Package: adductData Version: 1.29.0 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: 481d6b88c7d4190d192cdd1b1c1cc3f0 NeedsCompilation: no Title: Data from untargeted MS of modifications to Cys34 of serum albumin Description: mzXML files from Grigoryan et al 2016 (Anal Chem). biocViews: ExperimentData,MassSpectrometryData,ExperimentHub Author: Josie Hayes Maintainer: Josie Hayes VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/adductData git_branch: devel git_last_commit: ce0c4f7 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/adductData_1.29.0.tar.gz vignettes: vignettes/adductData/inst/doc/adductData.html vignetteTitles: Raw mzXML data using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/adductData/inst/doc/adductData.R dependencyCount: 65 Package: affycompData Version: 1.51.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp License: GPL (>= 2) MD5sum: 9d4698577948a6f340d2c4e261cb4928 NeedsCompilation: no Title: affycomp data Description: Data needed by the affycomp package. biocViews: MicroarrayData Author: Rafael A. Irizarry and Zhijin Wu with contributions from Simon Cawley Maintainer: Robert D Shear URL: https://bioconductor.org/packages/affycompData BugReports: https://github.com/rafalab/affyCompData/issues git_url: https://git.bioconductor.org/packages/affycompData git_branch: devel git_last_commit: a10f998 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/affycompData_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: affycomp dependencyCount: 8 Package: affydata Version: 1.61.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Imports: methods Suggests: hgu95av2cdf, hgu133acdf License: GPL (>= 2) MD5sum: 05f9cc2fcee187e77527302a1fbc45f6 NeedsCompilation: no Title: Affymetrix Data for Demonstration Purpose Description: Example datasets of a slightly large size. They represent 'real world examples', unlike the artificial examples included in the package affy. biocViews: ExperimentData, Tissue, MicroarrayData, TissueMicroarrayData Author: Laurent Gautier Maintainer: Robert D Shear URL: https://bioconductor.org/packages/affydata BugReports: https://github.com/rafalab/affydata/issues git_url: https://git.bioconductor.org/packages/affydata git_branch: devel git_last_commit: d3df454 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/affydata_1.61.0.tar.gz vignettes: vignettes/affydata/inst/doc/affydata.pdf vignetteTitles: affydata primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/affydata/inst/doc/affydata.R dependsOnMe: affyContam suggestsMe: affy, affyPLM, arrayMvout, Biostrings, gcrma, Harman, mimager, puma, pvac, TurboNorm, vsn dependencyCount: 12 Package: Affyhgu133A2Expr Version: 1.49.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 5a024895eee1c175fd08c0862a3691e3 NeedsCompilation: no Title: Affymetrix Human Genome U133A 2.0 Array (GPL571) Expression Data Package Description: Contains pre-built human (GPL571) databases of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133A2Expr git_branch: devel git_last_commit: f0c221f git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/Affyhgu133A2Expr_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: Affyhgu133aExpr Version: 1.51.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 1515585affa3c8cbb0d8f0face1b24fd NeedsCompilation: no Title: Affymetrix Human hgu133a Array (GPL96) Expression Data Package Description: Contains pre-built human (GPL96) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133aExpr git_branch: devel git_last_commit: 17ee22b git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/Affyhgu133aExpr_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: Affyhgu133Plus2Expr Version: 1.47.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 357a5550eba04d3f29bdd1aff7a69bbf NeedsCompilation: no Title: Affyhgu133Plus2Expr (GPL570) Expression Data Package Description: Contains pre-built human (GPL570) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133Plus2Expr git_branch: devel git_last_commit: 2322455 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/Affyhgu133Plus2Expr_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: AffymetrixDataTestFiles Version: 0.51.0 Depends: R (>= 2.5.0) License: LGPL-2.1 MD5sum: 92ef276370f4ee98db4b4ebbb6fb7529 NeedsCompilation: no Title: Affymetrix Data Files (CEL, CDF, CHP, EXP, PGF, PSI) for Testing Description: This package contains annotation data files and sample data files of Affymetrix file formats. The files originate from the Affymetrix' Fusion SDK distribution and other official sources. biocViews: ExperimentData, MicroarrayData Author: Henrik Bengtsson [aut, cre], James Bullard [aut], Kasper Daniel Hansen [aut] Maintainer: Henrik Bengtsson git_url: https://git.bioconductor.org/packages/AffymetrixDataTestFiles git_branch: devel git_last_commit: 3241be0 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/AffymetrixDataTestFiles_0.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: affxparser, affyILM, aroma.affymetrix dependencyCount: 0 Package: Affymoe4302Expr Version: 1.51.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: f697bc0c26a0d41227a6b44dde32709b NeedsCompilation: no Title: Affymetrix Mouse Genome 430 2.0 Array (GPL1261) Expression Data Package Description: Contains pre-built mouse (GPL1261) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Mus_musculus_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affymoe4302Expr git_branch: devel git_last_commit: 49103ec git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/Affymoe4302Expr_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: airway Version: 1.33.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: knitr, GEOquery, markdown License: LGPL MD5sum: 9abde008ca08c4739fe423356e79d064 NeedsCompilation: no Title: RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014 Description: This package provides a RangedSummarizedExperiment object of read counts in genes for an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. Details on the gene model and read counting procedure are provided in the package vignette. The citation for the experiment is: Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri R Jr, Tantisira KG, Weiss ST, Lu Q. 'RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells.' PLoS One. 2014 Jun 13;9(6):e99625. PMID: 24926665. GEO: GSE52778. biocViews: ExperimentData, SequencingData, RNASeqData, GEO Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/airway git_branch: devel git_last_commit: 806179e git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/airway_1.33.0.tar.gz vignettes: vignettes/airway/inst/doc/airway.html vignetteTitles: Airway smooth muscle cells hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/airway/inst/doc/airway.R dependsOnMe: rnaseqGene importsMe: NetActivity suggestsMe: apeglm, awst, BioCor, carnation, CeTF, DelayedArray, DESeq2, DNEA, dominatR, EnhancedVolcano, ExperimentSubset, funOmics, geyser, gg4way, IHW, InteractiveComplexHeatmap, iSEEde, iSEEpathways, iSEEu, MLInterfaces, OPWeight, pathwayPCA, PCAtools, plyxp, ReducedExperiment, Rvisdiff, scToppR, SummarizedExperiment, tidybulk, tidyprint, tidySummarizedExperiment, TTMap, VISTA, weitrix, XAItest, IHWpaper, RegParallel, seqgendiff dependencyCount: 25 Package: ALL Version: 1.55.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Suggests: rpart License: Artistic-2.0 MD5sum: 84d034264d8a17c6ac88ebdd1c26c08e NeedsCompilation: no Title: A data package Description: Data of T- and B-cell Acute Lymphocytic Leukemia from the Ritz Laboratory at the DFCI (includes Apr 2004 versions) biocViews: ExperimentData, CancerData, LeukemiaCancerData Author: Xiaochun Li Maintainer: Robert Gentleman git_url: https://git.bioconductor.org/packages/ALL git_branch: devel git_last_commit: c705298 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ALL_1.55.0.tar.gz vignettes: vignettes/ALL/inst/doc/ALLintro.pdf vignetteTitles: ALL data intro hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ALL/inst/doc/ALLintro.R importsMe: ConsensusClusterPlus suggestsMe: a4, a4Base, a4Classif, a4Preproc, Biobase, BioNet, CellMapper, ChromHeatMap, clipper, esetVis, genefilter, GeneSelectMMD, graphite, GSAR, GSEAlm, MLInterfaces, npGSEA, pathRender, rScudo, SNAGEE, topGO, SNAGEEdata, MMDvariance, nlcv dependencyCount: 7 Package: ALLMLL Version: 1.53.0 Depends: R (>= 2.10), affy (>= 1.23.4) License: GPL-2 MD5sum: 1b7c993a1bc8e959adc07c991b3e2a14 NeedsCompilation: no Title: A subset of arrays from a large acute lymphoblastic leukemia (ALL) study Description: This package provides probe-level data for 20 HGU133A and 20 HGU133B arrays which are a subset of arrays from a large ALL study. The data is for the MLL arrays. This data was published in Mary E. Ross, Xiaodong Zhou, Guangchun Song, Sheila A. Shurtleff, Kevin Girtman, W. Kent Williams, Hsi-Che Liu, Rami Mahfouz, Susana C. Raimondi, Noel Lenny, Anami Patel, and James R. Downing (2003) Classification of pediatric acute lymphoblastic leukemia by gene expression profiling Blood 102: 2951-2959 biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData Author: B. M. Bolstad git_url: https://git.bioconductor.org/packages/ALLMLL git_branch: devel git_last_commit: c02b4ee git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ALLMLL_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQualityMetrics, pvac dependencyCount: 12 Package: AmpAffyExample Version: 1.53.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Suggests: hgu133acdf License: LGPL (>= 2) MD5sum: 73e76127d2dc1149ba7c61df991f2ea9 NeedsCompilation: no Title: Example of Amplified Data Description: Six arrays. Three from amplified RNA, three from the typical procedure. biocViews: ExperimentData, MicroarrayData Author: Rafael A. Irizarry Maintainer: Robert D Shear URL: https://bioconductor.org/packages/AmpAffyExample BugReports: https://github.com/rafalab/AmpAffyExample/issues git_url: https://git.bioconductor.org/packages/AmpAffyExample git_branch: devel git_last_commit: f102229 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/AmpAffyExample_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: AffyRNADegradation dependencyCount: 12 Package: antiProfilesData Version: 1.49.0 Depends: Biobase, Suggests: frma, GEOquery, GEOmetadb License: Artistic-2.0 MD5sum: d17baaf2d68846412db2b5f99b9acb0d NeedsCompilation: no Title: Normal colon and cancer preprocessed affy data for antiProfile building. Description: Colon normal tissue and cancer samples used in Corrada Bravo, et al. gene expression anti-profiles paper: BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272. Measurements are z-scores obtained from the GeneExpression Barcode in the 'frma' package biocViews: ExperimentData, MicroarrayData, Tissue, CancerData, ColonCancerData Author: Hector Corrada Bravo, Matthew McCall and Rafael A. Irizarry Maintainer: Hector Corrada Bravo git_url: https://git.bioconductor.org/packages/antiProfilesData git_branch: devel git_last_commit: f2dab5c git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/antiProfilesData_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: antiProfiles, epivizr, epivizrChart, messina dependencyCount: 7 Package: aracne.networks Version: 1.39.0 Depends: R (>= 3.3), viper License: file LICENSE MD5sum: 9cf075976460c9f6593359eb7ff9c34f NeedsCompilation: no Title: ARACNe-inferred gene networks from TCGA tumor datasets Description: This package contains ARACNe-inferred networks from TCGA tumor datasets. It also contains a function to export them into plain-text format. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData Author: Federico M. Giorgi Maintainer: Federico M. Giorgi , Mariano Alvarez git_url: https://git.bioconductor.org/packages/aracne.networks git_branch: devel git_last_commit: ccb820f git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/aracne.networks_1.39.0.tar.gz vignettes: vignettes/aracne.networks/inst/doc/aracne.networks.pdf vignetteTitles: Using aracne.networks hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/aracne.networks/inst/doc/aracne.networks.R dependencyCount: 88 Package: ARRmData Version: 1.49.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: 61dff3440f23f322bdacbf749aff60ec NeedsCompilation: no Title: Example dataset for normalization of Illumina 450k Methylation data Description: Raw Beta values from 36 samples across 3 groups from Illumina 450k methylation arrays biocViews: ExperimentData, MethylationArrayData Author: Jean-Philippe Fortin, Celia M.T. Greenwood, Aurelie Labbe Maintainer: Jean-Philippe Fortin git_url: https://git.bioconductor.org/packages/ARRmData git_branch: devel git_last_commit: 359b678 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ARRmData_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ARRmNormalization dependencyCount: 0 Package: AshkenazimSonChr21 Version: 1.43.0 Suggests: knitr, VariantAnnotation License: Artistic-2.0 MD5sum: 9192e7c51c87b37955bac954751c0c72 NeedsCompilation: no Title: Annotated variants on the chromosome 21, human genome 19, Ashkenazim Trio son sample Description: SonVariantsChr21 is a dataset of annotated genomic variants coming from Complete Genomics whole genome sequencing. Data comes from GIAB project, Ashkenazim Trio, sample HG002 run 1. Both vcf and annotated data frame are provided. biocViews: GenomicVariation, Sequencing, WholeGenome Author: Tomasz Stokowy Maintainer: Who to complain to VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/AshkenazimSonChr21 git_branch: devel git_last_commit: 8bd87c5 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/AshkenazimSonChr21_1.43.0.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: 1.33.0 Depends: R (>= 3.5) Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 698915dcf1f381a117ece2efb78f6382 NeedsCompilation: no Title: Example of 1D NMR spectra data for ASICS package Description: 1D NMR example spectra and additional data for use with the ASICS package. Raw 1D Bruker spectral data files were found in the MetaboLights database (https://www.ebi.ac.uk/metabolights/, study MTBLS1). biocViews: ExperimentData, Homo_sapiens_Data Author: Gaëlle Lefort [aut, cre], Rémi Servien [aut], Nathalie Villa-Vialaneix [aut] Maintainer: Gaëlle Lefort VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ASICSdata git_branch: devel git_last_commit: a4b6bb4 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ASICSdata_1.33.0.tar.gz vignettes: vignettes/ASICSdata/inst/doc/ASICSdata.html vignetteTitles: ASICSdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: AssessORFData Version: 1.31.0 Depends: R (>= 3.5.0), RSQLite (>= 1.1) Imports: DECIPHER, utils Suggests: AssessORF, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 2f5d834fedb379fcc41a1b900435a687 NeedsCompilation: no Title: Data and Files for the AssessORF Package Description: This package provides access to mapping and results objects generated by the AssessORF package, as well as the genome sequences for the strains corresponding to those objects. biocViews: OrganismData, Bacillus_subtilis_Data, Escherichia_coli_Data, Pseudomonas_aeruginosa_Data, Staphylococcus_aureus_Data, Genome, Proteome, SequencingData Author: Deepank Korandla [aut], Nicholas Cooley [cre] (ORCID: ) Maintainer: Nicholas Cooley VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/AssessORFData git_branch: devel git_last_commit: e6d5433 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/AssessORFData_1.31.0.tar.gz vignettes: vignettes/AssessORFData/inst/doc/AssessORFDataGuide.pdf vignetteTitles: Using AssessORFData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/AssessORFData/inst/doc/AssessORFDataGuide.R suggestsMe: AssessORF dependencyCount: 31 Package: AWAggregatorData Version: 1.3.0 Depends: ExperimentHub Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: d960de26e389722317bece9ce2562003 NeedsCompilation: no Title: Attribute-Weighted Aggregation Data Description: The AWAggregatorData package contains the data associated with the AWAggregator R package. It includes two pre-trained random forest models, one incorporating the average coefficient of variation as a feature, and the other one not including it. It also contains the PSMs in Benchmark Set 1~3 derived from the psm.tsv output files generated by FragPipe, which are used to train the random forest models. biocViews: ExperimentData, PackageTypeData, ExperimentHub, MassSpectrometryData, Proteome Author: Jiahua Tan [aut, cre] (ORCID: ), Gian L. Negri [aut] (ORCID: ), Gregg B. Morin [aut] (ORCID: ), David D. Y. Chen [aut] (ORCID: ) Maintainer: Jiahua Tan URL: https://github.com/Tan-Jiahua/AWAggregatorData VignetteBuilder: knitr BugReports: https://github.com/Tan-Jiahua/AWAggregatorData/issues git_url: https://git.bioconductor.org/packages/AWAggregatorData git_branch: devel git_last_commit: 1ef37b1 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/AWAggregatorData_1.3.0.tar.gz vignettes: vignettes/AWAggregatorData/inst/doc/AWAggregatorData-vignette.html vignetteTitles: AWAggregatorData vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/AWAggregatorData/inst/doc/AWAggregatorData-vignette.R suggestsMe: AWAggregator dependencyCount: 64 Package: bcellViper Version: 1.49.0 Depends: R(>= 2.14.0), Biobase, methods License: GPL (>=2) MD5sum: 6d0080f21791b23d70acc7d791987d8a NeedsCompilation: no Title: Human B-cell transcriptional interactome and normal human B-cell expression data Description: This package provides a human B-cell context-specific transcriptional regulatory network and a human normal B-cells dataset for the examples in package viper. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData Author: Mariano Javier Alvarez Maintainer: Mariano Javier Alvarez git_url: https://git.bioconductor.org/packages/bcellViper git_branch: devel git_last_commit: d59c388 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/bcellViper_1.49.0.tar.gz vignettes: vignettes/bcellViper/inst/doc/bcellViper.pdf vignetteTitles: Using bcellViper hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bcellViper/inst/doc/bcellViper.R suggestsMe: GenomicSuperSignature, pageRank, viper dependencyCount: 7 Package: beadarrayExampleData Version: 1.51.0 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>= 2.0.0) License: GPL-2 MD5sum: b8b8d313863f5387b82a525676ed7065 NeedsCompilation: no Title: Example data for the beadarray package Description: An small dataset that can be used to run examples from the beadarray vignette and examples biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/beadarrayExampleData git_branch: devel git_last_commit: a4db882 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/beadarrayExampleData_1.51.0.tar.gz vignettes: vignettes/beadarrayExampleData/inst/doc/beadarrayExampleData.pdf vignetteTitles: beadarrayExampleData: example data for the beadarray package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/beadarrayExampleData/inst/doc/beadarrayExampleData.R suggestsMe: beadarray, MiRaGE dependencyCount: 66 Package: BeadArrayUseCases Version: 1.51.0 Imports: beadarray (>= 2.3.18), limma, GEOquery Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db License: GPL-2 MD5sum: 44b1dd7d2d91113261ca93e6e00d3ecb NeedsCompilation: no Title: Analysing Illumina BeadArray expression data using Bioconductor Description: Example data files and use cases for processing Illumina BeadArray expression data using Bioconductor biocViews: MicroarrayData Author: Mark Dunning, Wei Shi, Andy Lynch, Mike Smith, Matt Ritchie Maintainer: Mike Smith git_url: https://git.bioconductor.org/packages/BeadArrayUseCases git_branch: devel git_last_commit: 3bc582d git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/BeadArrayUseCases_1.51.0.tar.gz vignettes: vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.pdf vignetteTitles: BeadArrayUseCases.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.R dependencyCount: 100 Package: BeadSorted.Saliva.EPIC Version: 1.21.0 Depends: R (>= 4.1), minfi(>= 1.36.0), ExperimentHub Suggests: knitr, rmarkdown License: GPL-3 MD5sum: a6a09e99b1f8c24912d5508e9a045e50 NeedsCompilation: no Title: Illumina EPIC data on BeadSorted child saliva cells Description: Raw data objects used to estimate saliva cell proportion estimates in ewastools. The FlowSorted.Saliva.EPIC object is constructed from samples assayed by Lauren Middleton et. al. (2021). biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData, Genome, MethylationArrayData, ExperimentHub Author: Jonah Fisher [aut, cre], Kelly Bakulski [aut], Lauren Middleton [aut] Maintainer: Jonah Fisher VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/BeadSorted.Saliva.EPIC git_branch: devel git_last_commit: 7c910b1 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/BeadSorted.Saliva.EPIC_1.21.0.tar.gz vignettes: vignettes/BeadSorted.Saliva.EPIC/inst/doc/BeadSorted.Saliva.EPIC.html vignetteTitles: BeadSorted.Saliva.EPIC.html hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BeadSorted.Saliva.EPIC/inst/doc/BeadSorted.Saliva.EPIC.R dependencyCount: 152 Package: beta7 Version: 1.51.0 Depends: R (>= 2.4.0), marray License: LGPL MD5sum: 973100550efa4878a1c5d90ef56312ed NeedsCompilation: no Title: Rodriguez et al. (2004) Differential Gene Expression by Memory/Effector T Helper Cells Bearing the Gut-Homing Receptor Integrin alpha4 beta7. Description: Data from 6 gpr files aims to identify differential expressed genes between the beta 7+ and beta 7- memory T helper cells. biocViews: ExperimentData, Homo_sapiens_Data, CGHData, MicroarrayData Author: Jean Yang Maintainer: Jean Yang git_url: https://git.bioconductor.org/packages/beta7 git_branch: devel git_last_commit: c514620 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/beta7_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 8 Package: BioImageDbs Version: 1.21.0 Depends: R (>= 4.1.0) Imports: ExperimentHub, AnnotationHub, markdown, rmarkdown, EBImage, magick, magrittr, filesstrings, animation, einsum Suggests: knitr, BiocStyle, purrr License: Artistic-2.0 MD5sum: eb60b4f97bfc918cd7ef144e65dca77d NeedsCompilation: no Title: Bio- and biomedical imaging dataset for machine learning and deep learning (for ExperimentHub) Description: The package provides a bioimage dataset for the image analysis using machine learning and deep learning. The dataset includes microscopy imaging data with supervised labels. The data is provided as R list data that can be loaded to Keras/tensorflow in R. biocViews: ExperimentHub, ExperimentData, CellCulture, Tissue Author: Satoshi Kume [aut, cre] (ORCID: ), Kozo Nishida [aut] (ORCID: ) Maintainer: Satoshi Kume URL: https://kumes.github.io/BioImageDbs/ VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/BioImageDbs git_branch: devel git_last_commit: 5064eca git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/BioImageDbs_1.21.0.tar.gz vignettes: vignettes/BioImageDbs/inst/doc/BioImageBbs_Datasets.html, vignettes/BioImageDbs/inst/doc/BioImageDbs.html vignetteTitles: The BioImageBbs Datasets, Providing Bioimage Dataset for ExperimentHub hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BioImageDbs/inst/doc/BioImageBbs_Datasets.R, vignettes/BioImageDbs/inst/doc/BioImageDbs.R dependencyCount: 101 Package: BioPlex Version: 1.17.1 Depends: R (>= 4.1.0), SummarizedExperiment Imports: BiocFileCache, GEOquery, graph, methods, utils Suggests: AnnotationDbi, AnnotationHub, BiocStyle, DEXSeq, ExperimentHub, depmap, knitr, rmarkdown License: Artistic-2.0 MD5sum: 663b20c7a205962adb7d529ddf22dbeb NeedsCompilation: no Title: R-side access to BioPlex protein-protein interaction data Description: The BioPlex package implements access to the BioPlex protein-protein interaction networks and related resources from within R. Besides protein-protein interaction networks for HEK293 and HCT116 cells, this includes access to CORUM protein complex data, and transcriptome and proteome data for the two cell lines. Functionality focuses on importing the various data resources and storing them in dedicated Bioconductor data structures, as a foundation for integrative downstream analysis of the data. biocViews: CellCulture, ColonCancerData, ExperimentHub, ExpressionData, GEO, Genome, Homo_sapiens_Data, MassSpectrometryData, Proteome, ReproducibleResearch, RNASeqData Author: Ludwig Geistlinger [aut, cre], Robert Gentleman [aut] Maintainer: Ludwig Geistlinger URL: https://github.com/ccb-hms/BioPlex VignetteBuilder: knitr BugReports: https://github.com/ccb-hms/BioPlex/issues git_url: https://git.bioconductor.org/packages/BioPlex git_branch: devel git_last_commit: 6576d48 git_last_commit_date: 2026-01-26 Date/Publication: 2026-04-21 source.ver: src/contrib/BioPlex_1.17.1.tar.gz vignettes: vignettes/BioPlex/inst/doc/BasicChecks.html, vignettes/BioPlex/inst/doc/BioPlex.html vignetteTitles: 2. Data checks, 1. Data retrieval hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BioPlex/inst/doc/BasicChecks.R, vignettes/BioPlex/inst/doc/BioPlex.R dependencyCount: 85 Package: biotmleData Version: 1.37.0 Depends: R (>= 3.5.0) Suggests: Biobase, SummarizedExperiment License: file LICENSE MD5sum: 127c9e11b91a07e09ff8462b51bc5305 NeedsCompilation: no Title: Example experimental microarray data set for the "biotmle" R package Description: Microarray data (from the Illumina Ref-8 BeadChips platform) and phenotype-level data from an epidemiological investigation of benzene exposure, packaged using "SummarizedExperiemnt", for use as an example with the "biotmle" R package. biocViews: GeneExpression, DifferentialExpression, Sequencing, Microarray, RNASeq Author: Nima Hejazi [aut, cre] Maintainer: Nima Hejazi git_url: https://git.bioconductor.org/packages/biotmleData git_branch: devel git_last_commit: a95c22d git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/biotmleData_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: biotmle dependencyCount: 0 Package: biscuiteerData Version: 1.27.0 Depends: R (>= 4.1.0), ExperimentHub Imports: AnnotationHub, utils, curl, GenomicRanges Suggests: knitr, rmarkdown, markdown License: GPL-3 MD5sum: 6e334afdca2adc791c6f082a05b10b95 NeedsCompilation: no Title: Data Package for Biscuiteer Description: Contains default datasets used by the Bioconductor package biscuiteer. biocViews: ExperimentHub, ExperimentData, Genome, Homo_sapiens_Data Author: Tim Triche, Jr. [aut, cre], Wanding Zhou [aut], Ben Johnson [aut], Jacob Morrison [aut], Lyong Heo [aut] Maintainer: "Jacob Morrison" VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/biscuiteerData git_branch: devel git_last_commit: c4e2658 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/biscuiteerData_1.27.0.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: 65 Package: bladderbatch Version: 1.51.0 Depends: Biobase License: Artistic-2.0 MD5sum: a9bd000e949093294bb9254dfbe45b42 NeedsCompilation: no Title: Bladder gene expression data illustrating batch effects Description: This package contains microarray gene expression data on 57 bladder samples from 5 batches. The data are used as an illustrative example for the sva package. biocViews: ExperimentData, CancerData, MicroarrayData Author: Jeffrey T. Leek Maintainer: Jeffrey T. Leek git_url: https://git.bioconductor.org/packages/bladderbatch git_branch: devel git_last_commit: 51d6b54 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/bladderbatch_1.51.0.tar.gz vignettes: vignettes/bladderbatch/inst/doc/bladderbatch.pdf vignetteTitles: bladderbatchTutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bladderbatch/inst/doc/bladderbatch.R importsMe: RUVcorr suggestsMe: BatchQC, Harman, sva dependencyCount: 7 Package: blimaTestingData Version: 1.33.0 Depends: R(>= 3.0.0) Suggests: blima, beadarray, illuminaHumanv4.db, BiocStyle License: GPL-3 MD5sum: 9ec1baeaa813b2f106428dd73cbf3bfa NeedsCompilation: no Title: Data for testing of the package blima. Description: Experiment data package. The set were prepared using microarray images of human mesenchymal cells treated with various supplements. This package is intended to provide example data to test functionality provided by blima. biocViews: MicroarrayData, ExperimentData, GEO Author: Vojtech Kulvait Maintainer: Vojtech Kulvait URL: https://bitbucket.org/kulvait/blima git_url: https://git.bioconductor.org/packages/blimaTestingData git_branch: devel git_last_commit: c176de3 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/blimaTestingData_1.33.0.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: 1.33.0 Depends: R (>= 3.5.0) Imports: beeswarm, Biobase, DESeq2, devtools, dplyr, ggdendro, ggplot2, glmnet, graphics, grDevices, grid, gtable, ipflasso, methods, RColorBrewer, reshape2, scales, stats, SummarizedExperiment, survival, tibble Suggests: BiocStyle, knitr, rmarkdown, abind, AnnotationDbi, biomaRt, broom, colorspace, cowplot, dendsort, doParallel, foreach, forestplot, genefilter, ggbeeswarm, ggtern, gridExtra, hexbin, limma, magrittr, Matrix, maxstat, nat, org.Hs.eg.db, pheatmap, piano, readxl, Rtsne, tidyr, xtable License: LGPL (>= 3) MD5sum: 20c94ac3dd8f1a68c7faddb7079bdd72 NeedsCompilation: no Title: "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oleś M, Lu J et al. - experimental data and complete analysis Description: The package contains data of the Primary Blood Cancer Encyclopedia (PACE) project together with a complete executable transcript of the statistical analysis and reproduces figures presented in the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oleś M, Lu J et al., J. Clin. Invest. (2018) 128(1):427-445. doi:10.1172/JCI93801. biocViews: ExperimentData, ReproducibleResearch, CancerData, LeukemiaCancerData Author: Małgorzata Oleś, Sascha Dietrich, Junyan Lu, Britta Velten, Andreas Mock, Vladislav Kim, Wolfgang Huber Maintainer: Małgorzata Oleś VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/BloodCancerMultiOmics2017 git_branch: devel git_last_commit: 852576d git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/BloodCancerMultiOmics2017_1.33.0.tar.gz vignettes: vignettes/BloodCancerMultiOmics2017/inst/doc/BloodCancerMultiOmics2017-dataOverview.html, vignettes/BloodCancerMultiOmics2017/inst/doc/BloodCancerMultiOmics2017.html vignetteTitles: BloodCancerMultiOmics2017 - data overview, BloodCancerMultiOmics2017 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BloodCancerMultiOmics2017/inst/doc/BloodCancerMultiOmics2017-dataOverview.R, vignettes/BloodCancerMultiOmics2017/inst/doc/BloodCancerMultiOmics2017.R dependencyCount: 156 Package: bodymapRat Version: 1.29.0 Depends: R (>= 3.6.0), SummarizedExperiment, ExperimentHub Imports: utils Suggests: rmarkdown, knitr, BiocStyle, testthat License: CC BY 4.0 MD5sum: 5c077e89002530e2d965bb233f888d91 NeedsCompilation: no Title: Experimental dataset from the rat BodyMap project Description: This package contains a SummarizedExperiment from the Yu et al. (2013) paper that performed the rat BodyMap across 11 organs and 4 developmental stages. Raw FASTQ files were downloaded and mapped using STAR. Data is available on ExperimentHub as a data package. biocViews: SequencingData, RNASeqData, ExpressionData, ExperimentData, ExperimentHub Author: Stephanie Hicks [aut, cre] (ORCID: ), Kwame Okrah [aut] Maintainer: Stephanie Hicks VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/bodymapRat git_branch: devel git_last_commit: 3be6fa2 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/bodymapRat_1.29.0.tar.gz vignettes: vignettes/bodymapRat/inst/doc/bodymapRat.html vignetteTitles: The bodymapRat data user's guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bodymapRat/inst/doc/bodymapRat.R suggestsMe: qsmooth dependencyCount: 75 Package: breakpointRdata Version: 1.31.0 Depends: R (>= 3.5) Suggests: knitr, BiocStyle, License: file LICENSE MD5sum: 5303b584f178285f06c140d555f96aff NeedsCompilation: no Title: Strand-seq data for demonstration purposes Description: Strand-seq data to demonstrate functionalities of breakpointR package. biocViews: ExperimentData, Homo_sapiens_Data, SequencingData, DNASeqData, Genome, SingleCellData Author: David Porubsky, Aaron Taudt, Ashley Sanders Maintainer: David Porubsky URL: https://github.com/daewoooo/breakpointRdata VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/breakpointRdata git_branch: devel git_last_commit: 2c64e53 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/breakpointRdata_1.31.0.