaTranscriptExpr Version: 1.18.0 Depends: R (>= 3.3.0) Suggests: rtracklayer, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: 0b60db6e5deb47ef3ca351ba96cea648 NeedsCompilation: no Title: Data package with transcript expression obtained with kallisto from pasilla knock-down RNA-Seq data from Brooks et al. Description: Provides kallisto workflow and transcript expression of RNA-Seq data from Brooks et al. biocViews: Drosophila_melanogaster_Data, Genome, RNASeqData, ExperimentData, SequencingData, ExpressionData, GEO Author: Malgorzata Nowicka [aut, cre] Maintainer: Malgorzata Nowicka VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/PasillaTranscriptExpr git_branch: RELEASE_3_12 git_last_commit: 03d7bd7 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/PasillaTranscriptExpr_1.18.0.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: 1.26.0 Depends: R (>= 1.14.0) License: GPL-3 MD5sum: 7e3f6b58403749727af386484b41563c NeedsCompilation: no Title: Experimental data for the PathNet package Description: This package contains the data employed in the vignette of the PathNet package. These data belong to the following publication: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J., Source Code for Biology and Medicine 2012 Sep 24;7(1):10. biocViews: ExperimentData, PathwayInteractionDatabase Author: Bhaskar Dutta , Anders Wallqvist , and Jaques Reifman Maintainer: Ludwig Geistlinger git_url: https://git.bioconductor.org/packages/PathNetData git_branch: RELEASE_3_12 git_last_commit: b8cddbb git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/PathNetData_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PathNet dependencyCount: 0 Package: pathprintGEOData Version: 1.20.0 Depends: R (>= 3.4) Suggests: pathprint, SummarizedExperiment License: GPL MD5sum: c36a4a01d3aeca864e22f3218578964c NeedsCompilation: no Title: Pathway fingerprint vectors representing a subsection of arrays from the GEO data repository Description: Pathway Fingerprint vectors that have been pre-calculated for ~390,000 publicly available arrays from the GEO corpus, spanning 6 species and 31 platforms. All data are accompanied by their associated metadata. biocViews: ExperimentData, ExpressionData, MicroarrayData, GEO, Homo_sapiens_Data, Mus_musculus_Data, Drosophila_melanogaster_Data, Rattus_norvegicus_Data, Caenorhabditis_elegans_Data, Danio_rerio_Data,Genome, SequencingData, OneChannelData, TwoChannelData,PathwayInteractionDatabase Author: Gabriel Altschuler, Sokratis Kariotis Maintainer: Sokratis Kariotis PackageStatus: Deprecated git_url: https://git.bioconductor.org/packages/pathprintGEOData git_branch: RELEASE_3_12 git_last_commit: 545e7c7 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/pathprintGEOData_1.20.0.tar.gz vignettes: vignettes/pathprintGEOData/inst/doc/usingPathprintGEOData.pdf vignetteTitles: pathprintGEOData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pathprintGEOData/inst/doc/usingPathprintGEOData.R dependencyCount: 0 Package: pcaGoPromoter.Hs.hg19 Version: 1.26.0 License: GPL (>= 2) MD5sum: 6276608a745d2e02550f625fa7e2d003 NeedsCompilation: no Title: pcaGoPromoter.Hs.hg19 is a data package used by pcaGoPromoter Description: Contains the data for transciption factors analysis of organism Homo Sapiens with package pcaGoPromoter biocViews: Homo_sapiens_Data Author: Morten Hansen Maintainer: Morten Hansen PackageStatus: Deprecated git_url: https://git.bioconductor.org/packages/pcaGoPromoter.Hs.hg19 git_branch: RELEASE_3_12 git_last_commit: c1f37ef git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/pcaGoPromoter.Hs.hg19_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: pcaGoPromoter.Mm.mm9 Version: 1.26.0 License: GPL (>= 2) MD5sum: f8537b219b1a7c35d1a26b6ea2b0de3c NeedsCompilation: no Title: pcaGoPromoter.Mm.mm9 is a data package used by pcaGoPromoter Description: Contains the data for transciption factors analysis of organism Mus musculus with package pcaGoPromoter biocViews: Mus_musculus_Data Author: Morten Hansen, Maintainer: Morten Hansen PackageStatus: Deprecated git_url: https://git.bioconductor.org/packages/pcaGoPromoter.Mm.mm9 git_branch: RELEASE_3_12 git_last_commit: fdfcb4f git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/pcaGoPromoter.Mm.mm9_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: pcaGoPromoter.Rn.rn4 Version: 1.26.0 License: GPL (>= 2) MD5sum: 2086f764f93b01317fabb0615bc52071 NeedsCompilation: no Title: pcaGoPromoter.Rn.rn4 is a data package used by pcaGoPromoter Description: Contains the data for transciption factors analysis of organism Rattus norvegicus with package pcaGoPromoter biocViews: Rattus_norvegicus_Data Author: Morten Hansen Maintainer: Morten Hansen, PackageStatus: Deprecated git_url: https://git.bioconductor.org/packages/pcaGoPromoter.Rn.rn4 git_branch: RELEASE_3_12 git_last_commit: 5262b47 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/pcaGoPromoter.Rn.rn4_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: PCHiCdata Version: 1.18.0 Depends: R (>= 3.2), Chicago Suggests: testthat, BiocStyle, knitr License: Artistic-2.0 MD5sum: eb70f3ccb1adbc8919388c55902f84ec 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: Paula Freire-Pritchett VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/PCHiCdata git_branch: RELEASE_3_12 git_last_commit: 3d342b9 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/PCHiCdata_1.18.0.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: 72 Package: pcxnData Version: 2.12.0 Depends: R (>= 3.4) Suggests: pcxn License: MIT + file LICENSE MD5sum: 1931ae0b35e02acd7c06f412c658c7d7 NeedsCompilation: no Title: Correlation coefficients and p values between pre-defined pathway/gene sets Description: PCxN database contains correlation coefficients and p values between pre-defined gene sets within MSigDB H hallmark gene sets, MSigDB C2 CP (Canonical pathways), MSigDB C5 GO BP gene sets and Pathprint respectively, as well as adjusted pathway correlations to account for the shared genes between pathway pairs. biocViews: ExperimentData, ExpressionData, MicroarrayData, GEO, Homo_sapiens_Data, OneChannelData, PathwayInteractionDatabase Author: Sokratis Kariotis, Yered Pita-Juarez, Wenbin Wei, Winston Hide Maintainer: Sokratis Kariotis git_url: https://git.bioconductor.org/packages/pcxnData git_branch: RELEASE_3_12 git_last_commit: bb367e2 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/pcxnData_2.12.0.tar.gz vignettes: vignettes/pcxnData/inst/doc/usingpcxnData.pdf vignetteTitles: pcxnData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/pcxnData/inst/doc/usingpcxnData.R dependsOnMe: pcxn dependencyCount: 0 Package: pd.atdschip.tiling Version: 0.28.0 Depends: R (>= 2.14.0), 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: 62557a240f954bd28636afe2a01734f6 NeedsCompilation: no Title: Platform Design Info for Affymetrix Atdschip_tiling Description: Platform Design Info for Affymetrix Atdschip_tiling biocViews: Arabidopsis_thaliana_Data, MicroarrayData, SNPData Author: Kristof De Beuf Maintainer: Kristof De Beuf git_url: https://git.bioconductor.org/packages/pd.atdschip.tiling git_branch: RELEASE_3_12 git_last_commit: 0eff76b git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/pd.atdschip.tiling_0.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 54 Package: pepDat Version: 1.10.0 Depends: R(>= 3.0.0) Imports: GenomicRanges Suggests: knitr License: Artistic-2.0 MD5sum: c761ec707c83cd3a216065db41625767 NeedsCompilation: no Title: Peptide microarray data package Description: Provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV. biocViews: MicroarrayData Author: Renan Sauteraud, Raphael Gottardo Maintainer: Renan Sauteraud VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/pepDat git_branch: RELEASE_3_12 git_last_commit: 6dd4be5 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/pepDat_1.10.0.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: 17 Package: PepsNMRData Version: 1.8.0 Depends: R (>= 3.5) Suggests: knitr, markdown, rmarkdown, BiocStyle License: GPL-2 | file LICENSE MD5sum: 023e8a1b78b0f10590c67f2dc7308e30 NeedsCompilation: no Title: Datasets for the PepsNMR package Description: This package contains all the datasets used in the PepsNMR package. biocViews: ExperimentData, OrganismData, Homo_sapiens_Data Author: Manon Martin [aut, cre], Bernadette Govaerts [aut, ths], Pascal de Tullio [dtc] Maintainer: Manon Martin BugReports: https://github.com/ManonMartin/PepsNMRData/issues git_url: https://git.bioconductor.org/packages/PepsNMRData git_branch: RELEASE_3_12 git_last_commit: 557d701 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/PepsNMRData_1.8.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: PepsNMR dependencyCount: 0 Package: PhyloProfileData Version: 1.4.0 Depends: R (>= 3.6.0) Imports: ExperimentHub, Biostrings Suggests: knitr License: MIT + file LICENSE MD5sum: d5da0364c4e4205ff9b4d96c75eb6da9 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: Ingo Ebersberger, Arpit Jain, Hannah Mülbaier, Vinh Tran Maintainer: Vinh Tran URL: https://github.com/BIONF/PhyloProfileData VignetteBuilder: knitr BugReports: https://github.com/trvinh/PhyloProfileData/issues git_url: https://git.bioconductor.org/packages/PhyloProfileData git_branch: RELEASE_3_12 git_last_commit: f963b1b git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/PhyloProfileData_1.4.0.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: plasFIA Version: 1.18.0 Depends: proFIA License: LGPL MD5sum: 68bda04abd8377f101776fdfed8378b2 NeedsCompilation: no Title: FIA-HRMS plasma dataset Description: Positive Ionization FIA-HRMS data of human plasma spiked with a pool of 40 compounds acquired in FIA-HRMS mode on an orbitrap fusion. plasFIA also include the result of the processing by the proFIA package with adapted parameters for an Orbitrap Fusion. biocViews: ExperimentData, MassSpectrometryData Author: Alexis Delabriere, Etienne Thevenot, Ulli Hohenester and Christophe Junot. Maintainer: Alexis Delabriere git_url: https://git.bioconductor.org/packages/plasFIA git_branch: RELEASE_3_12 git_last_commit: 9fc459b git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/plasFIA_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: proFIA dependencyCount: 103 Package: ppiData Version: 0.28.0 Depends: graph Imports: AnnotationDbi Suggests: org.Sc.sgd.db, ppiStats License: Artistic-2.0 MD5sum: 4c12874544a3ce347b66a04169957c61 NeedsCompilation: no Title: A package that contains the bait to prey directed graphs for protein-protein interactions. Description: This package contains the directed graphs for protein interaction data as derived from Y2H and APMS as well as the code used to obtain the y2h data from IntAct Repository. biocViews: ExperimentData Author: Tony Chiang Maintainer: Bioconductor Package Maintainer git_url: https://git.bioconductor.org/packages/ppiData git_branch: RELEASE_3_12 git_last_commit: 86de2bb git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ppiData_0.28.0.tar.gz vignettes: vignettes/ppiData/inst/doc/ppiData.pdf vignetteTitles: Using the package ppiStats hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ppiData/inst/doc/ppiData.R dependsOnMe: PCpheno, ppiStats suggestsMe: ScISI dependencyCount: 27 Package: prebsdata Version: 1.26.0 Depends: R (>= 2.14.0) License: Artistic-2.0 MD5sum: 68d86474c0b61b7adc5950b96b53c3e7 NeedsCompilation: no Title: Data for 'prebs' package Description: This package contains data required to run examples in 'prebs' package. The data files include: 1) Small sample bam files for demonstration purposes 2) Probe sequence mappings for Custom CDF (taken from http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp) 3) Probe sequence mappings for manufacturer's CDF (manually created using bowtie) biocViews: ExperimentData, SequencingData, RNASeqData Author: Karolis Uziela and Antti Honkela Maintainer: Karolis Uziela git_url: https://git.bioconductor.org/packages/prebsdata git_branch: RELEASE_3_12 git_last_commit: 827eed6 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/prebsdata_1.26.0.tar.gz vignettes: vignettes/prebsdata/inst/doc/prebsdata.pdf vignetteTitles: prebsdata User Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: prebs, SigFuge dependencyCount: 0 Package: PREDAsampledata Version: 0.30.0 Depends: R (>= 2.10.0), methods, PREDA, Biobase, affy, annotate Suggests: hgu133plus2.db, hgu133plus2cdf License: Artistic-2.0 MD5sum: 196ea85e4e11d75d7904fd42e52705d3 NeedsCompilation: no Title: expression and copy number data on clear cell renal carcinoma samples Description: Sample data for PREDA package. (annotations objects synchronized with GeneAnnot custom CDFs version 2.2.0) biocViews: ExperimentData, Tissue, CancerData, KidneyCancerData, MicroarrayData, TissueMicroarrayData, ArrayExpress Author: I. Cifola et al. in Cristina Battaglia Lab, University of Milan Maintainer: Francesco Ferrari git_url: https://git.bioconductor.org/packages/PREDAsampledata git_branch: RELEASE_3_12 git_last_commit: 7fe7bf2 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/PREDAsampledata_0.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PREDA dependencyCount: 54 Package: ProData Version: 1.28.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL MD5sum: f6ad22c62345f4264ea027e603ab7ed5 NeedsCompilation: no Title: SELDI-TOF data of Breast cancer samples Description: A data package of SELDI-TOF protein mass spectrometry data of 167 breast cancer and normal samples. biocViews: ExperimentData, CancerData, BreastCancerData, MassSpectrometryData, NCI Author: Xiaochun Li Maintainer: Xiaochun Li git_url: https://git.bioconductor.org/packages/ProData git_branch: RELEASE_3_12 git_last_commit: 39a00e5 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ProData_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CorrectedFDR dependencyCount: 7 Package: pRolocdata Version: 1.28.0 Depends: R (>= 3.6.3), MSnbase Imports: Biobase, utils Suggests: pRoloc (>= 1.13.8), testthat License: GPL-2 MD5sum: 5ee41d08e66faba9bfb7e174bdba5c05 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, Oliver M. Crook and Lisa M. Breckels Maintainer: Laurent Gatto URL: https://github.com/lgatto/pRolocdata BugReports: https://github.com/lgatto/pRolocdata/issues git_url: https://git.bioconductor.org/packages/pRolocdata git_branch: RELEASE_3_12 git_last_commit: 1764dcb git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/pRolocdata_1.28.