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: 1.51.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 2ca060c17d2725d6b0e2ccbcd0254342 NeedsCompilation: no Title: Gene expression dataset published by Schmidt et al. [2008] (MAINZ). Description: Gene expression data from the breast cancer study published by Schmidt et al. in 2008, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerMAINZ git_branch: devel git_last_commit: 63e1110 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/breastCancerMAINZ_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: DART, genefu dependencyCount: 0 Package: breastCancerNKI Version: 1.51.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 84681a63f2c25e89f6b2f82edfaa60a1 NeedsCompilation: no Title: Genexpression dataset published by van't Veer et al. [2002] and van de Vijver et al. [2002] (NKI). Description: Genexpression data from a breast cancer study published by van't Veer et al. in 2002 and van de Vijver et al. in 2002, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, CGHData, MicroarrayData, OneChannelData, ChipOnChipData Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerNKI git_branch: devel git_last_commit: 94e1974 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/breastCancerNKI_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, SigCheck, seventyGeneData dependencyCount: 0 Package: breastCancerTRANSBIG Version: 1.51.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 203577ae1681ddbd9c2a4027e4c02ef1 NeedsCompilation: no Title: Gene expression dataset published by Desmedt et al. [2007] (TRANSBIG). Description: Gene expression data from a breast cancer study published by Desmedt et al. in 2007, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerTRANSBIG git_branch: devel git_last_commit: 44c0527 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/breastCancerTRANSBIG_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, GSgalgoR dependencyCount: 0 Package: breastCancerUNT Version: 1.51.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: fa4a2a90da801e40ff66c79c014829c9 NeedsCompilation: no Title: Gene expression dataset published by Sotiriou et al. [2007] (UNT). Description: Gene expression data from a breast cancer study published by Sotiriou et al. in 2007, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, TwoChannelData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerUNT git_branch: devel git_last_commit: a892b68 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/breastCancerUNT_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu dependencyCount: 0 Package: breastCancerUPP Version: 1.51.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 7c524832c2e5096d027f161a4346d9cc NeedsCompilation: no Title: Gene expression dataset published by Miller et al. [2005] (UPP). Description: Gene expression data from a breast cancer study published by Miller et al. in 2005, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerUPP git_branch: devel git_last_commit: 07d3f80 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/breastCancerUPP_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, GSgalgoR dependencyCount: 0 Package: breastCancerVDX Version: 1.51.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 1e4ec1617aec1afe8a44bbbdb1d91eb1 NeedsCompilation: no Title: Gene expression datasets published by Wang et al. [2005] and Minn et al. [2007] (VDX). Description: Gene expression data from a breast cancer study published by Wang et al. in 2005 and Minn et al. in 2007, provided as an eSet. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData, BreastCancerData, LungCancerData, MicroarrayData, OneChannelData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerVDX git_branch: devel git_last_commit: d97ce98 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/breastCancerVDX_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: AIMS, DART, genefu dependencyCount: 0 Package: bronchialIL13 Version: 1.51.0 Depends: R(>= 2.10.0), affy (>= 1.23.4) License: GPL-2 MD5sum: 21b52bc7e5d53cb7a557da9e1b0bf040 NeedsCompilation: no Title: time course experiment involving il13 Description: derived from CNMC (pepr.cnmcresearch.org) http://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=95 Human Bronchial Cell line A549 biocViews: ExperimentData, MicroarrayData Author: Vince Carey Maintainer: Vince Carey URL: http://www.biostat.harvard.edu/~carey git_url: https://git.bioconductor.org/packages/bronchialIL13 git_branch: devel git_last_commit: cf3b2f1 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/bronchialIL13_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 12 Package: bsseqData Version: 0.51.0 Depends: R (>= 3.5.0), bsseq (>= 1.16.0) License: Artistic-2.0 MD5sum: 98c4a17246dd5db3de172de78fa19511 NeedsCompilation: no Title: Example whole genome bisulfite data for the bsseq package Description: Example whole genome bisulfite data for the bsseq package biocViews: Genome, CancerData, ColonCancerData, SequencingData Author: Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/bsseqData git_branch: devel git_last_commit: b051d29 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/bsseqData_0.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: bsseq, methylSig dependencyCount: 91 Package: bugphyzz Version: 1.7.1 Depends: R (>= 4.4) Imports: dplyr, utils, purrr, stringr, tidyr, tidyselect, BiocFileCache, httr2, tools, S4Vectors Suggests: DT, forcats, ggplot2, htmltools, knitr, rmarkdown, sessioninfo, testthat, EnrichmentBrowser, MicrobiomeBenchmarkData, mia, stats, rlang, limma, mgsub, methods, readr, crayon, tibble, magrittr, tidytext, BiocStyle License: Artistic-2.0 MD5sum: c320ea89679562d18a394d624fdb6af4 NeedsCompilation: no Title: A harmonized data resource and software for enrichment analysis of microbial physiologies Description: bugphyzz is an electronic database of standardized microbial annotations. It facilitates the creation of microbial signatures based on shared attributes, which are utilized for bug set enrichment analysis. The data also includes annotations imputed with ancestra state reconstruction methods. biocViews: MicrobiomeData, ReproducibleResearch Author: Samuel Gamboa [aut, cre] (ORCID: ), Levi Waldron [aut] (ORCID: ), Kelly Eckenrode [aut], Jonathan Ye [aut], Jennifer Wokaty [aut], NCI [fnd] (GrantNo.: R01CA230551) Maintainer: Samuel Gamboa URL: https://github.com/waldronlab/bugphyzz VignetteBuilder: knitr BugReports: https://github.com/waldronlab/bugphyzz/issues git_url: https://git.bioconductor.org/packages/bugphyzz git_branch: devel git_last_commit: 7b909fe git_last_commit_date: 2026-04-29 Date/Publication: 2026-04-30 source.ver: src/contrib/bugphyzz_1.7.1.tar.gz vignettes: vignettes/bugphyzz/inst/doc/bugphyzz.html, vignettes/bugphyzz/inst/doc/sources.html vignetteTitles: bugphyzz, Sources hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bugphyzz/inst/doc/bugphyzz.R, vignettes/bugphyzz/inst/doc/sources.R dependencyCount: 46 Package: cancerdata Version: 1.51.0 Depends: R (>= 2.10.1), Biobase License: GPL (>= 2) MD5sum: 789c8048d4a39db4d10cf2cacb84ed65 NeedsCompilation: no Title: Development and validation of diagnostic tests from high-dimensional molecular data: Datasets Description: Dataset for the R package cancerclass biocViews: CancerData, MicroarrayData Author: Jan Budczies, Daniel Kosztyla Maintainer: Daniel Kosztyla git_url: https://git.bioconductor.org/packages/cancerdata git_branch: devel git_last_commit: cd39671 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/cancerdata_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: cancerclass dependencyCount: 7 Package: CardinalWorkflows Version: 1.45.0 Depends: R (>= 2.10), Cardinal, methods Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: e71a6e038c1ae6437b84aad8e3f73652 NeedsCompilation: no Title: Datasets and workflows for the Cardinal MSI Description: Datasets and workflows for Cardinal: DESI and MALDI examples including pig fetus, cardinal painting, and human RCC. biocViews: ExperimentData, MassSpectrometryData, ImagingMassSpectrometryData Author: Kylie A. Bemis Maintainer: Kylie A. Bemis VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/CardinalWorkflows git_branch: devel git_last_commit: b44cc41 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/CardinalWorkflows_1.45.0.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: 32 Package: ccdata Version: 1.39.0 Depends: R (>= 3.3) License: MIT + file LICENSE MD5sum: a07f7d69c68c9043c33fade0cbd18c78 NeedsCompilation: no Title: Data for Combination Connectivity Mapping (ccmap) Package Description: This package contains microarray gene expression data generated from the Connectivity Map build 02 and LINCS l1000. The data are used by the ccmap package to find drugs and drug combinations to mimic or reverse a gene expression signature. biocViews: ExperimentData, MicroarrayData, ExpressionData Author: Alex Pickering Maintainer: Alex Pickering git_url: https://git.bioconductor.org/packages/ccdata git_branch: devel git_last_commit: 24e95ee git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ccdata_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: retriever dependencyCount: 0 Package: CCl4 Version: 1.51.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), limma License: Artistic-2.0 MD5sum: af1c0985b7e9775c027eec4ce0c85848 NeedsCompilation: no Title: Carbon Tetrachloride (CCl4) treated hepatocytes Description: NChannelSet for rat hepatocytes treated with Carbon Tetrachloride (CCl4) data from LGC company. biocViews: ExperimentData, Genome, Rattus_norvegicus_Data, MicroarrayData Author: Audrey Kauffmann, Wolfgang Huber Maintainer: Audrey Kauffmann git_url: https://git.bioconductor.org/packages/CCl4 git_branch: devel git_last_commit: d42f3fc git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/CCl4_1.51.0.tar.gz vignettes: vignettes/CCl4/inst/doc/CCl4.pdf vignetteTitles: CCl4 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CCl4/inst/doc/CCl4.R suggestsMe: arrayQualityMetrics dependencyCount: 10 Package: celarefData Version: 1.31.0 Depends: R (>= 3.5.0) Suggests: ExperimentHub, knitr, rmarkdown License: GPL-3 MD5sum: a57cce7741036402b4a19fbdd0d16170 NeedsCompilation: no Title: Processed scRNA data for celaref Vignette - cell labelling by reference Description: This experiment data contains some processed data used in the celaref package vignette. These are publically available datasets, that have been processed by celaref package, and can be manipulated further with it. biocViews: ExperimentData, SingleCellData, ExperimentHub Author: Sarah Williams [aut, cre] Maintainer: Sarah Williams VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/celarefData git_branch: devel git_last_commit: 54cbbbd git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/celarefData_1.31.0.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: 1.23.0 Depends: SummarizedExperiment Imports: utils, methods, Matrix, ExperimentHub, AnnotationHub, AnnotationDbi, S4Vectors, DelayedArray, DelayedMatrixStats, gypsum, alabaster.base, alabaster.matrix, alabaster.se, DBI, RSQLite, jsonlite Suggests: testthat, knitr, rmarkdown, BiocStyle, DT, jsonvalidate, BiocManager, ensembldb License: GPL-3 MD5sum: 0d66e36da68884a223dc3553bf5763f9 NeedsCompilation: no Title: Index of Reference Cell Type Datasets Description: Provides a collection of reference expression datasets with curated cell type labels, for use in procedures like automated annotation of single-cell data or deconvolution of bulk RNA-seq. biocViews: ExperimentHub, ExperimentData, ExpressionData, SequencingData, RNASeqData Author: Dvir Aran [aut], Aaron Lun [aut, cre, cph], Daniel Bunis [aut], Jared Andrews [aut], Friederike Dündar [aut] Maintainer: Aaron Lun URL: https://github.com/LTLA/celldex VignetteBuilder: knitr BugReports: https://support.bioconductor.org/ git_url: https://git.bioconductor.org/packages/celldex git_branch: devel git_last_commit: 4740fc9 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/celldex_1.23.0.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 importsMe: singleCellTK suggestsMe: scDiagnostics, scGraphVerse, SingleR, sketchR, tidySingleCellExperiment dependencyCount: 95 Package: CellMapperData Version: 1.39.0 Depends: ExperimentHub, CellMapper Suggests: BiocStyle License: Artistic-2.0 MD5sum: 9eca8ddcf41f70f14ebdfecfb0bbec3c NeedsCompilation: no Title: Pre-processed data for use with the CellMapper package Description: Experiment data package. Contains microarray data from several large expression compendia that have been pre-processed for use with the CellMapper package. This pre-processed data is recommended for routine searches using the CellMapper package. biocViews: ExperimentData, MicroarrayData, ExpressionData Author: Brad Nelms Maintainer: Brad Nelms git_url: https://git.bioconductor.org/packages/CellMapperData git_branch: devel git_last_commit: e501816 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/CellMapperData_1.39.0.tar.gz vignettes: vignettes/CellMapperData/inst/doc/CellMapperData.pdf vignetteTitles: CellMapperData Introduction hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CellMapperData/inst/doc/CellMapperData.R suggestsMe: CellMapper dependencyCount: 65 Package: cfToolsData Version: 1.11.0 Depends: R (>= 4.3.0) Imports: utils, ExperimentHub Suggests: BiocStyle, knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0) License: file LICENSE MD5sum: 22164af0740f75129698ca0c72918c78 NeedsCompilation: no Title: ExperimentHub data for the cfTools package Description: The cfToolsData package supplies the data for the cfTools package. It contains two pre-trained deep neural network (DNN) models for the cfSort function. Additionally, it includes the shape parameters of beta distribution characterizing methylation markers associated with four tumor types for the CancerDetector function, as well as the parameters characterizing methylation markers specific to 29 primary human tissue types for the cfDeconvolve function. biocViews: ExperimentHub, ExperimentData, ReproducibleResearch, DiseaseModel, CancerData, Tissue Author: Ran Hu [aut, cre] (ORCID: ), Shuo Li [aut] (ORCID: ), Xianghong Jasmine Zhou [aut] (ORCID: ), Wenyuan Li [aut] (ORCID: ) Maintainer: Ran Hu URL: https://github.com/jasminezhoulab/cfToolsData VignetteBuilder: knitr BugReports: https://github.com/jasminezhoulab/cfToolsData/issues git_url: https://git.bioconductor.org/packages/cfToolsData git_branch: devel git_last_commit: 7ac0856 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/cfToolsData_1.11.0.tar.gz vignettes: vignettes/cfToolsData/inst/doc/cfToolsData.html vignetteTitles: cfToolsData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/cfToolsData/inst/doc/cfToolsData.R importsMe: cfTools dependencyCount: 64 Package: ChAMPdata Version: 2.45.0 Depends: R (>= 3.5.0), GenomicRanges (>= 1.22.4), BiocGenerics (>= 0.16.1) License: GPL-3 MD5sum: 08a82f8d6ab82e7798aa060f47425731 NeedsCompilation: no Title: Data Packages for ChAMP package Description: Provides datasets needed for ChAMP including a test dataset and blood controls for CNA analysis. biocViews: ExperimentData Author: Yuan Tian [ctb,aut], Tiffany Morris [cre,aut], Lee Stirling [ctb] and Andrew Teschendorff [ctb] Maintainer: Yuan Tian git_url: https://git.bioconductor.org/packages/ChAMPdata git_branch: devel git_last_commit: 5956fab git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ChAMPdata_2.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: methyLImp2 dependencyCount: 11 Package: ChimpHumanBrainData Version: 1.51.0 Depends: affy,qvalue,limma,hexbin,statmod Suggests: hgu95av2cdf License: MIT MD5sum: 7e6cae4de6b2d3715d622584844ca705 NeedsCompilation: no Title: Chimp and human brain data package Description: This data package contains chimp and human brain data extracted from the ArrayExpress accession E-AFMX-2. Both human and chimp RNAs were run on human hgu95av2 Affymetrix arrays. It is a useful dataset for tutorials. biocViews: Tissue, Homo_sapiens_Data, Pan_troglodytes_Data, MicroarrayData, TissueMicroarrayData, GEO Author: Roman Jaksik, Naomi Altman, and Sean Davis Maintainer: Sean Davis git_url: https://git.bioconductor.org/packages/ChimpHumanBrainData git_branch: devel git_last_commit: fcca614 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ChimpHumanBrainData_1.51.0.tar.gz vignettes: vignettes/ChimpHumanBrainData/inst/doc/DiffExpressVignette.pdf vignetteTitles: DiffExpressVignette.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ChimpHumanBrainData/inst/doc/DiffExpressVignette.R dependencyCount: 43 Package: ChIPDBData Version: 1.3.0 Imports: ExperimentHub Suggests: knitr, rmarkdown, BiocStyle, AnnotationHub, TFEA.ChIP, DESeq2, testthat (>= 3.0.0) License: GPL-3 MD5sum: ea2db42e5413dac21377081b1386e74e NeedsCompilation: no Title: ChIP-seq Target Databases for TFEA.ChIP Description: Provides curated gene target databases derived from ChIP-seq datasets, formatted as ChIPDB objects for use with TFEA.ChIP. biocViews: ExperimentData, ExperimentHub, Homo_sapiens_Data, ENCODE, SequencingData Author: Yosra Berrouayel [aut, cre] (ORCID: ), Luis del Peso [aut] (ORCID: ) Maintainer: Yosra Berrouayel URL: https://github.com/yberda/ChIPDBData VignetteBuilder: knitr BugReports: https://github.com/yberda/ChIPDBData/issues git_url: https://git.bioconductor.org/packages/ChIPDBData git_branch: devel git_last_commit: c6e5ccf git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ChIPDBData_1.3.0.tar.gz vignettes: vignettes/ChIPDBData/inst/doc/using_chipdb.html vignetteTitles: Using ChIPDBData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ChIPDBData/inst/doc/using_chipdb.R dependencyCount: 64 Package: chipenrich.data Version: 2.37.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, BiocGenerics, methods, GenomicRanges, GenomeInfoDb, IRanges, readr, rtracklayer, S4Vectors, utils Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat, GO.db, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene License: GPL-3 MD5sum: 76ebb7431782ee7aa098eaf56ba481c6 NeedsCompilation: no Title: Companion package to chipenrich Description: Supporting data for the chipenrich package. Includes pre-defined gene sets, gene locus definitions, and mappability estimates. biocViews: ChIPSeq, Epigenetics, FunctionalGenomics, GeneSetEnrichment, HistoneModification, Regression Author: Ryan P. Welch [aut, cph], Chee Lee [aut], Raymond G. Cavalcante [aut], Kai Wang [cre], Laura J. Scott [ths], Maureen A. Sartor [ths] Maintainer: Kai Wang VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/chipenrich.data git_branch: devel git_last_commit: b8b9ce8 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/chipenrich.data_2.37.0.tar.gz vignettes: vignettes/chipenrich.data/inst/doc/chipenrich.data-vignette.html vignetteTitles: chipenrich.data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/chipenrich.data/inst/doc/chipenrich.data-vignette.R importsMe: chipenrich dependencyCount: 90 Package: ChIPexoQualExample Version: 1.37.0 Depends: R (>= 3.3) Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: bf39074e364e43b2497bc9fc23911038 NeedsCompilation: no Title: Example data for the ChIPexoQual package, which implements a quality control pipeline for ChIP-exo data Description: Data for the ChIPexoQual package, consisting of (3) chromosome 1 aligned reads from a ChIP-exo experiment for FoxA1 in mouse liver cell lines aligned to the mm9 genome. biocViews: ExperimentData, Genome Author: Rene Welch, Dongjun Chung, Sunduz Keles Maintainer: Rene Welch URL: http://www.github.com/keleslab/ChIPexoQualExample VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ChIPexoQualExample git_branch: devel git_last_commit: d307abc git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ChIPexoQualExample_1.37.0.tar.gz vignettes: vignettes/ChIPexoQualExample/inst/doc/vignette.html vignetteTitles: ChIPexoQualExample hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ChIPexoQualExample/inst/doc/vignette.R suggestsMe: ChIPexoQual dependencyCount: 0 Package: chipseqDBData Version: 1.29.0 Imports: AnnotationHub, ExperimentHub, Rsamtools, S4Vectors Suggests: knitr, BiocStyle, rmarkdown License: CC BY 4.0 MD5sum: e7daeaee78ffcd157ae39cb5dfc01650 NeedsCompilation: no Title: Data for the chipseqDB Workflow Description: Sorted and indexed BAM files for ChIP-seq libraries, for use in the chipseqDB workflow. BAM indices are also included. biocViews: SequencingData, ChIPSeqData, ExperimentHub Author: Aaron Lun [aut, cre] Maintainer: Aaron Lun VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/chipseqDBData git_branch: devel git_last_commit: 1ad7393 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/chipseqDBData_1.29.0.tar.gz vignettes: vignettes/chipseqDBData/inst/doc/chipseqDBData.html vignetteTitles: File manifest and statistics hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/chipseqDBData/inst/doc/chipseqDBData.R dependsOnMe: csawBook suggestsMe: chipseqDB dependencyCount: 77 Package: ChIPXpressData Version: 1.51.0 Depends: bigmemory License: GPL (>=2) MD5sum: 94c705ff84596f222cbc62cf3b126a55 NeedsCompilation: no Title: ChIPXpress Pre-built Databases Description: Contains pre-built mouse (GPL1261) and human (GPL570) database of gene expression profiles to be used for ChIPXpress ranking. biocViews: Homo_sapiens_Data, Mus_musculus_Data, GEO Author: George Wu Maintainer: George Wu git_url: https://git.bioconductor.org/packages/ChIPXpressData git_branch: devel git_last_commit: 40d374f git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ChIPXpressData_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ChIPXpress dependencyCount: 7 Package: CLL Version: 1.53.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: LGPL MD5sum: 4132e9632df135ab64cb9d70fa955450 NeedsCompilation: no Title: A Package for CLL Gene Expression Data Description: The CLL package contains the chronic lymphocytic leukemia (CLL) gene expression data. The CLL data had 24 samples that were either classified as progressive or stable in regards to disease progression. The data came from Dr. Sabina Chiaretti at Division of Hematology, Department of Cellular Biotechnologies and Hematology, University La Sapienza, Rome, Italy and Dr. Jerome Ritz at Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts. biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData Author: Elizabeth Whalen Maintainer: Robert Gentleman git_url: https://git.bioconductor.org/packages/CLL git_branch: devel git_last_commit: 13ef6b7 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/CLL_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 12 Package: CLLmethylation Version: 1.33.0 Depends: R (>= 3.5.0) Imports: SummarizedExperiment, ExperimentHub Suggests: BiocStyle, ggplot2, knitr, rmarkdown License: LGPL MD5sum: a0f71ea614e7e4c2a5e0527cb41bb5e2 NeedsCompilation: no Title: Methylation data of primary CLL samples in PACE project Description: The package includes DNA methylation data for the primary Chronic Lymphocytic Leukemia samples included in the Primary Blood Cancer Encyclopedia (PACE) project. Raw data from the 450k DNA methylation arrays is stored in the European Genome-Phenome Archive (EGA) under accession number EGAS0000100174. For more information concerning the project please refer to the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) and R/Bioconductor package BloodCancerMultiOmics2017. biocViews: ExperimentData, DiseaseModel, CancerData, LeukemiaCancerData Author: Malgorzata Oles, Andreas Mock Maintainer: Malgorzata Oles , Andreas Mock VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/CLLmethylation git_branch: devel git_last_commit: 3b088a5 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/CLLmethylation_1.33.0.tar.gz vignettes: vignettes/CLLmethylation/inst/doc/CLLmethylation.html vignetteTitles: CLLmethylation hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CLLmethylation/inst/doc/CLLmethylation.R dependencyCount: 75 Package: CluMSIDdata Version: 1.29.0 Depends: R (>= 3.6) License: MIT + file LICENSE MD5sum: cc20b6808e75aa6df280ef42174e26e9 NeedsCompilation: no Title: Data for the CluMSID package Description: This package contains various LC-MS/MS and GC-MS data that is used in vignettes and examples in the CluMSID package. biocViews: ExperimentData, MassSpectrometryData Author: Tobias Depke [aut, cre] Maintainer: Tobias Depke git_url: https://git.bioconductor.org/packages/CluMSIDdata git_branch: devel git_last_commit: c85180d git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/CluMSIDdata_1.29.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: clustifyrdatahub Version: 1.23.0 Depends: R (>= 4.0), ExperimentHub Imports: utils Suggests: clustifyr, Seurat, usethis, rmarkdown, knitr, tidyr, BiocStyle License: MIT + file LICENSE MD5sum: e226d6cd287b1f07321d399cb95b041e NeedsCompilation: no Title: External data sets for clustifyr in ExperimentHub Description: References made from external single-cell mRNA sequencing data sets, stored as average gene expression matrices. For use with clustifyr to assign cell type identities. biocViews: SingleCellData, SequencingData, MicroarrayData, ExperimentHub, RNASeqData, PackageTypeData, ExpressionData Author: Rui Fu [aut] (ORCID: ), Kent Riemondy [aut, cre] (ORCID: ), RNA Bioscience Initiative [fnd], Austin Gillen [ctb] (ORCID: ), Jay Hesselberth [ctb] (ORCID: ), Sidhant Puntambekar [ctb] Maintainer: Kent Riemondy URL: https://rnabioco.github.io/clustifyrdatahub/ VignetteBuilder: knitr BugReports: https://github.com/rnabioco/clustifyrdatahub/issues git_url: https://git.bioconductor.org/packages/clustifyrdatahub git_branch: devel git_last_commit: 61513ac git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/clustifyrdatahub_1.23.0.tar.gz vignettes: vignettes/clustifyrdatahub/inst/doc/clustifyrdatahub.html vignetteTitles: clustifyrdatahub hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/clustifyrdatahub/inst/doc/clustifyrdatahub.R dependencyCount: 64 Package: cMap2data Version: 1.49.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: d82c47ddee189e84aad243b4a5cd3607 NeedsCompilation: no Title: Connectivity Map (version 2) Data Description: Data package which provides default drug profiles for the DrugVsDisease package as well as associated gene lists and data clusters used by the DrugVsDisease package. biocViews: Homo_sapiens_Data, MicroarrayData, GEO Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/cMap2data git_branch: devel git_last_commit: abcc752 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/cMap2data_1.49.0.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: 1.49.0 Depends: R (>= 2.10), cnvGSA License: LGPL MD5sum: c1ed1d4c6a8e243fb26a7083304a137d NeedsCompilation: no Title: Data used in the vignette of the cnvGSA package Description: This package contains the data used in the vignette of the cnvGSA package. biocViews: ExperimentData, Genome, CopyNumberVariationData Author: Joseph Lugo Maintainer: Joseph Lugo git_url: https://git.bioconductor.org/packages/cnvGSAdata git_branch: devel git_last_commit: e675f1d git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/cnvGSAdata_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: cnvGSA dependencyCount: 21 Package: COHCAPanno Version: 1.49.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: f89fa8ad496867e3d110e406c9063c53 NeedsCompilation: no Title: Annotations for City of Hope CpG Island Analysis Pipeline Description: Provides genomic location, nearby CpG island and nearby gene information for common Illumina methylation array platforms biocViews: Homo_sapiens_Data, MicroarrayData, MethylationArrayData, CpGIslandData, GEO, ArrayExpress Author: Charles Warden Maintainer: Charles Warden git_url: https://git.bioconductor.org/packages/COHCAPanno git_branch: devel git_last_commit: 8c5ff5d git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/COHCAPanno_1.49.0.tar.gz vignettes: vignettes/COHCAPanno/inst/doc/COHCAPanno.pdf vignetteTitles: COHCAPanno Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/COHCAPanno/inst/doc/COHCAPanno.R dependencyCount: 0 Package: colonCA Version: 1.55.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: d0e44261d1d932a28133db6d1f0a3d42 NeedsCompilation: no Title: exprSet for Alon et al. (1999) colon cancer data Description: exprSet for Alon et al. (1999) colon cancer data biocViews: ExperimentData, Tissue, CancerData, ColonCancerData, MicroarrayData, TissueMicroarrayData Author: Sylvia Merk Maintainer: W Sylvia Merk git_url: https://git.bioconductor.org/packages/colonCA git_branch: devel git_last_commit: 051bff0 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/colonCA_1.55.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: clustComp, copa dependencyCount: 7 Package: CONFESSdata Version: 1.41.0 Depends: R (>= 3.3) License: GPL-2 MD5sum: 169b6ca3978d6bbe6d15cf66278d60aa NeedsCompilation: no Title: Example dataset for CONFESS package Description: Example text-converted C01 image files for use in the CONFESS Bioconductor package. biocViews: HighThroughputImagingData,CellCulture,Homo_sapiens_Data,ExpressionData Author: Diana LOW and Efthimios MOTAKIS Maintainer: Diana LOW git_url: https://git.bioconductor.org/packages/CONFESSdata git_branch: devel git_last_commit: 4692173 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/CONFESSdata_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CONFESS dependencyCount: 0 Package: ConnectivityMap Version: 1.49.0 Depends: R (>= 2.15.1) Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: da0ab89631c20a50217eb38e51af086f NeedsCompilation: no Title: Functional connections between drugs, genes and diseases as revealed by common gene-expression changes Description: The Broad Institute's Connectivity Map (cmap02) is a "large reference catalogue of gene-expression data from cultured human cells perturbed with many chemicals and genetic reagents", containing more than 7000 gene expression profiles and 1300 small molecules. biocViews: ExperimentData, CancerData, MicroarrayData Author: Paul Shannon Maintainer: Paul Shannon git_url: https://git.bioconductor.org/packages/ConnectivityMap git_branch: devel git_last_commit: a2fe08b git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ConnectivityMap_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: COPDSexualDimorphism.data Version: 1.49.0 License: LGPL-2.1 MD5sum: 9f3e034ee54c93cba0359ca216e84619 NeedsCompilation: no Title: Data to support sexually dimorphic and COPD differential analysis for gene expression and methylation. Description: Datasets to support COPDSexaulDimorphism Package. biocViews: ExperimentData, Tissue, COPDData Author: J Fah Sathirapongsasuti Maintainer: J Fah Sathirapongsasuti git_url: https://git.bioconductor.org/packages/COPDSexualDimorphism.data git_branch: devel git_last_commit: 7dfbe5f git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/COPDSexualDimorphism.data_1.49.0.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: 1.45.0 Depends: R (>= 3.5.0) Suggests: BiocStyle License: GPL-2 MD5sum: e9de3dee1f6681a458fb84f21138bc03 NeedsCompilation: no Title: Helper files for CopywriteR Description: This package contains the helper files that are required to run the Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content and mappability files for the reference genomes hg18, hg19, hg38, mm9 and mm10. In addition, it contains a blacklist filter to remove regions that display CNV. Files are stored as GRanges objects from the GenomicRanges Bioconductor package. biocViews: Homo_sapiens, GenomicSequence Author: Thomas Kuilman Maintainer: Oscar Krijgsman git_url: https://git.bioconductor.org/packages/CopyhelpeR git_branch: devel git_last_commit: 8a0b95c git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/CopyhelpeR_1.45.0.tar.gz vignettes: vignettes/CopyhelpeR/inst/doc/CopyhelpeR.pdf vignetteTitles: CopyhelpeR hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CopyhelpeR/inst/doc/CopyhelpeR.R dependencyCount: 0 Package: CopyNeutralIMA Version: 1.31.0 Depends: R (>= 3.5.0) Imports: ExperimentHub,Rdpack (>= 0.8) Suggests: BiocStyle,knitr,rmarkdown,minfi,conumee,minfiData License: Artistic-2.0 MD5sum: 8cb042af8c26d9a7e93d5971f2c18cc1 NeedsCompilation: no Title: Copy Neutral Illumina Methylation Arrays Description: Provides a set of genomic copy neutral samples hybridized using Illumina Methylation arrays (450k and EPIC). biocViews: ExperimentData,Homo_sapiens_Data,MicroarrayData,TwoChannelData,MethylationArrayData,GEO Author: Xavier Pastor Hostench [aut, cre], Moritz Przybilla [aut] Maintainer: Xavier Pastor Hostench VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/CopyNeutralIMA git_branch: devel git_last_commit: 4b09c65 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/CopyNeutralIMA_1.31.0.tar.gz vignettes: vignettes/CopyNeutralIMA/inst/doc/CopyNeutralIMA.html vignetteTitles: CopyNeutralIMA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CopyNeutralIMA/inst/doc/CopyNeutralIMA.R dependencyCount: 66 Package: CoSIAdata Version: 1.13.0 Depends: R (>= 4.3.0), ExperimentHub (>= 2.6.0), Suggests: BiocStyle (>= 2.26.0), utils (>= 4.3.0), AnnotationHub (>= 3.7.3), knitr (>= 1.42) License: MIT + file LICENSE MD5sum: d5f516d010fcf7e280486912dae9f201 NeedsCompilation: no Title: VST normalized RNA-Sequencing data with annotations for multiple species samples from Bgee Description: Variance Stabilized Transformation of Read Counts derived from Bgee RNA-Seq Expression Data. Expression Data includes annotations and is across 6 species (Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Drosophila melanogaster, and Caenorhabditis elegans) and across more than 132 tissues. The data is represented as a RData files and is available in ExperimentHub. biocViews: ExperimentHub, RNASeqData, ExperimentData, PackageTypeData, OrganismData, Tissue,Caenorhabditis_elegans_Data, Danio_rerio_Data, Drosophila_melanogaster_Data, Homo_sapiens_Data, Mus_musculus_Data, Rattus_norvegicus_Data, SequencingData, ExpressionData Author: Anisha Haldar [aut] (ORCID: ), Vishal H. Oza [aut] (ORCID: ), Amanda D. Clark [cre, aut] (ORCID: ), Nathaniel S. DeVoss [aut] (ORCID: ), Brittany N. Lasseigne [aut] (ORCID: ) Maintainer: Amanda D. Clark VignetteBuilder: knitr BugReports: https://github.com/lasseignelab/CoSIAdata/issues git_url: https://git.bioconductor.org/packages/CoSIAdata git_branch: devel git_last_commit: 7119107 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/CoSIAdata_1.13.0.tar.gz vignettes: vignettes/CoSIAdata/inst/doc/CoSIAdata_vignette.html vignetteTitles: CoSIAdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/CoSIAdata/inst/doc/CoSIAdata_vignette.R dependencyCount: 64 Package: COSMIC.67 Version: 1.49.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, SummarizedExperiment, VariantAnnotation Suggests: testthat, BiocStyle, knitr License: GPL-3 MD5sum: 7efb8ee58c1da68f8de1444892341df3 NeedsCompilation: no Title: COSMIC.67 Description: COSMIC: Catalogue Of Somatic Mutations In Cancer, version 67 (2013-10-24) biocViews: ExperimentData, Genome, CancerData Author: Julian Gehring Maintainer: Julian Gehring VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/COSMIC.67 git_branch: devel git_last_commit: 0acb73f git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/COSMIC.67_1.49.0.tar.gz vignettes: vignettes/COSMIC.67/inst/doc/COSMIC.67.pdf vignetteTitles: COSMIC.67 - PDF hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/COSMIC.67/inst/doc/COSMIC.67.R importsMe: appreci8R dependencyCount: 78 Package: CRCL18 Version: 1.33.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 9bc632274ffcea521221c3e8b22dddd8 NeedsCompilation: no Title: CRC cell line dataset Description: colorectal cancer mRNA and miRNA on 18 cell lines biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/CRCL18 git_branch: devel git_last_commit: 07b897b git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/CRCL18_1.33.0.tar.gz vignettes: vignettes/CRCL18/inst/doc/CRCL18Vignette.pdf vignetteTitles: CRCL18 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CRCL18/inst/doc/CRCL18Vignette.R dependencyCount: 7 Package: crisprScoreData Version: 1.17.0 Depends: ExperimentHub Imports: AnnotationHub, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: f8ff974067a9fbcc402aebe7bba773cf NeedsCompilation: no Title: Pre-trained models for the crisprScore package Description: Provides an interface to access pre-trained models for on-target and off-target gRNA activity prediction algorithms implemented in the crisprScore package. Pre-trained model data are stored in the ExperimentHub database. Users should consider using the crisprScore package directly to use and load the pre-trained models. biocViews: ExperimentHub, Homo_sapiens_Data Author: Jean-Philippe Fortin [aut, cre, cph] Maintainer: Jean-Philippe Fortin URL: https://github.com/crisprVerse/crisprScoreData/issues VignetteBuilder: knitr BugReports: https://github.com/crisprVerse/crisprScoreData git_url: https://git.bioconductor.org/packages/crisprScoreData git_branch: devel git_last_commit: 1a3af4f git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/crisprScoreData_1.17.0.tar.gz vignettes: vignettes/crisprScoreData/inst/doc/crisprScoreData.html vignetteTitles: crisprScoreData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/crisprScoreData/inst/doc/crisprScoreData.R dependsOnMe: crisprScore importsMe: crisprVerse dependencyCount: 64 Package: curatedAdipoArray Version: 1.25.0 Depends: R (>= 4.0) Suggests: knitr, rmarkdown, ExperimentHub, SummarizedExperiment License: GPL-3 + file LICENSE MD5sum: a13d3c8be6176a0f0e946fc37695dba1 NeedsCompilation: no Title: A Curated Microarrays Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Under Genetic and Pharmacological Perturbations Description: A curated dataset of Microarrays samples. The samples are MDI- induced pre-adipocytes (3T3-L1) at different time points/stage of differentiation under different types of genetic (knockdown/overexpression) and pharmacological (drug treatment) perturbations. The package documents the data collection and processing. In addition to the documentation, the package contains the scripts that was used to generated the data. biocViews: ExperimentData, ExperimentHub, GEO, MicroarrayData Author: Mahmoud Ahmed [aut, cre] (ORCID: ) Maintainer: Mahmoud Ahmed URL: https://github.com/MahShaaban/curatedAdipoArray VignetteBuilder: knitr BugReports: https://github.com/MahShaaban/curatedAdipoArray/issues git_url: https://git.bioconductor.org/packages/curatedAdipoArray git_branch: devel git_last_commit: 0d3caeb git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/curatedAdipoArray_1.25.0.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: 1.29.0 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: ef15be255b2eb2e64025fc0472e72f25 NeedsCompilation: no Title: A Curated ChIP-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Description: A curated dataset of publicly available ChIP-sequencing of transcription factors, chromatin remodelers and histone modifications in the 3T3-L1 pre-adipocyte cell line. The package document the data collection, pre-processing and processing of the data. In addition to the documentation, the package contains the scripts that was used to generated the data. biocViews: ExperimentData, ExperimentHub, GEO, ChIPSeqData, SequencingData Author: Mahmoud Ahmed [aut, cre] (ORCID: ) Maintainer: Mahmoud Ahmed URL: https://github.com/MahShaaban/curatedAdipoChIP VignetteBuilder: knitr BugReports: https://github.com/MahShaaban/curatedAdipoChIP/issues git_url: https://git.bioconductor.org/packages/curatedAdipoChIP git_branch: devel git_last_commit: 3bea9ce git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/curatedAdipoChIP_1.29.0.tar.gz vignettes: vignettes/curatedAdipoChIP/inst/doc/curatedAdipoChIP.html vignetteTitles: Using curatedAdipoChIP hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedAdipoChIP/inst/doc/curatedAdipoChIP.R dependencyCount: 75 Package: curatedAdipoRNA Version: 1.29.0 Depends: R (>= 3.6), SummarizedExperiment Suggests: knitr, rmarkdown, DESeq2, fastqcr, devtools, testthat, readr, dplyr, tidyr, ggplot2, S4Vectors License: GPL-3 MD5sum: 9904f3b016f85a85e7778fce37e6c342 NeedsCompilation: no Title: A Curated RNA-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Description: A curated dataset of RNA-Seq samples. The samples are MDI-induced pre-phagocytes (3T3-L1) at different time points/stage of differentiation. The package document the data collection, pre-processing and processing. In addition to the documentation, the package contains the scripts that was used to generated the data. biocViews: ExperimentData, GEO, RNASeqData, SequencingData Author: Mahmoud Ahmed [aut, cre] (ORCID: ) Maintainer: Mahmoud Ahmed URL: https://github.com/MahShaaban/curatedAdipoRNA VignetteBuilder: knitr BugReports: https://github.com/MahShaaban/curatedAdipoRNA/issues git_url: https://git.bioconductor.org/packages/curatedAdipoRNA git_branch: devel git_last_commit: 314a7a2 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/curatedAdipoRNA_1.29.0.tar.gz vignettes: vignettes/curatedAdipoRNA/inst/doc/curatedadiporna_vignette.html vignetteTitles: Using curatedAdipoRNA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedAdipoRNA/inst/doc/curatedadiporna_vignette.R dependencyCount: 25 Package: curatedBladderData Version: 1.49.0 Depends: R (>= 2.10.0), affy Suggests: BiocStyle, survival, xtable, sva, genefilter, logging License: Artistic-2.0 MD5sum: cf03aa5e8c4e1df9209633a26daf0f6d NeedsCompilation: no Title: Bladder Cancer Gene Expression Analysis Description: The curatedBladderData package provides relevant functions and data for gene expression analysis in patients with bladder cancer. biocViews: ExperimentData, CancerData, OvarianCancerData, MicroarrayData, ExpressionData Author: Markus Riester Maintainer: Markus Riester URL: https://github.com/lima1/curatedBladderData git_url: https://git.bioconductor.org/packages/curatedBladderData git_branch: devel git_last_commit: d95abf4 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/curatedBladderData_1.49.0.tar.gz vignettes: vignettes/curatedBladderData/inst/doc/curatedBladderData_vignette.pdf vignetteTitles: curatedBladderData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedBladderData/inst/doc/curatedBladderData_vignette.R suggestsMe: covEB dependencyCount: 12 Package: curatedCRCData Version: 2.45.1 Depends: R (>= 4.0.0), Biobase Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 5a75484a7a52c6fb9305fa5d8720bd80 NeedsCompilation: no Title: Colorectal Cancer Gene Expression Analysis Description: The curatedCRC package provides relevant functions and data for gene expression analysis in patients with colorectal cancer. biocViews: ExperimentData, CancerData, ExpressionData Author: Princy Parsana [aut], Markus Riester [aut], Curtis Huttenhower [aut], Levi Waldron [aut, cre] (ORCID: ), National Cancer Institute [fnd] (5U24CA180996) Maintainer: Levi Waldron URL: https://github.com/waldronlab/curatedCRCData VignetteBuilder: knitr BugReports: https://github.com/waldronlab/curatedCRCData/issues git_url: https://git.bioconductor.org/packages/curatedCRCData git_branch: devel git_last_commit: 33355a8 git_last_commit_date: 2026-04-29 Date/Publication: 2026-04-30 source.ver: src/contrib/curatedCRCData_2.45.1.tar.gz vignettes: vignettes/curatedCRCData/inst/doc/curatedCRCData_vignette.html vignetteTitles: curatedCRCData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedCRCData/inst/doc/curatedCRCData_vignette.R dependencyCount: 7 Package: curatedMetagenomicData Version: 3.19.0 Depends: R (>= 4.1.0), SummarizedExperiment, TreeSummarizedExperiment Imports: AnnotationHub, ExperimentHub, S4Vectors, dplyr, magrittr, mia, purrr, rlang, stringr, tibble, tidyr, tidyselect Suggests: BiocStyle, DT, knitr, readr, rmarkdown, scater, testthat, utils, uwot, vegan, OmicsMLRepoR, lefser License: Artistic-2.0 MD5sum: 50d012cc0eb61e3ca29ea26d5b70a6a7 NeedsCompilation: no Title: Curated Metagenomic Data of the Human Microbiome Description: The curatedMetagenomicData package provides standardized, curated human microbiome data for novel analyses. It includes gene families, marker abundance, marker presence, pathway abundance, pathway coverage, and relative abundance for samples collected from different body sites. The bacterial, fungal, and archaeal taxonomic abundances for each sample were calculated with MetaPhlAn3, and metabolic functional potential was calculated with HUMAnN3. The manually curated sample metadata and standardized metagenomic data are available as (Tree)SummarizedExperiment objects. biocViews: ExperimentHub, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch Author: Lucas schiffer [aut, cre] (ORCID: ), Levi Waldron [aut], Edoardo Pasolli [ctb], Jennifer Wokaty [ctb], Sean Davis [ctb], Audrey Renson [ctb], Chloe Mirzayi [ctb], Paolo Manghi [ctb], Samuel Gamboa-Tuz [ctb], Marcel Ramos [ctb], Valerie Obenchain [ctb], Kelly Eckenrode [ctb], Nicola Segata [ctb], Sehyun Oh [ctb], Yoon-Ji Jung [ctb] Maintainer: Lucas schiffer URL: https://github.com/waldronlab/curatedMetagenomicData VignetteBuilder: knitr BugReports: https://github.com/waldronlab/curatedMetagenomicData/issues git_url: https://git.bioconductor.org/packages/curatedMetagenomicData git_branch: devel git_last_commit: 5cacdd9 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/curatedMetagenomicData_3.19.0.tar.gz vignettes: vignettes/curatedMetagenomicData/inst/doc/curatedMetagenomicData.html vignetteTitles: curatedMetagenomicData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedMetagenomicData/inst/doc/curatedMetagenomicData.R suggestsMe: CrcBiomeScreen, lefser, MMUPHin dependencyCount: 154 Package: curatedOvarianData Version: 1.51.1 Depends: Biobase, R (>= 4.6.0) Imports: BiocGenerics Suggests: BiocStyle, futile.logger, genefilter, knitr, logging, metafor, rmarkdown, RUnit, survival, sva, xtable License: Artistic-2.0 MD5sum: 80b1533eac08729050cf16e8e94cee4d 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, MicroarrayData Author: Benjamin Ganzfried [aut], Markus Riester [aut], Steve Skates [aut], Victoria Wang [aut], Thomas Risch [aut], Benjamin Haibe-Kains [aut], Svitlana Tyekucheva [aut], Jie Ding [aut], Ina Jazic [aut], Michael Birrer [aut], Giovanni Parmigiani [aut], Curtis Huttenhower [aut], Levi Waldron [aut, cre] (ORCID: ), NCI [fnd] (GrantNo.: U24CA289073) Maintainer: Levi Waldron URL: http://bcb.dfci.harvard.edu/ovariancancer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/curatedOvarianData git_branch: devel git_last_commit: 151f781 git_last_commit_date: 2026-04-29 Date/Publication: 2026-04-30 source.ver: src/contrib/curatedOvarianData_1.51.1.tar.gz vignettes: vignettes/curatedOvarianData/inst/doc/curatedOvarianData.html vignetteTitles: curatedOvarianData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedOvarianData/inst/doc/curatedOvarianData.R suggestsMe: doppelgangR, TOP dependencyCount: 7 Package: curatedPCaData Version: 1.9.0 Depends: R (>= 4.4.0), S4Vectors (>= 0.23.18), MultiAssayExperiment, RaggedExperiment Imports: ExperimentHub, AnnotationHub, utils, methods, rlang, stats, reshape2 Suggests: BiocStyle, knitr, ggplot2, rmarkdown, survival, survminer, ComplexHeatmap, corrplot, formatR License: CC BY 4.0 MD5sum: 9a295f6be40a9ffac92244363c5951c8 NeedsCompilation: no Title: Curated Prostate Cancer Data Description: The package curatedPCaData offers a selection of annotated prostate cancer datasets featuring multiple omics, manually curated metadata, and derived downstream variables. The studies are offered as MultiAssayExperiment (MAE) objects via ExperimentHub, and comprise of clinical characteristics tied to gene expression, copy number alteration and somatic mutation data. Further, downstream features computed from these multi-omics data are offered. Multiple vignettes help grasp characteristics of the various studies and provide example exploratory and meta-analysis of leveraging the multiple studies provided here-in. biocViews: ExperimentHub, ExperimentData, ProstateCancerData, CancerData, Homo_sapiens_Data, MicroarrayData, RNASeqData, ExpressionData, CopyNumberVariationData, Somatic, GEO, ReproducibleResearch Author: Teemu Daniel Laajala [aut, cre] (ORCID: ), Jordan Creed [ctb], Christelle Colin Leitzinger [ctb], Varsha Sreekanth [ctb], Federico Calboli [ctb], Kalaimathy Singaravelu [ctb], Michael Orman [ctb], Alex Soupir [ctb], Anni Halkola [ctb] Maintainer: Teemu Daniel Laajala URL: https://github.com/Syksy/curatedPCaData VignetteBuilder: knitr BugReports: https://github.com/Syksy/curatedPCaData/issues git_url: https://git.bioconductor.org/packages/curatedPCaData git_branch: devel git_last_commit: 6316670 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/curatedPCaData_1.9.0.tar.gz vignettes: vignettes/curatedPCaData/inst/doc/overview.html vignetteTitles: Overview to curatedPCaData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedPCaData/inst/doc/overview.R dependencyCount: 80 Package: curatedTBData Version: 2.9.0 Depends: R (>= 4.3.0) Imports: AnnotationHub, ExperimentHub, MultiAssayExperiment, rlang, stats Suggests: BiocStyle, DT, dplyr, HGNChelper, knitr, methods, rmarkdown, SummarizedExperiment, sva, testthat License: MIT + file LICENSE MD5sum: e90d005fcdac5cf1f1f5544cb7072b56 NeedsCompilation: no Title: Curation of existing tuberculosis transcriptomic studies Description: The curatedTBData is an R package that provides standardized, curated tuberculosis(TB) transcriptomic studies. The initial release of the package contains 49 studies. The curatedTBData package allows users to access tuberculosis trancriptomic efficiently and to make efficient comparison for different TB gene signatures across multiple datasets. biocViews: ExperimentHub, GEO, Homo_sapiens_Data Author: Xutao Wang [aut, cre], W. Evan Johnson [aut], Prasad Patil [aut] Maintainer: Xutao Wang URL: https://github.com/compbiomed/curatedTBData VignetteBuilder: knitr BugReports: https://github.com/compbiomed/curatedTBData/issues git_url: https://git.bioconductor.org/packages/curatedTBData git_branch: devel git_last_commit: 3f32eb1 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/curatedTBData_2.9.0.tar.gz vignettes: vignettes/curatedTBData/inst/doc/curatedTBData.html vignetteTitles: curatedTBData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/curatedTBData/inst/doc/curatedTBData.R suggestsMe: BatchQC dependencyCount: 76 Package: curatedTCGAData Version: 1.35.0 Depends: R (>= 4.5.0), MultiAssayExperiment Imports: AnnotationHub, ExperimentHub, HDF5Array, methods, S4Vectors, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, RaggedExperiment, readr, rmarkdown, TCGAutils, testthat License: Artistic-2.0 MD5sum: 5305de652649011766b2721a124222b3 NeedsCompilation: no Title: Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects Description: This package provides publicly available data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects. MultiAssayExperiment integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. It also links assay barcodes with patient identifiers, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-'omics experiment. biocViews: Homo_sapiens_Data, ReproducibleResearch, CancerData, ExperimentHub Author: Marcel Ramos [aut, cre] (ORCID: ), Levi Waldron [ctb], Lucas Schiffer [ctb], Ludwig Geistlinger [ctb], Valerie Obenchain [ctb], Martin Morgan [ctb], NCI [fnd] (GrantNo.: U24CA289073) Maintainer: Marcel Ramos VignetteBuilder: knitr BugReports: https://github.com/waldronlab/curatedTCGAData/issues git_url: https://git.bioconductor.org/packages/curatedTCGAData git_branch: devel git_last_commit: adb1593 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/curatedTCGAData_1.35.0.tar.gz vignettes: vignettes/curatedTCGAData/inst/doc/curatedTCGAData.html vignetteTitles: curatedTCGAData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedTCGAData/inst/doc/curatedTCGAData.R importsMe: AMARETTO suggestsMe: CNVRanger, glmSparseNet, imageFeatureTCGA, TCGAutils dependencyCount: 83 Package: CytoMethIC Version: 1.9.0 Depends: R (>= 4.4.0), ExperimentHub Imports: utils, stats, tools, sesame, methods, sesameData, BiocParallel, BiocManager Suggests: tibble, BiocStyle, randomForest, testthat, knitr, rmarkdown, e1071, xgboost, keras, tensorflow License: Artistic-2.0 MD5sum: d620c2451f7ff111e8031944a2dba5d8 NeedsCompilation: no Title: DNA methylation-based machine learning models Description: This package provides model data and functions for easily using machine learning models that use data from the DNA methylome to classify cancer type and phenotype from a sample. The primary motivation for the development of this package is to abstract away the granular and accessibility-limiting code required to utilize machine learning models in R. Our package provides this abstraction for RandomForest, e1071 Support Vector, Extreme Gradient Boosting, and Tensorflow models. This is paired with an ExperimentHub component, which contains models developed for epigenetic cancer classification and predicting phenotypes. This includes CNS tumor classification, Pan-cancer classification, race prediction, cell of origin classification, and subtype classification models. The package links to our models on ExperimentHub. The package currently supports HM450, EPIC, EPICv2, MSA, and MM285. biocViews: ExperimentData, MicroarrayData, Genome, ExperimentHub, MethylationArrayData, CancerData, PackageTypeData Author: Wanding Zhou [aut] (ORCID: ), Jacob Fanale [aut, cre] (ORCID: ) Maintainer: Jacob Fanale URL: https://github.com/zhou-lab/CytoMethIC VignetteBuilder: knitr BugReports: https://github.com/zhou-lab/CytoMethIC/issues git_url: https://git.bioconductor.org/packages/CytoMethIC git_branch: devel git_last_commit: 193109c git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/CytoMethIC_1.9.0.tar.gz vignettes: vignettes/CytoMethIC/inst/doc/CytoMethIC.html, vignettes/CytoMethIC/inst/doc/Oncology.html vignetteTitles: 1. Basic Information, 2. CytoMethIC Oncology hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CytoMethIC/inst/doc/CytoMethIC.R, vignettes/CytoMethIC/inst/doc/Oncology.R dependencyCount: 109 Package: DAPARdata Version: 1.41.0 Depends: R (>= 4.4.0), MSnbase Imports: utils Suggests: knitr, DAPAR, BiocStyle License: GPL-2 MD5sum: d53e5c68fb0c3d5ceef55483ce290bcf NeedsCompilation: no Title: Data accompanying the DAPAR and Prostar packages Description: Mass-spectrometry based UPS proteomics data sets from Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssie D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianferani S, Ferro M, Dorssaeler AV, Burlet-Schiltz O, Schaeffer C, Coute Y, Gonzalez de Peredo A. Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods. Data Brief. 2015 Dec 17;6:286-94 and Giai Gianetto, Q., Combes, F., Ramus, C., Bruley, C., Coute, Y., Burger, T. (2016). Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments. Proteomics, 16(1), 29-32. biocViews: ExperimentData, MassSpectrometryData, Proteome Author: Samuel Wieczorek [cre,aut], Thomas Burger [aut], Enora Fremy [aut] Maintainer: Samuel Wieczorek URL: http://www.prostar-proteomics.org/ VignetteBuilder: knitr BugReports: https://github.com/edyp-lab/DAPARdata/issues git_url: https://git.bioconductor.org/packages/DAPARdata git_branch: devel git_last_commit: 1733867 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/DAPARdata_1.41.0.tar.gz vignettes: vignettes/DAPARdata/inst/doc/dapardata.html vignetteTitles: DAPARdata User Manual hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DAPARdata/inst/doc/dapardata.R dependencyCount: 2 Package: davidTiling Version: 1.53.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db License: LGPL MD5sum: ce5a9e65d84ecc7c24d982203a68b436 NeedsCompilation: no Title: Data and analysis scripts for David, Huber et al. yeast tiling array paper Description: This package contains the data for the paper by L. David et al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix genechips, an ExpressionSet object with the raw feature data, a probe annotation data structure for the chip and the yeast genome annotation (GFF file) that was used. In addition, some custom-written analysis functions are provided, as well as R scripts in the scripts directory. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, MicroarrayData, ReproducibleResearch Author: Wolfgang Huber , Joern Toedling Maintainer: Wolfgang Huber URL: http://www.ebi.ac.uk/huber git_url: https://git.bioconductor.org/packages/davidTiling git_branch: devel git_last_commit: a880251 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/davidTiling_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 76 Package: depmap Version: 1.27.0 Depends: R (>= 4.1.0), methods, dplyr Imports: utils, ExperimentHub, AnnotationHub, BiocFileCache, httr2, curl, tibble Suggests: knitr, rmarkdown, BiocStyle, viridis, gridExtra, ggplot2, readr, stringr, tidyverse, magick License: Artistic-2.0 MD5sum: 406ded5cf78c7b3411cc03d38b7d7f2e NeedsCompilation: no Title: Cancer Dependency Map Data Package Description: The depmap package is a data package that accesses datsets from the Broad Institute DepMap cancer dependency study using ExperimentHub. Datasets from the most current release are available, including RNAI and CRISPR-Cas9 gene knockout screens quantifying the genetic dependency for select cancer cell lines. Additional datasets are also available pertaining to the log copy number of genes for select cell lines, protein expression of cell lines as measured by reverse phase protein lysate microarray (RPPA), 'Transcript Per Million' (TPM) data, as well as supplementary datasets which contain metadata and mutation calls for the other datasets found in the current release. The 19Q3 release adds the drug_dependency dataset, that contains cancer cell line dependency data with respect to drug and drug-candidate compounds. The 20Q2 release adds the proteomic dataset that contains quantitative profiling of proteins via mass spectrometry. This package will be updated on a quarterly basis to incorporate the latest Broad Institute DepMap Public cancer dependency datasets. All data made available in this package was generated by the Broad Institute DepMap for research purposes and not intended for clinical use. This data is distributed under the Creative Commons license (Attribution 4.0 International (CC BY 4.0)). biocViews: ExperimentHub, ExperimentData, ReproducibleResearch, RepositoryData, AssayDomainData, CopyNumberVariationData, DiseaseModel, CancerData, BreastCancerData, ColonCancerData, KidneyCancerData, LeukemiaCancerData, LungCancerData, OvarianCancerData, ProstateCancerData, OrganismData, Homo_sapiens_Data, PackageTypeData, SpecimenSource, CellCulture, Genome, Proteome, StemCell, Tissue Author: Laurent Gatto [cre, aut] (ORCID: ), Theo Killian [aut], Alexander Peltzer [ctb] (ORCID: ) Maintainer: Laurent Gatto VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/depmap git_branch: devel git_last_commit: c9de6f9 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/depmap_1.27.0.tar.gz vignettes: vignettes/depmap/inst/doc/depmap.html, vignettes/depmap/inst/doc/using_depmap.html vignetteTitles: depmap, depmap use cases hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/depmap/inst/doc/depmap.R, vignettes/depmap/inst/doc/using_depmap.R importsMe: CBNplot, DeepTarget suggestsMe: CRISPRball, mastR, BioPlex dependencyCount: 64 Package: derfinderData Version: 2.31.0 Depends: R (>= 3.5.0) Suggests: sessioninfo, knitr (>= 1.6), RefManageR, rmarkdown (>= 0.3.3), BiocStyle License: Artistic-2.0 MD5sum: 1890b50a0980083e8d30444ec3326ac6 NeedsCompilation: no Title: Processed BigWigs from BrainSpan for examples Description: Processed 22 samples from BrainSpan keeping only the information for chromosome 21. Data is stored in the BigWig format and is used for examples in other packages. biocViews: ExperimentData, Homo_sapiens_Data, RNASeqData Author: Leonardo Collado-Torres [aut, cre] (ORCID: ), Andrew Jaffe [aut] (ORCID: ), Jeffrey Leek [aut, ths] (ORCID: ) Maintainer: Leonardo Collado-Torres URL: https://github.com/leekgroup/derfinderData VignetteBuilder: knitr BugReports: https://github.com/leekgroup/derfinderData/issues git_url: https://git.bioconductor.org/packages/derfinderData git_branch: devel git_last_commit: ecaed85 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/derfinderData_2.31.0.tar.gz vignettes: vignettes/derfinderData/inst/doc/derfinderData.html vignetteTitles: Introduction to derfinderData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/derfinderData/inst/doc/derfinderData.R suggestsMe: derfinder, derfinderPlot dependencyCount: 0 Package: DeSousa2013 Version: 1.49.0 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: f3c923c8fb724f8b893e877a2c847aac NeedsCompilation: no Title: Poor prognosis colon cancer is defined by a molecularly distinct subtype and precursor lesion Description: This package reproduces the main pipeline to analyze the AMC-AJCCII-90 microarray data set in De Sousa et al. accepted by Nature Medicine in 2013. biocViews: CancerData, ColonCancerData, MicroarrayData Author: Xin Wang Maintainer: Xin Wang git_url: https://git.bioconductor.org/packages/DeSousa2013 git_branch: devel git_last_commit: f62b055 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/DeSousa2013_1.49.0.tar.gz vignettes: vignettes/DeSousa2013/inst/doc/DeSousa2013-Vignette.pdf vignetteTitles: Main vignette:Poor prognosis colon cancer is defined by a molecular distinct subtype and develops from serrated precursor lesions hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DeSousa2013/inst/doc/DeSousa2013-Vignette.R dependencyCount: 123 Package: DExMAdata Version: 1.21.0 Depends: R (>= 4.1) Imports: Biobase Suggests: BiocStyle License: GPL-2 MD5sum: 5c2c95cf0399ee4658d8b4e333788a8c NeedsCompilation: no Title: Data package for DExMA package Description: Data objects needed to allSameID() function of DExMA package. There are also some objects that are necessary to be able to apply the examples of the DExMA package, which illustrate package functionality. biocViews: ExperimentData, OrganismData, MicroarrayData Author: Juan Antonio Villatoro-García [aut, cre], Pedro Carmona-Sáez [aut] Maintainer: Juan Antonio Villatoro-García git_url: https://git.bioconductor.org/packages/DExMAdata git_branch: devel git_last_commit: b1f306a git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/DExMAdata_1.21.0.tar.gz vignettes: vignettes/DExMAdata/inst/doc/DExMAdata.pdf vignetteTitles: Data for DExMA package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DExMAdata/inst/doc/DExMAdata.R dependsOnMe: DExMA dependencyCount: 7 Package: diffloopdata Version: 1.41.0 Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 3d40e18577574c052a5f201777e365b3 NeedsCompilation: no Title: Example ChIA-PET Datasets for the diffloop Package Description: ChIA-PET example datasets and additional data for use with the diffloop package. biocViews: ExperimentData, SequencingData Author: Caleb Lareau [aut], Martin Aryee [aut, cre] Maintainer: Caleb Lareau VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/diffloopdata git_branch: devel git_last_commit: 1b46013 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/diffloopdata_1.41.0.tar.gz vignettes: vignettes/diffloopdata/inst/doc/diffloopdata.html vignetteTitles: diffloopdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: diggitdata Version: 1.45.0 Depends: R(>= 2.14.0), Biobase, methods Imports: viper License: GPL (>=2) MD5sum: df40e2bf63c7227c6cff589b73b259b1 NeedsCompilation: no Title: Example data for the diggit package Description: This package provides expression