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: proteomics suggestsMe: MSnbase, pRoloc, pRolocGUI, RforProteomics dependencyCount: 74 Package: prostateCancerCamcap Version: 1.18.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 2b1fa1c883bf7dbded0cb728abd53f70 NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Ross-Adams (2015) Prostate Cancer dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerCamcap git_branch: RELEASE_3_12 git_last_commit: 65f5bfc git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/prostateCancerCamcap_1.18.0.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: 1.18.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 37acc8f486549ba417079204c202e237 NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Grasso (2012) Prostate Cancer dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerGrasso git_branch: RELEASE_3_12 git_last_commit: cd66d64 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/prostateCancerGrasso_1.18.0.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: 1.18.0 Depends: Biobase , R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: dd95c3fe63eed97ff7dcb7dee3de8ccb NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Stockholm dataset biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerStockholm git_branch: RELEASE_3_12 git_last_commit: 0b0c3e1 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/prostateCancerStockholm_1.18.0.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: 1.18.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery, org.Hs.eg.db License: Artistic-2.0 MD5sum: 315f32f75f7b8f7e3577c0f80d6a60e1 NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Taylor et al (2010) dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerTaylor git_branch: RELEASE_3_12 git_last_commit: 4f5143f git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/prostateCancerTaylor_1.18.0.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: 1.18.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 12a3ae30f7460c5cc6ed4236e6c3a904 NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Varambally dataset biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerVarambally git_branch: RELEASE_3_12 git_last_commit: 8f71824 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/prostateCancerVarambally_1.18.0.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: PtH2O2lipids Version: 1.16.0 Depends: R (>= 3.3), xcms, CAMERA, LOBSTAHS, methods, utils Suggests: gplots, RColorBrewer, cluster, vegan, clustsig License: MIT + file LICENSE MD5sum: 4974fcaef00b3f026cd9c25576a4e050 NeedsCompilation: no Title: P. tricornutum HPLC-ESI-MS Lipid Data from van Creveld et al. (2015) Description: Annotated HPLC-ESI-MS lipid data in positive ionization mode from an experiment in which cultures of the marine diatom Phaeodactylum tricornutum were treated with various concentrations of hydrogen peroxide (H2O2) to induce oxidative stress. The experiment is described in Graff van Creveld, et al., 2015, "Early perturbation in mitochondria redox homeostasis in response to environmental stress predicts cell fate in diatoms," ISME Journal 9:385-395. PtH2O2lipids consists of two objects: A CAMERA xsAnnotate object (ptH2O2lipids$xsAnnotate) and LOBSTAHS LOBSet object (ptH2O2lipids$xsAnnotate$LOBSet). The LOBSet includes putative compound assignments from the default LOBSTAHS database. Isomer annotation is recorded in three other LOBSet slots. biocViews: ReproducibleResearch, CellCulture, MassSpectrometryData, Phaeodactylum_tricornutum_data Author: Shiri Graff van Creveld [aut], Shilo Rosenwasser [aut], Daniella Schatz [aut], Ilan Koren [aut], Assaf Vardi [aut], James Collins [cre] Maintainer: James Collins URL: http://dx.doi.org/10.1038/ismej.2014.136, https://github.com/vanmooylipidomics/PtH2O2lipids, http://www.whoi.edu/page.do?pid=133616&tid=282&cid=192529 BugReports: https://github.com/vanmooylipidomics/PtH2O2lipids/issues/new git_url: https://git.bioconductor.org/packages/PtH2O2lipids git_branch: RELEASE_3_12 git_last_commit: 906a1b5 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/PtH2O2lipids_1.16.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: LOBSTAHS dependencyCount: 127 Package: pumadata Version: 2.26.0 Depends: R (>= 3.2.0), Biobase (>= 2.5.5),puma, oligo(>= 1.32.0) License: LGPL MD5sum: 2077713140f2990ee39a20b6eb03edf1 NeedsCompilation: no Title: Various data sets for use with the puma package Description: This is a simple data package including various data sets derived from the estrogen data for use with the puma (Propagating Uncertainty in Microarray Analysis) package. biocViews: ExperimentData, MicroarrayData, SNPData Author: Richard Pearson Maintainer: Xuejun liu URL: http://umber.sbs.man.ac.uk/resources/puma git_url: https://git.bioconductor.org/packages/pumadata git_branch: RELEASE_3_12 git_last_commit: 0a89e6f git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/pumadata_2.26.0.tar.gz vignettes: vignettes/pumadata/inst/doc/pumadata.pdf vignetteTitles: pumadata User Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pumadata/inst/doc/pumadata.R suggestsMe: puma dependencyCount: 57 Package: PWMEnrich.Dmelanogaster.background Version: 4.24.0 Depends: methods, PWMEnrich License: GPL-3 MD5sum: e6b46ce8b619bd07902b43b1a0596d31 NeedsCompilation: no Title: D. melanogaster background for PWMEnrich Description: PWMEnrich pre-compiled background objects for Drosophila melanogaster and MotifDb D. melanogaster motifs. biocViews: Drosophila_melanogaster_Data Author: Robert Stojnic Maintainer: Diego Diez git_url: https://git.bioconductor.org/packages/PWMEnrich.Dmelanogaster.background git_branch: RELEASE_3_12 git_last_commit: 91f16e6 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/PWMEnrich.Dmelanogaster.background_4.24.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 21 Package: PWMEnrich.Hsapiens.background Version: 4.24.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: f9110634c557cbef10df0b45788b5b7b NeedsCompilation: no Title: H. sapiens background for PWMEnrich Description: PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs. biocViews: Homo_sapiens_Data, CGHData Author: Robert Stojnic Maintainer: Diego Diez git_url: https://git.bioconductor.org/packages/PWMEnrich.Hsapiens.background git_branch: RELEASE_3_12 git_last_commit: 9cf6a9a git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/PWMEnrich.Hsapiens.background_4.24.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 21 Package: PWMEnrich.Mmusculus.background Version: 4.24.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: 7064bd9b2897bc609ae70da70659e69d NeedsCompilation: no Title: M. musculus background for PWMEnrich Description: PWMEnrich pre-compiled background objects for M.musculus (mouse) and MotifDb M. musculus motifs. biocViews: Mus_musculus_Data Author: Robert Stojnic Maintainer: Diego Diez git_url: https://git.bioconductor.org/packages/PWMEnrich.Mmusculus.background git_branch: RELEASE_3_12 git_last_commit: 4c7cff2 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/PWMEnrich.Mmusculus.background_4.24.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 21 Package: pwrEWAS.data Version: 1.4.0 Imports: ExperimentHub Suggests: knitr, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: cb3ce70b6132afcde57b4a294f01738c NeedsCompilation: no Title: pwrEWAS.data: Reference data accompanying pwrEWAS Description: This package provides reference data required for pwrEWAS. pwrEWAS is a user-friendly tool to estimate power in EWAS as a function of sample and effect size for two-group comparisons of DNAm (e.g., case vs control, exposed vs non-exposed, etc.). biocViews: ExperimentHub, MethylationArrayData, MicroarrayData, TissueMicroarrayData, Tissue Author: Stefan Graw Maintainer: Stefan Graw VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/pwrEWAS.data git_branch: RELEASE_3_12 git_last_commit: be93ea2 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/pwrEWAS.data_1.4.0.tar.gz vignettes: vignettes/pwrEWAS.data/inst/doc/pwrEWAS.data.pdf vignetteTitles: pwrEWAS.data: Reference data accompanying pwrEWAS hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: pwrEWAS dependencyCount: 77 Package: QDNAseq.hg19 Version: 1.20.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: bda22c86fc59317e07ac4f9041a263f7 NeedsCompilation: no Title: QDNAseq bin annotation for hg19 Description: This package provides QDNAseq bin annotations for the human genome build hg19. biocViews: ExperimentData, OrganismData, Homo_sapiens_Data Author: Daoud Sie [aut, cre] Maintainer: Daoud Sie URL: https://github.com/tgac-vumc/QDNAseq.hg19 BugReports: https://github.com/tgac-vumc/QDNAseq.hg19/issues git_url: https://git.bioconductor.org/packages/QDNAseq.hg19 git_branch: RELEASE_3_12 git_last_commit: dec68e5 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/QDNAseq.hg19_1.20.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: biscuiteer, QDNAseq dependencyCount: 49 Package: QDNAseq.mm10 Version: 1.20.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: cd65e7df93f4a4765f7f338b62191de6 NeedsCompilation: no Title: Bin annotation mm10 Description: This package provides QDNAseq bin annotations for the mouse genome build mm10. biocViews: ExperimentData, OrganismData, Mus_musculus_Data Author: Daoud Sie [aut, cre] Maintainer: Daoud Sie URL: https://github.com/tgac-vumc/QDNAseq.mm10 BugReports: https://github.com/tgac-vumc/QDNAseq.mm10/issues git_url: https://git.bioconductor.org/packages/QDNAseq.mm10 git_branch: RELEASE_3_12 git_last_commit: a71709e git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/QDNAseq.mm10_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: biscuiteer, QDNAseq dependencyCount: 49 Package: qPLEXdata Version: 1.8.0 Depends: R (>= 3.5), qPLEXanalyzer Imports: utils, knitr, MSnbase, dplyr License: GPL-2 MD5sum: a9545e21a0e553f6faf5787984f8c4f7 NeedsCompilation: no Title: Data accompanying qPLEXanalyzer package Description: qPLEX-RIME and Full proteome TMT mass spectrometry datasets. biocViews: ExperimentData, MassSpectrometryData, Proteome Author: Kamal Kishore Developer [aut, cre] Maintainer: Kamal Kishore Developer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/qPLEXdata git_branch: RELEASE_3_12 git_last_commit: 869fe2a git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/qPLEXdata_1.8.0.tar.gz vignettes: vignettes/qPLEXdata/inst/doc/qPLEXdata.pdf vignetteTitles: qPLEXdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/qPLEXdata/inst/doc/qPLEXdata.R suggestsMe: qPLEXanalyzer dependencyCount: 98 Package: QUBICdata Version: 1.18.0 Depends: R (>= 3.1) Suggests: knitr, rmarkdown License: Unlimited | file LICENSE MD5sum: da5cf90f8d08212eaef5a718a6da2be1 NeedsCompilation: no Title: Data employed in the vignette of the QUBIC package Description: The data employed in the vignette of the QUBIC package. These data belong to Many Microbe Microarrays Database and STRING v10. biocViews: Escherichia_coli_Data, OrganismData, ExperimentData Author: Yu Zhang [aut, cre], Qin Ma [aut] Maintainer: Yu Zhang URL: http://github.com/zy26/QUBICdata VignetteBuilder: knitr BugReports: http://github.com/zy26/QUBICdata/issues git_url: https://git.bioconductor.org/packages/QUBICdata git_branch: RELEASE_3_12 git_last_commit: cea4c13 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/QUBICdata_1.18.0.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: rcellminerData Version: 2.12.0 Depends: R (>= 3.1.1), Biobase Suggests: knitr, testthat, BiocStyle, rcellminer License: LGPL-3 + file LICENSE MD5sum: c981f721c32746a7d63c8d0ba2a78c66 NeedsCompilation: no Title: rcellminerData: Molecular Profiles and Drug Response for the NCI-60 Cell Lines Description: The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data. biocViews: CancerData, CopyNumberVariationData, ExpressionData, SNPData, NCI, MicroarrayData, miRNAData Author: Augustin Luna, Vinodh Rajapakse, Fabricio Sousa Maintainer: Augustin Luna , Vinodh Rajapakse , Fathi Elloumi VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/rcellminerData git_branch: RELEASE_3_12 git_last_commit: a135de0 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/rcellminerData_2.12.0.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: 1.10.0 Depends: R (>= 3.3) Imports: data.table License: GPL-3 MD5sum: 9618daa214589c03ea720088cfcb6c29 NeedsCompilation: no Title: RcisTarget motif databases for human (hg19) - Subset of 4.6k motifs Description: RcisTarget databases: Gene-based motif rankings and annotation to transcription factors. This package contains a subset of 4.6k motifs (cisbp motifs), scored only within 500bp upstream and the TSS. See RcisTarget tutorial to download the full databases, containing 20k motifs and search space up to 10kbp around the TSS. biocViews: Homo_sapiens_Data Author: Sara Aibar, Gert Hulselmans, Stein Aerts. Laboratory of Computational Biology, KU Leuven Center for Human Genetics. Leuven, Belgium. Maintainer: Sara Aibar URL: http://scenic.aertslab.org git_url: https://git.bioconductor.org/packages/RcisTarget.hg19.motifDBs.cisbpOnly.500bp git_branch: RELEASE_3_12 git_last_commit: 5491126 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.10.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RcisTarget dependencyCount: 2 Package: ReactomeGSA.data Version: 1.4.0 Depends: R (>= 3.6), limma, edgeR, ReactomeGSA, Seurat License: Artistic-2.0 MD5sum: adbf24701a53d3e0b3c169c175226e38 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] () Maintainer: Johannes Griss URL: https://github.com/reactome/ReactomeGSA.data/issues BugReports: https://github.com/reactome/ReactomeGSA.data git_url: https://git.bioconductor.org/packages/ReactomeGSA.data git_branch: RELEASE_3_12 git_last_commit: 34d0432 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/ReactomeGSA.data_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ReactomeGSA dependencyCount: 145 Package: RegParallel Version: 1.8.0 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 License: GPL-3 MD5sum: 132d98edb956ba2fa222f919aa96d64f NeedsCompilation: no Title: Standard regression functions in R enabled for parallel processing over large data-frames Description: In many analyses, a large amount of variables have to be tested independently against the trait/endpoint of interest, and also adjusted for covariates and confounding factors at the same time. The major bottleneck in these is the amount of time that it takes to complete these analyses. With RegParallel, a large number of tests can be performed simultaneously. On a 12-core system, 144 variables can be tested simultaneously, with 1000s of variables processed in a matter of seconds via 'nested' parallel processing. Works for logistic regression, linear regression, conditional logistic regression, Cox proportional hazards and survival models, and Bayesian logistic regression. Also caters for generalised linear models that utilise survey weights created by the 'survey' CRAN package and that utilise 'survey::svyglm'. biocViews: DiseaseModel Author: Kevin Blighe [aut, cre], Sarega Gurudas [ctb], Jessica Lasky-Su [aut] Maintainer: Kevin Blighe URL: https://github.com/kevinblighe/RegParallel VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RegParallel git_branch: RELEASE_3_12 git_last_commit: 1526474 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RegParallel_1.8.0.