profile and CNV data for glioblastoma from TCGA, and transcriptional and post-translational regulatory networks assembled with the ARACNe and MINDy algorithms, respectively. biocViews: ExperimentData, Cancer Author: Mariano Javier Alvarez Maintainer: Mariano Javier Alvarez git_url: https://git.bioconductor.org/packages/diggitdata git_branch: devel git_last_commit: 0300b11 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/diggitdata_1.45.0.tar.gz vignettes: vignettes/diggitdata/inst/doc/diggitdata.pdf vignetteTitles: Using bcellViper hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/diggitdata/inst/doc/diggitdata.R suggestsMe: diggit dependencyCount: 88 Package: DLBCL Version: 1.53.0 Depends: R(>= 2.11.0), Biobase, graph License: GPL (>=2) MD5sum: fca94d681f1b945f646e3bafa77bb610 NeedsCompilation: no Title: Diffuse large B-cell lymphoma expression data Description: This package provides additional expression data on diffuse large B-cell lymphomas for the BioNet package. biocViews: ExperimentData, CancerData, MicroarrayData, ChipOnChipData Author: Marcus Dittrich and Daniela Beisser Maintainer: Marcus Dittrich URL: http://bionet.bioapps.biozentrum.uni-wuerzburg.de/ git_url: https://git.bioconductor.org/packages/DLBCL git_branch: devel git_last_commit: 0ff2295 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/DLBCL_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: BioNet, mwcsr dependencyCount: 9 Package: DMRcatedata Version: 2.31.0 Depends: R (>= 4.0), ExperimentHub Imports: GenomicFeatures, Gviz, readxl, plyr, rtracklayer, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr License: GPL-3 MD5sum: 3ca5c5e6c134397cc64e365f53bccded NeedsCompilation: no Title: Data Package for DMRcate Description: This package contains 9 data objects supporting functionality and examples of the Bioconductor package DMRcate. biocViews: ExperimentHub, ExperimentData, SNPData, Homo_sapiens_Data, Mus_musculus_Data, SequencingData, MicroarrayData, Genome Author: Tim Peters Maintainer: Tim Peters VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DMRcatedata git_branch: devel git_last_commit: 11234be git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/DMRcatedata_2.31.0.tar.gz vignettes: vignettes/DMRcatedata/inst/doc/DMRcatedata.pdf vignetteTitles: The DMRcate package user's guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DMRcatedata/inst/doc/DMRcatedata.R dependencyCount: 208 Package: DMRsegaldata Version: 1.1.0 Depends: R (>= 4.5.0), ExperimentHub Suggests: knitr, rmarkdown, BiocStyle, ExperimentHubData License: GPL (>= 2) MD5sum: 4460702f3e55e0c179a15bbe9f21f269 NeedsCompilation: no Title: Example DNAm Data for DMRsegal Description: Data package providing example DNA methylation files used in the DMRsegal vignette and examples. Includes a sorted beta matrix as a tab-delimited, bgzip-compressed file and a matching phenotype table. The data contains 10 healthy and 10 cancer samples, and preprocessing has already been performed on the beta values. biocViews: ExperimentHub, ExperimentData, SNPData, SequencingData, MicroarrayData, Genome Author: Vasileios Lemonidis [aut, cre, cph] (ORCID: ), Center for Oncological Research, University of Antwerp [cph, fnd], Stichting Tegen Kanker [fnd] Maintainer: Vasileios Lemonidis URL: https://github.com/CMG-UA/DMRsegal VignetteBuilder: knitr BugReports: https://github.com/CMG-UA/DMRsegal/issues git_url: https://git.bioconductor.org/packages/DMRsegaldata git_branch: devel git_last_commit: ce339a5 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/DMRsegaldata_1.1.0.tar.gz vignettes: vignettes/DMRsegaldata/inst/doc/DMRsegaldata.html vignetteTitles: Introduction to DMRsegaldata hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DMRsegaldata/inst/doc/DMRsegaldata.R dependencyCount: 64 Package: DNAZooData Version: 1.13.0 Depends: R (>= 4.2), HiCExperiment Imports: BiocFileCache, S4Vectors, rjson, utils, tools Suggests: dplyr, testthat, methods, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 9dee44b778939f47fc0ba2cd7e8b4ce9 NeedsCompilation: no Title: DNA Zoo data package Description: DNAZooData is a data package giving programmatic access to genome assemblies and Hi-C contact matrices uniformly processed by the [DNA Zoo Consortium](https://www.dnazoo.org/). The matrices are available in the multi-resolution `.hic` format. A URL to corrected genome assemblies in `.fastq` format is also provided to the end-user. biocViews: ExperimentData, SequencingData Author: Jacques Serizay [aut, cre] Maintainer: Jacques Serizay URL: https://github.com/js2264/DNAZooData VignetteBuilder: knitr BugReports: https://github.com/js2264/DNAZooData/issues git_url: https://git.bioconductor.org/packages/DNAZooData git_branch: devel git_last_commit: fc17f13 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/DNAZooData_1.13.0.tar.gz vignettes: vignettes/DNAZooData/inst/doc/DNAZooData.html vignetteTitles: DNAZooData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/DNAZooData/inst/doc/DNAZooData.R dependencyCount: 88 Package: dominatRData Version: 1.1.0 Depends: R (>= 4.5.0) Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 18837e6e512d73afd45dd263e48defde NeedsCompilation: no Title: Datasets for R Package dominatR Description: dominatRData is a data package useful for showcasing dominatR examples. dominatR is an R package for quantifying and visualizing feature dominance in datasets. dominatR makes use of entropy-based triangular projections and compositional comparison metrics. biocViews: ExperimentData, ChIPSeqData, Tissue, PackageTypeData Author: Simon Lizarazo [aut, cre] (ORCID: ), Ethan Chen [ctb], Rajendra K C [ctb], Kevin Van Bortle [ctb] Maintainer: Simon Lizarazo URL: https://github.com/VanBortleLab/dominatRData VignetteBuilder: knitr BugReports: https://github.com/VanBortleLab/dominatRData/issues git_url: https://git.bioconductor.org/packages/dominatRData git_branch: devel git_last_commit: f277c56 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/dominatRData_1.1.0.tar.gz vignettes: vignettes/dominatRData/inst/doc/dominatRData.html vignetteTitles: Introduction to dominatR hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/dominatRData/inst/doc/dominatRData.R suggestsMe: dominatR dependencyCount: 0 Package: DonaPLLP2013 Version: 1.51.0 Depends: EBImage, parallel License: Artistic-2.0 MD5sum: 9c95b0b1d576ec0420c404e9b822de02 NeedsCompilation: no Title: Supplementary data package for Dona et al. (2013) containing example images and tables Description: An experiment data package associated with the publication Dona et al. (2013). Package contains runnable vignettes showing an example image segmentation for one posterior lateral line primordium, and also the data table and code used to analyze tissue-scale lifetime-ratio statistics. biocViews: ExperimentData, Tissue Author: Erika Dona, Joseph D. Barry, Guillaume Valentin, Charlotte Quirin, Anton Khmelinskii, Andreas Kunze, Sevi Durdu, Lionel R. Newton, Ana Fernandez-Minan, Wolfgang Huber, Michael Knop, Darren Gilmour Maintainer: Joseph D. Barry git_url: https://git.bioconductor.org/packages/DonaPLLP2013 git_branch: devel git_last_commit: 6e62b24 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/DonaPLLP2013_1.51.0.tar.gz vignettes: vignettes/DonaPLLP2013/inst/doc/PLLPanalysis.pdf, vignettes/DonaPLLP2013/inst/doc/PLLPstatistics.pdf vignetteTitles: PLLP image analysis, PLLP tissue-scale ratio statistics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DonaPLLP2013/inst/doc/PLLPanalysis.R, vignettes/DonaPLLP2013/inst/doc/PLLPstatistics.R dependencyCount: 46 Package: DoReMiTra Version: 1.3.0 Depends: R (>= 4.5.0) Imports: ExperimentHub, SummarizedExperiment, AnnotationHub, utils, glue, S4Vectors, scater Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, DT License: MIT + file LICENSE MD5sum: 4fdfc4432233658a64ada147022391f8 NeedsCompilation: no Title: Orchestrating Blood Radiation Transcriptomic Data Description: DoReMiTra is an R data package providing access to curated transcriptomic datasets related to blood radiation, with a focus on neutron, x-ray, and gamma ray studies. It is designed to facilitate radiation biology research and support data exploration and reproducibility in radiation transcriptomics. All datasets are provided as SummarizedExperiment objects, allowing seamless integration with the Bioconductor ecosystem. biocViews: ExperimentData, RNASeqData, ExperimentHub, ExpressionData, GEO, PackageTypeData Author: Ahmed Salah [aut, cre] (ORCID: ), Federico Marini [aut] (ORCID: ) Maintainer: Ahmed Salah URL: https://github.com/AhmedSAHassan/DoReMiTra VignetteBuilder: knitr BugReports: https://github.com/AhmedSAHassan/DoReMiTra/issues git_url: https://git.bioconductor.org/packages/DoReMiTra git_branch: devel git_last_commit: 4da68ce git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/DoReMiTra_1.3.0.tar.gz vignettes: vignettes/DoReMiTra/inst/doc/DoReMiTra.html vignetteTitles: The DoReMiTra User's Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/DoReMiTra/inst/doc/DoReMiTra.R dependencyCount: 127 Package: dressCheck Version: 0.51.0 Depends: R (>= 2.10.1), methods, Biobase (>= 2.5.5) Suggests: survival, chron License: Artistic-2.0 MD5sum: 98a90f5b697aeb916d8417ec5038bb3d NeedsCompilation: no Title: data and software for checking Dressman JCO 25(5) 2007 Description: data and software for checking Dressman JCO 25(5) 2007 biocViews: ExperimentData, Genome Author: Vincent Carey Maintainer: Vincent Carey git_url: https://git.bioconductor.org/packages/dressCheck git_branch: devel git_last_commit: 80e0b1c git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/dressCheck_0.51.0.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: 1.23.0 Imports: utils, ExperimentHub, AnnotationHub, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, testthat, DropletUtils License: GPL-3 MD5sum: 16d7f3d32742fad3e01012f83384bb6d NeedsCompilation: no Title: Test Files for Single-Cell Droplet Utilities Description: Assorted files generated from droplet-based single-cell protocols, to be used for testing functions in DropletUtils. Primarily intended for storing files that directly come out of processing pipelines like 10X Genomics' CellRanger software, prior to the formation of a SingleCellExperiment object. Unlike other packages, this is not designed to provide objects that are immediately ready for analysis. biocViews: ExperimentHub, ExperimentData, ExpressionData, SequencingData, RNASeqData, SingleCellData Author: Aaron Lun [ctb, cre] Maintainer: Aaron Lun VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DropletTestFiles git_branch: devel git_last_commit: cdd76ae git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/DropletTestFiles_1.23.0.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, TENxIO dependencyCount: 64 Package: DrugVsDiseasedata Version: 1.49.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 86338d6aeb28591d7d84c7f3f686783b NeedsCompilation: no Title: Drug versus Disease Data Description: Data package which provides default disease expression profiles, clusters and annotation information for use with the DrugVsDisease package. biocViews: Homo_sapiens_Data, MicroarrayData Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/DrugVsDiseasedata git_branch: devel git_last_commit: 9038eae git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/DrugVsDiseasedata_1.49.0.tar.gz vignettes: vignettes/DrugVsDiseasedata/inst/doc/DrugVsDiseasedata.pdf vignetteTitles: DrugVsDiseasedata hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DrugVsDiseasedata/inst/doc/DrugVsDiseasedata.R dependsOnMe: DrugVsDisease dependencyCount: 0 Package: DuoClustering2018 Version: 1.31.0 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: b8ca11b1143b124259ec5c04e42938ba NeedsCompilation: no Title: Data, Clustering Results and Visualization Functions From Duò et al (2018) Description: Preprocessed experimental and simulated scRNA-seq data sets used for evaluation of clustering methods for scRNA-seq data in Duò et al (2018). Also contains results from applying several clustering methods to each of the data sets, and functions for plotting method performance. biocViews: SingleCellData, ExperimentData Author: Angelo Duò, Charlotte Soneson Maintainer: Angelo Duò VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DuoClustering2018 git_branch: devel git_last_commit: 6894b97 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/DuoClustering2018_1.31.0.tar.gz vignettes: vignettes/DuoClustering2018/inst/doc/combine_data_clustering.html, vignettes/DuoClustering2018/inst/doc/plot_performance.html, vignettes/DuoClustering2018/inst/doc/run_clustering.html vignetteTitles: Visualize data sets and clustering results with iSEE, Plot performance summaries, Apply clustering method hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DuoClustering2018/inst/doc/combine_data_clustering.R, vignettes/DuoClustering2018/inst/doc/plot_performance.R, vignettes/DuoClustering2018/inst/doc/run_clustering.R suggestsMe: corral, scry dependencyCount: 81 Package: DvDdata Version: 1.49.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 636caee8fb13755201def1eb6730611f NeedsCompilation: no Title: Drug versus Disease Data Description: Data package which provides default drug and disease expression profiles for the DvD package. biocViews: GEO Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/DvDdata git_branch: devel git_last_commit: d9349a5 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/DvDdata_1.49.0.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: 1.53.0 Depends: R (>= 1.4.1), marray, GEOquery Suggests: dyebias, convert, Biobase License: GPL-3 MD5sum: d53d31e4189bf95d734b5b00d5545d04 NeedsCompilation: no Title: Example data for the dyebias package, which implements the GASSCO method. Description: Data for the dyebias package, consisting of 4 self-self hybrizations of self-spotted yeast slides, as well as data from Array Express accession E-MTAB-32 biocViews: ExperimentData, SAGEData, CGHData, MicroarrayData, TwoChannelData, ArrayExpress Author: Philip Lijnzaad and Thanasis Margaritis Maintainer: Philip Lijnzaad URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad git_url: https://git.bioconductor.org/packages/dyebiasexamples git_branch: devel git_last_commit: 354f761 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/dyebiasexamples_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: dyebias dependencyCount: 76 Package: easierData Version: 1.19.0 Depends: R (>= 4.1.0) Imports: ExperimentHub, AnnotationHub, utils, SummarizedExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 172b3566b7c8bd71ce782f97bb1cf4e1 NeedsCompilation: no Title: easier internal data and exemplary dataset from IMvigor210CoreBiologies package Description: Access to internal data required for the functional performance of easier package and exemplary bladder cancer dataset with both processed RNA-seq data and information on response to ICB therapy generated by Mariathasan et al. "TGF-B attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells", published in Nature, 2018 [doi:10.1038/nature25501](https://doi.org/10.1038/nature25501). The data is made available via [`IMvigor210CoreBiologies`](http://research-pub.gene.com/IMvigor210CoreBiologies/) package under the CC-BY license. biocViews: RNASeqData, ExperimentHub, ReproducibleResearch, ImmunoOncologyData, CancerData, ExperimentData Author: Oscar Lapuente-Santana [aut, cre] (ORCID: ), Federico Marini [aut] (ORCID: ), Arsenij Ustjanzew [aut] (ORCID: ), Francesca Finotello [aut] (ORCID: ), Federica Eduati [aut] (ORCID: ) Maintainer: Oscar Lapuente-Santana VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/easierData git_branch: devel git_last_commit: 3a9b249 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/easierData_1.19.0.tar.gz vignettes: vignettes/easierData/inst/doc/easierData.html vignetteTitles: easier data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/easierData/inst/doc/easierData.R dependencyCount: 75 Package: EatonEtAlChIPseq Version: 0.51.0 Depends: GenomicRanges (>= 1.5.42), ShortRead, rtracklayer License: Artistic 2.0 MD5sum: 9de75fa4bf358ff180aa66afef476881 NeedsCompilation: no Title: ChIP-seq data of ORC-binding sites in Yeast excerpted from Eaton et al. 2010 Description: ChIP-seq analysis subset from "Conserved nucleosome positioning defines replication origins" (PMID 20351051) biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, ChIPSeqData, GEO Author: Patrick Aboyoun Maintainer: Patrick Aboyoun git_url: https://git.bioconductor.org/packages/EatonEtAlChIPseq git_branch: devel git_last_commit: e9820af git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/EatonEtAlChIPseq_0.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 70 Package: ecoliLeucine Version: 1.53.0 Depends: R (>= 1.9.0), affy (>= 1.23.4), ecolicdf License: GPL (>= 2) MD5sum: 28a4ee84e618d595ff6a4f9ccc103583 NeedsCompilation: no Title: Experimental data with Affymetrix E. coli chips Description: Experimental data with Affymetrix E. coli chips, as reported in She-pin Hung, Pierre Baldi, and G. Wesley Hatfield, J. Biol. Chem., Vol. 277, Issue 43, 40309-40323, October 25, 2002 biocViews: ExperimentData, MicroarrayData Author: Laurent Gautier Maintainer: Laurent Gautier git_url: https://git.bioconductor.org/packages/ecoliLeucine git_branch: devel git_last_commit: 0e70fc5 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ecoliLeucine_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ecolitk dependencyCount: 47 Package: EGSEAdata Version: 1.41.0 Depends: R (>= 3.4) Suggests: EGSEA License: file LICENSE MD5sum: 4058c29de0c3cae625863cd7b2dd84f2 NeedsCompilation: no Title: Gene set collections for the EGSEA package Description: This package includes gene set collections that are used for the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. It includes Human and Mouse versions of the MSidDB (Subramanian, et al. (2005) PNAS, 102(43):15545-15550) and GeneSetDB (Araki, et al. (2012) FEBS Open Bio, 2:76-82) collections. biocViews: ExperimentData, Homo_sapiens_Data, Mus_musculus_Data, Rattus_norvegicus_Data Author: Monther Alhamdoosh, Yifang Hu and Gordon K. Smyth Maintainer: Monther Alhamdoosh git_url: https://git.bioconductor.org/packages/EGSEAdata git_branch: devel git_last_commit: f2aaa38 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/EGSEAdata_1.41.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: ELMER.data Version: 2.37.0 Depends: R (>= 3.5.0) Imports: GenomicRanges Suggests: BiocStyle, knitr, dplyr, devtools, DT, rmarkdown License: GPL-3 MD5sum: 5559723523598090e42306cc25c45a19 NeedsCompilation: no Title: Data for the ELMER package Description: Supporting data for the ELMER package. It includes: - elmer.data.example.promoter: mae.promoter - elmer.data.example: data - EPIC.hg38.manifest - EPIC.hg19.manifest - hm450.hg38.manifest - hm450.hg19.manifest - hocomoco.table - human.TF - LUSC_meth_refined: Meth - LUSC_RNA_refined: GeneExp - Probes.motif.hg19.450K - Probes.motif.hg19.EPIC - Probes.motif.hg38.450K - Probes.motif.hg38.EPIC - TF.family - TF.subfamily - Human_genes__GRCh37_p13 - Human_genes__GRCh38_p12 - Human_genes__GRCh37_p13__tss - Human_genes__GRCh38_p12__tss biocViews: AssayDomainData, TechnologyData, OrganismData Author: Tiago Chedraoui Silva, Lijing Yao Simon Coetzee, Benjamin P. Berman Maintainer: Tiago Chedraoui Silva VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ELMER.data git_branch: devel git_last_commit: f051777 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ELMER.data_2.37.0.tar.gz vignettes: vignettes/ELMER.data/inst/doc/vignettes.html vignetteTitles: ELMER.data: Supporting data for the ELMER package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ELMER.data/inst/doc/vignettes.R dependencyCount: 11 Package: emtdata Version: 1.21.0 Depends: R (>= 4.1) Imports: edgeR, ExperimentHub, SummarizedExperiment Suggests: testthat (>= 3.0.0), stringr, plyr, prettydoc, BiocStyle, Homo.sapiens, RColorBrewer, rmarkdown, BiocFileCache, knitr License: GPL-3 MD5sum: 1fe72ee85bca06e0e3f64a5d0ecf4a09 NeedsCompilation: no Title: An ExperimentHub Package for data sets with an Epithelial to Mesenchymal Transition (EMT) Description: This package provides pre-processed RNA-seq data where the epithelial to mesenchymal transition was induced on cell lines. These data come from three publications Cursons et al. (2015), Cursons etl al. (2018) and Foroutan et al. (2017). In each of these publications, EMT was induces across multiple cell lines following treatment by TGFb among other stimulants. This data will be useful in determining the regulatory programs modified in order to achieve an EMT. Data were processed by the Davis laboratory in the Bioinformatics division at WEHI. biocViews: ExperimentHub, Homo_sapiens_Data, RNASeqData, ExpressionData Author: Malvika D. Kharbanda [aut, cre] (ORCID: ), Chin Wee Tan [aut] (ORCID: ), Dharmesh D. Bhuva [aut] (ORCID: ) Maintainer: Malvika D. Kharbanda URL: https://github.com/DavisLaboratory/emtdata VignetteBuilder: knitr BugReports: https://github.com/DavisLaboratory/emtdata/issues git_url: https://git.bioconductor.org/packages/emtdata git_branch: devel git_last_commit: 48bda00 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/emtdata_1.21.0.tar.gz vignettes: vignettes/emtdata/inst/doc/emtdataR.html vignetteTitles: emtdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/emtdata/inst/doc/emtdataR.R dependencyCount: 79 Package: EMTscoreData Version: 1.1.0 Imports: SummarizedExperiment, Seurat, SingleCellExperiment, AnnotationHub, ExperimentHub, ggplot2 Suggests: BiocFileCache, SeuratObject, knitr, rmarkdown, googledrive, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: c4999ff72036d93b1f6505f0adc0f4c1 NeedsCompilation: no Title: Single-cell RNA-seq datasets of EMT responses from Cook et al. (2020) Description: Provides 12 single-cell RNA-seq datasets profiling epithelial–mesenchymal transition (EMT) in human cancer cell lines (MCF7, OVCA420, DU145, and A549) under TGF-beta stimulation, kinase inhibition, and time-course conditions, as reported by Cook DP and Vanderhyden BC (2020). The datasets are distributed via ExperimentHub as SingleCellExperiment objects. biocViews: ExperimentHub, SingleCellData, ExpressionData, CancerData, RNASeqData Author: Haimei Wen [aut, cre] (ORCID: ), Tian Hong [fnd] Maintainer: Haimei Wen URL: https://github.com/wenmm/EMTscoreData VignetteBuilder: knitr BugReports: https://github.com/wenmm/EMTscoreData/issues git_url: https://git.bioconductor.org/packages/EMTscoreData git_branch: devel git_last_commit: c9557df git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/EMTscoreData_1.1.0.tar.gz vignettes: vignettes/EMTscoreData/inst/doc/EMTscoreData.html vignetteTitles: EMTscoreData Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/EMTscoreData/inst/doc/EMTscoreData.R dependencyCount: 183 Package: eoPredData Version: 1.7.0 Depends: ExperimentHub Suggests: BiocStyle, knitr, rmarkdown, RefManageR, planet, mixOmics License: MIT + file LICENSE MD5sum: 93676f0ceedc24d5892e591b29535d3d NeedsCompilation: no Title: ExperimentHub package containing model data for predicting preeclampsia status for based on plcaental DNA methylation profile Description: Provides access to eoPred pretrained model hosted on ExperimentHub. Model was trained on placental DNA methylation preeclampsia samples using mixOmics splsda. There are two resources: 1. the model object, and 2. a testing data set used to demonstrate the function. biocViews: ExperimentData, ExperimentHub, GEO, Tissue, MethylationArrayData, Homo_sapiens_Data Author: Iciar Boyano [aut], Victor Yuan [aut, cre] Maintainer: Victor Yuan URL: https://github.com/wvictor14/eoPredData VignetteBuilder: knitr BugReports: https://github.com/wvictor14/eoPredData/issues git_url: https://git.bioconductor.org/packages/eoPredData git_branch: devel git_last_commit: 023e9ab git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/eoPredData_1.7.0.tar.gz vignettes: vignettes/eoPredData/inst/doc/eoPredData.html vignetteTitles: eoPredData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/eoPredData/inst/doc/eoPredData.R dependencyCount: 64 Package: EpiMix.data Version: 1.15.0 Depends: R (>= 4.2.0), ExperimentHub (>= 0.99.6) Suggests: rmarkdown, knitr License: GPL-3 MD5sum: fb885226de8dd262da8ed2005b39414b NeedsCompilation: no Title: Data for the EpiMix package Description: Supporting data for the EpiMix R package. It include: - HM450_lncRNA_probes.rda - HM450_miRNA_probes.rda - EPIC_lncRNA_probes.rda - EPIC_miRNA_probes.rda - EpigenomeMap.rda - LUAD.sample.annotation - TCGA_BatchData - MET.data - mRNA.data - microRNA.data - lncRNA.data - Sample_EpiMixResults_lncRNA - Sample_EpiMixResults_miRNA - Sample_EpiMixResults_Regular - Sample_EpiMixResults_Enhancer - lncRNA expression data of tumors from TCGA that are stored in the ExperimentHub. biocViews: ExperimentData, ExperimentHub, Genome, RNASeqData, ExpressionData Author: Yuanning Zheng [aut, cre] Maintainer: Yuanning Zheng VignetteBuilder: knitr BugReports: https://github.com/gevaertlab/EpiMix/issues git_url: https://git.bioconductor.org/packages/EpiMix.data git_branch: devel git_last_commit: 3c653e6 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/EpiMix.data_1.15.0.tar.gz vignettes: vignettes/EpiMix.data/inst/doc/RetrieveData.html vignetteTitles: vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/EpiMix.data/inst/doc/RetrieveData.R dependencyCount: 64 Package: epimutacionsData Version: 1.17.0 Depends: R (>= 4.2.0) Suggests: rmarkdown, BiocStyle, knitr, ExperimentHub, minfi License: MIT + file LICENSE MD5sum: 9d41ded1e697ed10099e09f0e89e1bb3 NeedsCompilation: no Title: Data for epimutacions package Description: This package includes the data necessary to run functions and examples in epimutacions package. Collection of DNA methylation data. The package contains 2 datasets: (1) Control ( GEO: GSE104812), (GEO: GSE97362) case samples; and (2) reference panel (GEO: GSE127824). It also contains candidate regions to be epimutations in 450k methylation arrays. biocViews: ExperimentHub, Homo_sapiens_Data, MethylationArrayData, MicroarrayData Author: Leire Abarrategui [aut, cre], Juan R. Gonzalez [aut], Carlos Ruiz-Arenas [aut], Carles Hernandez-Ferrer [aut] Maintainer: Leire Abarrategui URL: https://github.com/LeireAbarrategui/epimutacionsData VignetteBuilder: knitr BugReports: https://github.com/LeireAbarrategui/epimutacionsData/issues git_url: https://git.bioconductor.org/packages/epimutacionsData git_branch: devel git_last_commit: 6586c33 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/epimutacionsData_1.17.0.tar.gz vignettes: vignettes/epimutacionsData/inst/doc/epimutacionsData.html vignetteTitles: data repository for epimutacions package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/epimutacionsData/inst/doc/epimutacionsData.R dependencyCount: 0 Package: EpipwR.data Version: 1.7.0 Imports: ExperimentHub Suggests: knitr, rmarkdown, sessioninfo License: Artistic-2.0 MD5sum: c810239d8168eaefb118b3ee0df53cd2 NeedsCompilation: no Title: EpipwR.data: Reference data for EpipwR Description: This package provides reference data for EpipwR. EpipwR is a fast and efficient power analysis for continuous and binary phenotypes of epigenomic-wide association studies. This package is only meant to be used in conjunction with EpipwR. biocViews: ExperimentHub, MethylationArrayData, MicroarrayData, TissueMicroarrayData, Tissue, ExperimentData Author: Jackson Barth [aut, cre] (ORCID: ), Austin Reynolds [aut] Maintainer: Jackson Barth URL: https://github.com/jbarth216/EpipwR.data VignetteBuilder: knitr BugReports: https://github.com/jbarth216/EpipwR.data git_url: https://git.bioconductor.org/packages/EpipwR.data git_branch: devel git_last_commit: cba09c2 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/EpipwR.data_1.7.0.tar.gz vignettes: vignettes/EpipwR.data/inst/doc/EpipwR.data.html vignetteTitles: EpipwR.data: Reference data for EpipwR hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/EpipwR.data/inst/doc/EpipwR.data.R importsMe: EpipwR dependencyCount: 64 Package: estrogen Version: 1.59.0 Suggests: affy, hgu95av2.db, hgu95av2cdf, vsn, knitr, genefilter License: LGPL MD5sum: 8b2fdf4c663bedb8f5927181d4d4b0bb NeedsCompilation: no Title: Microarray dataset that can be used as example for 2x2 factorial designs Description: Data from 8 Affymetrix genechips, looking at a 2x2 factorial design (with 2 repeats per level). biocViews: ExperimentData, MicroarrayData Author: Wolfgang Huber, Robert Gentleman Maintainer: Wolfgang Huber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/estrogen git_branch: devel git_last_commit: 79cc12d git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/estrogen_1.59.0.tar.gz vignettes: vignettes/estrogen/inst/doc/estrogen.pdf vignetteTitles: estrogen hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/estrogen/inst/doc/estrogen.R dependencyCount: 0 Package: etec16s Version: 1.41.0 Depends: R (>= 3.3), Biobase, metagenomeSeq(>= 1.12.0) License: Artistic-2.0 MD5sum: 30c19fef193fa648a656a840321a0c51 NeedsCompilation: no Title: Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment Description: 16S rRNA gene sequencing data to study changes in the faecal microbiota of 12 volunteers during a human challenge study with ETEC (H10407) and subsequent treatment with ciprofloxacin. biocViews: ExperimentData, SequencingData, MicrobiomeData Author: Joseph N. Paulson Maintainer: Joseph N. Paulson git_url: https://git.bioconductor.org/packages/etec16s git_branch: devel git_last_commit: 87d5411 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/etec16s_1.41.0.tar.gz vignettes: vignettes/etec16s/inst/doc/etec16s.pdf vignetteTitles: etec16s hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/etec16s/inst/doc/etec16s.R dependencyCount: 33 Package: ewceData Version: 1.21.0 Depends: R (>= 4.1), ExperimentHub Suggests: knitr, BiocStyle, ggplot2, cowplot, rmarkdown, markdown, rbibutils, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 5948c7d052f996948a61df46d6f9d773 NeedsCompilation: no Title: The ewceData package provides reference data required for ewce Description: This package provides reference data required for ewce. Expression Weighted Celltype Enrichment (EWCE) is used to determine which cell types are enriched within gene lists. The package provides tools for testing enrichments within simple gene lists (such as human disease associated genes) and those resulting from differential expression studies. The package does not depend upon any particular Single Cell Transcriptome dataset and user defined datasets can be loaded in and used in the analyses. biocViews: ExperimentData, ExperimentHub, ExpressionData, Genome, Proteome, MicroarrayData, SequencingData, SingleCellData, RNASeqData Author: Alan Murphy [aut] (ORCID: ), Hiranyamaya Dash [cre] (ORCID: ), Nathan Skene [aut] (ORCID: ) Maintainer: Hiranyamaya Dash URL: https://github.com/neurogenomics/ewceData VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ewceData git_branch: devel git_last_commit: 29b7bce git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ewceData_1.21.0.tar.gz vignettes: vignettes/ewceData/inst/doc/ewceData.html vignetteTitles: Data package for Expression Weighted Celltype Enrichment EWCE hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ewceData/inst/doc/ewceData.R importsMe: EWCE dependencyCount: 64 Package: faahKO Version: 1.51.0 Depends: R (>= 3.5) Imports: xcms (>= 4.5.4) Suggests: MSnbase (>= 2.33.3) License: LGPL MD5sum: 19e1b431906633ee8076961bcb5a5939 NeedsCompilation: no Title: Saghatelian et al. (2004) FAAH knockout LC/MS data Description: Positive ionization mode data in NetCDF file format. Centroided subset from 200-600 m/z and 2500-4500 seconds. Data originally reported in "Assignment of Endogenous Substrates to Enzymes by Global Metabolite Profiling" Biochemistry; 2004; 43(45). Also includes detected peaks in an xcmsSet. biocViews: ExperimentData, MassSpectrometryData Author: Colin A. Smith Maintainer: Steffen Neumann URL: http://dx.doi.org/10.1021/bi0480335 git_url: https://git.bioconductor.org/packages/faahKO git_branch: devel git_last_commit: 620ca15 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/faahKO_1.51.