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: 84 Package: restfulSEData Version: 1.12.0 Depends: R (>= 3.4), SummarizedExperiment, ExperimentHub Imports: utils, methods Suggests: knitr License: Artistic-2.0 MD5sum: 3b5a5f351916c2b5b16bff0709dfe2bb NeedsCompilation: no Title: Example metadata for the "restfulSE" R package Description: Metadata RangedSummarizedExperiment shell for use with restfulSE. biocViews: ExperimentData, Mus_musculus_Data, Homo_sapiens_Data, ExpressionData, SequencingData Author: Vincent Carey [aut], Shweta Gopaulakrishnan [cre, aut] Maintainer: Bioconductor Package Maintainer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/restfulSEData git_branch: RELEASE_3_12 git_last_commit: a0966bb git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/restfulSEData_1.12.0.tar.gz vignettes: vignettes/restfulSEData/inst/doc/restfulSEData.pdf vignetteTitles: restfulSEData -- SummarizedExperiment shells for remote assay data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/restfulSEData/inst/doc/restfulSEData.R suggestsMe: restfulSE dependencyCount: 91 Package: RforProteomics Version: 1.28.1 Depends: R (>= 3.5), MSnbase (>= 2.5.3) Imports: R.utils, shiny, biocViews, BiocManager Suggests: AnnotationDbi, rpx (>= 1.16.1), DT, knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, isobar, MALDIquant (>= 1.12), MALDIquantForeign, readBrukerFlexData, synapter, synapterdata, 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, DEP, corrplot, beanplot, Heatplus, gplots, VennDiagram, protViz, genefilter, plotly, gridExtra, dplyr, lubridate, magick, cleaver License: Artistic-2.0 MD5sum: 71957a7234ce2c5758dea84b1254771d NeedsCompilation: no Title: Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication Description: This package contains code to illustrate the 'Using R and Bioconductor for proteomics data analysis' and 'Visualisation of proteomics data using R and Bioconductor' manuscripts. The vignettes describe the code and data needed to reproduce the examples and figures described in the paper and functionality for proteomics visualisation. It also contain various function to discover R software for mass spectrometry and proteomics. biocViews: ExperimentData, MassSpectrometryData, ReproducibleResearch Author: Laurent Gatto [aut, cre], Sebastian Gibb [ctb], Vlad Petyuk [ctb], Thomas Pedersen Lin [ctb] Maintainer: Laurent Gatto URL: http://lgatto.github.com/RforProteomics/ VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RforProteomics git_branch: RELEASE_3_12 git_last_commit: 96a57e3 git_last_commit_date: 2021-01-15 Date/Publication: 2021-01-18 source.ver: src/contrib/RforProteomics_1.28.1.tar.gz vignettes: vignettes/RforProteomics/inst/doc/RforProteomics.html, vignettes/RforProteomics/inst/doc/RProtVis.html vignetteTitles: Using R for proteomics data analysis, Visualisation of proteomics data using R and Bioconductor hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RforProteomics/inst/doc/RforProteomics.R, vignettes/RforProteomics/inst/doc/RProtVis.R suggestsMe: MSstatsQC, qcmetrics dependencyCount: 102 Package: RGMQLlib Version: 1.10.0 Depends: R(>= 3.4.2) Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 29dad94fa077f0b9aa608ec34a5f441c NeedsCompilation: no Title: RGMQLlib, java libraries to run GMQL scala API Description: A package that contains scala libraries to call GMQL from R used by RGMQL package. It contains a scalable data management engine written in Scala programming language. biocViews: ExperimentData,RepositoryData Author: Simone Pallotta, Marco Masseroli Maintainer: Simone Pallotta URL: http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/ VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RGMQLlib git_branch: RELEASE_3_12 git_last_commit: 8f25360 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RGMQLlib_1.10.0.tar.gz vignettes: vignettes/RGMQLlib/inst/doc/RGMQLlib.pdf vignetteTitles: RGMQLlib: scala Libraries to support GMQL hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: RGMQL dependencyCount: 0 Package: rheumaticConditionWOLLBOLD Version: 1.28.0 Depends: R (>= 2.10.0) Suggests: genefilter, Biobase, hgu133plus2.db License: Artistic-2.0 MD5sum: e6dd8c70198e59afc648fe567e55ca58 NeedsCompilation: no Title: Normalized gene expression dataset published by Wollbold et al. [2009] (WOLLBOLD). Description: Normalized gene expression data from rheumatic diseases from study published by Wollbold et al. in 2009, provided as an eSet. biocViews: ExperimentData, Tissue, MicroarrayData, MultiChannelData, ChipOnChipData, TissueMicroarrayData, GEO, ArrayExpress Author: Alejandro Quiroz-Zarate, John Quackenbush Maintainer: Alejandro Quiroz-Zarate URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/rheumaticConditionWOLLBOLD git_branch: RELEASE_3_12 git_last_commit: 48b344b git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/rheumaticConditionWOLLBOLD_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: RITANdata Version: 1.14.0 Depends: R (>= 3.4) License: file LICENSE MD5sum: 61372f17e03d8dcfc9651d8822b73127 NeedsCompilation: no Title: This package contains the annotation and network data sets Description: Data such as is contained in these two R data files in this package are required for the RITAN package. Users may use their own or additional resources in conjunction with RITANdata. See the RITAN vignettes for more information. biocViews: AnnotationData, Homo_sapiens Author: Michael Zimmermann Maintainer: Michael Zimmermann VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RITANdata git_branch: RELEASE_3_12 git_last_commit: e9a2293 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RITANdata_1.14.0.tar.gz vignettes: vignettes/RITANdata/inst/doc/RITANdata.html vignetteTitles: Vignette Title hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/RITANdata/inst/doc/RITANdata.R importsMe: RITAN dependencyCount: 0 Package: RMassBankData Version: 1.28.0 Suggests: RMassBank License: Artistic-2.0 MD5sum: 3cc5ee0065cf23bedc59addd8fb7baa3 NeedsCompilation: no Title: Test dataset for RMassBank Description: Example spectra, example compound list(s) and an example annotation list for a narcotics dataset; required to test RMassBank. The package is described in the man page for RMassBankData. Includes new XCMS test data. biocViews: ExperimentData, MassSpectrometryData Author: Michael Stravs, Emma Schymanski, Steffen Neumann Maintainer: Michael Stravs, Emma Schymanski git_url: https://git.bioconductor.org/packages/RMassBankData git_branch: RELEASE_3_12 git_last_commit: 0fe2270 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RMassBankData_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: RNAinteractMAPK Version: 1.28.2 Depends: R (>= 2.12.0), sparseLDA, RNAinteract Imports: grid, gdata, MASS, genefilter, methods, fields, utils, lattice, Biobase Suggests: qvalue License: Artistic-2.0 MD5sum: 4f2bbb8a9aadd75159d44d8556bea3ff NeedsCompilation: no Title: Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi Description: This package includes all data used in the paper -Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi- by Horn, Sandmann, Fischer et al.., Nat. Methods, 2011. The package vignette shows the R code to reproduce all figures in the paper. biocViews: ExperimentData, MicrotitrePlateAssayData, Drosophila_melanogaster_Data, CellCulture Author: Bernd Fischer [aut], Wolfgang Huber [ctb], Mike Smith [cre] Maintainer: Mike Smith git_url: https://git.bioconductor.org/packages/RNAinteractMAPK git_branch: RELEASE_3_12 git_last_commit: 425e384 git_last_commit_date: 2020-12-22 Date/Publication: 2020-12-24 source.ver: src/contrib/RNAinteractMAPK_1.28.2.tar.gz vignettes: vignettes/RNAinteractMAPK/inst/doc/RNAinteractMAPK.pdf vignetteTitles: RNAinteractMAPK hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RNAinteractMAPK/inst/doc/RNAinteractMAPK.R suggestsMe: DmelSGI dependencyCount: 113 Package: RNAmodR.Data Version: 1.4.0 Depends: R (>= 3.6), ExperimentHub, ExperimentHubData (>= 1.9.2) Imports: utils Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, sessioninfo, testthat License: Artistic-2.0 MD5sum: 76a39b40b6dc9e54d5f0513896e93153 NeedsCompilation: no Title: Example data for the RNAmodR package Description: RNAmodR.Data contains example data, which is used for vignettes and example workflows in the RNAmodR and dependent packages. biocViews: ExperimentData, SequencingData, RNASeqData Author: Felix G.M. Ernst [aut, cre], Denis L.J. Lafontaine [ctb, fnd] Maintainer: Felix G.M. Ernst URL: https://github.com/FelixErnst/RNAmodR.Data VignetteBuilder: knitr BugReports: https://github.com/FelixErnst/RNAmodR.Data/issues git_url: https://git.bioconductor.org/packages/RNAmodR.Data git_branch: RELEASE_3_12 git_last_commit: 8fe16f1 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RNAmodR.Data_1.4.0.tar.gz vignettes: vignettes/RNAmodR.Data/inst/doc/RNAmodR.Data.html vignetteTitles: RNAmodR.Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RNAmodR.Data/inst/doc/RNAmodR.Data.R suggestsMe: RNAmodR, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq dependencyCount: 130 Package: RNAseqData.HNRNPC.bam.chr14 Version: 0.28.0 Suggests: GenomicAlignments, BiocManager License: LGPL MD5sum: 1025906a7f6a12e4342a628d563011ca NeedsCompilation: no Title: Aligned reads from RNAseq experiment: Transcription profiling by high throughput sequencing of HNRNPC knockdown and control HeLa cells Description: The package contains 8 BAM files, 1 per sequencing run. Each BAM file was obtained by (1) aligning the reads (paired-end) to the full hg19 genome with TopHat2, and then (2) subsetting to keep only alignments on chr14. See accession number E-MTAB-1147 in the ArrayExpress database for details about the experiment, including links to the published study (by Zarnack et al., 2012) and to the FASTQ files. biocViews: ExperimentData, Genome, Homo_sapiens_Data, SequencingData, GEO, NCI, RNASeqData, ArrayExpress Author: Hervé Pagès Maintainer: Hervé Pagès URL: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1147/ git_url: https://git.bioconductor.org/packages/RNAseqData.HNRNPC.bam.chr14 git_branch: RELEASE_3_12 git_last_commit: 8a9881d git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RNAseqData.HNRNPC.bam.chr14_0.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: sequencing suggestsMe: BiocParallel, GenomicAlignments, GenomicFiles, GenomicRanges, roar, Rsamtools, SplicingGraphs dependencyCount: 0 Package: RNASeqRData Version: 1.8.0 Depends: R (>= 3.5.0) Suggests: png, grid License: Artistic-2.0 MD5sum: 61afda2f15d7fc1239252c5c59329d8e NeedsCompilation: no Title: RNASeqRData: sample data for RNASeqR software package demonstration Description: RNASeqRData is a helper experiment package for vignette demonstration purpose in RNASeqR software package. biocViews: ExperimentData, Saccharomyces_cerevisiae_Data Author: Kuan-Hao Chao Maintainer: Kuan-Hao Chao git_url: https://git.bioconductor.org/packages/RNASeqRData git_branch: RELEASE_3_12 git_last_commit: 095ea4b git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RNASeqRData_1.8.0.tar.gz vignettes: vignettes/RNASeqRData/inst/doc/RNASeqRData.html vignetteTitles: RNASeqRData.html hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RNASeqR dependencyCount: 0 Package: RnaSeqSampleSizeData Version: 1.22.0 Depends: edgeR,R (>= 2.10) Suggests: BiocStyle, knitr License: GPL (>= 2) MD5sum: ddef4d25b2214d2607342546e4349b77 NeedsCompilation: no Title: RnaSeqSampleSizeData Description: RnaSeqSampleSizeData package provides the read counts and dispersion distribution from real RNA-seq experiments. It can be used by RnaSeqSampleSize package to estimate sample size and power for RNA-seq experiment design. biocViews: ExperimentData, CancerData, RNASeqData Author: Shilin Zhao, Chung-I Li, Yan Guo, Quanhu Sheng, Yu Shyr Maintainer: Shilin Zhao VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RnaSeqSampleSizeData git_branch: RELEASE_3_12 git_last_commit: 0e389c8 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RnaSeqSampleSizeData_1.22.0.tar.gz vignettes: vignettes/RnaSeqSampleSizeData/inst/doc/RnaSeqSampleSizeData.pdf vignetteTitles: RnaSeqSampleSizeData: Read counts and dispersion distribution from real data for sample size estimation of RNA-seq experiments hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RnaSeqSampleSizeData/inst/doc/RnaSeqSampleSizeData.R dependsOnMe: RnaSeqSampleSize dependencyCount: 11 Package: RnBeads.hg19 Version: 1.22.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 1358bfdb643b632aeaaca13ada2e68e8 NeedsCompilation: no Title: RnBeads.hg19 Description: Automatically generated RnBeads annotation package for the assembly hg19. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.hg19 git_branch: RELEASE_3_12 git_last_commit: c27ee43 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RnBeads.hg19_1.22.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RnBeads dependencyCount: 17 Package: RnBeads.hg38 Version: 1.22.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: b0e5d03c6a3e1b76cd9503d7676bfa50 NeedsCompilation: no Title: RnBeads.hg38 Description: Automatically generated RnBeads annotation package for the assembly hg38. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.hg38 git_branch: RELEASE_3_12 git_last_commit: 1e100ef git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RnBeads.hg38_1.22.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 17 Package: RnBeads.mm10 Version: 1.22.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 3dcef33b4fb917282b932410facf6dfa NeedsCompilation: no Title: RnBeads.mm10 Description: Automatically generated RnBeads annotation package for the assembly mm10. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.mm10 git_branch: RELEASE_3_12 git_last_commit: a5c65a5 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RnBeads.mm10_1.22.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 17 Package: RnBeads.mm9 Version: 1.22.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: e7464eae153a04268efc60dc41e934c0 NeedsCompilation: no Title: RnBeads.mm9 Description: Automatically generated RnBeads annotation package for the assembly mm9. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.mm9 git_branch: RELEASE_3_12 git_last_commit: 8f7475c git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RnBeads.mm9_1.22.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RnBeads dependencyCount: 17 Package: RnBeads.rn5 Version: 1.22.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 1a5a8735c728edb6f3c64a72ef2d680d NeedsCompilation: no Title: RnBeads.rn5 Description: Automatically generated RnBeads annotation package for the assembly rn5. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.rn5 git_branch: RELEASE_3_12 git_last_commit: d1dc5ff git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RnBeads.rn5_1.22.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 17 Package: RRBSdata Version: 1.10.0 Depends: R (>= 3.1.0), BiSeq (>= 1.9.2) License: LGPL-3 MD5sum: 1fd71908f0416a54d9445d091918f2b3 NeedsCompilation: no Title: An RRBS data set with 12 samples and 10,000 simulated DMRs Description: RRBS data set comprising 12 samples with simulated differentially methylated regions (DMRs). biocViews: ExperimentData, CancerData, SequencingData, CpGIslandData Author: Katja Hebestreit, Hans-Ulrich Klein Maintainer: Katja Hebestreit git_url: https://git.bioconductor.org/packages/RRBSdata git_branch: RELEASE_3_12 git_last_commit: b573878 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RRBSdata_1.10.0.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: 80 Package: rRDPData Version: 1.10.0 Depends: rRDP License: GPL-2 MD5sum: 51a4076759f1dcbd9656a845d7ac64c1 NeedsCompilation: no Title: Database for the Default RDP Classifier Description: Database used by the default RDP Classifier biocViews: SequencingData, MicrobiomeData Author: Michael Hahsler, Anurag Nagar Maintainer: Michael Hahsler SystemRequirements: Java git_url: https://git.bioconductor.org/packages/rRDPData git_branch: RELEASE_3_12 git_last_commit: 5d9752b git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/rRDPData_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: rRDP dependencyCount: 16 Package: RTCGA.clinical Version: 20151101.20.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 49276179a16b54de3cd2b7fac99ba008 NeedsCompilation: no Title: Clinical datasets from The Cancer Genome Atlas Project Description: Package provides clinical datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Clinical data format is explained here https://wiki.nci.nih.gov/display/TCGA/Clinical+Data+Overview. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.clinical git_branch: RELEASE_3_12 git_last_commit: 098f383 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RTCGA.clinical_20151101.20.0.tar.gz vignettes: vignettes/RTCGA.clinical/inst/doc/downloading_clinical_datasets.html vignetteTitles: Using RTCGA to download clinical data as included in RTCGA.clinical hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.clinical/inst/doc/downloading_clinical_datasets.R suggestsMe: RTCGA dependencyCount: 133 Package: RTCGA.CNV Version: 1.18.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 56553c5cfc97460e6e1baa782b97a37b NeedsCompilation: no Title: CNV (Copy-number variation) datasets from The Cancer Genome Atlas Project Description: Package provides CNV (based on Merge snp) datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Retrieving +Data+Using+the+Data+Matrix. Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Przemyslaw Biecek Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.CNV git_branch: RELEASE_3_12 git_last_commit: de50b10 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RTCGA.CNV_1.18.0.tar.gz vignettes: vignettes/RTCGA.CNV/inst/doc/downloading_cnv_datasets.html, vignettes/RTCGA.CNV/inst/doc/frequency_of_cnv_for_mdm3.html vignetteTitles: Using RTCGA to download CNV data as included in RTCGA.CNV, Using RTCGA to estimate ratio of MDM2 duplications hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.CNV/inst/doc/downloading_cnv_datasets.R, vignettes/RTCGA.CNV/inst/doc/frequency_of_cnv_for_mdm3.R suggestsMe: RTCGA dependencyCount: 133 Package: RTCGA.methylation Version: 1.18.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: e35fd39ede52974f7a370301d0cd100b NeedsCompilation: no Title: Methylation datasets from The Cancer Genome Atlas Project Description: Package provides methylation (humanmethylation27) datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/DNA+methylation Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Marcin Kosinski [aut, cre], Witold Chodor [aut] Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.methylation git_branch: RELEASE_3_12 git_last_commit: 6f0d63b git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RTCGA.methylation_1.18.0.tar.gz vignettes: vignettes/RTCGA.methylation/inst/doc/downloading_methylation_datasets.html vignetteTitles: Using RTCGA to download methylation data as included in RTCGA.methylation hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.methylation/inst/doc/downloading_methylation_datasets.R suggestsMe: RTCGA dependencyCount: 133 Package: RTCGA.miRNASeq Version: 1.18.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 1689a88880bd360d1c70106f11f64262 NeedsCompilation: no Title: miRNASeq datasets from The Cancer Genome Atlas Project Description: Package provides miRNASeq datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/miRNASeq#miRNASeq-DataOverview Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.miRNASeq git_branch: RELEASE_3_12 git_last_commit: a3170df git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RTCGA.miRNASeq_1.18.0.tar.gz vignettes: vignettes/RTCGA.miRNASeq/inst/doc/downloading_miRNASeq_datasets.html vignetteTitles: Using RTCGA to download miRNASeq data as included in RTCGA.miRNASeq hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.miRNASeq/inst/doc/downloading_miRNASeq_datasets.R suggestsMe: RTCGA dependencyCount: 133 Package: RTCGA.mRNA Version: 1.18.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 4efaa7ff5133a37f3018daf851edbf17 NeedsCompilation: no Title: mRNA datasets from The Cancer Genome Atlas Project Description: Package provides mRNA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Gene+expression+data Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.mRNA git_branch: RELEASE_3_12 git_last_commit: 4e20464 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RTCGA.mRNA_1.18.0.tar.gz vignettes: vignettes/RTCGA.mRNA/inst/doc/downloading_mRNA_datasets.html vignetteTitles: Using RTCGA to download mRNA data as included in RTCGA.mRNA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.mRNA/inst/doc/downloading_mRNA_datasets.R suggestsMe: CancerSubtypes, RTCGA dependencyCount: 133 Package: RTCGA.mutations Version: 20151101.20.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: d2ed408e34a0429e0638afef954ce189 NeedsCompilation: no Title: Mutations datasets from The Cancer Genome Atlas Project Description: Package provides mutations datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Mutations data format is explained here https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+(MAF)+Specification. There is extra one column with patients' barcodes. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.mutations git_branch: RELEASE_3_12 git_last_commit: 25d0255 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RTCGA.mutations_20151101.20.0.tar.gz vignettes: vignettes/RTCGA.mutations/inst/doc/downloading_mutations_datasets.html vignetteTitles: Using RTCGA to download mutations data as included in RTCGA.mutations hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.mutations/inst/doc/downloading_mutations_datasets.R suggestsMe: RTCGA dependencyCount: 133 Package: RTCGA.PANCAN12 Version: 1.18.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 46773c210d21b9adaa0b6fee183b1b7c NeedsCompilation: no Title: PanCan 12 from Genome Cancer Browser Description: Package provides clinical, expression, cnv and mutation data from Genome Cancer Browser. biocViews: AnnotationData Author: Przemyslaw Biecek Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.PANCAN12 git_branch: RELEASE_3_12 git_last_commit: 6486bf5 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RTCGA.PANCAN12_1.18.0.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, RTCGA dependencyCount: 133 Package: RTCGA.rnaseq Version: 20151101.20.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 9b949ae0aef4bb42381eedc853d6cd25 NeedsCompilation: no Title: Rna-seq datasets from The Cancer Genome Atlas Project Description: Package provides rna-seq datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Rna-seq data format is explained here https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2. Data source is illumina hiseq Level 3 RSEM normalized expression data. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.rnaseq git_branch: RELEASE_3_12 git_last_commit: 09009ff git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RTCGA.rnaseq_20151101.20.0.tar.gz vignettes: vignettes/RTCGA.rnaseq/inst/doc/downloading_rnaseq_datasets.html vignetteTitles: Using RTCGA to download RNAseq data as included in RTCGA.rnaseq hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.rnaseq/inst/doc/downloading_rnaseq_datasets.R suggestsMe: RTCGA, FSelectorRcpp dependencyCount: 133 Package: RTCGA.RPPA Version: 1.18.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 633094117181e59aae4b4dde340b4c05 NeedsCompilation: no Title: RPPA datasets from The Cancer Genome Atlas Project Description: Package provides RPPA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Protein+Array +Data+Format+Specification?src=search biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.RPPA git_branch: RELEASE_3_12 git_last_commit: 982cbf4 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RTCGA.RPPA_1.18.0.tar.gz vignettes: vignettes/RTCGA.RPPA/inst/doc/downloading_RPPA_datasets.html vignetteTitles: Using RTCGA to download RPPA data as included in RTCGA.RPPA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.RPPA/inst/doc/downloading_RPPA_datasets.R suggestsMe: RTCGA dependencyCount: 133 Package: RUVnormalizeData Version: 1.10.0 Depends: R (>= 2.10.0), Biobase License: GPL-3 MD5sum: 248e26e3fa9bff5a7aac430397cd1822 NeedsCompilation: no Title: Gender data for the RUVnormalize package Description: Microarray gene expression data from the study of Vawter et al., 2004. biocViews: MicroarrayData Author: Laurent Jacob Maintainer: Laurent Jacob git_url: https://git.bioconductor.org/packages/RUVnormalizeData git_branch: RELEASE_3_12 git_last_commit: 781ff5e git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/RUVnormalizeData_1.10.0.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: 1.14.1 Depends: R (>= 3.4), SummarizedExperiment Suggests: BiocStyle License: Artistic-2.0 MD5sum: 3981f88bbe0a20afbe85843c0bd4581f NeedsCompilation: no Title: Pre-processed data for use with the sampleClassifier package Description: This package contains two microarray and two RNA-seq datasets that have been preprocessed for use with the sampleClassifier package. The RNA-seq data are derived from Fagerberg et al. (2014) and the Illumina Body Map 2.0 data. The microarray data are derived from Roth et al. (2006) and Ge et al. (2005). biocViews: ExperimentData, ExpressionData, MicroarrayData, SequencingData, RNASeqData, ArrayExpress Author: Khadija El Amrani Maintainer: Khadija El Amrani git_url: https://git.bioconductor.org/packages/sampleClassifierData git_branch: RELEASE_3_12 git_last_commit: 558c056 git_last_commit_date: 2021-01-19 Date/Publication: 2021-01-21 source.ver: src/contrib/sampleClassifierData_1.14.1.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 suggestsMe: sampleClassifier dependencyCount: 26 Package: SBGNview.data Version: 1.4.1 Depends: R (>= 3.6) Imports: knitr, rmarkdown, bookdown Suggests: SummarizedExperiment License: AGPL-3 MD5sum: 853cf8c818d5f406bb2c6be72c93182c NeedsCompilation: no Title: Demo gene expression datasets for SBGNview package Description: This package contains: 1. A microarray gene expression dataset from a human breast cancer study. 2. A RNA-Seq gene expression dataset from a mouse study on IFNG knockout. 3. ID mapping tables between gene IDs and SBGN-ML file glyph IDs. 4. Percent of orthologs detected in other species of the genes in a pathway. Cutoffs of this percentage for defining if a pathway exists in another species. 5. XML text of SBGN-ML files for all pre-collected pathways. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO, RNASeqData Author: Xiaoxi Dong*, Kovidh Vegesna*, Weijun Luo Maintainer: Weijun Luo VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/SBGNview.data git_branch: RELEASE_3_12 git_last_commit: 24dae23 git_last_commit_date: 2021-02-25 Date/Publication: 2021-03-01 source.ver: src/contrib/SBGNview.data_1.4.1.tar.gz vignettes: vignettes/SBGNview.data/inst/doc/SBGNview.data.vignette.html vignetteTitles: SBGNview functions hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SBGNview.data/inst/doc/SBGNview.data.vignette.R dependsOnMe: SBGNview dependencyCount: 24 Package: SCATEData Version: 1.0.0 Depends: ExperimentHub, GenomicAlignments, GenomicRanges, base Imports: utils Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 6670e17bf9845cf95c848d8df0ce3bbd NeedsCompilation: no Title: Data for SCATE (Single-cell ATAC-seq Signal Extraction and Enhancement) Description: SCATEData is an ExperimentHub package for SCATE which is a software tool for extracting and enhancing the sparse and discrete Single-cell ATAC-seq Signal. biocViews: ExperimentHub, ExperimentData Author: Zhicheng Ji [aut], Weiqiang Zhou [aut], Wenpin Hou [cre, aut] (), Hongkai Ji [aut] Maintainer: Wenpin Hou VignetteBuilder: knitr BugReports: https://github.com/Winnie09/SCATEData/issues git_url: https://git.bioconductor.org/packages/SCATEData git_branch: RELEASE_3_12 git_last_commit: 4c42627 git_last_commit_date: 2020-10-27 Date/Publication: 2020-11-09 source.ver: src/contrib/SCATEData_1.0.0.tar.gz vignettes: vignettes/SCATEData/inst/doc/SCATEData_package.html vignetteTitles: 1. SCATEData package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/SCATEData/inst/doc/SCATEData_package.R dependsOnMe: SCATE dependencyCount: 103 Package: SCLCBam Version: 1.22.0 Depends: R(>= 2.10) Suggests: BiocStyle License: GPL-2 MD5sum: 97a1d00b7bc1ce93f5bb8199c8f5a507 NeedsCompilation: no Title: Sequence data from chromosome 4 of a small-cell lung tumor Description: Whole-exome sequencing data from a murine small-cell lung tumor; only contains data of chromosome 4. biocViews: SequencingData, LungCancerData Author: Thomas Kuilman Maintainer: Oscar Krijgsman git_url: https://git.bioconductor.org/packages/SCLCBam git_branch: RELEASE_3_12 git_last_commit: 207d811 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/SCLCBam_1.22.0.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 suggestsMe: CopywriteR dependencyCount: 0 Package: scRNAseq Version: 2.4.0 Depends: SingleCellExperiment Imports: utils, methods, BiocGenerics, S4Vectors, GenomicRanges, SummarizedExperiment, ExperimentHub, AnnotationHub, AnnotationDbi, ensembldb, GenomicFeatures Suggests: BiocStyle, knitr, rmarkdown, BiocFileCache, testthat License: CC0 MD5sum: 2a68fa4f52d25c91dda4354ae49b4838 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] Maintainer: Aaron Lun VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/scRNAseq git_branch: RELEASE_3_12 git_last_commit: 61f2c38 git_last_commit_date: 2020-10-27 Date/Publication: 2020-11-09 source.ver: src/contrib/scRNAseq_2.4.0.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 importsMe: singleCellTK suggestsMe: batchelor, bluster, dittoSeq, iSEE, iSEEu, scater, scDblFinder, scFeatureFilter, scone, scran, scuttle, SingleCellExperiment, SingleR, snifter, SummarizedBenchmark, velociraptor, zellkonverter, zinbwave dependencyCount: 116 Package: scTHI.data Version: 1.2.0 Depends: R (>= 4.0) License: GPL-2 MD5sum: a5b6b2a786120dff265800f5beeaa108 NeedsCompilation: no Title: The package contains examples of single cell data used in vignettes and examples of the scTHI package; data contain both tumor cells and immune cells from public dataset of glioma Description: Data for the vignette and tutorial of the package scTHI. biocViews: ExperimentData, SingleCellData Author: Francesca Pia Caruso [aut], Michele Ceccarelli [aut, cre] Maintainer: Michele Ceccarelli git_url: https://git.bioconductor.org/packages/scTHI.data git_branch: RELEASE_3_12 git_last_commit: b6a8c5a git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/scTHI.data_1.2.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: scTHI dependencyCount: 0 Package: seq2pathway.data Version: 1.22.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 8fb6db12ac9673267562e1404d959c06 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: Xinan Holly Yang git_url: https://git.bioconductor.org/packages/seq2pathway.data git_branch: RELEASE_3_12 git_last_commit: 5ba32cf git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/seq2pathway.data_1.22.0.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: 1.24.0 Depends: R (>= 2.10) Imports: utils, Biobase License: GPL-3 MD5sum: 0fc3dca59ff6ec7f05397f0c71e86ce3 NeedsCompilation: no Title: RNA-seq data generated from SEQC (MAQC-III) study Description: The SEQC/MAQC-III Consortium has produced benchmark RNA-seq data for the assessment of RNA sequencing technologies and data analysis methods (Nat Biotechnol, 2014). Billions of sequence reads have been generated from ten different sequencing sites. This package contains the summarized read count data for ~2000 sequencing libraries. It also includes all the exon-exon junctions discovered from the study. TaqMan RT-PCR data for ~1000 genes and ERCC spike-in sequence data are included in this package as well. biocViews: ExperimentData, RNASeqData, qPCRData, SequencingData Author: Yang Liao and Wei Shi with contributions from Gordon K Smyth and Steve Lianoglou. Maintainer: Yang Liao and Wei Shi URL: http://bioconductor.org/packages/release/data/experiment/html/seqc.html git_url: https://git.bioconductor.org/packages/seqc git_branch: RELEASE_3_12 git_last_commit: 64b0931 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/seqc_1.24.0.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: seqCNA.annot Version: 1.26.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 4113813d5c84463543ae336d3b5011d5 NeedsCompilation: no Title: Annotation for the copy number analysis of deep sequencing cancer data with seqCNA Description: Provides annotation on GC content, mappability and genomic features for various genomes biocViews: Genome, CopyNumberVariationData Author: David Mosen-Ansorena Maintainer: David Mosen-Ansorena git_url: https://git.bioconductor.org/packages/seqCNA.annot git_branch: RELEASE_3_12 git_last_commit: 1e2cfa6 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/seqCNA.annot_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: seqCNA dependencyCount: 0 Package: serumStimulation Version: 1.26.0 Depends: R (>= 2.10) License: GPL (>= 2) MD5sum: f7f0e6996e6e155adbf439a1e7508320 NeedsCompilation: no Title: serumStimulation is a data package which is used by examples in package pcaGoPromoter Description: Contains 13 micro array data results from a serum stimulation experiment biocViews: ExperimentData, MicroarrayData Author: Morten Hansen Maintainer: Morten Hansen, git_url: https://git.bioconductor.org/packages/serumStimulation git_branch: RELEASE_3_12 git_last_commit: 9162b24 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/serumStimulation_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: sesameData Version: 1.8.10 Depends: R (>= 4.0), ExperimentHub, AnnotationHub, rmarkdown Imports: utils, curl Suggests: GenomicRanges, BiocGenerics, sesame, testthat, knitr License: Artistic-2.0 MD5sum: e426c8dd46c862c9a0bd42790fcb836c NeedsCompilation: no Title: Supporting Data for SeSAMe Package Description: Provides supporting annotation and test data for SeSAMe package. This includes chip tango addresses, mapping information, performance annotation, and trained predictor for Infinium array data. This package provides user access to essential annotation data for working with many generations of the Infinium DNA methylation array. Current we support human array (HM27, HM450, EPIC), mouse array (MM285) and the HorvathMethylChip40 (Mammal40) array. biocViews: ExperimentData, MicroarrayData, Genome, ExperimentHub, MethylationArrayData Author: Wanding Zhou [aut, cre], Hui Shen [aut], Timothy Triche [ctb] Maintainer: Wanding Zhou VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/sesameData git_branch: RELEASE_3_12 git_last_commit: e98950a git_last_commit_date: 2021-04-25 Date/Publication: 2021-04-26 source.ver: src/contrib/sesameData_1.8.10.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: MethReg suggestsMe: ELMER dependencyCount: 86 Package: seventyGeneData Version: 1.26.0 Depends: R (>= 2.13.0) Suggests: Biobase, gdata, limma, breastCancerNKI License: Artistic-2.0 MD5sum: f79a5b674497a5b11a044ec86673a1a6 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 Maintainer: Luigi Marchionni URL: http://luigimarchionni.org/breastTSP.html git_url: https://git.bioconductor.org/packages/seventyGeneData git_branch: RELEASE_3_12 git_last_commit: 6f93804 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/seventyGeneData_1.26.0.tar.gz vignettes: vignettes/seventyGeneData/inst/doc/seventyGeneData.pdf vignetteTitles: Working with the seventyGeneData package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/seventyGeneData/inst/doc/seventyGeneData.R dependencyCount: 0 Package: shinyMethylData Version: 1.10.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: e201fa0f3ea58fcfb78a5b3183748ca8 NeedsCompilation: no Title: Example dataset of input data for shinyMethyl Description: Extracted data from 369 TCGA Head and Neck Cancer DNA methylation samples. The extracted data serve as an example dataset for the package shinyMethyl. Original samples are from 450k methylation arrays, and were obtained from The Cancer Genome Atlas (TCGA). 310 samples are from tumor, 50 are matched normals and 9 are technical replicates of a control cell line. biocViews: Genome, CancerData Author: Jean-Philippe Fortin [cre, aut], Kasper Daniel Hansen [aut] Maintainer: Jean-Philippe Fortin git_url: https://git.bioconductor.org/packages/shinyMethylData git_branch: RELEASE_3_12 git_last_commit: 47df22d git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/shinyMethylData_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: shinyMethyl dependencyCount: 0 Package: signatureSearchData Version: 1.4.0 Depends: R (>= 3.6) Imports: ExperimentHub, utils, affy, limma, Biobase, magrittr, dplyr, R.utils, stats, signatureSearch, rhdf5 Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 638bec4cef7d3195b0effb863d68f52e 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 , Thomas Girke Maintainer: Yuzhu Duan VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/signatureSearchData git_branch: RELEASE_3_12 git_last_commit: 6e452bf git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/signatureSearchData_1.4.0.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 dependencyCount: 166 Package: simpIntLists Version: 1.26.0 License: GPL (>= 2) MD5sum: d655210439afa09dab079e3efe24a04d NeedsCompilation: no Title: The package contains BioGRID interactions for various organisms in a simple format Description: The package contains BioGRID interactions for arabidopsis(thale cress), c.elegans, fruit fly, human, mouse, yeast( budding yeast ) and S.pombe (fission yeast) . Entrez ids, official names and unique ids can be used to find proteins. The format of interactions are lists. For each gene/protein, there is an entry in the list with "name" containing name of the gene/protein and "interactors" containing the list of genes/proteins interacting with it. biocViews: ExperimentData, Arabidopsis_thaliana_Data Author: Kircicegi Korkmaz, Volkan Atalay, Rengul Cetin-Atalay Maintainer: Kircicegi Korkmaz git_url: https://git.bioconductor.org/packages/simpIntLists git_branch: RELEASE_3_12 git_last_commit: 11e24c3 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/simpIntLists_1.26.0.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 suggestsMe: GeneNetworkBuilder dependencyCount: 0 Package: Single.mTEC.Transcriptomes Version: 1.18.0 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 License: LGPL MD5sum: dc96320ac09f9b5816d9cb0a70419d9b NeedsCompilation: no Title: Single Cell Transcriptome Data and Analysis of Mouse mTEC cells Description: This data package contains the code used to analyse the single-cell RNA-seq and the bulk ATAC-seq data from the manuscript titled: Single-cell transcriptome analysis reveals coordinated ectopic-gene expression patterns in medullary thymic epithelial cells. This paper was published in Nature Immunology 16,933-941(2015). The data objects provided in this package has been pre-processed: the raw data files can be downloaded from ArrayExpress under the accession identifiers E-MTAB-3346 and E-MTAB-3624. The vignette of this data package provides a documented and reproducible workflow that includes the code that was used to generate each statistic and figure from the manuscript. biocViews: ExperimentData Author: Alejandro Reyes Maintainer: Alejandro Reyes VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/Single.mTEC.Transcriptomes git_branch: RELEASE_3_12 git_last_commit: f6ad28b git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/Single.mTEC.Transcriptomes_1.18.0.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: 1.2.4 Depends: R (>= 4.0.0), MultiAssayExperiment Imports: AnnotationHub, BiocFileCache, BiocGenerics, ExperimentHub, HCAMatrixBrowser, HDF5Array, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, Matrix, methods, utils Suggests: knitr, scran License: Artistic-2.0 MD5sum: 2f13c8eebf694b3a36d1d2b5f8f56e08 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. The current focus is on datasets that use new technologies such as scNMT and scM&T. biocViews: ExperimentData, SingleCellData, ReproducibleResearch, ExperimentHub, GEO Author: Marcel Ramos [aut, cre] (), Ricard Argelaguet [aut], Dario Righelli [aut], Kelly Eckenrode [aut], Levi Waldron [aut] Maintainer: Marcel Ramos VignetteBuilder: knitr BugReports: https://github.com/waldronlab/SingleCellMultiModal/issues git_url: https://git.bioconductor.org/packages/SingleCellMultiModal git_branch: RELEASE_3_12 git_last_commit: de087cd git_last_commit_date: 2021-01-22 Date/Publication: 2021-01-28 source.ver: src/contrib/SingleCellMultiModal_1.2.4.tar.gz vignettes: vignettes/SingleCellMultiModal/inst/doc/CITEseq.html, vignettes/SingleCellMultiModal/inst/doc/ECCITEseq.html, vignettes/SingleCellMultiModal/inst/doc/PBMC.html, vignettes/SingleCellMultiModal/inst/doc/scNMT.html, vignettes/SingleCellMultiModal/inst/doc/SCoPE2.html, vignettes/SingleCellMultiModal/inst/doc/seqFISH.html vignetteTitles: CITEseq Cord Blood, ECCITEseq Peripheral Blood, PBMC 10x multiome, scNMT Mouse Gastrulation, SCoPE2: macrophage vs monocytes, seqFISH Mouse Visual Cortex 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/PBMC.R, vignettes/SingleCellMultiModal/inst/doc/scNMT.R, vignettes/SingleCellMultiModal/inst/doc/SCoPE2.R, vignettes/SingleCellMultiModal/inst/doc/seqFISH.R dependencyCount: 110 Package: SNAData Version: 1.36.0 Depends: R (>= 2.4.0), graph Suggests: Rgraphviz License: LGPL MD5sum: b37133b8d98bd2e5b3e9f5dde1d9b746 NeedsCompilation: no Title: Social Networks Analysis Data Examples Description: Data from Wasserman & Faust (1999) "Social Network Analysis" biocViews: ExperimentData Author: Denise Scholtens Maintainer: Denise Scholtens git_url: https://git.bioconductor.org/packages/SNAData git_branch: RELEASE_3_12 git_last_commit: fc0ef6a git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/SNAData_1.36.0.