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 1 Package: fabiaData Version: 1.51.0 Depends: R (>= 2.10.0), Biobase Imports: utils Suggests: fabia License: LGPL (>= 2.1) MD5sum: ab60f12c2872c60c2f4802617e8a4f37 NeedsCompilation: no Title: Data sets for FABIA (Factor Analysis for Bicluster Acquisition) Description: Supplying gene expression data sets for the demos of the biclustering method "Factor Analysis for Bicluster Acquisition" (FABIA). The following three data sets are provided: A) breast cancer (van't Veer, Nature, 2002), B) multiple tissues (Su, PNAS, 2002), and C) diffuse large-B-cell lymphoma (Rosenwald, N Engl J Med, 2002). biocViews: CancerData, BreastCancerData, MicroarrayData Author: Sepp Hochreiter Maintainer: Sepp Hochreiter URL: http://www.bioinf.jku.at/software/fabia/fabia.html git_url: https://git.bioconductor.org/packages/fabiaData git_branch: devel git_last_commit: 4136acf git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/fabiaData_1.51.0.tar.gz vignettes: vignettes/fabiaData/inst/doc/fabiaData.pdf vignetteTitles: fabiaData: Manual for the R Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/fabiaData/inst/doc/fabiaData.R dependencyCount: 7 Package: FANTOM3and4CAGE Version: 1.49.0 Depends: R (>= 2.15.0) License: GPL-3 MD5sum: 9074ed9fdc6166ea055b23d914f2c8e5 NeedsCompilation: no Title: CAGE data from FANTOM3 and FANTOM4 projects Description: CAGE (Cap Analysis Gene Expression) data from FANTOM3 and FANTOM4 projects produced by RIKEN Omics Science Center. biocViews: ExperimentData, Tissue Author: Vanja Haberle, Department of Biology, University of Bergen, Norway Maintainer: Vanja Haberle git_url: https://git.bioconductor.org/packages/FANTOM3and4CAGE git_branch: devel git_last_commit: f98e3bb git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/FANTOM3and4CAGE_1.49.0.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: 1.51.0 Depends: R (>= 2.10.0), lumi Suggests: genefilter, affy License: GPL (>2) MD5sum: 93bba3b847b95394bac2d8a8bc59f682 NeedsCompilation: no Title: Illumina DASL example microarray data Description: A subset of GSE17565 (April et al. 2009) containing 32 FFPE samples of Burkitts Lymphoma and Breast Adenocarcinoma, with a dilution series in technical duplicate. biocViews: Tissue, Genome, MicroarrayData, TissueMicroarrayData, GEO Author: Levi Waldron Maintainer: Levi Waldron git_url: https://git.bioconductor.org/packages/ffpeExampleData git_branch: devel git_last_commit: ee4ce2c git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ffpeExampleData_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ffpe dependencyCount: 168 Package: fibroEset Version: 1.55.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: 8fb40c77e391a537ffbc5652acfea0b2 NeedsCompilation: no Title: exprSet for Karaman et al. (2003) fibroblasts data Description: exprSet for Karaman et al. (2003) human, bonobo and gorilla fibroblasts data biocViews: ExperimentData, Genome, Homo_sapiens_Data, MicroarrayData, ChipOnChipData Author: Sylvia Merk Maintainer: Sylvia Merk git_url: https://git.bioconductor.org/packages/fibroEset git_branch: devel git_last_commit: 4bbd90b git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/fibroEset_1.55.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: biocGraph, clusterStab, geneplotter dependencyCount: 7 Package: FieldEffectCrc Version: 1.23.0 Depends: utils Imports: BiocStyle, RUnit, SummarizedExperiment, ExperimentHub (>= 0.99.6), AnnotationHub, DESeq2 Suggests: knitr, rmarkdown, BiocGenerics, sva, BiocManager License: Artistic-2.0 MD5sum: 8167d507ead12bfb74033d3dfe83dd43 NeedsCompilation: no Title: Tumor, tumor-adjacent normal, and healthy colorectal transcriptomes as SummarizedExperiment objects Description: Processed RNA-seq data for 1,139 human primary colorectal tissue samples across three phenotypes, including tumor, normal adjacent-to-tumor, and healthy, available as Synapse ID syn22237139 on synapse.org. Data have been parsed into SummarizedExperiment objects available via ExperimentHub to facilitate reproducibility and extension of results from Dampier et al. (PMCID: PMC7386360, PMID: 32764205). biocViews: ExperimentData, ReproducibleResearch, Tissue, Homo_sapiens_Data, ColonCancerData, RNASeqData, ExpressionData, ExperimentHub, SequencingData Author: Christopher Dampier [aut, cre] (ORCID: ), Bioconductor Package Maintainer [ctb] Maintainer: Christopher Dampier URL: http://bioconductor.org/packages/release/bioc/html/FieldEffectCrc.html VignetteBuilder: knitr BugReports: https://github.com/Bioconductor/FieldEffectCrc/ git_url: https://git.bioconductor.org/packages/FieldEffectCrc git_branch: devel git_last_commit: 22e600e git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/FieldEffectCrc_1.23.0.tar.gz vignettes: vignettes/FieldEffectCrc/inst/doc/FieldEffectCrc.html vignetteTitles: SummarizedExperiments of colorectal transcriptomes hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FieldEffectCrc/inst/doc/FieldEffectCrc.R dependencyCount: 114 Package: FIs Version: 1.41.0 Depends: R (>= 3.3) License: GPL-3 MD5sum: 1dc10d7d0555e6d654c3981734df2b84 NeedsCompilation: no Title: Human Functional Interactions (FIs) for splineTimeR package Description: Data set containing two complete lists of identified functional interaction partners in Human. Data are derived from Reactome and BioGRID databases. biocViews: PathwayInteractionDatabase, Homo_sapiens_Data Author: Agata Michna Maintainer: Herbert Braselmann , Martin Selmansberger git_url: https://git.bioconductor.org/packages/FIs git_branch: devel git_last_commit: 2994acc git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/FIs_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: splineTimeR dependencyCount: 0 Package: fission Version: 1.33.0 Depends: R (>= 2.10), SummarizedExperiment Suggests: knitr, markdown License: LGPL MD5sum: 78137914e746660b1389be78b23275d7 NeedsCompilation: no Title: RangedSummarizedExperiment for time course RNA-Seq of fission yeast in response to stress, by Leong et al., Nat Commun 2014. Description: This package provides a RangedSummarizedExperiment object of read counts in genes for a time course RNA-Seq experiment of fission yeast (Schizosaccharomyces pombe) in response to oxidative stress (1M sorbitol treatment) at 0, 15, 30, 60, 120 and 180 mins. The samples are further divided between a wild-type group and a group with deletion of atf21. The read count matrix was prepared and provided by the author of the study: Leong HS, Dawson K, Wirth C, Li Y, Connolly Y, Smith DL, Wilkinson CR, Miller CJ. "A global non-coding RNA system modulates fission yeast protein levels in response to stress". Nat Commun 2014 May 23;5:3947. PMID: 24853205. GEO: GSE56761. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData, GEO Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/fission git_branch: devel git_last_commit: a0a3080 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/fission_1.33.0.tar.gz vignettes: vignettes/fission/inst/doc/fission.html vignetteTitles: Fission yeast time course hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/fission/inst/doc/fission.R dependsOnMe: ROCpAI, rnaseqGene dependencyCount: 25 Package: Fletcher2013a Version: 1.49.0 Depends: R (>= 2.15), limma Imports: Biobase ,VennDiagram, gplots,grid License: GPL (>= 2) MD5sum: c61029005bd4c79a506947ef6678f3b5 NeedsCompilation: no Title: Gene expression data from breast cancer cells under FGFR2 signalling perturbation Description: The package Fletcher2013a contains time-course gene expression data from MCF-7 cells treated under different experimental systems in order to perturb FGFR2 signalling. The data comes from Fletcher et al. (Nature Comms 4:2464, 2013) where further details about the background and the experimental design of the study can be found. biocViews: ExperimentData, ExpressionData, CancerData, BreastCancerData, MicroarrayData Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin Meyer. Maintainer: Mauro Castro URL: http://dx.doi.org/10.1038/ncomms3464 git_url: https://git.bioconductor.org/packages/Fletcher2013a git_branch: devel git_last_commit: 3f2f39b git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/Fletcher2013a_1.49.0.tar.gz vignettes: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.pdf vignetteTitles: Main vignette:Fletcher2013a hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.R suggestsMe: NetActivity dependencyCount: 21 Package: flowPloidyData Version: 1.39.0 Suggests: knitr, rmarkdown, flowCore License: GPL-3 MD5sum: 244ec05bba9abe2527eed6ee0fd10800 NeedsCompilation: no Title: Example Flow Cytometry Data Description: A collection of raw flow cytometry data for use in vignettes for the flowPloidy package. biocViews: FlowCytometryData Author: Tyler Smith Maintainer: Tyler Smith VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/flowPloidyData git_branch: devel git_last_commit: 8099dbb git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/flowPloidyData_1.39.0.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: 1.51.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 08359625e7796694687e113e01f0b01d NeedsCompilation: no Title: Illumina HumanMethylation data on sorted blood cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays, and an object depicting which CpGs on the array are associated with cell type. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Andrew E Jaffe Maintainer: Andrew E Jaffe git_url: https://git.bioconductor.org/packages/FlowSorted.Blood.450k git_branch: devel git_last_commit: 603b71d git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/FlowSorted.Blood.450k_1.51.0.tar.gz vignettes: vignettes/FlowSorted.Blood.450k/inst/doc/FlowSorted.Blood.450k.pdf vignetteTitles: FlowSorted Blood 450k Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.Blood.450k/inst/doc/FlowSorted.Blood.450k.R dependsOnMe: methylCC, methylationArrayAnalysis suggestsMe: minfi, wateRmelon, FlowSorted.Blood.EPIC dependencyCount: 146 Package: FlowSorted.Blood.EPIC Version: 2.17.0 Depends: R (>= 3.5), minfi(>= 1.21.2), ExperimentHub Imports: genefilter, nlme, quadprog, graphics, stats, utils, AnnotationHub, SummarizedExperiment, S4Vectors Suggests: knitr,rmarkdown, FlowSorted.CordBlood.450k, FlowSorted.Blood.450k(>= 1.0.1), EpiDISH,FlowSorted.CordBloodNorway.450k, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Enhances: FlowSorted.CordBloodCombined.450k(>= 1.11.5) License: GPL-3 MD5sum: 4c153891f4370740f82ed1ff0ee375b2 NeedsCompilation: no Title: Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells Description: Raw data objects to be used for blood cell proportion estimation in minfi and similar packages. The FlowSorted.Blood.EPIC object is based in samples assayed by Brock Christensen and colleagues; for details see Salas et al. 2018. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, Genome, TissueMicroarrayData, MethylationArrayData Author: Lucas A. Salas [cre, aut], Devin C. Koestler [aut], Rondi A. Butler [ctb], Helen M. Hansen [ctb], John K. Wiencke [ctb], Karl T. Kelsey [ctb], Brock C. Christensen [ctb], Kasper Daniel Hansen [ctb] (author and maintainer of the original minfi estimateCellCounts and internal functions), Jean-Philippe Fortin [ctb] (contributor in the original minfi estimateCellCounts and internal functions), Shan V. Andrews [ctb] (contributor in the original minfi estimateCellCounts and internal functions), E. Andres Houseman [ctb] (author of the original quadratic programming function used for cell projection), Andrew E Jaffe [ctb] (author of the original estimateCellCounts and internal functions within minfi) Maintainer: Lucas A. Salas URL: https://github.com/immunomethylomics/FlowSorted.Blood.EPIC VignetteBuilder: knitr BugReports: https://github.com/immunomethylomics/FlowSorted.Blood.EPIC/issues. git_url: https://git.bioconductor.org/packages/FlowSorted.Blood.EPIC git_branch: devel git_last_commit: 67491cd git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/FlowSorted.Blood.EPIC_2.17.0.tar.gz vignettes: vignettes/FlowSorted.Blood.EPIC/inst/doc/FlowSorted.Blood.EPIC.html vignetteTitles: FlowSorted.Blood.EPIC hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.Blood.EPIC/inst/doc/FlowSorted.Blood.EPIC.R importsMe: HiBED suggestsMe: wateRmelon, FlowSorted.CordBloodCombined.450k dependencyCount: 152 Package: FlowSorted.CordBlood.450k Version: 1.41.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: e12728cfa34f4c3831db1be164bab416 NeedsCompilation: no Title: Illumina 450k data on sorted cord blood cells Description: Raw data objects to be used for cord blood cell proportion estimation in minfi. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Shan V. Andrews [cre, aut], Kelly M. Bakulski [aut] Maintainer: Shan V. Andrews git_url: https://git.bioconductor.org/packages/FlowSorted.CordBlood.450k git_branch: devel git_last_commit: e56c436 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/FlowSorted.CordBlood.450k_1.41.0.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: 146 Package: FlowSorted.CordBloodCombined.450k Version: 1.29.0 Depends: R (>= 3.6), minfi (>= 1.21.2), ExperimentHub(>= 1.9.1) Imports: SummarizedExperiment, IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b4.hg19, utils, AnnotationHub Suggests: FlowSorted.Blood.EPIC, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: GPL-3 MD5sum: 2fe081e21fb3616bd9572b6429751e57 NeedsCompilation: no Title: Illumina 450k/EPIC data on FACS and MACS umbilical blood cells Description: Raw data objects to be used for umbilical cord blood cell proportion estimation in minfi and similar packages. The FlowSorted.CordBloodCombined.450k object is based in samples assayed by Bakulski et al, Gervin et al., de Goede et al., and Lin et al. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, Genome, TissueMicroarrayData, MethylationArrayData, ExperimentHub Author: Lucas A. Salas [cre, aut], Kristina Gervin [aut], Meaghan C. Jones [aut], Kelly M. Bakulski [ctb], Devin C. Koestler [ctb], John K. Wiencke [ctb], Karl T. Kelsey [ctb], Robert Lyle [ctb], Brock C. Christensen [ctb], Janine Felix [ctb] Maintainer: Lucas A. Salas URL: https://github.com/immunomethylomics/FlowSorted.CordBloodCombined.450k VignetteBuilder: knitr BugReports: https://github.com/immunomethylomics/FlowSorted.CordBloodCombined.450k/issues. git_url: https://git.bioconductor.org/packages/FlowSorted.CordBloodCombined.450k git_branch: devel git_last_commit: 0cdd791 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/FlowSorted.CordBloodCombined.450k_1.29.0.tar.gz vignettes: vignettes/FlowSorted.CordBloodCombined.450k/inst/doc/FlowSorted.CordBloodCombined.450k.html vignetteTitles: FlowSorted.CordBloodCombined.450k hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.CordBloodCombined.450k/inst/doc/FlowSorted.CordBloodCombined.450k.R dependencyCount: 154 Package: FlowSorted.CordBloodNorway.450k Version: 1.39.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 3c0a9abd338d931e4b27bc26903d63b4 NeedsCompilation: no Title: Illumina HumanMethylation data on sorted cord blood cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays, for cell type composition estimation. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: kristina gervin [cre, aut], Kasper Daniel Hansen [aut] Maintainer: kristina gervin URL: https://bitbucket.com/kasperdanielhansen/Illumina_CordBlood git_url: https://git.bioconductor.org/packages/FlowSorted.CordBloodNorway.450k git_branch: devel git_last_commit: 00e62bd git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/FlowSorted.CordBloodNorway.450k_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 146 Package: FlowSorted.DLPFC.450k Version: 1.49.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 6d1d68412ebba92e302dd5db8c27a866 NeedsCompilation: no Title: Illumina HumanMethylation data on sorted frontal cortex cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Andrew E Jaffe, Zachary A. Kaminsky Maintainer: Andrew E Jaffe git_url: https://git.bioconductor.org/packages/FlowSorted.DLPFC.450k git_branch: devel git_last_commit: c63b41c git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/FlowSorted.DLPFC.450k_1.49.0.tar.gz vignettes: vignettes/FlowSorted.DLPFC.450k/inst/doc/FlowSorted.DLPFC.450k.pdf vignetteTitles: FlowSorted DLPFC 450k Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.DLPFC.450k/inst/doc/FlowSorted.DLPFC.450k.R importsMe: HiBED dependencyCount: 146 Package: flowWorkspaceData Version: 3.25.0 License: GPL-2 MD5sum: 04bf305f8fd1f86fd1e507c788640a3b NeedsCompilation: no Title: A data package containing two flowJo, one diva xml workspace and the associated fcs files as well as three GatingSets for testing the flowWorkspace, openCyto and CytoML packages. Description: The necessary external data to run the flowWorkspace and openCyto vignette is found in this package. biocViews: ExperimentData, FlowCytometryData Author: Greg Finak Maintainer: Mike Jiang git_url: https://git.bioconductor.org/packages/flowWorkspaceData git_branch: devel git_last_commit: dad6b3b git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/flowWorkspaceData_3.25.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CytoML, flowClust, flowCore, flowWorkspace, ggcyto, openCyto dependencyCount: 0 Package: fourDNData Version: 1.13.0 Depends: R (>= 4.2) Imports: BiocFileCache, HiCExperiment, GenomicRanges, IRanges, S4Vectors, utils, tools Suggests: rtracklayer, dplyr, testthat, methods, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 4840bfcb935383e0f8b18cf000ef1400 NeedsCompilation: no Title: 4DN data package Description: fourDNData is a data package giving programmatic access to Hi-C contact matrices uniformly processed by the [4DN consortium](https://www.4dnucleome.org/). The matrices are available in the multi-resolution `.mcool` format. biocViews: ExperimentData, SequencingData Author: Jacques Serizay [aut, cre] Maintainer: Jacques Serizay URL: https://github.com/js2264/fourDNData VignetteBuilder: knitr BugReports: https://github.com/js2264/fourDNData/issues git_url: https://git.bioconductor.org/packages/fourDNData git_branch: devel git_last_commit: 61c9833 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/fourDNData_1.13.0.tar.gz vignettes: vignettes/fourDNData/inst/doc/fourDNData.html vignetteTitles: fourDNData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/fourDNData/inst/doc/fourDNData.R dependencyCount: 87 Package: frmaExampleData Version: 1.49.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: de068a5b0f3a11184fdf3e941b948842 NeedsCompilation: no Title: Frma Example Data Description: Data files used by the examples in frma and frmaTools packages biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/frmaExampleData git_branch: devel git_last_commit: 49cfd65 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/frmaExampleData_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: frma, frmaTools dependencyCount: 0 Package: gageData Version: 2.51.0 Depends: R (>= 2.10) Suggests: gage, pathview, genefilter License: GPL (>=2.0) MD5sum: a60e71f5947e874ec34ba9a3e059f361 NeedsCompilation: no Title: Auxillary data for gage package Description: This is a supportive data package for the software package, gage. However, the data supplied here are also useful for gene set or pathway analysis or microarray data analysis in general. In this package, we provide two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and BMP6 (originally published as an demo dataset for GAGE, also registered as GSE13604 in GEO). This package also includes commonly used gene set data based on KEGG pathways and GO terms for major research species, including human, mouse, rat and budding yeast. Mapping data between common gene IDs for budding yeast are also included. biocViews: ExperimentData, StemCell, CancerData, BreastCancerData, MicroarrayData, GEO Author: Weijun Luo Maintainer: Weijun Luo git_url: https://git.bioconductor.org/packages/gageData git_branch: devel git_last_commit: 9566944 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/gageData_2.51.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: gage dependencyCount: 0 Package: gaschYHS Version: 1.51.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 652f0a2f89c28bec583a9c98a4145320 NeedsCompilation: no Title: ExpressionSet for response of yeast to heat shock and other environmental stresses Description: Data from PMID 11102521 biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data Author: Audrey Gasch and colleagues Maintainer: Vince Carey URL: http://genome-www.stanford.edu/yeast_stress/data/rawdata/complete_dataset.txt git_url: https://git.bioconductor.org/packages/gaschYHS git_branch: devel git_last_commit: 8cacd13 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/gaschYHS_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: gcspikelite Version: 1.51.0 Depends: R (>= 2.5.0) License: LGPL MD5sum: d6c9c64421b96ed1b359e467a96c08e4 NeedsCompilation: no Title: Spike-in data for GC/MS data and methods within flagme Description: Spike-in data for GC/MS data and methods within flagme biocViews: MassSpectrometryData Author: Mark Robinson Maintainer: Mark Robinson git_url: https://git.bioconductor.org/packages/gcspikelite git_branch: devel git_last_commit: 647dcd8 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/gcspikelite_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: erah dependencyCount: 0 Package: gDNAinRNAseqData Version: 1.13.0 Depends: R (>= 4.3) Imports: RCurl, XML, ExperimentHub, BiocGenerics, Rsamtools Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 87a6b23064820c3fb3cee0896ff8e7d8 NeedsCompilation: no Title: RNA-seq data with different levels of gDNA contamination Description: Provides access to BAM files generated from RNA-seq data produced with different levels of gDNA contamination. It currently allows one to download a subset of the data published by Li et al., BMC Genomics, 23:554, 2022. This subset of data is formed by BAM files with about 100,000 alignments with three different levels of gDNA contamination. biocViews: ExperimentHub, ExperimentData, ExpressionData, SequencingData, RNASeqData, Homo_sapiens_Data Author: Robert Castelo [aut, cre] (ORCID: ) Maintainer: Robert Castelo URL: https://github.com/functionalgenomics/gDNAinRNAseqData VignetteBuilder: knitr BugReports: https://github.com/functionalgenomics/gDNAinRNAseqData git_url: https://git.bioconductor.org/packages/gDNAinRNAseqData git_branch: devel git_last_commit: 34e1e2a git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/gDNAinRNAseqData_1.13.0.tar.gz vignettes: vignettes/gDNAinRNAseqData/inst/doc/gDNAinRNAseqData.html vignetteTitles: RNA-seq data with different levels of gDNA contamination hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/gDNAinRNAseqData/inst/doc/gDNAinRNAseqData.R suggestsMe: gDNAx dependencyCount: 79 Package: gDRtestData Version: 1.11.1 Depends: R (>= 4.2) Imports: checkmate, data.table Suggests: BiocStyle, gDRstyle (>= 1.7.1), knitr, qs2, reshape2, rmarkdown, SummarizedExperiment, testthat, yaml License: Artistic-2.0 MD5sum: 75a96ea08eb99ce42018acda77902d28 NeedsCompilation: no Title: gDRtestData - R data package with testing dose response data Description: R package with internal dose-response test data. Package provides functions to generate input testing data that can be used as the input for gDR pipeline. It also contains qs2 files with MAE data processed by gDR. biocViews: ExperimentData, TechnologyData Author: Aleksander Chlebowski [aut], Bartosz Czech [aut] (ORCID: ), Arkadiusz Gladki [cre, aut] (ORCID: ), Marc Hafner [aut] (ORCID: ), Marcin Kamianowski [aut], Sergiu Mocanu [aut], Natalia Potocka [aut], Dariusz Scigocki [aut], Janina Smola [aut], Allison Voung [aut] Maintainer: Arkadiusz Gladki URL: https://github.com/gdrplatform/gDRtestData, https://gdrplatform.github.io/gDRtestData/ VignetteBuilder: knitr BugReports: https://github.com/gdrplatform/gDRtestData/issues git_url: https://git.bioconductor.org/packages/gDRtestData git_branch: devel git_last_commit: 94e8bcc git_last_commit_date: 2026-04-30 Date/Publication: 2026-04-30 source.ver: src/contrib/gDRtestData_1.11.1.tar.gz vignettes: vignettes/gDRtestData/inst/doc/gDRtestData.html vignetteTitles: gDRtestData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/gDRtestData/inst/doc/gDRtestData.R suggestsMe: gDR, gDRcore, gDRimport, gDRutils dependencyCount: 5 Package: geneLenDataBase Version: 1.49.0 Depends: R (>= 2.11.0) Imports: utils, rtracklayer, GenomicFeatures, txdbmaker License: LGPL (>= 2) MD5sum: c702d40f78608b62f889e8448cc7cdc3 NeedsCompilation: no Title: Lengths of mRNA transcripts for a number of genomes Description: Length of mRNA transcripts for a number of genomes and gene ID formats, largely based on UCSC table browser. Data objects are provided as individual pieces of information to be retrieved and loaded. A variety of different gene identifiers and genomes is supported to ensure wide applicability. biocViews: ExperimentData, Genome Author: Matthew Young [aut], Nadia Davidson [aut], Federico Marini [ctb, cre] (ORCID: ) Maintainer: Federico Marini URL: https://github.com/federicomarini/geneLenDataBase BugReports: https://github.com/federicomarini/geneLenDataBase/issues git_url: https://git.bioconductor.org/packages/geneLenDataBase git_branch: devel git_last_commit: 9203043 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/geneLenDataBase_1.49.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: goseq importsMe: SMITE dependencyCount: 100 Package: genomationData Version: 1.45.0 Suggests: knitr License: GPL-3 MD5sum: 5d6127219d964df01d73c9ce8beac5f1 NeedsCompilation: no Title: Experimental data for showing functionalities of the genomation package Description: The package contains Chip Seq, Methylation and Cage data, downloaded from Encode biocViews: ExperimentData, Genome, StemCell, SequencingData, ChIPSeqData, ChipOnChipData, ENCODE Author: Altuna Akalin, Vedran Franke Maintainer: Vedran Franke VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/genomationData git_branch: devel git_last_commit: 077e49c git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/genomationData_1.45.0.tar.gz vignettes: vignettes/genomationData/inst/doc/genomationData-knitr.pdf vignetteTitles: genomationData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/genomationData/inst/doc/genomationData-knitr.R suggestsMe: genomation dependencyCount: 0 Package: GenomicDistributionsData Version: 1.21.0 Depends: R (>= 4.1) Imports: ExperimentHub (>= 1.14.0), AnnotationHub, AnnotationFilter, data.table, utils, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges, ensembldb Suggests: knitr, BiocStyle, rmarkdown License: BSD_2_clause + file LICENSE MD5sum: 4937a8c7303fc00d5e5e6733090b9b15 NeedsCompilation: no Title: Reference data for GenomicDistributions package Description: This package provides ready to use reference data for GenomicDistributions package. Raw data was obtained from ensembldb and processed with helper functions. Data files are available for the following genome assemblies: hg19, hg38, mm9 and mm10. biocViews: ExperimentHub, ExperimentData, Genome Author: Michal Stolarczyk [aut], Kristyna Kupkova [aut, cre], Jose Verdezoto [aut], John Lawson [ctb], Jason Smith [ctb], Nathan C. Sheffield [ctb] Maintainer: Kristyna Kupkova VignetteBuilder: knitr BugReports: http://github.com/databio/GenomicDistributionsData git_url: https://git.bioconductor.org/packages/GenomicDistributionsData git_branch: devel git_last_commit: e024c0a git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/GenomicDistributionsData_1.21.0.tar.gz vignettes: vignettes/GenomicDistributionsData/inst/doc/intro.html vignetteTitles: 1. Getting started with GenomicDistributionsData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/GenomicDistributionsData/inst/doc/intro.R suggestsMe: GenomicDistributions dependencyCount: 104 Package: GeuvadisTranscriptExpr Version: 1.41.0 Depends: R (>= 3.5.0) Suggests: limma, rtracklayer, GenomicRanges, Rsamtools, VariantAnnotation, tools, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: 08f91d1ab8c38e81b741dfe233b33130 NeedsCompilation: no Title: Data package with transcript expression and bi-allelic genotypes from the GEUVADIS project Description: Provides transcript expression and bi-allelic genotypes corresponding to the chromosome 19 for CEU individuals from the GEUVADIS project, Lappalainen et al. biocViews: Homo_sapiens_Data, SNPData, Genome, RNASeqData, SequencingData, ExpressionData Author: Malgorzata Nowicka [aut, cre] Maintainer: Malgorzata Nowicka VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GeuvadisTranscriptExpr git_branch: devel git_last_commit: 0f70ea9 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/GeuvadisTranscriptExpr_1.41.0.tar.gz vignettes: vignettes/GeuvadisTranscriptExpr/inst/doc/GeuvadisTranscriptExpr.pdf vignetteTitles: Preprocessing and preparation of transcript expression and genotypes from the GEUVADIS project for sQTL analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GeuvadisTranscriptExpr/inst/doc/GeuvadisTranscriptExpr.R suggestsMe: DRIMSeq dependencyCount: 0 Package: GIGSEAdata Version: 1.31.0 Depends: R (>= 3.5) Suggests: GIGSEA, knitr, rmarkdown License: LGPL-3 MD5sum: e4f5d1f6f08f69bc02143eb59b55aa84 NeedsCompilation: no Title: Gene set collections for the GIGSEA package Description: The gene set collection used for the GIGSEA package. biocViews: ExperimentData, Homo_sapiens_Data Author: Shijia Zhu Maintainer: Shijia Zhu VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GIGSEAdata git_branch: devel git_last_commit: 8032f73 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/GIGSEAdata_1.31.0.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: 1.55.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: LGPL MD5sum: 887d101450da0085a83b91b718ee47d8 NeedsCompilation: no Title: exprSets for golub leukemia data Description: representation of public golub data with some covariate data of provenance unknown to the maintainer at present; now employs ExpressionSet format biocViews: ExperimentData, Genome, CancerData, LeukemiaCancerData Author: Todd Golub Maintainer: Vince Carey git_url: https://git.bioconductor.org/packages/golubEsets git_branch: devel git_last_commit: c8b3775 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/golubEsets_1.55.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: adSplit, Biobase, GlobalAncova, globaltest, idiogram, MLInterfaces, pvca, RDRToolbox, twilight dependencyCount: 7 Package: gpaExample Version: 1.25.0 Depends: R (>= 4.0.0) License: GPL (>= 2) MD5sum: bc25e38cd36a9e1547f715b987571a1c NeedsCompilation: no Title: Example data for the GPA package (Genetic analysis incorporating Pleiotropy and Annotation) Description: Example data for the GPA package, consisting of the p-values of 1,219,805 SNPs for five psychiatric disorder GWAS from the psychiatric GWAS consortium (PGC), with the annotation data using genes preferentially expressed in the central nervous system (CNS). biocViews: ExperimentData, Homo_sapiens_Data, SNPData Author: Dongjun Chung, Carter Allen Maintainer: Dongjun Chung URL: http://dongjunchung.github.io/GPA/ git_url: https://git.bioconductor.org/packages/gpaExample git_branch: devel git_last_commit: 58fc0b5 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/gpaExample_1.25.