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: 1.26.0 Depends: R (>= 2.6.0) Suggests: ALL, hgu95av2.db, SNAGEE License: Artistic-2.0 MD5sum: 9951bf260fe26f22b0c69b704e13cccf NeedsCompilation: no Title: SNAGEE data Description: SNAGEE data - gene list and correlation matrix biocViews: MicroarrayData Author: David Venet Maintainer: David Venet URL: http://fleming.ulb.ac.be/SNAGEE git_url: https://git.bioconductor.org/packages/SNAGEEdata git_branch: RELEASE_3_12 git_last_commit: e4e0b31 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/SNAGEEdata_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: SNAGEE dependencyCount: 0 Package: SNPhoodData Version: 1.20.0 Depends: R (>= 3.2) Suggests: BiocStyle,knitr,rmarkdown License: LGPL (>= 3) MD5sum: 3fa7b5d70c31be14b6864b7993dd6ce4 NeedsCompilation: no Title: Additional and more complex example data for the SNPhood package Description: This companion package for SNPhood provides some example datasets of a larger size than allowed for the SNPhood package. They include full and real-world examples for performing analyses with the SNPhood package. biocViews: ExperimentData Author: Christian Arnold, Judith Zaugg Maintainer: Christian Arnold VignetteBuilder: knitr BugReports: christian.arnold@embl.de git_url: https://git.bioconductor.org/packages/SNPhoodData git_branch: RELEASE_3_12 git_last_commit: 233b829 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/SNPhoodData_1.20.0.tar.gz vignettes: vignettes/SNPhoodData/inst/doc/SNPhoodData.html vignetteTitles: The *SNPhoodData* package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: SNPhood dependencyCount: 0 Package: SomatiCAData Version: 1.28.0 Depends: R (>= 2.14) License: Artistic-2.0 MD5sum: 0e95d82bf6efb7d3208ea5bf74ef888a NeedsCompilation: no Title: An example cancer whole genome sequencing data for the SomatiCA package Description: An example cancer whole genome sequencing data for the SomatiCA package biocViews: ExperimentData, Genome, CancerData, SequencingData Author: Mengjie Chen Maintainer: Mengjie Chen git_url: https://git.bioconductor.org/packages/SomatiCAData git_branch: RELEASE_3_12 git_last_commit: 1aba49c git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/SomatiCAData_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: SomaticCancerAlterations Version: 1.26.0 Depends: R (>= 3.0.0) Imports: GenomicRanges, exomeCopy, stringr, IRanges, S4Vectors Suggests: testthat, ggbio, ggplot2, knitr License: GPL-3 MD5sum: 01eab508abaff3a3500479b8bfa82c05 NeedsCompilation: no Title: Somatic Cancer Alterations Description: Collection of somatic cancer alteration datasets biocViews: ExperimentData, Genome, CancerData, Project1000genomes, NCI Author: Julian Gehring (EMBL Heidelberg) Maintainer: Julian Gehring VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/SomaticCancerAlterations git_branch: RELEASE_3_12 git_last_commit: e6b9385 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/SomaticCancerAlterations_1.26.0.tar.gz vignettes: vignettes/SomaticCancerAlterations/inst/doc/SomaticCancerAlterations-html.html vignetteTitles: SomaticCancerAlterations - HTML hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SomaticCancerAlterations/inst/doc/SomaticCancerAlterations-html.R suggestsMe: SomaticSignatures dependencyCount: 34 Package: spatialLIBD Version: 1.2.1 Depends: SingleCellExperiment, R (>= 3.6) Imports: shiny, golem, ggplot2, cowplot, plotly, viridisLite, shinyWidgets, Polychrome, sessioninfo, grid, grDevices, methods, AnnotationHub, utils, png, scater, DT, ExperimentHub, RColorBrewer, SummarizedExperiment, stats, graphics, S4Vectors, IRanges, fields, benchmarkme, SpatialExperiment, BiocFileCache, jsonlite, tibble, readbitmap Suggests: knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager License: Artistic-2.0 MD5sum: 5d1f8b2ef147899634e29e036ec077f7 NeedsCompilation: no Title: LIBD Visium spatial transcriptomics human pilot data inspector Description: Inspect interactively the spatial transcriptomics 10x Genomics Visium data from Maynard, Collado-Torres et al, 2020 analyzed by Lieber Institute for Brain Development researchers and collaborators. biocViews: Homo_sapiens_Data, ExperimentHub, SequencingData, SingleCellData, ExpressionData, Tissue, PackageTypeData Author: Leonardo Collado-Torres [aut, cre] (), Kristen R. Maynard [ctb] (), Andrew E. Jaffe [ctb] (), Brenda Pardo [ctb] () Maintainer: Leonardo Collado-Torres URL: https://github.com/LieberInstitute/spatialLIBD VignetteBuilder: knitr BugReports: https://support.bioconductor.org/t/spatialLIBD git_url: https://git.bioconductor.org/packages/spatialLIBD git_branch: RELEASE_3_12 git_last_commit: a78c6d3 git_last_commit_date: 2020-12-17 Date/Publication: 2020-12-21 source.ver: src/contrib/spatialLIBD_1.2.1.tar.gz vignettes: vignettes/spatialLIBD/inst/doc/spatialLIBD.html vignetteTitles: Introduction to spatialLIBD hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/spatialLIBD/inst/doc/spatialLIBD.R suggestsMe: BayesSpace dependencyCount: 196 Package: SpikeIn Version: 1.32.0 Depends: R (>= 1.6), affy (>= 1.23.4) License: Artistic-2.0 MD5sum: 0a55a618bef51e548e2201d3fa8d7fe8 NeedsCompilation: no Title: Affymetrix Spike-In Experiment Data Description: Contains the HGU133 and HGU95 spikein experiment data. biocViews: ExperimentData, MicroarrayData Author: Rafael Irizarry Maintainer: Rafael A. Irizarry git_url: https://git.bioconductor.org/packages/SpikeIn git_branch: RELEASE_3_12 git_last_commit: 07cde8e git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/SpikeIn_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PECA dependencyCount: 13 Package: SpikeInSubset Version: 1.30.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5), affy (>= 1.23.4) License: LGPL MD5sum: 8d161157f44ae59e5e95e8be8fef2b68 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: Rafael A. Irizarry git_url: https://git.bioconductor.org/packages/SpikeInSubset git_branch: RELEASE_3_12 git_last_commit: 7628919 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/SpikeInSubset_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: logitT dependencyCount: 13 Package: spqnData Version: 1.2.0 Depends: R (>= 4.0), SummarizedExperiment License: Artistic-2.0 MD5sum: 60ab50fa06b3eb5014ce6e19cc7e6422 NeedsCompilation: no Title: Data for the spqn package Description: Bulk RNA-seq from GTEx on 4,000 randomly selected, expressed genes. Data has been processed for co-expression analysis. biocViews: Homo_sapiens_Data, ExpressionData, Tissue, RNASeqData Author: Yi Wang [cre, aut], Kasper Daniel Hansen [aut] Maintainer: Yi Wang git_url: https://git.bioconductor.org/packages/spqnData git_branch: RELEASE_3_12 git_last_commit: 09e8a13 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/spqnData_1.2.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: spqn dependencyCount: 26 Package: stemHypoxia Version: 1.26.0 Depends: R (>= 2.14.1) License: GPL (>=2) MD5sum: 3fb87ef5cdeaddd8553e2ed31066f7d9 NeedsCompilation: no Title: Differentiation of Human Embryonic Stem Cells under Hypoxia gene expression dataset by Prado-Lopez et al. (2010) Description: Expression profiling using microarray technology to prove if 'Hypoxia Promotes Efficient Differentiation of Human Embryonic Stem Cells to Functional Endothelium' by Prado-Lopez et al. (2010) Stem Cells 28:407-418. Full data available at Gene Expression Omnibus series GSE37761. biocViews: ExperimentData, Tissue, StemCell, Homo_sapiens_Data, CancerData, MicroarrayData, TissueMicroarrayData, GEO Author: Cristobal Fresno and Elmer A. Fernandez Maintainer: Cristobal Fresno URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37761, http://onlinelibrary.wiley.com/doi/10.1002/stem.295/abstract git_url: https://git.bioconductor.org/packages/stemHypoxia git_branch: RELEASE_3_12 git_last_commit: 66be421 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/stemHypoxia_1.26.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: lmdme dependencyCount: 0 Package: stjudem Version: 1.30.0 Depends: R (>= 2.10), utils License: LGPL (>= 2) MD5sum: 020817d16c315fc572f13d1145861702 NeedsCompilation: no Title: Microarray Data from Yeoh et al. in MACAT format Description: This is a microarray data set on acute lymphoblastic leukemia, published in 2002 (Yeoh et al.Cancer Cell 2002). The experiments were conducted in the St.Jude Children's Research Hospital, Memphis, Tenessee, USA. The raw data was preprocessed by variance stabilizing normalization (Huber et al.) on probe and subsequent summarization of probe expression values into probe set expression values using median polish. biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData, ChipOnChipData Author: Benjamin Georgi, Matthias Heinig, Sebastian Schmeier, Joern Toedling Maintainer: Joern Toedling git_url: https://git.bioconductor.org/packages/stjudem git_branch: RELEASE_3_12 git_last_commit: fefa5d7 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/stjudem_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: macat dependencyCount: 1 Package: SVM2CRMdata Version: 1.22.0 Depends: R(>= 3.2.0) License: LGPL (>= 2) MD5sum: b6da6180ff95e623d6f9637f874d8ad4 NeedsCompilation: no Title: An example dataset for use with the SVM2CRM package Description: An example dataset for use with the SVM2CRM package. biocViews: ExperimentData, ChIPSeq, HistoneModification, Preprocessing, DataImport Author: Guidantonio Malagoli Tagliazucchi Maintainer: Guidantonio Malagoli Tagliazucchi git_url: https://git.bioconductor.org/packages/SVM2CRMdata git_branch: RELEASE_3_12 git_last_commit: 0309604 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/SVM2CRMdata_1.22.0.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: synapterdata Version: 1.28.0 Depends: R (>= 2.10), synapter (>= 1.99.2) Imports: utils License: GPL-2 MD5sum: a2be9b10dcda1e3f3c41ec9c797b8438 NeedsCompilation: no Title: Data accompanying the synapter package Description: Data independant acquisition of UPS1 protein mix in an E. coli background obtained on a Waters Synapt G2 instrument. biocViews: ExperimentData, MassSpectrometryData Author: Laurent Gatto, Sebastian Gibb and Pavel V. Shliaha Maintainer: Laurent Gatto git_url: https://git.bioconductor.org/packages/synapterdata git_branch: RELEASE_3_12 git_last_commit: 08f1c73 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/synapterdata_1.28.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: synapter, RforProteomics dependencyCount: 101 Package: systemPipeRdata Version: 1.18.2 Depends: methods Imports: BiocGenerics, jsonlite, remotes Suggests: RUnit, BiocStyle, knitr, rmarkdown, systemPipeR License: Artistic-2.0 MD5sum: 89ff9c9ff7ef9d4a1101b1019b181e71 NeedsCompilation: no Title: systemPipeRdata: Workflow templates and sample data Description: systemPipeRdata is a helper package to generate with a single command NGS workflow templates that are intended to be used by its parent package systemPipeR. The latter is an environment for building end-to-end analysis pipelines with automated report generation for next generation sequence (NGS) applications such as RNA-Seq, RIBO-Seq, ChIP-Seq, VAR-Seq and many others. Detailed examples for using systemPipeRdata are given in systemPipeR's overview vignette. biocViews: Genetics, Infrastructure, DataImport, Sequencing, RNASeq, ChIPSeq, MethylSeq, SNP, GeneExpression, Coverage, GeneSetEnrichment, Alignment, QualityControl, ImmunoOncology, RiboSeq, WorkflowStep Author: Thomas Girke Maintainer: Thomas Girke URL: https://github.com/tgirke/systemPipeRdata VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/systemPipeRdata git_branch: RELEASE_3_12 git_last_commit: 38a38e3 git_last_commit_date: 2021-05-01 Date/Publication: 2021-05-03 source.ver: src/contrib/systemPipeRdata_1.18.2.tar.gz vignettes: 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: 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: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: 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 importsMe: RNASeqR suggestsMe: systemPipeR, systemPipeShiny dependencyCount: 9 Package: TabulaMurisData Version: 1.8.0 Depends: R (>= 3.5) Imports: ExperimentHub, utils Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran, scater, iSEE, testthat License: MIT + file LICENSE MD5sum: 594d805f9c6d0f27d27c387bfd9009d4 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] () Maintainer: Charlotte Soneson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TabulaMurisData git_branch: RELEASE_3_12 git_last_commit: 03b050d git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/TabulaMurisData_1.8.0.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: 77 Package: TargetScoreData Version: 1.26.0 Suggests: TargetScore, gplots License: GPL-2 MD5sum: 31e4471f23f72d785dd56ef323748780 NeedsCompilation: no Title: TargetScoreData Description: Precompiled and processed miRNA-overexpression fold-changes from 84 Gene Expression Omnibus (GEO) series corresponding to 6 platforms, 77 human cells or tissues, and 113 distinct miRNAs. Accompanied with the data, we also included in this package the sequence feature scores from TargetScanHuman 6.1 including the context+ score and the probabilities of conserved targeting for each miRNA-mRNA interaction. Thus, the user can use these static sequence-based scores together with user-supplied tissue/cell-specific fold-change due to miRNA overexpression to predict miRNA targets using the package TargetScore (download separately) biocViews: ExperimentData, RNASeqData, miRNAData Author: Yue Li Maintainer: Yue Li git_url: https://git.bioconductor.org/packages/TargetScoreData git_branch: RELEASE_3_12 git_last_commit: db41481 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/TargetScoreData_1.26.0.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: 1.28.0 License: GPL (>= 2) MD5sum: a747a8e44a7cddeacc2074a375776b65 NeedsCompilation: no Title: Example GC-MS data for TargetSearch Package Description: This package provides example GC-MS data for TargetSearch Package. biocViews: ExperimentData, Escherichia_coli_Data Author: Alvaro Cuadros-Inostroza, Henning Redestig, Matt Hannah Maintainer: Alvaro Cuadros-Inostroza git_url: https://git.bioconductor.org/packages/TargetSearchData git_branch: RELEASE_3_12 git_last_commit: 98d93e0 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/TargetSearchData_1.28.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: TargetSearch dependencyCount: 0 Package: tartare Version: 1.4.0 Depends: R (>= 3.6), AnnotationHub (>= 2.16), ExperimentHub (>= 1.0) Imports: utils Suggests: BiocStyle, knitr, testthat, tools License: GPL-3 MD5sum: 5a72965c07427ac22bf8eb4d200a1b6e NeedsCompilation: no Title: Raw ground spectra recorded on Thermo Fisher Scientific mass spectrometers Description: provides raw files (size=278MBytes) 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 rawDiag package (Trachsel, 2018 ) and the Spectra MsBackends. biocViews: ExperimentData, MassSpectrometryData, ExperimentHub Author: Christian Panse [aut, cre] (), Tobias Kockmann [aut] () Maintainer: Christian Panse URL: https://github.com/cpanse/tartare VignetteBuilder: knitr BugReports: https://github.com/cpanse/tartare/issues git_url: https://git.bioconductor.org/packages/tartare git_branch: RELEASE_3_12 git_last_commit: fafd789 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/tartare_1.4.0.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 dependencyCount: 77 Package: TBX20BamSubset Version: 1.26.0 Depends: Rsamtools (>= 1.9.8) Imports: xtable License: LGPL MD5sum: 1998a04cdc3472b7a00471bf2efbb539 NeedsCompilation: no Title: Subset of BAM files from the "TBX20" experiment Description: Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. A subset of the RNA-Seq data. biocViews: ExperimentData, SequencingData, RNASeqData Author: D. Bindreither Maintainer: D. Bindreither git_url: https://git.bioconductor.org/packages/TBX20BamSubset git_branch: RELEASE_3_12 git_last_commit: 4d093dd git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/TBX20BamSubset_1.26.0.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: APAlyzer dependencyCount: 30 Package: TCGAbiolinksGUI.data Version: 1.10.0 Depends: R (>= 3.5.0) Suggests: BiocStyle, knitr, readr, DT License: GPL-3 MD5sum: bb7f8eb16b13e00ec659e4719c42cceb NeedsCompilation: no Title: Data for the TCGAbiolinksGUI package Description: Supporting data for the TCGAbiolinksGUI package. biocViews: AssayDomainData, TechnologyData, OrganismData Author: Tiago Chedraoui Silva Maintainer: Tiago Chedraoui Silva URL: https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data VignetteBuilder: knitr BugReports: https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data/issues git_url: https://git.bioconductor.org/packages/TCGAbiolinksGUI.data git_branch: RELEASE_3_12 git_last_commit: c5c0e4c git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/TCGAbiolinksGUI.data_1.10.0.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 dependsOnMe: TCGAbiolinksGUI importsMe: TCGAbiolinks dependencyCount: 0 Package: TCGAcrcmiRNA Version: 1.10.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: bcf3267c998bce384b1294b76803600d NeedsCompilation: no Title: TCGA CRC 450 miRNA dataset Description: colorectal cancer miRNA profile provided by TCGA biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/TCGAcrcmiRNA git_branch: RELEASE_3_12 git_last_commit: ec8776b git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/TCGAcrcmiRNA_1.10.0.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: 1.10.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 60f50f5dfe358d4bfd393daeca07aaf4 NeedsCompilation: no Title: TCGA CRC 450 mRNA dataset Description: colorectal cancer mRNA profile provided by TCGA biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/TCGAcrcmRNA git_branch: RELEASE_3_12 git_last_commit: 9ad8507 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/TCGAcrcmRNA_1.10.0.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: 1.26.0 License: GPL-2 MD5sum: 7212b9155400bcb2ac808e36cb57f238 NeedsCompilation: no Title: The Cancer Genome Atlas Illumina 450k methylation example data Description: The Cancer Genome Atlas (TCGA) is applying genomics technologies to over 20 different types of cancer. This package contains a small set of 450k array data in idat format. biocViews: Genome, CancerData, MethylationArrayData Author: Sean Davis Maintainer: Sean Davis git_url: https://git.bioconductor.org/packages/TCGAMethylation450k git_branch: RELEASE_3_12 git_last_commit: c182148 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/TCGAMethylation450k_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: methylumi dependencyCount: 0 Package: tcgaWGBSData.hg19 Version: 1.8.0 Depends: R (>= 3.5.0), ExperimentHub Imports: bsseq, knitr License: GPL-2 MD5sum: 0491742975afb83b01f8cd5a4c60c241 NeedsCompilation: no Title: Data Description: Data package for WGBS Data in TCGA. Data is stored as SummarizedExperiment Format. See vignette on how to extract the data and perform differential methylation analysis. biocViews: Genome, SequencingData, ExperimentData, Homo_sapiens_Data, CancerData Author: Divy Kangeyan Maintainer: Divy Kangeyan VignetteBuilder: knitr BugReports: https://github.com/aryeelab/tcgaWGBSData.hg19/issues git_url: https://git.bioconductor.org/packages/tcgaWGBSData.hg19 git_branch: RELEASE_3_12 git_last_commit: 8a8967a git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/tcgaWGBSData.hg19_1.8.0.tar.gz vignettes: vignettes/tcgaWGBSData.hg19/inst/doc/tcgaWGBSData.hg19.html vignetteTitles: Vignette Title hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tcgaWGBSData.hg19/inst/doc/tcgaWGBSData.hg19.R dependencyCount: 135 Package: TCGAWorkflowData Version: 1.14.0 Depends: R (>= 3.5.0) Imports: SummarizedExperiment Suggests: knitr, rmarkdown, pander, testthat License: GPL-3 MD5sum: 7322a7c134fe9c97e2e860ec8885ecf0 NeedsCompilation: no Title: Data for TCGA Workflow Description: This experimental data package contains 11 data sets necessary to follow the "TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages". biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData, CancerData Author: Tiago Chedraoui Silva Maintainer: Tiago Chedraoui Silva URL: https://f1000research.com/articles/5-1542/v2 VignetteBuilder: knitr BugReports: https://github.com/BioinformaticsFMRP/TCGAWorkflow/issues git_url: https://git.bioconductor.org/packages/TCGAWorkflowData git_branch: RELEASE_3_12 git_last_commit: c2b1aa3 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/TCGAWorkflowData_1.14.0.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 importsMe: TCGAWorkflow dependencyCount: 26 Package: TENxBrainData Version: 1.10.0 Depends: SingleCellExperiment, HDF5Array Imports: AnnotationHub (>= 2.9.22), ExperimentHub Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel, data.table License: CC BY 4.0 MD5sum: e085743f73d5fada27265ce1956f4286 NeedsCompilation: no Title: Data from the 10X 1.3 Million Brain Cell Study Description: Single-cell RNA-seq data for 1.3 million brain cells from E18 mice, generated by 10X Genomics. biocViews: SequencingData, RNASeqData, ExpressionData, SingleCellData Author: Aaron Lun [aut], Martin Morgan [aut], Bioconductor Package Maintainer [cre] Maintainer: Bioconductor Package Maintainer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TENxBrainData git_branch: RELEASE_3_12 git_last_commit: b17ec93 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/TENxBrainData_1.10.0.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: HDF5Array dependencyCount: 96 Package: TENxBUSData Version: 1.4.0 Imports: ExperimentHub, AnnotationHub, utils, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle License: BSD_2_clause + file LICENSE MD5sum: 845b21dc544617f8e05677225fc41762 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] () Maintainer: Lambda Moses URL: https://github.com/BUStools/TENxBUSData VignetteBuilder: knitr BugReports: https://github.com/BUStools/TENxBUSData/issues git_url: https://git.bioconductor.org/packages/TENxBUSData git_branch: RELEASE_3_12 git_last_commit: 6c30472 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/TENxBUSData_1.4.0.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: 77 Package: TENxPBMCData Version: 1.8.0 Depends: SingleCellExperiment, HDF5Array Imports: AnnotationHub, ExperimentHub Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel License: CC BY 4.0 MD5sum: b4fadbce37bf648c02a3626fc755349c 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, SingleCellData Author: Kasper D. Hansen [aut], Davide Risso [aut], Stephanie Hicks [aut, cre] Maintainer: Stephanie Hicks VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TENxPBMCData git_branch: RELEASE_3_12 git_last_commit: 5f34edd git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/TENxPBMCData_1.8.0.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 importsMe: singleCellTK suggestsMe: celda, ExperimentSubset, fcoex, glmGamPoi, iSEE, mbkmeans, schex, scry dependencyCount: 96 Package: timecoursedata Version: 1.0.0 Depends: R (>= 4.0), SummarizedExperiment Suggests: testthat (>= 1.0.0), knitr, rmarkdown, covr, BiocStyle License: BSD 3-clause License + file LICENSE MD5sum: ed81142a31e819fb0fab8140ae5cd8a1 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] (), Nelle Varoquaux [aut, cre] () Maintainer: Nelle Varoquaux VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/timecoursedata git_branch: RELEASE_3_12 git_last_commit: 337b3bd git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/timecoursedata_1.0.0.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: 26 Package: TimerQuant Version: 1.20.0 Depends: shiny Imports: ggplot2, grid, gridExtra, deSolve, dplyr, locfit Suggests: BiocStyle, reshape2, knitr, shinyBS License: Artistic-2.0 MD5sum: 2e01e61900332c9c245f0b8d704194b7 NeedsCompilation: no Title: Timer Quantification Description: Supplementary Data package for tandem timer methods paper by Barry et al. (2015) including TimerQuant shiny applications. biocViews: ExperimentData, Danio_rerio_Data, HighThroughputImagingData, Tissue Author: Joseph Barry Maintainer: Joseph Barry VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TimerQuant git_branch: RELEASE_3_12 git_last_commit: 7757f9d git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/TimerQuant_1.20.0.tar.gz vignettes: vignettes/TimerQuant/inst/doc/genPaperFigures.pdf, vignettes/TimerQuant/inst/doc/mathematicalDerivations.pdf vignetteTitles: Supplementary Methods - automatic generation of paper figures, Supplementary Methods - mathematical derivations hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TimerQuant/inst/doc/genPaperFigures.R, vignettes/TimerQuant/inst/doc/mathematicalDerivations.R dependencyCount: 65 Package: tinesath1cdf Version: 1.28.0 License: Artistic-2.0 MD5sum: 5fe7aec027da2e8e73f3a15828f59759 NeedsCompilation: no Title: tinesath1cdf Description: A package containing an environment represeting the newcdf/tinesATH1.cdf.cdf file. biocViews: Arabidopsis_thaliana_Data, ChipOnChipData Author: Tine Casneuf Maintainer: Tine Casneuf git_url: https://git.bioconductor.org/packages/tinesath1cdf git_branch: RELEASE_3_12 git_last_commit: 790d139 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/tinesath1cdf_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: XhybCasneuf dependencyCount: 0 Package: tinesath1probe Version: 1.28.0 Depends: R (>= 1.6), AnnotationDbi (>= 1.11.9) License: LGPL MD5sum: f3ac30fde273358f9a68faa36aad58dd NeedsCompilation: no Title: Probe sequence data for microarrays of type tinesath1 Description: This package was automatically created by package matchprobes version 1.4.0. The probe sequence data was obtained from http://www.affymetrix.com. biocViews: Arabidopsis_thaliana_Data, SequencingData, MicroarrayData Author: The Bioconductor Project www.bioconductor.org Maintainer: Tine Casneuf git_url: https://git.bioconductor.org/packages/tinesath1probe git_branch: RELEASE_3_12 git_last_commit: 71e5153 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/tinesath1probe_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 26 Package: tissueTreg Version: 1.10.0 Depends: R (>= 3.5) Suggests: BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq, SummarizedExperiment License: GPL (>= 2) MD5sum: 3b1721e4047f6446069ce776038636cd NeedsCompilation: no Title: TWGBS and RNA-seq data from tissue T regulatory cells from mice Description: The package provides ready to use epigenomes (obtained from TWGBS) and transcriptomes (RNA-seq) from various tissues as obtained in the study (Delacher and Imbusch 2017, PMID: 28783152). Regulatory T cells (Treg cells) perform two distinct functions: they maintain self-tolerance, and they support organ homeostasis by differentiating into specialized tissue Treg cells. The underlying dataset characterises the epigenetic and transcriptomic modifications for specialized tissue Treg cells. biocViews: ExperimentData, Tissue, Mus_musculus_Data, SequencingData, RNASeqData Author: Charles Imbusch [aut, cre], Michael Delacher [aut], Markus Feuerer [aut], Benedikt Brors [aut] Maintainer: Charles Imbusch URL: https://github.com/cimbusch/tissueTreg VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tissueTreg git_branch: RELEASE_3_12 git_last_commit: d504da1 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/tissueTreg_1.10.0.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: 1.0.1 Depends: R (>= 4.0), SingleCellExperiment Imports: methods, Matrix Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 950a8242d2704ac4eadf0c190c3111fd NeedsCompilation: no Title: A Collection of Tumour Microenvironment Single-cell RNA Sequencing Datasets and Correspodnding 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], Parisa Shooshtari [aut] Maintainer: Erik Christensen VignetteBuilder: knitr BugReports: https://github.com/shooshtarilab/TMExplorer/issues git_url: https://git.bioconductor.org/packages/TMExplorer git_branch: RELEASE_3_12 git_last_commit: e19400c git_last_commit_date: 2021-01-13 Date/Publication: 2021-01-14 source.ver: src/contrib/TMExplorer_1.0.1.