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GPA dependencyCount: 0 Package: grndata Version: 1.45.0 Depends: R (>= 2.10) Suggests: RUnit, BiocGenerics, knitr License: GPL-3 MD5sum: 44b4fbb6bc884abb994f383551dbbc30 NeedsCompilation: no Title: Synthetic Expression Data for Gene Regulatory Network Inference Description: Simulated expression data for five large Gene Regulatory Networks from different simulators biocViews: ExperimentData, NetworkInference, GeneExpression, Microarray, GeneRegulation, Network Author: Pau Bellot, Catharina Olsen, Patrick E Meyer Maintainer: Pau Bellot VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/grndata git_branch: devel git_last_commit: 427ca1d git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/grndata_1.45.0.tar.gz vignettes: vignettes/grndata/inst/doc/grndata.html vignetteTitles: GRNdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: GSBenchMark Version: 1.33.0 Depends: R (>= 2.13.1) License: GPL-2 MD5sum: 15fabb5ead6d045f13949c45cdc52f85 NeedsCompilation: no Title: Gene Set Benchmark Description: Benchmarks for Machine Learning Analysis of the Gene Sets. The package contains a list of pathways and gene expression data sets used in "Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)" (2010) by Eddy et al. biocViews: MicroarrayData Author: Bahman Afsari , Elana J. Fertig Maintainer: Bahman Afsari git_url: https://git.bioconductor.org/packages/GSBenchMark git_branch: devel git_last_commit: e1056b9 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/GSBenchMark_1.33.0.tar.gz vignettes: vignettes/GSBenchMark/inst/doc/GSBenchMark.pdf vignetteTitles: Working with the GSBenchMark package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GSBenchMark/inst/doc/GSBenchMark.R suggestsMe: GSReg dependencyCount: 0 Package: GSE103322 Version: 1.19.0 Depends: Biobase, GEOquery Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown, SummarizedExperiment, SingleCellExperiment License: Artistic-2.0 MD5sum: e451a1e16e69fa4284ad7eb003bb7e65 NeedsCompilation: no Title: GEO accession data GSE103322 as a SingleCellExperiment Description: Single cell RNA-Seq data for 5902 cells from 18 patients with oral cavity head and neck squamous cell carcinoma available as GEO accession [GSE103322] (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE103322). GSE103322 data have been parsed into a SincleCellExperiment object available in ExperimentHub. biocViews: ExperimentData, Genome, DNASeqData, RNASeqData, ExperimentData, ExpressionData, RNASeqData, Homo_sapiens_Data, CancerData, SingleCellData, GEO, ExperimentHub Author: Mariano Alvarez [aut, cre] Maintainer: Mariano Alvarez VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GSE103322 git_branch: devel git_last_commit: bc1f79b git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/GSE103322_1.19.0.tar.gz vignettes: vignettes/GSE103322/inst/doc/GSE103322.html vignetteTitles: scRNASeq HNSC data using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GSE103322/inst/doc/GSE103322.R dependencyCount: 75 Package: GSE13015 Version: 1.21.0 Depends: Biobase, GEOquery Imports: preprocessCore, SummarizedExperiment, GEOquery, Biobase Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown License: MIT License MD5sum: afb30ee436e75d85789bbd33e61383ff NeedsCompilation: no Title: GEO accession data GSE13015_GPL6106 as a SummarizedExperiment Description: Microarray expression matrix platform GPL6106 and clinical data for 67 septicemic patients and made them available as GEO accession [GSE13015](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13015). GSE13015 data have been parsed into a SummarizedExperiment object available in ExperimentHub. This data data could be used as an example supporting BloodGen3Module R package. biocViews: ExperimentData, MicroarrayData,ExperimentHub Author: Darawan Rinchai [aut, cre] (ORCID: ) Maintainer: Darawan Rinchai VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GSE13015 git_branch: devel git_last_commit: e08dab1 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/GSE13015_1.21.0.tar.gz vignettes: vignettes/GSE13015/inst/doc/GSE13015.html vignetteTitles: Expression data from GSE13015 using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/GSE13015/inst/doc/GSE13015.R dependencyCount: 76 Package: GSE159526 Version: 1.19.0 Suggests: ExperimentHub, BiocStyle, RefManageR, knitr, rmarkdown, testthat, minfi, tibble, sessioninfo License: MIT + file LICENSE MD5sum: f95abff6cead896a9f8a6bbc64868ec1 NeedsCompilation: no Title: Placental cell DNA methylation data from GEO accession GSE159526 Description: 19 term and 9 first trimester placental chorionic villi and matched cell-sorted samples ran on Illumina HumanMethylationEPIC DNA methylation microarrays. This data was made available on GEO accession [GSE159526](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159526). Both the raw and processed data has been made available on \code{ExperimentHub}. Raw unprocessed data formatted as an RGChannelSet object for integration and normalization using minfi and other existing Bioconductor packages. Processed normalized data is also available as a DNA methylation \code{matrix}, with a corresponding phenotype information as a \code{data.frame} object. biocViews: ExperimentData, ExperimentHub, GEO, Genome, Tissue, MethylationArrayData, Homo_sapiens_Data Author: Victor Yuan [aut, cre] (ORCID: ) Maintainer: Victor Yuan URL: https://github.com/wvictor14/GSE159526 VignetteBuilder: knitr BugReports: https://github.com/wvictor14/GSE159526/issues git_url: https://git.bioconductor.org/packages/GSE159526 git_branch: devel git_last_commit: a260d6d git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/GSE159526_1.19.0.tar.gz vignettes: vignettes/GSE159526/inst/doc/GSE159526.html vignetteTitles: Introduction to GSE159526 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/GSE159526/inst/doc/GSE159526.R dependencyCount: 0 Package: GSE62944 Version: 1.41.0 Depends: Biobase, GEOquery Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown, DESeq2 License: Artistic-2.0 MD5sum: 256b6508b3d97955c6780ddfb8e7ecf4 NeedsCompilation: no Title: GEO accession data GSE62944 as a SummarizedExperiment Description: TCGA processed RNA-Seq data for 9264 tumor and 741 normal samples across 24 cancer types and made them available as GEO accession [GSE62944](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944). GSE62944 data have been parsed into a SummarizedExperiment object available in ExperimentHub. biocViews: ExperimentData, Genome, DNASeqData, RNASeqData Author: Sonali Arora Maintainer: Bioconductor Package Maintainer URL: http://bioconductor.org/packages/release/bioc/html/GSE62944.html VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GSE62944 git_branch: devel git_last_commit: d7a279e git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/GSE62944_1.41.0.tar.gz vignettes: vignettes/GSE62944/inst/doc/GSE62944.html vignetteTitles: Raw TCGA data using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GSE62944/inst/doc/GSE62944.R dependencyCount: 75 Package: GSVAdata Version: 1.49.0 Depends: R (>= 4.0), Biobase, GSEABase, SummarizedExperiment Imports: methods, utils, Matrix, SpatialExperiment License: Artistic-2.0 MD5sum: f5805e6a0bdc0baba687438ea5d963e7 NeedsCompilation: no Title: Data employed in the vignette of the GSVA package Description: This package stores the data employed in the vignette of the GSVA package. These data belong to the following publications: Cahoy et al. J Neurosci 28:264-278, 2008; Carrel and Willard, Nature, 434:400-404, 2005; Huang et al. PNAS, 104:9758-9763, 2007; Pickrell et al. Nature, 464:768-722, 2010; Skaletsky et al. Nature, 423:825-837; Verhaak et al. Cancer Cell 17:98-110, 2010; Costa et al. FEBS J, 288:2311-2331, 2021. biocViews: ExperimentData, ExpressionData, SequencingData, Homo_sapiens_Data, CancerData, Tissue Author: Robert Castelo Maintainer: Robert Castelo git_url: https://git.bioconductor.org/packages/GSVAdata git_branch: devel git_last_commit: c59dc04 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/GSVAdata_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: singleCellTK suggestsMe: GSAR, GSVA dependencyCount: 79 Package: GWASdata Version: 1.51.0 Depends: GWASTools Suggests: ncdf4 License: Artistic-2.0 MD5sum: 0775fffdad6f0c49381fdc09c3ee578f NeedsCompilation: no Title: Data used in the examples and vignettes of the GWASTools package Description: Selected Affymetrix and Illlumina SNP data for HapMap subjects. Data provided by the Center for Inherited Disease Research at Johns Hopkins University and the Broad Institute of MIT and Harvard University. biocViews: ExperimentData, MicroarrayData, SNPData, HapMap Author: Stephanie Gogarten Maintainer: Stephanie Gogarten git_url: https://git.bioconductor.org/packages/GWASdata git_branch: devel git_last_commit: 8cb428d git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/GWASdata_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GENESIS, GWASTools dependencyCount: 95 Package: h5vcData Version: 2.33.0 Suggests: h5vc License: GPL (>= 3) MD5sum: 65ca18beeb78609fd47ee9e41cf2543f NeedsCompilation: no Title: Example data for the h5vc package Description: This package contains the data used in the vignettes and examples of the 'h5vc' package biocViews: CancerData Author: Paul Theodor Pyl Maintainer: Paul Theodor Pyl git_url: https://git.bioconductor.org/packages/h5vcData git_branch: devel git_last_commit: 04f6bc8 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/h5vcData_2.33.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: h5vc suggestsMe: HDF5Array dependencyCount: 0 Package: hapmap100khind Version: 1.55.0 Suggests: oligo License: GPL MD5sum: 284ee9ce18af6f20d43b44ad013eba66 NeedsCompilation: no Title: Sample data - Hapmap 100K HIND Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap100khind git_branch: devel git_last_commit: a849824 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/hapmap100khind_1.55.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmap100kxba Version: 1.55.0 Suggests: oligo License: GPL MD5sum: 4a6bad3d062fa37bd9f1fbdf52d16cb9 NeedsCompilation: no Title: Sample data - Hapmap 100K XBA Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap100kxba git_branch: devel git_last_commit: 7b18044 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/hapmap100kxba_1.55.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligo dependencyCount: 0 Package: hapmap500knsp Version: 1.55.0 Suggests: oligo License: GPL MD5sum: 11c3d6bac1fb08e06c27e65f4d6bfe3c NeedsCompilation: no Title: Sample data - Hapmap 500K NSP Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap500knsp git_branch: devel git_last_commit: 62abac1 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/hapmap500knsp_1.55.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmap500ksty Version: 1.55.0 Suggests: oligo License: GPL MD5sum: cb71f4f27083f8157234e635baf41505 NeedsCompilation: no Title: Sample data - Hapmap 500K STY Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap500ksty git_branch: devel git_last_commit: 8cb550e git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/hapmap500ksty_1.55.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmapsnp5 Version: 1.55.0 Suggests: oligo License: GPL MD5sum: 761020c865985c4bf4bbaa40c42fdd1a NeedsCompilation: no Title: Sample data - Hapmap SNP 5.0 Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData, SNPData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmapsnp5 git_branch: devel git_last_commit: 949e1ae git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/hapmapsnp5_1.55.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligoClasses dependencyCount: 0 Package: hapmapsnp6 Version: 1.55.0 Depends: R (>= 2.15) Suggests: oligo, oligoClasses License: GPL MD5sum: be14382b3818f0694b856b16cf642eba NeedsCompilation: no Title: Sample data - Hapmap SNP 6.0 Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, SNPData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmapsnp6 git_branch: devel git_last_commit: ff84557 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/hapmapsnp6_1.55.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: crlmm, oligoClasses dependencyCount: 0 Package: harbChIP Version: 1.51.0 Depends: R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5), Biostrings Imports: methods, stats License: Artistic-2.0 MD5sum: 4f55a743d9862026e4b0717a1f86962d NeedsCompilation: no Title: Experimental Data Package: harbChIP Description: data from a yeast ChIP-chip experiment biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/harbChIP git_branch: devel git_last_commit: a7dc8c2 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/harbChIP_1.51.0.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: 1.41.0 Depends: R (>= 3.5.0) Suggests: BiocGenerics, BiocStyle, knitr, rmarkdown, Harman (>= 1.23.3) License: GPL-3 MD5sum: 04bd48bee7bbda43f547b97785138c2d NeedsCompilation: no Title: Data for the Harman package Description: Datasets of accompany Harman, a PCA and constrained optimisation based technique. Contains three example datasets: IMR90, Human lung fibroblast cells exposed to nitric oxide; NPM, an experiment to test skin penetration of metal oxide nanoparticles following topical application of sunscreens in non-pregnant mice; OLF; an experiment to gauge the response of human olfactory neurosphere-derived (hONS) cells to ZnO nanoparticles. Since version 1.24, this package also contains the Infinium5 dataset, a set of batch correction adjustments across 5 Illumina Infinium Methylation BeadChip datasets. This file does not contain methylation data, but summary statistics of 5 datasets after correction. There is also an EpiSCOPE_sample file as exampling for the new methylation clustering functionality in Harman. biocViews: ExpressionData, MicroarrayData, ExperimentData, Homo_sapiens_Data, Mus_musculus_Data Author: Yalchin Oytam [aut], Josh Bowden [aut], Jason Ross [aut, cre] Maintainer: Jason Ross URL: http://www.bioinformatics.csiro.au/harman/ VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/HarmanData git_branch: devel git_last_commit: db17fbf git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/HarmanData_1.41.0.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: 1.35.0 Depends: R (>= 3.4.0) Imports: ExperimentHub Suggests: AnnotationHub, knitr, rmarkdown, igraph, survival, ANF, stats, testthat License: GPL-3 MD5sum: a5b145fb8e68ae63ca144e40e35eac6a NeedsCompilation: no Title: Processed Harmonized TCGA Data of Five Selected Cancer Types Description: This package contains the processed harmonized TCGA data of five cancer types used in "Tianle Ma and Aidong Zhang, Integrate Multi-omic Data Using Affinity Network Fusion (ANF) for Cancer Patient Clustering". biocViews: CancerData, ReproducibleResearch Author: Tianle Ma Maintainer: Tianle Ma VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/HarmonizedTCGAData git_branch: devel git_last_commit: 5858525 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/HarmonizedTCGAData_1.35.0.tar.gz vignettes: vignettes/HarmonizedTCGAData/inst/doc/HarmonizedTCGAData.html vignetteTitles: Patient Affinity Matrices Derived from Harmonized TCGA Dataset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HarmonizedTCGAData/inst/doc/HarmonizedTCGAData.R dependencyCount: 64 Package: HCAData Version: 1.29.0 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: 545ec45b40ac0c590bf7a831fc3a8d4e NeedsCompilation: no Title: Accessing The Datasets Of The Human Cell Atlas in R/Bioconductor Description: This package allows a direct access to the dataset generated by the Human Cell Atlas project for further processing in R and Bioconductor, in the comfortable format of SingleCellExperiment objects (available in other formats here: http://preview.data.humancellatlas.org/). biocViews: RNASeqData, SingleCellData, ExperimentData, ExpressionData, ExperimentHub Author: Federico Marini [aut, cre] (ORCID: ) Maintainer: Federico Marini URL: https://github.com/federicomarini/HCAData VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/HCAData git_branch: devel git_last_commit: b37a62e git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/HCAData_1.29.0.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: 83 Package: HCATonsilData Version: 1.11.0 Depends: R (>= 4.3.0) Imports: ExperimentHub, SingleCellExperiment, SpatialExperiment, HDF5Array, SummarizedExperiment, S4Vectors, htmltools, rmarkdown, base64enc, utils Suggests: knitr, ggplot2, testthat (>= 3.0.0), scater, Seurat, Signac, zellkonverter, iSEE, ggspavis, kableExtra, BiocStyle License: MIT + file LICENSE MD5sum: 89f935a433964b6541475cf57eb0af4a NeedsCompilation: no Title: Provide programmatic access to the tonsil cell atlas datasets Description: This package provides access to the scRNA-seq, scATAC-seq, multiome, CITE-seq and spatial transcriptomics (Visium) data generated by the tonsil cell atlas in the context of the Human Cell Atlas (HCA). The data is provided via the Bioconductor project in the form of SingleCellExperiments. Additionally, information on the whole compendium of identified cell types is provided in form of a glossary. biocViews: SingleCellData, ExperimentData, RNASeqData, ExperimentHub, ExpressionData, SpatialData Author: Ramon Massoni-Badosa [aut, cre] (ORCID: ), Federico Marini [aut] (ORCID: ), Alan O'Callaghan [aut], Helena L. Crowell [aut] (ORCID: ) Maintainer: Ramon Massoni-Badosa URL: https://github.com/massonix/HCATonsilData VignetteBuilder: knitr BugReports: https://github.com/massonix/HCATonsilData/issues git_url: https://git.bioconductor.org/packages/HCATonsilData git_branch: devel git_last_commit: 5d3b6bc git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/HCATonsilData_1.11.0.tar.gz vignettes: vignettes/HCATonsilData/inst/doc/HCATonsilData.html vignetteTitles: HCATonsilData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HCATonsilData/inst/doc/HCATonsilData.R dependencyCount: 101 Package: HD2013SGI Version: 1.53.0 Depends: R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots, limma, vcd, LSD,EBImage Suggests: BiocStyle License: Artistic-2.0 MD5sum: 0e4f1b5abab2e989b8542c80542d8c6e NeedsCompilation: no Title: Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping Description: This package contains the experimental data and a complete executable transcript (vignette) of the analysis of the HCT116 genetic interaction matrix presented in the paper "Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping" by C. Laufer, B. Fischer, M. Billmann, W. Huber, M. Boutros; Nature Methods (2013) 10:427-31. doi: 10.1038/nmeth.2436. biocViews: ExperimentData, CancerData, ColonCancerData, MicrotitrePlateAssayData, CellCulture, Homo_sapiens_Data, HighThroughputImagingData Author: Bernd Fischer Maintainer: Mike Smith SystemRequirements: GNU make git_url: https://git.bioconductor.org/packages/HD2013SGI git_branch: devel git_last_commit: f1a7dd4 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/HD2013SGI_1.53.0.tar.gz vignettes: vignettes/HD2013SGI/inst/doc/HD2013SGI.pdf vignetteTitles: HD2013SGI hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HD2013SGI/inst/doc/HD2013SGI.R suggestsMe: splots dependencyCount: 87 Package: HDCytoData Version: 1.33.0 Depends: ExperimentHub, SummarizedExperiment, flowCore Imports: utils, methods Suggests: BiocStyle, knitr, rmarkdown, Rtsne, umap, ggplot2, FlowSOM, mclust License: MIT + file LICENSE MD5sum: b359d7d6b8bf1570791e60cf519aa107 NeedsCompilation: no Title: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats Description: Data package containing a set of publicly available high-dimensional cytometry benchmark datasets, formatted into SummarizedExperiment and flowSet Bioconductor object formats, including all required metadata. Row metadata includes sample IDs, group IDs, patient IDs, reference cell population or cluster labels (where available), and labels identifying 'spiked in' cells (where available). Column metadata includes channel names, protein marker names, and protein marker classes (cell type or cell state). biocViews: ExperimentHub, ExperimentData, ExpressionData, FlowCytometryData, SingleCellData, Homo_sapiens_Data, ImmunoOncologyData Author: Lukas M. Weber [aut, cre], Charlotte Soneson [aut] Maintainer: Lukas M. Weber URL: https://github.com/lmweber/HDCytoData VignetteBuilder: knitr BugReports: https://github.com/lmweber/HDCytoData/issues git_url: https://git.bioconductor.org/packages/HDCytoData git_branch: devel git_last_commit: 95eb6bd git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/HDCytoData_1.33.0.tar.gz vignettes: vignettes/HDCytoData/inst/doc/Contribution_guidelines.html, vignettes/HDCytoData/inst/doc/Examples_and_use_cases.html, vignettes/HDCytoData/inst/doc/HDCytoData_package.html vignetteTitles: 3. Contribution guidelines, 2. Examples and use cases, 1. HDCytoData package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HDCytoData/inst/doc/Contribution_guidelines.R, vignettes/HDCytoData/inst/doc/Examples_and_use_cases.R, vignettes/HDCytoData/inst/doc/HDCytoData_package.R dependsOnMe: cytofWorkflow suggestsMe: CytoMDS, diffcyt, MDSvis, tidyFlowCore dependencyCount: 83 Package: healthyControlsPresenceChecker Version: 1.17.0 Depends: R (>= 4.0.0) Imports: xml2, GEOquery, geneExpressionFromGEO, magrittr Suggests: RUnit, BiocGenerics, markdown, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: dcb6e43e3d89f6612a0df679861643cf NeedsCompilation: no Title: Dowloads A Gene Expression Dataset From GEO And Checks If It Contains Data Of Healthy Controls Or Not Description: A function that reads in the GEO accession code of a gene expression dataset, retrieves its data from GEO, and checks if data of healthy controls are present in the dataset. It returns true if healthy controls data are found, and false otherwise. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL . biocViews: GEO, RepositoryData, ExpressionData Author: Davide Chicco [aut, cre] (ORCID: ) Maintainer: Davide Chicco URL: https://github.com/davidechicco/healthyControlsPresenceChecker VignetteBuilder: knitr BugReports: https://github.com/davidechicco/healthyControlsPresenceChecker/issues git_url: https://git.bioconductor.org/packages/healthyControlsPresenceChecker git_branch: devel git_last_commit: 2b322fd git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/healthyControlsPresenceChecker_1.17.0.tar.gz vignettes: vignettes/healthyControlsPresenceChecker/inst/doc/healthyControlsPresenceChecker.html vignetteTitles: healthyControlsPresenceChecker vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/healthyControlsPresenceChecker/inst/doc/healthyControlsPresenceChecker.R dependencyCount: 88 Package: healthyFlowData Version: 1.51.0 Depends: R (>= 2.15.0), flowCore Imports: methods License: Artistic-2.0 MD5sum: c06b403ac155e32db44d2717e28f4a94 NeedsCompilation: no Title: Healthy dataset used by the flowMatch package Description: A healthy dataset with 20 flow cytometry samples used by the flowMatch package. biocViews: FlowCytometryData Author: Ariful Azad Maintainer: Ariful Azad git_url: https://git.bioconductor.org/packages/healthyFlowData git_branch: devel git_last_commit: 5950af4 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/healthyFlowData_1.51.0.tar.gz vignettes: vignettes/healthyFlowData/inst/doc/healthyFlowData.pdf vignetteTitles: healthyFlowData: A healthy dataset with 20 flow cytometry samples used by the flowMatch package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/healthyFlowData/inst/doc/healthyFlowData.R suggestsMe: flowMatch dependencyCount: 22 Package: HEEBOdata Version: 1.51.0 License: LGPL MD5sum: bbfe7d2a554c0a559a7382e81d0ae1a1 NeedsCompilation: no Title: HEEBO set and HEEBO controls. Description: R objects describing the HEEBO oligo set. biocViews: ExperimentData Author: Agnes Paquet Maintainer: Agnes Paquet URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/ git_url: https://git.bioconductor.org/packages/HEEBOdata git_branch: devel git_last_commit: a82d0fc git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/HEEBOdata_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQuality dependencyCount: 0 Package: HelloRangesData Version: 1.39.0 Suggests: BiocStyle License: GPL (>= 2) MD5sum: aeaebc6ca44facaee889e65a3902bc41 NeedsCompilation: no Title: Data for the HelloRanges tutorial vignette Description: Provides the data that were used in the bedtools tutorial by Aaron Quinlan (http://quinlanlab.org/tutorials/bedtools/bedtools.html). Includes a subset of the DnaseI hypersensitivity data from "Maurano et al. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA. Science. 2012. Vol. 337 no. 6099 pp. 1190-1195." The rest of the tracks were originally downloaded from the UCSC table browser. See the HelloRanges vignette for a port of the bedtools tutorial to R. biocViews: ExperimentData, SequencingData Author: Michael Lawrence Maintainer: Michael Lawrence git_url: https://git.bioconductor.org/packages/HelloRangesData git_branch: devel git_last_commit: 5f2d796 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/HelloRangesData_1.39.0.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: 1.51.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 7d91b9cef2a731c84bbe693b5b2e21e6 NeedsCompilation: no Title: hgu133a data for barcode Description: Data used by the barcode package for microarrays of type hgu133a. biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/hgu133abarcodevecs git_branch: devel git_last_commit: 6b5e927 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/hgu133abarcodevecs_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hgu133plus2barcodevecs Version: 1.51.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 097934ed830296ccd02b736c998268a9 NeedsCompilation: no Title: hgu133plus2 data for barcode Description: Data used by the barcode package for microarrays of type hgu133plus2. biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/hgu133plus2barcodevecs git_branch: devel git_last_commit: 4580e54 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/hgu133plus2barcodevecs_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hgu133plus2CellScore Version: 1.33.0 Depends: R (>= 3.5.0) Imports: Biobase (>= 2.39.1) Suggests: knitr License: GPL-3 MD5sum: cf81f61d6799f1b14eb0666216af2308 NeedsCompilation: no Title: CellScore Standard Cell Types Expression Dataset [hgu133plus2] Description: The CellScore Standard Dataset contains expression data from a wide variety of human cells and tissues, which should be used as standard cell types in the calculation of the CellScore. All data was curated from public databases such as Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) or ArrayExpress (https://www.ebi.ac.uk/arrayexpress/). This standard dataset only contains data from the Affymetrix GeneChip Human Genome U133 Plus 2.0 microarrays. Samples were manually annotated using the database information or consulting the publications in which the datasets originated. The sample annotations are stored in the phenoData slot of the expressionSet object. Raw data (CEL files) were processed with the affy package to generate present/absent calls (mas5calls) and background-subtracted values, which were then normalized by the R-package yugene to yield the final expression values for the standard expression matrix. The annotation table for the microarray was retrieved from the BioC annotation package hgu133plus2. All data are stored in an expressionSet object. biocViews: ExpressionData, MicroarrayData, GEO, ExperimentData, Homo_sapiens_Data, Genome, ArrayExpress Author: Nancy Mah, Katerina Taskova Maintainer: Nancy Mah VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/hgu133plus2CellScore git_branch: devel git_last_commit: fc4b63c git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/hgu133plus2CellScore_1.33.0.tar.gz vignettes: vignettes/hgu133plus2CellScore/inst/doc/hgu133plus2Vignette.pdf vignetteTitles: R packages: hgu133plus2CellScore hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/hgu133plus2CellScore/inst/doc/hgu133plus2Vignette.R dependencyCount: 7 Package: hgu2beta7 Version: 1.53.0 Depends: R (>= 2.0.0) License: Artistic-2.0 MD5sum: 969c1c9e0f71744e0f30668c763196e5 NeedsCompilation: no Title: A data package containing annotation data for hgu2beta7 Description: Annotation data file for hgu2beta7 assembled using data from public data repositories biocViews: Genome Author: Chenwei Lin Maintainer: Bioconductor Package Maintainer git_url: https://git.bioconductor.org/packages/hgu2beta7 git_branch: devel git_last_commit: 8946d1d git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/hgu2beta7_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: HiBED Version: 1.11.0 Depends: R (>= 3.5.0) Imports: dplyr, FlowSorted.Blood.EPIC, tibble, FlowSorted.DLPFC.450k, minfi, utils, AnnotationHub, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, IlluminaHumanMethylation450kmanifest License: GPL-3 MD5sum: 583ca895266f5ff5bd3eb00326e4a1ec NeedsCompilation: no Title: HiBED Description: Hierarchical deconvolution for extensive cell type resolution in the human brain using DNA methylation. The HiBED deconvolution estimates proportions up to 7 cell types (GABAergic neurons, glutamatergic neurons, astrocytes, microglial cells, oligodendrocytes, endothelial cells, and stromal cells) in bulk brain tissues. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, Genome, MethylationArrayData, PackageTypeData Author: Ze Zhang [cre, aut] (ORCID: ), Lucas A. Salas [aut] Maintainer: Ze Zhang URL: https://github.com/SalasLab/HiBED VignetteBuilder: knitr BugReports: https://github.com/SalasLab/HiBED/issues. git_url: https://git.bioconductor.org/packages/HiBED git_branch: devel git_last_commit: 65a76d7 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/HiBED_1.11.0.tar.gz vignettes: vignettes/HiBED/inst/doc/HiBED.html vignetteTitles: HiBED hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HiBED/inst/doc/HiBED.R dependencyCount: 154 Package: HiCDataHumanIMR90 Version: 1.33.0 Depends: R (>= 3.5.0) Suggests: HiTC, BiocStyle License: GPL-3 MD5sum: 01f713c9417d12f281a7880c63bc90bf NeedsCompilation: no Title: Human IMR90 Fibroblast HiC data from Dixon et al. 2012 Description: The HiC data from Human Fibroblast IMR90 cell line (HindIII restriction) was retrieved from the GEO website, accession number GSE35156 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35156). The raw reads were processed as explained in Dixon et al. (Nature 2012). biocViews: ExperimentData, Genome, Homo_sapiens_Data, GEO Author: Nicolas Servant Maintainer: Nicolas Servant git_url: https://git.bioconductor.org/packages/HiCDataHumanIMR90 git_branch: devel git_last_commit: 3610e54 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/HiCDataHumanIMR90_1.33.0.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: 1.49.0 Suggests: ShortRead License: GPL-3 MD5sum: 873290e2a33af6e1a374bd8a789b76b3 NeedsCompilation: no Title: Human lymphoblastoid HiC data from Lieberman-Aiden et al. 2009 Description: The HiC data from human lymphoblastoid cell line (HindIII restriction) was retrieved from the sequence read archive and two ends of the paired reads were aligned separately with bowtie. biocViews: ExperimentData, Homo_sapiens_Data Author: Borbala Mifsud Maintainer: Borbala Mifsud git_url: https://git.bioconductor.org/packages/HiCDataLymphoblast git_branch: devel git_last_commit: bbb877f git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/HiCDataLymphoblast_1.49.0.tar.gz vignettes: vignettes/HiCDataLymphoblast/inst/doc/package_vignettes.pdf vignetteTitles: package_vignettes.