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: 27 Package: tofsimsData Version: 1.18.0 Depends: R (>= 3.2.0) Suggests: knitr, rmarkdown, tools License: GPL-3 MD5sum: 0d50184b61ff71003b1244abaa08d5a9 NeedsCompilation: no Title: Import, process and analysis of ToF-SIMS imaging data Description: This packages contains data to be used with the 'tofsims' package. biocViews: ExperimentData, MassSpectrometry, ImagingMassSpectrometry, DataImport Author: Lorenz Gerber, Viet Mai Hoang Maintainer: Lorenz Gerber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tofsimsData git_branch: RELEASE_3_12 git_last_commit: 73360be git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/tofsimsData_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: tofsims dependencyCount: 0 Package: topdownrdata Version: 1.12.0 Depends: topdownr License: GPL (>= 3) MD5sum: c47120469cb5ca3c8a436edbc3f853da 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://github.com/sgibb/topdownrdata/ BugReports: https://github.com/sgibb/topdownrdata/issues/ git_url: https://git.bioconductor.org/packages/topdownrdata git_branch: RELEASE_3_12 git_last_commit: e045a19 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/topdownrdata_1.12.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: topdownr dependencyCount: 78 Package: tweeDEseqCountData Version: 1.28.0 Depends: Biobase, R (>= 2.10) License: GPL (>=2) MD5sum: 7b1928bf23ebda984f9a537c9ba43535 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: Juan R Gonzalez and Mikel Esnaola (with contributions from Robert Castelo ) Maintainer: Juan R Gonzalez URL: http://www.creal.cat/jrgonzalez/software.htm git_url: https://git.bioconductor.org/packages/tweeDEseqCountData git_branch: RELEASE_3_12 git_last_commit: 197ce26 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/tweeDEseqCountData_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSAR, missMethyl, tweeDEseq dependencyCount: 7 Package: tximportData Version: 1.18.0 Suggests: knitr License: GPL (>= 2) MD5sum: 8cd06bd336aedef19f19fd75615c92e8 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. For details on version numbers, sample information, and details on calls, see the package vignette. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tximportData git_branch: RELEASE_3_12 git_last_commit: 24945f8 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/tximportData_1.18.0.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 suggestsMe: DESeq2, fishpond, HumanTranscriptomeCompendium, tximeta, tximport, variancePartition dependencyCount: 0 Package: VariantToolsData Version: 1.14.0 Depends: R (>= 2.10), VariantAnnotation (>= 1.7.35) Imports: BiocGenerics, GenomicRanges Suggests: VariantTools (>= 1.3.4), gmapR (>= 1.3.3), BiocStyle License: Artistic-2.0 MD5sum: 943b64e4ff261fe355a02a4a1b6eaa60 NeedsCompilation: no Title: Data for the VariantTools tutorial Description: Data from the sequencing of a 50/50 mixture of HapMap trio samples NA12878 (CEU) and NA19240 (YRI), subset to the TP53 region. biocViews: ExperimentData, SequencingData, HapMap, SNPData Author: Michael Lawrence Maintainer: Michael Lawrence git_url: https://git.bioconductor.org/packages/VariantToolsData git_branch: RELEASE_3_12 git_last_commit: 882b063 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/VariantToolsData_1.14.0.tar.gz vignettes: vignettes/VariantToolsData/inst/doc/intro.pdf vignetteTitles: VariantTools Example Data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/VariantToolsData/inst/doc/intro.R dependencyCount: 90 Package: vulcandata Version: 1.12.0 Imports: utils License: LGPL-3 MD5sum: ad53e1b94cd41c14df136d8ba7eb250a NeedsCompilation: no Title: VirtUaL ChIP-Seq data Analysis using Networks, dummy dataset Description: This package provides a dummy regulatory network and ChIP-Seq dataset for running examples in the vulcan package biocViews: ExperimentData, Homo_sapiens_Data, CancerData, ChIPSeqData Author: Federico M. Giorgi, Andrew N. Holding, Florian Markowetz Maintainer: Federico M. Giorgi git_url: https://git.bioconductor.org/packages/vulcandata git_branch: RELEASE_3_12 git_last_commit: 4e5dc2c git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/vulcandata_1.12.0.tar.gz vignettes: vignettes/vulcandata/inst/doc/vulcandata.pdf vignetteTitles: Vulcan: VirtUaL ChIP-Seq Analysis through Networks,, dummy datasets hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/vulcandata/inst/doc/vulcandata.R suggestsMe: vulcan dependencyCount: 1 Package: waveTilingData Version: 1.26.0 Depends: R (>= 2.14.0) License: GPL (>= 2) MD5sum: b52fb120bef93cb2dfca4493f2728957 NeedsCompilation: no Title: waveTiling Example Data Description: Experiment and Annotation Data files used by the examples / vignette in the waveTiling package biocViews: ExperimentData, Arabidopsis_thaliana_Data, MicroarrayData Author: Kristof De Beuf Maintainer: Kristof De Beuf PackageStatus: Deprecated git_url: https://git.bioconductor.org/packages/waveTilingData git_branch: RELEASE_3_12 git_last_commit: 4b0dba0 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/waveTilingData_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: WES.1KG.WUGSC Version: 1.22.0 License: GPL-2 MD5sum: 33e3d778c0da4283cb15eccca2fe72b5 NeedsCompilation: no Title: Whole Exome Sequencing (WES) of chromosome 22 401st to 500th exon from the 1000 Genomes (1KG) Project by the Washington University Genome Sequencing Center (WUGSC). Description: The assembled .bam files of whole exome sequencing data from the 1000 Genomes Project. 46 samples sequenced by the Washington University Genome Sequencing Center are included. biocViews: ExperimentData, Project1000genomes, SequencingData, DNASeqData, Homo_sapiens_Data Author: Yuchao Jiang, Nancy R. Zhang Maintainer: Yuchao Jiang git_url: https://git.bioconductor.org/packages/WES.1KG.WUGSC git_branch: RELEASE_3_12 git_last_commit: f341ebe git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/WES.1KG.WUGSC_1.22.0.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: 1.2.0 Depends: R (>= 3.6.0), GenomicRanges License: GPL-2 MD5sum: 150eaf7f0cf8a38f9f4eeea6c1d77894 NeedsCompilation: no Title: Mappability tracks of Whole-genome Sequencing from the ENCODE Project Description: This package provides whole-genome mappability tracks on human hg19/hg38 assembly. We employed the 100-mers mappability track from the ENCODE Project and computed weighted average of the mappability scores if multiple ENCODE regions overlap with the same bin. “Blacklist” bins, including segmental duplication regions and gaps in reference assembly from telomere, centromere, and/or heterochromatin regions are included. The dataset consists of three assembled .bam files of single-cell whole genome sequencing from 10X for illustration purposes. biocViews: ExperimentData, SequencingData, DNASeqData, SingleCellData, Homo_sapiens_Data, Genome, ENCODE Author: Rujin Wang Maintainer: Rujin Wang git_url: https://git.bioconductor.org/packages/WGSmapp git_branch: RELEASE_3_12 git_last_commit: 51622c7 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/WGSmapp_1.2.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: SCOPE dependencyCount: 17 Package: XhybCasneuf Version: 1.28.0 Depends: R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf , RColorBrewer , methods, grid License: Artistic-2.0 MD5sum: 06021f1c339927f0417d2eb228368700 NeedsCompilation: no Title: EBI/PSB cross-hybridisation study package Description: Cross-hybridisation study on the ATH1 Affymetrix GeneChip biocViews: ExperimentData, Tissue, MicroarrayData, TissueMicroarrayData Author: Tineke Casneuf Maintainer: Tineke Casneuf git_url: https://git.bioconductor.org/packages/XhybCasneuf git_branch: RELEASE_3_12 git_last_commit: db88792 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/XhybCasneuf_1.28.0.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: 36 Package: yeastCC Version: 1.30.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 4ffe10f0fecf43d1e888704d295b294e NeedsCompilation: no Title: Spellman et al. (1998) and Pramila/Breeden (2006) yeast cell cycle microarray data Description: ExpressionSet for Spellman et al. (1998) yeast cell cycle microarray experiment biocViews: ExperimentData, CellCulture, Saccharomyces_cerevisiae_Data, CancerData, MicroarrayData, OneChannelData, GEO Author: Sandrine Dudoit Maintainer: Sandrine Dudoit git_url: https://git.bioconductor.org/packages/yeastCC git_branch: RELEASE_3_12 git_last_commit: a34138a git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/yeastCC_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: LiquidAssociation suggestsMe: fastLiquidAssociation, ibh dependencyCount: 7 Package: yeastExpData Version: 0.36.0 Depends: R (>= 2.4), graph (>= 1.9.26) Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db License: GPL MD5sum: b761c451ec244671fc5ad1ff20464bbd NeedsCompilation: no Title: Yeast Experimental Data Description: A collection of different sets of experimental data from yeast. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data Author: R. Gentleman Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/yeastExpData git_branch: RELEASE_3_12 git_last_commit: 76d3d55 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/yeastExpData_0.36.0.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: BiocCaseStudies, ClusterJudge, ppiStats dependencyCount: 8 Package: yeastGSData Version: 0.28.0 License: Artistic-2.0 MD5sum: b23b5a8c2896b2c614069d45bc4c533a NeedsCompilation: no Title: Yeast Gold Standard Data Description: A collection of so-called gold (and other) standard data sets biocViews: ExperimentData, Saccharomyces_cerevisiae_Data Author: R. Gentleman Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/yeastGSData git_branch: RELEASE_3_12 git_last_commit: aa208a7 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/yeastGSData_0.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: yeastNagalakshmi Version: 1.26.0 License: Artistic-2.0 MD5sum: 8bbfff7430c654e9546aecaa4b3b0e9f NeedsCompilation: no Title: Yeast genome RNA sequencing data based on Nagalakshmi et. al. Description: The yeast genome data was retrieved from the sequence read archive, aligned with bwa, and converted to BAM format with samtools. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, SequencingData, BiocViews, ChIPSeqData Author: Martin Morgan Maintainer: Bioconductor Package Maintainer git_url: https://git.bioconductor.org/packages/yeastNagalakshmi git_branch: RELEASE_3_12 git_last_commit: 5f4bcd1 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/yeastNagalakshmi_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ShortRead dependencyCount: 0 Package: yeastRNASeq Version: 0.28.0 Depends: R (>= 2.4) Suggests: Biobase, ShortRead, IRanges License: GPL MD5sum: 4e3ca6ed952a67f0c652fac815525db7 NeedsCompilation: no Title: Yeast RNA-Seq Experimental Data from Lee et al. 2008 Description: A selection of RNA-Seq data from a yeast transcriptome experiment. biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData Author: James H. Bullard and Kasper D. Hansen Maintainer: J. Bullard git_url: https://git.bioconductor.org/packages/yeastRNASeq git_branch: RELEASE_3_12 git_last_commit: 2a96d83 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/yeastRNASeq_0.28.0.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: yri1kgv Version: 0.32.0 Depends: GGBase Imports: Biobase License: Artistic-2.0 MD5sum: 6ef0871237bcd859a0b87adbae5aaf4e NeedsCompilation: no Title: expression + genotype on 79 unrelated YRI individuals Description: expression + genotype on 79 unrelated YRI individuals biocViews: ArrayExpress Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/yri1kgv git_branch: RELEASE_3_12 git_last_commit: 622195e git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/yri1kgv_0.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: eQTL dependencyCount: 60 Package: yriMulti Version: 0.19.0 Depends: Homo.sapiens, geuvPack, MultiAssayExperiment (>= 1.3.14) Imports: GenomicFiles (>= 1.13.6), VariantAnnotation (>= 1.23.1), gQTLBase, SummarizedExperiment, GenomicRanges, dsQTL, GenomeInfoDb Suggests: erma, BiocStyle, knitr, rmarkdown, gQTLstats (>= 1.9.2), doParallel, geuvPack, knitcitations, bibtex License: Artistic-2.0 MD5sum: 1be47b590d01aa030ffae8e32754c23b NeedsCompilation: no Title: support for expression, methylation, DHS, VCF for YRI Description: expression, methylation, DHS for YRI Author: VJ Carey Maintainer: VJ Carey VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/yriMulti git_branch: master git_last_commit: 5558af5 git_last_commit_date: 2020-04-27 Date/Publication: 2020-04-30 source.ver: src/contrib/yriMulti_0.19.0.tar.gz vignettes: vignettes/yriMulti/inst/doc/yriMulti.pdf vignetteTitles: yriMulti -- HapMap YRI population,, multiassay interfaces hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/yriMulti/inst/doc/yriMulti.R dependencyCount: 129 Package: zebrafishRNASeq Version: 1.10.0 Depends: R (>= 2.10) Suggests: BiocStyle, knitr License: GPL MD5sum: 9c4a233f00916d399030cc394ec174f4 NeedsCompilation: no Title: Zebrafish RNA-Seq Experimental Data from Ferreira et al. (2014) Description: Gene-level read counts from RNA-Seq for gallein-treated and control zebrafish. biocViews: ExperimentData, Danio_rerio_Data, RNASeqData Author: Davide Risso Maintainer: Davide Risso VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/zebrafishRNASeq git_branch: RELEASE_3_12 git_last_commit: 5f95ce3 git_last_commit_date: 2020-10-27 Date/Publication: 2020-10-29 source.ver: src/contrib/zebrafishRNASeq_1.10.0.tar.gz vignettes: vignettes/zebrafishRNASeq/inst/doc/preprocessing.pdf 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: FunciSNP.data Version: 1.26.0 Depends: R (>= 2.14.0), IRanges Imports: rtracklayer License: GPL-3 Title: Various data sets for use with the FunciSNP package Description: Data sets needed for FunciSNP to integrate information from GWAS, 1000genomes and chromatin feature, in order to identify functional SNP in coding or non-coding regions. biocViews: SNPData, Project1000genomes, ENCODE Author: Simon G. Coetzee and Houtan Noushmehr, PhD Maintainer: Simon G. Coetzee URL: http://coetzeeseq.usc.edu/publication/Coetzee_SG_et_al_2012/ PackageStatus: Deprecated Package: Mulder2012 Version: 0.30.0 Depends: R (>= 2.14), org.Hs.eg.db, KEGG.db Imports: igraph, HTSanalyzeR, PANR, RedeR, pvclust, MASS Suggests: snow License: Artistic-2.0 Title: Predicting functional networks and modules of chromatin factors controlling adult stem cell fate from RNA interference screens Description: This package provides functions to reproduce results and figures in Mulder K. et. al. published in Nature Cell Biology 2012 and Wang X. et. al. published in PLoS Computational Biology 2012. biocViews: StemCell, CancerData Author: Xin Wang , Florian Markowetz Maintainer: Xin Wang PackageStatus: Deprecated