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HiCDataLymphoblast/inst/doc/package_vignettes.R suggestsMe: GOTHiC dependencyCount: 0 Package: HiContactsData Version: 1.15.0 Depends: ExperimentHub Imports: BiocFileCache, AnnotationHub Suggests: testthat, methods, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: d135c5ffa3bd4d7b4b52e8130071440d NeedsCompilation: no Title: HiContacts companion data package Description: Provides a collection of Hi-C files (pairs, (m)cool and fastq). These datasets can be read into R and further investigated and visualized with the HiContacts package. Data includes yeast Hi-C data generated by the Koszul lab from the Pasteur Institute. biocViews: ExperimentHub, ExperimentData, SequencingData Author: Jacques Serizay [aut, cre] Maintainer: Jacques Serizay URL: https://github.com/js2264/HiContactsData VignetteBuilder: knitr BugReports: https://github.com/js2264/HiContactsData/issues git_url: https://git.bioconductor.org/packages/HiContactsData git_branch: devel git_last_commit: 30ff320 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/HiContactsData_1.15.0.tar.gz vignettes: vignettes/HiContactsData/inst/doc/HiContactsData.html vignetteTitles: HiContactsData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HiContactsData/inst/doc/HiContactsData.R suggestsMe: HiCExperiment, HiContacts, HiSpaR, plyinteractions dependencyCount: 64 Package: HighlyReplicatedRNASeq Version: 1.25.0 Depends: SummarizedExperiment, ExperimentHub Imports: S4Vectors Suggests: BiocStyle, BiocFileCache, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 3a5d18df5b7c634bc63be8c8619ff043 NeedsCompilation: no Title: Collection of Bulk RNA-Seq Experiments With Many Replicates Description: Gene-level count matrix data for bulk RNA-seq dataset with many replicates. The data are provided as easy to use SummarizedExperiment objects. The source data that is made accessible through this package comes from https://github.com/bartongroup/profDGE48. biocViews: ExperimentHub, ExperimentData, ExpressionData, SequencingData, RNASeqData Author: Constantin Ahlmann-Eltze [aut, cre] (ORCID: ) Maintainer: Constantin Ahlmann-Eltze URL: https://github.com/const-ae/HighlyReplicatedRNASeq VignetteBuilder: knitr BugReports: https://github.com/const-ae/HighlyReplicatedRNASeq/issues git_url: https://git.bioconductor.org/packages/HighlyReplicatedRNASeq git_branch: devel git_last_commit: 3999d3f git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/HighlyReplicatedRNASeq_1.25.0.tar.gz vignettes: vignettes/HighlyReplicatedRNASeq/inst/doc/HighlyReplicatedRNASeq.html vignetteTitles: Exploring the 86 bulk RNA-seq samples from the Schurch et al. (2016) study hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HighlyReplicatedRNASeq/inst/doc/HighlyReplicatedRNASeq.R dependencyCount: 75 Package: HIVcDNAvantWout03 Version: 1.53.0 License: GPL (>= 2) MD5sum: 71cb6f3b50a3545a8479333011edec4e NeedsCompilation: no Title: T cell line infections with HIV-1 LAI (BRU) Description: The expression levels of approximately 4600 cellular RNA transcripts were assessed in CD4+ T cell lines at different times after infection with HIV-1BRU using DNA microarrays. This data corresponds to the first block of a 12 block array image (001030_08_1.GEL) in the first data set (2000095918 A) in the first experiment (CEM LAI vs HI-LAI 24hr). There are two data sets, which are part of a dye-swap experiment with replicates, representing the Cy3 (green) absorption intensities for channel 1 (hiv1raw) and the Cy5 (red) absorption intensities for channel 2 (hiv2raw). biocViews: ExperimentData, MicroarrayData, TwoChannelData, HIVData Author: Dr. Angelique van't Wout, Department of Microbiology, University of Washington Maintainer: Chris Fraley URL: http://expression.microslu.washington.edu/expression/vantwoutjvi2002.html git_url: https://git.bioconductor.org/packages/HIVcDNAvantWout03 git_branch: devel git_last_commit: 076d49a git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/HIVcDNAvantWout03_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: HMP16SData Version: 1.33.1 Depends: R (>= 4.1.0), SummarizedExperiment Imports: AnnotationHub, ExperimentHub, S4Vectors, assertthat, dplyr, kableExtra, knitr, magrittr, methods, readr, stringr, tibble, utils Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, circlize, cowplot, dendextend, devtools, ggplot2, gridExtra, haven, phyloseq, rmarkdown, roxygen2, stats, testthat, tidyr License: Artistic-2.0 MD5sum: 46fe5af4c6b9c8c1a8efc711b9e35f17 NeedsCompilation: no Title: 16S rRNA Sequencing Data from the Human Microbiome Project Description: HMP16SData is a Bioconductor ExperimentData package of the Human Microbiome Project (HMP) 16S rRNA sequencing data for variable regions 1–3 and 3–5. Raw data files are provided in the package as downloaded from the HMP Data Analysis and Coordination Center. Processed data is provided as SummarizedExperiment class objects via ExperimentHub. biocViews: ExperimentData, ExperimentHub, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch, SequencingData Author: Lucas schiffer [aut, cre] (ORCID: ), Rimsha Azhar [aut], Marcel Ramos [ctb], Ludwig Geistlinger [ctb], Levi Waldron [aut], NCI [fnd] (GrantNo.: R01CA230551) Maintainer: Lucas schiffer URL: https://github.com/waldronlab/HMP16SData VignetteBuilder: knitr BugReports: https://github.com/waldronlab/HMP16SData/issues git_url: https://git.bioconductor.org/packages/HMP16SData git_branch: devel git_last_commit: 7b262b8 git_last_commit_date: 2026-04-29 Date/Publication: 2026-04-30 source.ver: src/contrib/HMP16SData_1.33.1.tar.gz vignettes: vignettes/HMP16SData/inst/doc/HMP16SData.html vignetteTitles: HMP16SData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HMP16SData/inst/doc/HMP16SData.R dependencyCount: 108 Package: HSMMSingleCell Version: 1.33.0 Depends: R (>= 2.10) License: Artistic-2.0 MD5sum: b47e779d044dc68d09a57a4f55fa33c2 NeedsCompilation: no Title: Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM) Description: Skeletal myoblasts undergo a well-characterized sequence of morphological and transcriptional changes during differentiation. In this experiment, primary human skeletal muscle myoblasts (HSMM) were expanded under high mitogen conditions (GM) and then differentiated by switching to low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several hundred cells taken over a time-course of serum-induced differentiation. Between 49 and 77 cells were captured at each of four time points (0, 24, 48, 72 hours) following serum switch using the Fluidigm C1 microfluidic system. RNA from each cell was isolated and used to construct mRNA-Seq libraries, which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell. biocViews: ExperimentData, RNASeqData Author: Cole Trapnell Maintainer: Cole Trapnell git_url: https://git.bioconductor.org/packages/HSMMSingleCell git_branch: devel git_last_commit: e86ad46 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/HSMMSingleCell_1.33.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: monocle dependencyCount: 0 Package: HumanAffyData Version: 1.39.0 Depends: ExperimentHub, Biobase, R (>= 3.3) Suggests: BiocStyle License: Artistic-2.0 MD5sum: 0df98d32a9dcda6d871c1274e9bbf799 NeedsCompilation: no Title: GEO accession GSE64985 and ArrayExpress accession E-MTAB-62 as ExpressionSet objects Description: Re-analysis of human gene expression data generated on the Affymetrix HG_U133PlusV2 (EH176) and Affymetrix HG_U133A (EH177) platforms. The original data were normalized using robust multiarray averaging (RMA) to obtain an integrated gene expression atlas across diverse biological sample types and conditions. The entire compendia comprisee 9395 arrays for EH176 and 5372 arrays for EH177. biocViews: ExperimentData, GEO, ArrayExpress, Homo_sapiens_Data, MicroarrayData, ExpressionData Author: Brad Nelms Maintainer: Brad Nelms git_url: https://git.bioconductor.org/packages/HumanAffyData git_branch: devel git_last_commit: 8c81c82 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/HumanAffyData_1.39.0.tar.gz vignettes: vignettes/HumanAffyData/inst/doc/HumanAffyData.pdf vignetteTitles: Intro to the HumanAffyData package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HumanAffyData/inst/doc/HumanAffyData.R suggestsMe: CellMapper dependencyCount: 64 Package: humanHippocampus2024 Version: 1.5.0 Depends: R (>= 4.4) Imports: ExperimentHub, SummarizedExperiment,SpatialExperiment Suggests: testthat (>= 3.0.0), sessioninfo, rmarkdown, knitr, BiocStyle, ExperimentHubData, AnnotationHubData, RefManageR License: Artistic-2.0 MD5sum: ab481c702d22de4800fb35b9266267bc NeedsCompilation: no Title: Access to SRT and snRNA-seq data from spatial_HPC project Description: This is an ExperimentHub Data package that helps to access the spatially-resolved transcriptomics and single-nucleus RNA sequencing data. The datasets are generated from adjacent tissue sections of the anterior human hippocampus across ten adult neurotypical donors. The datasets are based on [spatial_hpc](https://github.com/LieberInstitute/spatial_hpc) project by Lieber Institute for Brain Development (LIBD) researchers and collaborators. biocViews: ExperimentHub, SequencingData, SpatialData, ExpressionData, Tissue, RNASeqData Author: Christine Hou [aut, cre] (ORCID: ) Maintainer: Christine Hou URL: https://github.com/LieberInstitute/spatial_hpc, https://christinehou11.github.io/humanHippocampus2024/ VignetteBuilder: knitr BugReports: https://support.bioconductor.org/t/humanHippocampus2024 git_url: https://git.bioconductor.org/packages/humanHippocampus2024 git_branch: devel git_last_commit: e7188ff git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/humanHippocampus2024_1.5.0.tar.gz vignettes: vignettes/humanHippocampus2024/inst/doc/humanHippocampus2024.html vignetteTitles: humanHippocampus2024 Tutorial hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/humanHippocampus2024/inst/doc/humanHippocampus2024.R dependencyCount: 80 Package: HumanRetinaLRSData Version: 1.1.0 Depends: R (>= 4.6.0), SummarizedExperiment Imports: osfr, BiocFileCache Suggests: testthat, knitr, rmarkdown, ggplot2, ggrepel License: MIT + file LICENSE MD5sum: 023b422942eb105d24319985b025a883 NeedsCompilation: no Title: Long-read RNA-seq gene count data from human retinal organoids Description: Dataset package containing gene and isoform count matrices, and sample metadata for long-read direct cDNA sequencing of human retinal organoids, 2D retinal ganglion cell (RGC) cultures, and flowthrough fractions from H9 and EP1 iPSC cell lines. Data were generated using Oxford Nanopore Technology (ONT) direct cDNA sequencing and mapped to the GRCh38 reference genome (GENCODE v46 annotation). The package provides accessor functions returning SummarizedExperiment objects for gene-level counts, isoform-level counts, and a matrix of allele-specific expression (ASE) gene counts. Data files are stored in flat CSV format in an Open Science Framework (OSF) repository and cached locally via BiocFileCache. biocViews: ExperimentData, RNASeqData, ExpressionData, Homo_sapiens_Data, CellCulture Author: Sowmya Parthiban [aut, cre] Maintainer: Sowmya Parthiban URL: https://github.com/sparthib/HumanRetinaLrsData VignetteBuilder: knitr BugReports: https://github.com/sparthib/HumanRetinaLrsData/issues git_url: https://git.bioconductor.org/packages/HumanRetinaLRSData git_branch: devel git_last_commit: 85415f6 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/HumanRetinaLRSData_1.1.0.tar.gz vignettes: vignettes/HumanRetinaLRSData/inst/doc/example_analysis.html vignetteTitles: Retinal Organoids counts data: Gene and Isoform Level Exploration hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HumanRetinaLRSData/inst/doc/example_analysis.R dependencyCount: 71 Package: humanStemCell Version: 0.53.0 Depends: Biobase (>= 2.5.5), hgu133plus2.db License: Artistic-2.0 MD5sum: 6d989486dc42ea30b9581fdc6b4ead8f NeedsCompilation: no Title: Human Stem Cells time course experiment Description: Affymetrix time course experiment on human stem cells (two time points: undifferentiated and differentiated). biocViews: ExperimentData, Homo_sapiens_Data Author: R. Gentleman, N. Le Meur, M. Tewari Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/humanStemCell git_branch: devel git_last_commit: c09a5e6 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/humanStemCell_0.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MiRaGE, rtracklayer dependencyCount: 44 Package: IHWpaper Version: 1.41.0 Depends: R (>= 3.3), IHW Imports: Rcpp, stats, splines, methods, utils, DESeq2, SummarizedExperiment, fdrtool, genefilter, qvalue, Biobase, BiocGenerics, BiocParallel, dplyr, grid, ggplot2, cowplot LinkingTo: Rcpp Suggests: testthat, RColorBrewer, wesanderson, scales, gridExtra, BiocStyle, knitr, rmarkdown, airway, locfdr, tidyr, latex2exp License: Artistic-2.0 MD5sum: 236b5c636f242d8218a192ad09d697d7 NeedsCompilation: yes Title: Reproduce figures in IHW paper Description: This package conveniently wraps all functions needed to reproduce the figures in the IHW paper (https://www.nature.com/articles/nmeth.3885) and the data analysis in https://rss.onlinelibrary.wiley.com/doi/10.1111/rssb.12411, cf. the arXiv preprint (http://arxiv.org/abs/1701.05179). Thus it is a companion package to the Bioconductor IHW package. biocViews: ReproducibleResearch, ExperimentData, RNASeqData, ExpressionData Author: Nikos Ignatiadis [aut, cre] Maintainer: Nikos Ignatiadis VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/IHWpaper git_branch: devel git_last_commit: 4458da4 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/IHWpaper_1.41.0.tar.gz vignettes: vignettes/IHWpaper/inst/doc/BH-explanation.html, vignettes/IHWpaper/inst/doc/explaining_tdr.html, vignettes/IHWpaper/inst/doc/grenander_vs_ecdf.html, vignettes/IHWpaper/inst/doc/hqtl_IHW_BY.html, vignettes/IHWpaper/inst/doc/IHW_bonferroni_simulations.html, vignettes/IHWpaper/inst/doc/real_data_examples_single_curve.html, vignettes/IHWpaper/inst/doc/real_data_examples.html, vignettes/IHWpaper/inst/doc/simulations_vignette.html, vignettes/IHWpaper/inst/doc/stratified_histograms.html, vignettes/IHWpaper/inst/doc/tdr_pvalue_rejection_thresholds.html, vignettes/IHWpaper/inst/doc/weights_vs_filtering.html vignetteTitles: "Various: BH explanation / visualization", "NMeth paper: Explaining tdr", "Various: Grenander Estimator as applied to IHW (vs ECDF)", "Stats paper: hQTL analysis with IHW-Benjamini-Yekutieli", "NMeth paper: IHW-Bonferroni simulations", "Various: Real data examples: 1-fold weight function", "NMeth paper: Real data examples", "NMeth paper: Simulation Figures", "NMeth paper: Stratified Histograms", "Various: tdr and pvalue rejection regions", "Various: Weights vs Independent Filtering" hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/IHWpaper/inst/doc/BH-explanation.R, vignettes/IHWpaper/inst/doc/explaining_tdr.R, vignettes/IHWpaper/inst/doc/grenander_vs_ecdf.R, vignettes/IHWpaper/inst/doc/hqtl_IHW_BY.R, vignettes/IHWpaper/inst/doc/IHW_bonferroni_simulations.R, vignettes/IHWpaper/inst/doc/real_data_examples_single_curve.R, vignettes/IHWpaper/inst/doc/real_data_examples.R, vignettes/IHWpaper/inst/doc/simulations_vignette.R, vignettes/IHWpaper/inst/doc/stratified_histograms.R, vignettes/IHWpaper/inst/doc/tdr_pvalue_rejection_thresholds.R, vignettes/IHWpaper/inst/doc/weights_vs_filtering.R dependencyCount: 98 Package: Illumina450ProbeVariants.db Version: 1.49.0 Depends: R (>= 3.0.1) License: GPL-3 MD5sum: 1ccba9853ade48f2cc4ae17415523825 NeedsCompilation: no Title: Annotation Package combining variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes Description: Includes details on variants for each probe on the 450k bead chip for each of the four populations (Asian, American, African and European) biocViews: Homo_sapiens_Data, CancerData, ChipOnChipData, SNPData Author: Lee Butcher Maintainer: Tiffany Morris git_url: https://git.bioconductor.org/packages/Illumina450ProbeVariants.db git_branch: devel git_last_commit: 257c5c7 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/Illumina450ProbeVariants.db_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: IlluminaDataTestFiles Version: 1.51.0 License: Artistic-2.0 MD5sum: 57ff4ef25177eed45c86109b6d0fdd5c NeedsCompilation: no Title: Illumina microarray files (IDAT) for testing Description: Example data for Illumina microarray output files, for testing purposes biocViews: MicroarrayData Author: Kasper Daniel Hansen, Mike L. Smith Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/IlluminaDataTestFiles git_branch: devel git_last_commit: 552d7c3 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/IlluminaDataTestFiles_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: illuminaio dependencyCount: 0 Package: imcdatasets Version: 1.21.0 Depends: R (>= 4.4.0), SingleCellExperiment, SpatialExperiment, cytomapper, Imports: methods, utils, ExperimentHub, S4Vectors, DelayedArray, HDF5Array Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat License: GPL-3 + file LICENSE MD5sum: 7bad119ba31346348f5e4b423776ffaa NeedsCompilation: no Title: Collection of publicly available imaging mass cytometry (IMC) datasets Description: The imcdatasets package provides access to publicly available IMC datasets. IMC is a technology that enables measurement of > 40 proteins from tissue sections. The generated images can be segmented to extract single cell data. Datasets typically consist of three elements: a SingleCellExperiment object containing single cell data, a CytoImageList object containing multichannel images and a CytoImageList object containing the cell masks that were used to extract the single cell data from the images. biocViews: ExperimentData, ExperimentHub, SingleCellData, SpatialData, Homo_sapiens_Data, ImmunoOncologyData, TechnologyData, PackageTypeData, ReproducibleResearch, Tissue Author: Nicolas Damond [aut, cre] (ORCID: ), Nils Eling [ctb] (ORCID: ), Fischer Jana [ctb] (ORCID: ) Maintainer: Nicolas Damond URL: https://github.com/BodenmillerGroup/imcdatasets VignetteBuilder: knitr BugReports: https://github.com/BodenmillerGroup/imcdatasets/issues git_url: https://git.bioconductor.org/packages/imcdatasets git_branch: devel git_last_commit: 2302612 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/imcdatasets_1.21.0.tar.gz vignettes: vignettes/imcdatasets/inst/doc/Guidelines_Contribution_Dataset-formatting.html, vignettes/imcdatasets/inst/doc/imcdatasets.html vignetteTitles: "Contributing guidelines and datasets format", "Accessing IMC datasets" hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/imcdatasets/inst/doc/Guidelines_Contribution_Dataset-formatting.R, vignettes/imcdatasets/inst/doc/imcdatasets.R dependencyCount: 150 Package: iModMixData Version: 1.3.0 Imports: ExperimentHub Suggests: knitr, testthat License: GPL-3 MD5sum: 832dcfdc1c98a062f395548e75e1dd7a NeedsCompilation: no Title: Data for iModMix Package Description: Provides example datasets for the iModMix package, including gene, protein, and metabolite partial correlation matrices derived from ccRCC4 and FloresData_K_TK studies. The data are preprocessed and ready to use for testing, demonstrating iModMix workflows, and exploring correlation networks. biocViews: ExperimentData, ExpressionData, MassSpectrometryData, ExperimentHub Author: Isis Narvaez-Bandera [aut, cre] (ORCID: ) Maintainer: Isis Narvaez-Bandera URL: https://github.com/biodatalab/iModMixData VignetteBuilder: knitr BugReports: https://github.com/biodatalab/iModMixData/issues git_url: https://git.bioconductor.org/packages/iModMixData git_branch: devel git_last_commit: d3ebce1 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/iModMixData_1.3.0.tar.gz vignettes: vignettes/iModMixData/inst/doc/iModMixData.html vignetteTitles: Using iModMixData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/iModMixData/inst/doc/iModMixData.R importsMe: iModMix dependencyCount: 64 Package: ITALICSData Version: 2.51.0 Depends: R (>= 2.0.0) License: GPL MD5sum: b3d72e40363136ca3093767a3909bdc0 NeedsCompilation: no Title: ITALICSData Description: Data needed to use the ITALICS package biocViews: ExperimentData, HapMap Author: Guillem Rigaill Maintainer: Guillem Rigaill URL: http://bioinfo.curie.fr git_url: https://git.bioconductor.org/packages/ITALICSData git_branch: devel git_last_commit: eadf406 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ITALICSData_2.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ITALICS dependencyCount: 0 Package: Iyer517 Version: 1.55.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: f35d0ecb2f4a1a6db74f29598f07f410 NeedsCompilation: no Title: exprSets for Iyer, Eisen et all 1999 Science paper Description: representation of public Iyer data from http://genome-www.stanford.edu/serum/clusters.html biocViews: ExperimentData Author: Vishy Iyer Maintainer: Vince Carey git_url: https://git.bioconductor.org/packages/Iyer517 git_branch: devel git_last_commit: d2051cf git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/Iyer517_1.55.0.tar.gz vignettes: vignettes/Iyer517/inst/doc/Iyer517.pdf vignetteTitles: Iyer517 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Iyer517/inst/doc/Iyer517.R suggestsMe: DendSer dependencyCount: 7 Package: JASPAR2014 Version: 1.49.0 Depends: R (>= 3.0.1), methods, Biostrings (>= 2.29.19) License: GPL-2 MD5sum: 4be966927ee1d72fa2cebb6401f491fe NeedsCompilation: no Title: Data package for JASPAR Description: Data package for JASPAR 2014. To search this databases, please use the package TFBSTools. biocViews: ExperimentData, SequencingData Author: Ge Tan Maintainer: Ge Tan URL: http://jaspar.genereg.net/ git_url: https://git.bioconductor.org/packages/JASPAR2014 git_branch: devel git_last_commit: 62f4a16 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/JASPAR2014_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MatrixRider, TFBSTools dependencyCount: 15 Package: JASPAR2016 Version: 1.41.0 Depends: R (>= 3.2.2), methods License: GPL-2 MD5sum: 986248489becb06f1237131267c4b787 NeedsCompilation: no Title: Data package for JASPAR 2016 Description: Data package for JASPAR 2016. To search this databases, please use the package TFBSTools (>= 1.8.1). biocViews: ExperimentData, MotifAnnotation, GeneRegulation Author: Ge Tan Maintainer: Ge Tan URL: http://jaspar.genereg.net/ git_url: https://git.bioconductor.org/packages/JASPAR2016 git_branch: devel git_last_commit: 1960efd git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/JASPAR2016_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: TFBSTools, CAGEWorkflow dependencyCount: 1 Package: JohnsonKinaseData Version: 1.9.0 Depends: R (>= 4.1.0) Imports: ExperimentHub, BiocParallel, checkmate, dplyr, stats, stringr, tidyr, purrr, utils Suggests: knitr, BiocStyle, ExperimentHubData, testthat (>= 3.0.0), rmarkdown License: MIT + file LICENSE MD5sum: a485f541647af4fc9be16711af249372 NeedsCompilation: no Title: Kinase PWMs based on data published by Johnson et al. 2023 and Yaron-Barir et al. 2024 Description: The packages provides position specific weight matrices (PWMs) for 303 human serine/threonine and 93 tyrosine kinases originally published in Johnson et al. 2023 (doi:10.1038/s41586-022-05575-3) and Yaron-Barir et al. 2024 (doi:10.1038/s41586-024-07407-y). The package includes basic functionality to score user provided phosphosites. It also includes pre-computed PWM scores ("background scores") for a large collection of curated human phosphosites which can be used to rank PWM scores relative to the background scores ("percentile rank"). biocViews: ExperimentHub, Homo_sapiens_Data, Proteome Author: Florian Geier [aut, cre] (ORCID: ) Maintainer: Florian Geier URL: https://github.com/fgeier/JohnsonKinaseData/ VignetteBuilder: knitr BugReports: https://support.bioconductor.org/t/JohnsonKinaseData git_url: https://git.bioconductor.org/packages/JohnsonKinaseData git_branch: devel git_last_commit: 2675c64 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/JohnsonKinaseData_1.9.0.tar.gz vignettes: vignettes/JohnsonKinaseData/inst/doc/JohnsonKinaseData.html vignetteTitles: JohnsonKinaseData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/JohnsonKinaseData/inst/doc/JohnsonKinaseData.R dependencyCount: 75 Package: KEGGandMetacoreDzPathwaysGEO Version: 1.33.0 Depends: R (>= 2.15.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: c0dc6ba4cc185de459b24cae2ed1d938 NeedsCompilation: no Title: Disease Datasets from GEO Description: This is a collection of 18 data sets for which the phenotype is a disease with a corresponding pathway in either KEGG or metacore database.This collection of datasets were used as gold standard in comparing gene set analysis methods. biocViews: ExperimentData, GEO Author: Gaurav Bhatti Maintainer: Gaurav Bhatti git_url: https://git.bioconductor.org/packages/KEGGandMetacoreDzPathwaysGEO git_branch: devel git_last_commit: 0576659 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/KEGGandMetacoreDzPathwaysGEO_1.33.0.tar.gz vignettes: vignettes/KEGGandMetacoreDzPathwaysGEO/inst/doc/KEGGandMetacoreDzPathwaysGEO.pdf vignetteTitles: KEGGandMetacoreDzPathwaysGEO Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/KEGGandMetacoreDzPathwaysGEO/inst/doc/KEGGandMetacoreDzPathwaysGEO.R dependencyCount: 7 Package: KEGGdzPathwaysGEO Version: 1.51.0 Depends: R (>= 2.13.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: 9771151b8e85f58b70f382fa3a2cedd5 NeedsCompilation: no Title: KEGG Disease Datasets from GEO Description: This is a collection of 24 data sets for which the phenotype is a disease with a corresponding pathway in the KEGG database.This collection of datasets were used as gold standard in comparing gene set analysis methods by the PADOG package. biocViews: MicroarrayData, GEO, ExperimentData Author: Gaurav Bhatti, Adi L. Tarca Maintainer: Gaurav Bhatti git_url: https://git.bioconductor.org/packages/KEGGdzPathwaysGEO git_branch: devel git_last_commit: 9bd5be1 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/KEGGdzPathwaysGEO_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: PADOG dependencyCount: 7 Package: kidpack Version: 1.55.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5) License: GPL-2 MD5sum: 20cbf2a20044ed20792cba913008e4b7 NeedsCompilation: no Title: DKFZ kidney package Description: kidney microarray data biocViews: ExperimentData, CancerData, KidneyCancerData, MicroarrayData, ArrayExpress Author: Wolfgang Huber Maintainer: Wolfgang Huber URL: http://www.dkfz.de/mga git_url: https://git.bioconductor.org/packages/kidpack git_branch: devel git_last_commit: 8987bbb git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/kidpack_1.55.0.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: 1.39.0 Depends: R (>= 3.3.0) License: MIT + file LICENSE MD5sum: e792f1694a8633d97270e0cfe7fca371 NeedsCompilation: no Title: LINCS Knock-Out Data Package Description: Contains consensus genomic signatures (CGS) for experimental cell-line specific gene knock-outs as well as baseline gene expression data for a subset of experimental cell-lines. Intended for use with package KEGGlincs. biocViews: ExpressionData, CancerData, Homo_sapiens_Data Author: Shana White Maintainer: Shana White git_url: https://git.bioconductor.org/packages/KOdata git_branch: devel git_last_commit: 2a207af git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/KOdata_1.39.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: KEGGlincs dependencyCount: 0 Package: leeBamViews Version: 1.49.0 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: 87bb131113824589daf93eb2789cf6d6 NeedsCompilation: no Title: leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009 Description: data from PMID 19096707; prototype for managing multiple NGS samples biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData, SNPData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/leeBamViews git_branch: devel git_last_commit: b5c21fd git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/leeBamViews_1.49.0.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: 59 Package: LegATo Version: 1.7.0 Depends: R (>= 4.4.0) Imports: animalcules, data.table, dplyr, ggplot2, magrittr, MultiAssayExperiment, plyr, rlang, S4Vectors, stringr, SummarizedExperiment, tibble, tidyr, tidyselect Suggests: BiocStyle, broom, broom.mixed, circlize, ComplexHeatmap, emmeans, geepack, ggalluvial, ggeffects, grDevices, knitr, lme4, lmerTest, methods, RColorBrewer, rmarkdown, spelling, TBSignatureProfiler, testthat (>= 3.0.0), TreeSummarizedExperiment, usethis, vegan License: MIT + file LICENSE MD5sum: 02ecdddab253423ab29b6a2336c5f6ad NeedsCompilation: no Title: LegATo: Longitudinal mEtaGenomic Analysis Toolkit Description: LegATo is a suite of open-source software tools for longitudinal microbiome analysis. It is extendable to several different study forms with optimal ease-of-use for researchers. Microbiome time-series data presents distinct challenges including complex covariate dependencies and variety of longitudinal study designs. This toolkit will allow researchers to determine which microbial taxa are affected over time by perturbations such as onset of disease or lifestyle choices, and to predict the effects of these perturbations over time, including changes in composition or stability of commensal bacteria. biocViews: MicrobiomeData, ReproducibleResearch, SequencingData Author: Aubrey Odom [aut, cre] (ORCID: ), Yilong Zhang [ctb] (Author of NMIT functions), Jared Pincus [csl] (ORCID: , other: Naming consultant of package), Jordan Pincus [art] (Artist of LegATo icon) Maintainer: Aubrey Odom URL: https://wejlab.github.io/LegATo-docs/ VignetteBuilder: knitr BugReports: https://github.com/wejlab/LegATo/issues git_url: https://git.bioconductor.org/packages/LegATo git_branch: devel git_last_commit: 6068fed git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/LegATo_1.7.0.tar.gz vignettes: vignettes/LegATo/inst/doc/LegATo_vignette.html vignetteTitles: LegATo Tutorial hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/LegATo/inst/doc/LegATo_vignette.R dependencyCount: 190 Package: leukemiasEset Version: 1.49.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 3d00b76e02c88a90783656fe9a240a24 NeedsCompilation: no Title: Leukemia's microarray gene expression data (expressionSet). Description: Expressionset containing gene expresion data from 60 bone marrow samples of patients with one of the four main types of leukemia (ALL, AML, CLL, CML) or non-leukemia. biocViews: Tissue, Genome, Homo_sapiens_Data, CancerData, LeukemiaCancerData, MicroarrayData, ChipOnChipData, TissueMicroarrayData, GEO Author: Sara Aibar, Celia Fontanillo and Javier De Las Rivas. Bioinformatics and Functional Genomics Group. Cancer Research Center (CiC-IBMCC, CSIC/USAL). Salamanca. Spain. Maintainer: Sara Aibar git_url: https://git.bioconductor.org/packages/leukemiasEset git_branch: devel git_last_commit: 61c6365 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/leukemiasEset_1.49.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: geNetClassifier, multiclassPairs dependencyCount: 7 Package: LiebermanAidenHiC2009 Version: 0.51.0 Depends: KernSmooth, IRanges License: LGPL MD5sum: c054ee9699aafcfca6f2438829eeea57 NeedsCompilation: no Title: Selected data from the HiC paper of E. Lieberman-Aiden et al. in Science (2009) Description: This package provides data that were presented in the article "Comprehensive mapping of long-range interactions reveals folding principles of the human genome", Science 2009 Oct 9;326(5950):289-93. PMID: 19815776 biocViews: ExperimentData, Genome, SequencingData, DNASeqData, ChIPSeqData, miRNAData, SmallRNAData, ChipOnChipData, GEO, NCI, ENCODE Author: Wolfgang Huber, Felix Klein Maintainer: Felix Klein git_url: https://git.bioconductor.org/packages/LiebermanAidenHiC2009 git_branch: devel git_last_commit: 6dc8b18 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/LiebermanAidenHiC2009_0.51.0.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: 1.45.0 Depends: R (>= 3.1.1), methylPipe Suggests: BSgenome.Hsapiens.UCSC.hg18 License: Artistic 2.0 MD5sum: f65e73321b56c2be2ee2a73a8a0c0e14 NeedsCompilation: no Title: BS-seq data of H1 and IMR90 cell line excerpted from Lister et al. 2009 Description: Base resolution bisulfite sequencing data of Human DNA methylomes biocViews: ExperimentData, Homo_sapiens_Data, SequencingData Author: Mattia Pelizzola [aut], Kamal Kishore [aut], Mattia Furlan [ctb, cre] Maintainer: Mattia Furlan git_url: https://git.bioconductor.org/packages/ListerEtAlBSseq git_branch: devel git_last_commit: 4ca3e04 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ListerEtAlBSseq_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 160 Package: LRcellTypeMarkers Version: 1.21.0 Depends: R (>= 4.1) Imports: ExperimentHub Suggests: LRcell, BiocStyle, knitr, rmarkdown, roxygen2, testthat License: MIT + file LICENSE MD5sum: af8550ca8386cd615bab25af1d8eb5a3 NeedsCompilation: no Title: Marker gene information for LRcell R Bioconductor package Description: This is an external ExperimentData package for LRcell. This data package contains the gene enrichment scores calculated from scRNA-seq dataset which indicates the gene enrichment of each cell type in certain brain region. LRcell package is used to identify specific sub-cell types that drives the changes observed in a bulk RNA-seq differential gene expression experiment. For more details, please visit: https://github.com/marvinquiet/LRcell. biocViews: ExperimentData, ExperimentHub, RNASeqData, SingleCellData, ExpressionData, PackageTypeData Author: Wenjing Ma [cre, aut] (ORCID: ) Maintainer: Wenjing Ma VignetteBuilder: knitr BugReports: https://github.com/marvinquiet/LRcellTypeMarkers/issues git_url: https://git.bioconductor.org/packages/LRcellTypeMarkers git_branch: devel git_last_commit: ff973a7 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/LRcellTypeMarkers_1.21.0.tar.gz vignettes: vignettes/LRcellTypeMarkers/inst/doc/LRcellTypeMarkers-vignette.html vignetteTitles: LRcellTypeMarkers: Marker gene information for LRcell R Bioconductor package using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/LRcellTypeMarkers/inst/doc/LRcellTypeMarkers-vignette.R suggestsMe: LRcell dependencyCount: 64 Package: lumiBarnes Version: 1.53.0 Depends: R (>= 2.0), Biobase (>= 2.5.5), lumi (>= 1.1.0) License: LGPL MD5sum: 2028960bfd297f0e664427b48fb59704 NeedsCompilation: no Title: Barnes Benchmark Illumina Tissues Titration Data Description: The Barnes benchmark dataset can be used to evaluate the algorithms for Illumina microarrays. It measured a titration series of two human tissues, blood and placenta, and includes six samples with the titration ratio of blood and placenta as 100:0, 95:5, 75:25, 50:50, 25:75 and 0:100. The samples were hybridized on HumanRef-8 BeadChip (Illumina, Inc) in duplicate. The data is loaded as an LumiBatch Object (see documents in the lumi package). biocViews: ExperimentData, Tissue, MicroarrayData, ChipOnChipData Author: Pan Du Maintainer: Pan Du git_url: https://git.bioconductor.org/packages/lumiBarnes git_branch: devel git_last_commit: 85b424c git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/lumiBarnes_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayMvout, lumi dependencyCount: 168 Package: LungCancerACvsSCCGEO Version: 1.49.0 Depends: R (>= 2.15.0) License: GPL-2 MD5sum: 4403ef6258d6a9c24c3d16bf9261013c NeedsCompilation: no Title: A lung cancer dataset that can be used with maPredictDSC package for developing outcome prediction models from Affymetrix CEL files. Description: This package contains 30 Affymetrix CEL files for 7 Adenocarcinoma (AC) and 8 Squamous cell carcinoma (SCC) lung cancer samples taken at random from 3 GEO datasets (GSE10245, GSE18842 and GSE2109) and other 15 samples from a dataset produced by the organizers of the IMPROVER Diagnostic Signature Challenge available from GEO (GSE43580). biocViews: CancerData, LungCancerData, MicroarrayData, GEO Author: Adi Laurentiu Tarca Maintainer: Adi Laurentiu Tarca URL: http://bioinformaticsprb.med.wayne.edu/ git_url: https://git.bioconductor.org/packages/LungCancerACvsSCCGEO git_branch: devel git_last_commit: 9261fef git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/LungCancerACvsSCCGEO_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: LungCancerLines Version: 0.51.0 Imports: Rsamtools License: Artistic-2.0 MD5sum: 3069c4089af84a38f9bd77805efdb0cd NeedsCompilation: no Title: Reads from Two Lung Cancer Cell Lines Description: Reads from an RNA-seq experiment between two lung cancer cell lines: H1993 (met) and H2073 (primary). The reads are stored as Fastq files and are meant for use with the TP53Genome object in the gmapR package. biocViews: ExperimentData, Genome, CancerData, LungCancerData, RNASeqData Author: Cory Barr, Michael Lawrence Maintainer: Michael Lawrence git_url: https://git.bioconductor.org/packages/LungCancerLines git_branch: devel git_last_commit: e26f7cb git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/LungCancerLines_0.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: gmapR, VariantTools dependencyCount: 29 Package: lungExpression Version: 0.51.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: eb7f5cbc8d813f6a797ed1c1e9f1eb3b NeedsCompilation: no Title: ExpressionSets for Parmigiani et al., 2004 Clinical Cancer Research paper Description: Data from three large lung cancer studies provided as ExpressionSets biocViews: ExperimentData, CancerData, LungCancerData Author: Robert Scharpf , Simens Zhong , Giovanni Parmigiani Maintainer: Robert Scharpf git_url: https://git.bioconductor.org/packages/lungExpression git_branch: devel git_last_commit: d675c95 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/lungExpression_0.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: globaltest dependencyCount: 7 Package: lydata Version: 1.39.0 License: MIT + file LICENSE MD5sum: d41a5b98442a8019561e58c0e09b02f0 NeedsCompilation: no Title: Example Dataset for crossmeta Package Description: Raw data downloaded from GEO for the compound LY294002. Raw data is from multiple platforms from Affymetrix and Illumina. This data is used to illustrate the cross-platform meta-analysis of microarray data using the crossmeta package. biocViews: ExperimentData, MicroarrayData Author: Alex Pickering Maintainer: Alex Pickering git_url: https://git.bioconductor.org/packages/lydata git_branch: devel git_last_commit: 1bcc032 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/lydata_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: M3DExampleData Version: 1.39.0 Depends: R (>= 3.3) License: GPL (>=2) MD5sum: b3bc2a04cfa165169bb4be087129d075 NeedsCompilation: no Title: M3Drop Example Data Description: Example data for M3Drop package. biocViews: Mus_musculus_Data, RNASeqData, ExpressionData, GEO, Tissue, ExperimentData Author: Tallulah Andrews Maintainer: Tallulah Andrews git_url: https://git.bioconductor.org/packages/M3DExampleData git_branch: devel git_last_commit: e07b595 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/M3DExampleData_1.39.0.tar.gz hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: celda, M3Drop dependencyCount: 0 Package: macrophage Version: 1.29.0 Depends: R (>= 3.5.0) Suggests: knitr, markdown License: GPL (>= 2) MD5sum: 658903a51565d12ff9ec09c857f87332 NeedsCompilation: no Title: Human macrophage immune response Description: This package provides the output of running Salmon on a set of 24 RNA-seq samples from Alasoo, et al. "Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response", published in Nature Genetics, January 2018. For details on version numbers and how the samples were processed see the package vignette. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/macrophage git_branch: devel git_last_commit: f222c52 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/macrophage_1.29.0.tar.gz vignettes: vignettes/macrophage/inst/doc/macrophage.html vignetteTitles: Salmon quantifications for human macrophage immune response experiment hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/macrophage/inst/doc/macrophage.R suggestsMe: DeeDeeExperiment, fishpond, GeneTonic, mosdef, quantiseqr, tximeta, fluentGenomics dependencyCount: 0 Package: MACSdata Version: 1.21.0 License: file LICENSE MD5sum: 6ae40a6686d3cc21bef8b6047d51c107 NeedsCompilation: no Title: Test datasets for the MACSr package Description: Test datasets from the MACS3 test examples are use in the examples of the `MACSr` package. All 9 datasets are uploaded to the `ExperimentHub`. The original data can be found at: https://github.com/macs3-project/MACS/. biocViews: ExperimentHub, ExperimentData, ChIPSeqData Author: Qiang Hu [aut, cre] Maintainer: Qiang Hu git_url: https://git.bioconductor.org/packages/MACSdata git_branch: devel git_last_commit: fc15089 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/MACSdata_1.21.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: MACSr dependencyCount: 0 Package: mammaPrintData Version: 1.49.0 Depends: R (>= 2.13.0) Suggests: Biobase, readxl, limma License: Artistic-2.0 MD5sum: 095fac12b6fc984b1d4738253fb3b73c NeedsCompilation: no Title: RGLists from the Glas and Buyse breast cancer studies Description: Gene expression data for the two breast cancer cohorts published by Glas and Buyse in 2006. This cohorts were used to implement and validate the mammaPrint breast cancer test. biocViews: ExperimentData, ExpressionData, CancerData, BreastCancerData, MicroarrayData, TwoChannelData Author: Luigi Marchionni Maintainer: Luigi Marchionni URL: http://luigimarchionni.org/breastTSP.html git_url: https://git.bioconductor.org/packages/mammaPrintData git_branch: devel git_last_commit: 0073dec git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/mammaPrintData_1.49.0.tar.gz vignettes: vignettes/mammaPrintData/inst/doc/mammaPrintData.pdf vignetteTitles: Working with the mammaPrintData package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mammaPrintData/inst/doc/mammaPrintData.R dependencyCount: 0 Package: maqcExpression4plex Version: 1.57.0 Suggests: oligo, pdInfoBuilder License: GPL MD5sum: e539800366b01979b2da56832bf475bf NeedsCompilation: no Title: Sample Expression Data - MAQC / HG18 - NimbleGen Description: Data from human (HG18) 4plex NimbleGen array. It has 24k genes with 3 60mer probes per gene. biocViews: ExperimentData, CancerData Author: NimbleGen Systems Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/maqcExpression4plex git_branch: devel git_last_commit: 020fd04 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/maqcExpression4plex_1.57.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligo dependencyCount: 0 Package: MAQCsubset Version: 1.51.0 Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), lumi, methods Suggests: genefilter, codelink License: Artistic-2.0 MD5sum: 8e63c735bac8f47e7976bbb068cafceb NeedsCompilation: no Title: Experimental Data Package: MAQCsubset Description: Data Package automatically created on Sun Nov 19 15:59:29 2006. biocViews: ExperimentData, MicroarrayData, GEO Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/MAQCsubset git_branch: devel git_last_commit: d39e9ae git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/MAQCsubset_1.51.0.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: 168 Package: marinerData Version: 1.13.0 Imports: utils, ExperimentHub Suggests: knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0) License: GPL-3 MD5sum: f1f406b40b0bef3469a86cfe229b8664 NeedsCompilation: no Title: ExperimentHub data for the mariner package Description: Subsampled Hi-C in HEK cells expressing the NHA9 fusion with an F to S mutated IDR ("FS") or without any mutations to the IDR ("Wildtype" or "WT"). These files are used for testing mariner functions and some examples. biocViews: ExperimentHub, ExperimentData, SequencingData Author: Eric Davis [aut, cre] (ORCID: ) Maintainer: Eric Davis VignetteBuilder: knitr BugReports: https://support.bioconductor.org/t/marinerData git_url: https://git.bioconductor.org/packages/marinerData git_branch: devel git_last_commit: d9675c5 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/marinerData_1.13.0.tar.gz vignettes: vignettes/marinerData/inst/doc/marinerData.html vignetteTitles: marinerData package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/marinerData/inst/doc/marinerData.R suggestsMe: mariner dependencyCount: 64 Package: mCSEAdata Version: 1.33.0 Depends: R (>= 3.5) Imports: GenomicRanges Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 9d056d43ac182f5ba484fbf54f108f46 NeedsCompilation: no Title: Data package for mCSEA package Description: Data objects necessary to some mCSEA package functions. There are also example data objects to illustrate mCSEA package functionality. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData, ExperimentData Author: Jordi Martorell Marugán Maintainer: Jordi Martorell Marugán VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mCSEAdata git_branch: devel git_last_commit: a4473cb git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/mCSEAdata_1.33.0.tar.gz vignettes: vignettes/mCSEAdata/inst/doc/mCSEAdata.html vignetteTitles: Data for mCSEA package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mCSEAdata/inst/doc/mCSEAdata.R dependencyCount: 11 Package: mcsurvdata Version: 1.31.0 Depends: R (>= 3.5), ExperimentHub Imports: AnnotationHub, Biobase Suggests: BiocStyle, knitr License: GPL (>=2) MD5sum: 5e46ae70104d135a31f06208d3511947 NeedsCompilation: no Title: Meta cohort survival data Description: This package stores two merged expressionSet objects that contain the gene expression profile and clinical information of -a- six breast cancer cohorts and -b- four colorectal cancer cohorts. Breast cancer data are employed in the vignette of the hrunbiased package for survival analysis of gene signatures. biocViews: ExperimentData, Homo_sapiens_Data, GEO, MicroarrayData Author: Adria Caballe Mestres [aut, cre], Antoni Berenguer Llergo [aut], Camille Stephan-Otto Attolini [aut] Maintainer: Adria Caballe Mestres URL: https://github.com/adricaba/mcsurvdata VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mcsurvdata git_branch: devel git_last_commit: 51b5d7a git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/mcsurvdata_1.31.0.tar.gz vignettes: vignettes/mcsurvdata/inst/doc/mcsurvdata.html vignetteTitles: analysis vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mcsurvdata/inst/doc/mcsurvdata.R dependencyCount: 64 Package: MEDIPSData Version: 1.49.0 Depends: R (>= 3.5) Suggests: MEDIPS, GenomicRanges, qsea License: GPL (>= 2) MD5sum: f1f152d13be83dec84056bee86b847d1 NeedsCompilation: no Title: Example data for MEDIPS and QSEA packages Description: Example data for MEDIPS and QSEA packages, consisting of chromosome 22 MeDIP and control/Input sample data. Additionally, the package contains MeDIP seq data from 3 NSCLC samples and adjacent normal tissue (chr 20-22). All data has been aligned to human genome hg19. biocViews: ExperimentData, Genome, SequencingData Author: Lukas Chavez Maintainer: Lukas Chavez git_url: https://git.bioconductor.org/packages/MEDIPSData git_branch: devel git_last_commit: b8c3d21 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/MEDIPSData_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MEDIPS, qsea dependencyCount: 0 Package: MEEBOdata Version: 1.51.0 License: LGPL MD5sum: a2bd3aab6d705e5a7823a96482989bee NeedsCompilation: no Title: MEEBO set and MEEBO controls. Description: R objects describing the MEEBO set. biocViews: ExperimentData Author: Agnes Paquet Maintainer: Agnes Paquet URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/ git_url: https://git.bioconductor.org/packages/MEEBOdata git_branch: devel git_last_commit: 1e6c46d git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/MEEBOdata_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQuality dependencyCount: 0 Package: MetaGxBreast Version: 1.33.0 Depends: R (>= 3.6.0), Biobase, AnnotationHub, ExperimentHub Imports: stats, lattice, impute, SummarizedExperiment Suggests: testthat, xtable, tinytex License: Apache License (>= 2) MD5sum: bdf0ed32ba9d8caf0326b22082a22ba8 NeedsCompilation: no Title: Transcriptomic Breast Cancer Datasets Description: A collection of Breast Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium. biocViews: ExpressionData, ExperimentHub, CancerData, Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData, ExperimentData Author: Michael Zon [aut], Deena M.A. Gendoo [aut], Christopher Eeles [ctb], Benjamin Haibe-Kains [aut, cre] Maintainer: Benjamin Haibe-Kains git_url: https://git.bioconductor.org/packages/MetaGxBreast git_branch: devel git_last_commit: 8d29f74 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/MetaGxBreast_1.33.0.tar.gz vignettes: vignettes/MetaGxBreast/inst/doc/MetaGxBreast.pdf vignetteTitles: MetaGxBreast: a package for breast cancer gene expression analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MetaGxBreast/inst/doc/MetaGxBreast.R dependencyCount: 76 Package: MetaGxOvarian Version: 1.33.0 Depends: Biobase, AnnotationHub, ExperimentHub, SummarizedExperiment, R (>= 3.6.0) Imports: stats, lattice, impute Suggests: testthat, xtable, rmarkdown, knitr, BiocStyle, markdown License: Artistic-2.0 MD5sum: c354827ea2251efd3c8bdc6248d10e8c NeedsCompilation: no Title: Transcriptomic Ovarian Cancer Datasets Description: A collection of Ovarian Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium. biocViews: ExpressionData, ExperimentHub, CancerData, Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData, ExperimentData Author: Michael Zon [aut], Vandana Sandhu [aut], Christopher Eeles [ctb], Benjamin Haibe-Kains [aut, cre] Maintainer: Benjamin Haibe-Kains VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MetaGxOvarian git_branch: devel git_last_commit: 432564f git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/MetaGxOvarian_1.33.0.tar.gz vignettes: vignettes/MetaGxOvarian/inst/doc/MetaGxOvarian.html vignetteTitles: MetaGxOvarian: A Package for Ovarian Cancer Gene Expression Analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MetaGxOvarian/inst/doc/MetaGxOvarian.R dependencyCount: 76 Package: MetaGxPancreas Version: 1.33.0 Depends: SummarizedExperiment, ExperimentHub, R (>= 3.6.0) Imports: stats, impute, S4Vectors, AnnotationHub Suggests: testthat, knitr, BiocStyle, rmarkdown, markdown License: Artistic-2.0 MD5sum: 3c5777c69d22c2f242a2d6d35c897193 NeedsCompilation: no Title: Transcriptomic Pancreatic Cancer Datasets Description: A collection of pancreatic Cancer transcriptomic datasets that are part of the MetaGxData package compendium. This package contains multiple pancreas cancer datasets that have been downloaded from various resources and turned into SummarizedExperiment objects. The details of how the authors normalized the data can be found in the experiment data section of the objects. Additionally, the location the data was obtained from can be found in the url variables of the experiment data portion of each SE. biocViews: ExpressionData, ExperimentHub, CancerData, Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData, ExperimentData, SequencingData Author: Michael Zon [aut], Vandana Sandhu [aut], Christopher Eeles [ctb], Michael Tran Cao-Anh [ctb], Benjamin Haibe-Kains [aut, cre] Maintainer: Benjamin Haibe-Kains VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MetaGxPancreas git_branch: devel git_last_commit: 006b935 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/MetaGxPancreas_1.33.0.tar.gz vignettes: vignettes/MetaGxPancreas/inst/doc/MetaGxPancreas.html vignetteTitles: MetaGxPancreas: A Package for Pancreatic Cancer Gene Expression Analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MetaGxPancreas/inst/doc/MetaGxPancreas.R dependencyCount: 76 Package: metaMSdata Version: 1.49.0 License: GPL (>= 2) MD5sum: 1820a131f96067b5a3102d2346df9b31 NeedsCompilation: no Title: Example CDF data for the metaMS package Description: Example CDF data for the metaMS package biocViews: ExperimentData, MassSpectrometryData Author: Ron Wehrens [aut, cre], Pietro Franceschi [aut], Georg Weingart [ctb] Maintainer: Yann Guitton git_url: https://git.bioconductor.org/packages/metaMSdata git_branch: devel git_last_commit: bb65a05 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/metaMSdata_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: MetaScope Version: 2.1.0 Depends: R (>= 4.2.0) Imports: BiocFileCache, Biostrings, data.table (>= 1.16.2), dplyr, ggplot2, magrittr, Matrix, MultiAssayExperiment, purrr, Rbowtie2, readr, rlang, Rsamtools, S4Vectors, stringr, SummarizedExperiment, taxonomizr, tibble, tidyr, tools Suggests: animalcules, BiocStyle, biomformat, GenomicRanges, IRanges, knitr, lintr, plyr, R.utils, RCurl, rmarkdown, Rsubread, spelling, sys, testthat, usethis Enhances: BiocParallel License: GPL (>= 3) MD5sum: c9c6f34413f99820eda571fb894958e5 NeedsCompilation: no Title: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data Description: This package contains tools and methods for preprocessing microbiome data. Functionality includes library generation, demultiplexing, alignment, and microbe identification. It is in part an R translation of the PathoScope 2.0 pipeline. biocViews: MicrobiomeData, ReproducibleResearch, SequencingData Author: Sean Lu [aut, cre] (ORCID: ), Aubrey Odom [aut] (ORCID: ), Rahul Varki [aut] (ORCID: ), W. Evan Johnson [aut] (ORCID: ) Maintainer: Sean Lu URL: https://github.com/wejlab/metascope https://wejlab.github.io/metascope-docs/ VignetteBuilder: knitr BugReports: https://github.com/wejlab/MetaScope/issues git_url: https://git.bioconductor.org/packages/MetaScope git_branch: devel git_last_commit: 9b1edc6 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/MetaScope_2.1.0.tar.gz vignettes: vignettes/MetaScope/inst/doc/MetaScope_vignette.html vignetteTitles: "Introduction to MetaScope" hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MetaScope/inst/doc/MetaScope_vignette.R dependencyCount: 99 Package: MethylAidData Version: 1.45.0 Depends: MethylAid, R (>= 3.2) Suggests: BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC License: GPL (>= 2) MD5sum: c55b573055615f2bfb1c4aa2b75eb02e NeedsCompilation: no Title: MethylAid-summarized data for 2800 Illumina 450k array samples and 2620 EPIC array samples Description: A data package containing summarized Illumina 450k array data on 2800 samples and summarized EPIC data for 2620 samples. The data can be use as a background data set in the interactive application. biocViews: ExperimentData, TechnologyData, MicroarrayData, MethylationArrayData Author: Davy Cats, Tyler J. Gorrie-Stone, Bastiaan T. Heijmans, John W. Holloway, BIOS Consortium, Maarten van Iterson, Faisal I. Rezwam, Leonard Schalkwyk Maintainer: M. van Iterson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MethylAidData git_branch: devel git_last_commit: bd179ce git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/MethylAidData_1.45.0.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: 171 Package: methylclockData Version: 1.21.0 Imports: ExperimentHubData, ExperimentHub, utils Suggests: knitr, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: d7933b27fcb99c1bbc0a7b2f32fb4431 NeedsCompilation: no Title: Data for methylclock package Description: Collection of 9 datasets, andrews and bakulski cord blood, blood gse35069, blood gse35069 chen, blood gse35069 complete, combined cord blood, cord bloo d gse68456, gervin and lyle cord blood, guintivano dlpfc and saliva gse48472". Data downloaded from [meffil](https://github.com/perishky/meffil/). Data used to estimate cell counts using Extrinsic epigenetic age acceleration (EEAA) method Collection of 12 datasets to use with MethylClock package to estimate chronological and gestational DNA methylationwith estimators to use wit different methylation clocks biocViews: SpecimenSource, ExperimentHub, Tissue, OrganismData, Homo_sapiens_Data Author: Juan R. Gonzalez [aut], Dolors Pelegri-Siso [aut, cre] Maintainer: Dolors Pelegri-Siso URL: https://github.com/isglobal-brge/methylclockData VignetteBuilder: knitr BugReports: https://github.com/isglobal-brge/methylclockData/issues git_url: https://git.bioconductor.org/packages/methylclockData git_branch: devel git_last_commit: 69601c0 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/methylclockData_1.21.0.tar.gz vignettes: vignettes/methylclockData/inst/doc/methylcockData.html vignetteTitles: References for metilclock using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/methylclockData/inst/doc/methylcockData.R dependsOnMe: methylclock dependencyCount: 119 Package: MethylSeqData Version: 1.23.0 Depends: SummarizedExperiment Imports: ExperimentHub, HDF5Array, rhdf5, GenomeInfoDb, S4Vectors, GenomicRanges, stats, IRanges, utils Suggests: BiocFileCache, BiocStyle, data.table, knitr, rmarkdown License: CC0 MD5sum: ab471adc17b1e8e743158493aab68487 NeedsCompilation: no Title: Collection of Public DNA Methylation Sequencing Datasets Description: Base-level (i.e. cytosine-level) counts for a collection of public bisulfite-seq datasets (e.g., WGBS and RRBS), provided as SummarizedExperiment objects with sample- and base-level metadata. biocViews: ExperimentHub, ExperimentData, SequencingData, Homo_sapiens_Data, Mus_musculus_Data, MethylSeqData Author: Peter Hickey [aut, cre] Maintainer: Peter Hickey VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MethylSeqData git_branch: devel git_last_commit: 3240f36 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/MethylSeqData_1.23.0.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: 84 Package: MicrobiomeBenchmarkData Version: 1.15.1 Depends: R (>= 4.2), SummarizedExperiment, TreeSummarizedExperiment Imports: BiocFileCache, tools, S4Vectors, ape, utils Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0), mia, ggplot2, tidyr, dplyr, magrittr, tibble, purrr License: Artistic-2.0 MD5sum: d63e732551f9cd358ae4958737d57552 NeedsCompilation: no Title: Datasets for benchmarking in microbiome research Description: The MicrobiomeBenchmarkData package provides functionality to access microbiome datasets suitable for benchmarking. These datasets have some biological truth, which allows to have expected results for comparison. The datasets come from various published sources and are provided as TreeSummarizedExperiment objects. Currently, only datasets suitable for benchmarking differential abundance methods are available. biocViews: ExperimentData, MicrobiomeData, ReproducibleResearch, SequencingData Author: Samuel Gamboa [aut, cre] (ORCID: ), Levi Waldron [aut] (ORCID: ), Marcel Ramos [ctb], NCI [fnd] (GrantNo.: R01CA230551) Maintainer: Samuel Gamboa URL: https://github.com/waldronlab/MicrobiomeBenchmarkData, http://waldronlab.io/MicrobiomeBenchmarkData/ VignetteBuilder: knitr BugReports: https://github.com/waldronlab/MicrobiomeBenchmarkData/issues git_url: https://git.bioconductor.org/packages/MicrobiomeBenchmarkData git_branch: devel git_last_commit: ed900aa git_last_commit_date: 2026-04-29 Date/Publication: 2026-04-30 source.ver: src/contrib/MicrobiomeBenchmarkData_1.15.1.tar.gz vignettes: vignettes/MicrobiomeBenchmarkData/inst/doc/datasets.html, vignettes/MicrobiomeBenchmarkData/inst/doc/MicrobiomeBenchmarkData.html, vignettes/MicrobiomeBenchmarkData/inst/doc/recalibrare_spikein_data.html vignetteTitles: Datasets in MicrobiomeBenchmarkData, MicrobiomeBenchmarkData, Recalibration of the Stammler_2016_16S_spikein dataset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MicrobiomeBenchmarkData/inst/doc/datasets.R, vignettes/MicrobiomeBenchmarkData/inst/doc/MicrobiomeBenchmarkData.R, vignettes/MicrobiomeBenchmarkData/inst/doc/recalibrare_spikein_data.R suggestsMe: bugphyzz dependencyCount: 84 Package: microbiomeDataSets Version: 1.21.0 Depends: R (>= 4.1), SummarizedExperiment, TreeSummarizedExperiment, MultiAssayExperiment Imports: methods, utils, BiocGenerics, ExperimentHub, Biostrings, ape Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, testthat License: CC0 MD5sum: a8ed691e84c86b14e90ec38c90fcc81d NeedsCompilation: no Title: Experiment Hub based microbiome datasets Description: microbiomeDataSets is a collection of microbiome datasets loaded from Bioconductor'S ExperimentHub infrastructure. The datasets serve as reference for workflows and vignettes published adjacent to the microbiome analysis tools on Bioconductor. Additional datasets can be added overtime and additions from authors are welcome. biocViews: ExperimentHub, ExperimentData, MicrobiomeData, SequencingData Author: Leo Lahti [cre, aut] (ORCID: ), Felix G.M. Ernst [aut] (ORCID: ), Sudarshan Shetty [aut] (ORCID: ), Chouaib Benchraka [ctb] (ORCID: ), Yagmur Simsek [ctb] Maintainer: Leo Lahti VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/microbiomeDataSets git_branch: devel git_last_commit: e26aadc git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/microbiomeDataSets_1.21.0.tar.gz vignettes: vignettes/microbiomeDataSets/inst/doc/microbiomeDataSets.html vignetteTitles: microbiomeDataSets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/microbiomeDataSets/inst/doc/microbiomeDataSets.R suggestsMe: mia dependencyCount: 96 Package: microRNAome Version: 1.35.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: BiocGenerics, RUnit License: GPL (>= 2) MD5sum: e233ff15e661aebbdd7cd9125ccfbb39 NeedsCompilation: no Title: SummarizedExperiment for the microRNAome project Description: This package provides a SummarizedExperiment object of read counts for microRNAs across tissues, cell-types, and cancer cell-lines. The read count matrix was prepared and provided by the author of the study: Towards the human cellular microRNAome. biocViews: ExperimentData, CellCulture, CancerData, SequencingData, RNASeqData, miRNAData Author: Matthew N. McCall , Marc K. Halushka , Arun H. Patil Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/microRNAome git_branch: devel git_last_commit: edc55f6 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/microRNAome_1.35.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 25 Package: minfiData Version: 0.59.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2), IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 License: Artistic-2.0 MD5sum: 9daa026d63aaec0fed436362d687f4a1 NeedsCompilation: no Title: Example data for the Illumina Methylation 450k array Description: Data from 6 samples across 2 groups from 450k methylation arrays. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData Author: Kasper Daniel Hansen, Martin Aryee, Winston Timp Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/minfiData git_branch: devel git_last_commit: 6bb3fa2 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/minfiData_0.59.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: methylationArrayAnalysis suggestsMe: bigmelon, conumee, ENmix, funtooNorm, Harman, MethylAid, minfi, MultiDataSet, recountmethylation, regionalpcs, shinyepico, shinyMethyl, skewr, MethylAidData dependencyCount: 148 Package: minfiDataEPIC Version: 1.39.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2), IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: Artistic-2.0 MD5sum: c7d984fd607cec7704b5685d7fb39be1 NeedsCompilation: no Title: Example data for the Illumina Methylation EPIC array Description: Data from 3 technical replicates of the cell line GM12878 from the EPIC methylation array. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData Author: Jean-Philippe Fortin, Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/minfiDataEPIC git_branch: devel git_last_commit: 35f2e75 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/minfiDataEPIC_1.39.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MethylAid, minfi, recountmethylation, REMP, MethylAidData dependencyCount: 148 Package: minionSummaryData Version: 1.43.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: d981808da28c8ea34311f37c99ce8afc NeedsCompilation: no Title: Summarised MinION sequencing data published by Ashton et al. 2015 Description: Summarised MinION sequencing data for Salmonella Typhi published by Ashton et al. in 2015. Three replicate runs are each provided as Fast5Summary objects. biocViews: ExperimentData, SequencingData Author: Mike Smith [aut, cre] Maintainer: Mike Smith VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/minionSummaryData git_branch: devel git_last_commit: f103208 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/minionSummaryData_1.43.0.tar.gz vignettes: vignettes/minionSummaryData/inst/doc/creating-Styphi-Dataset.html vignetteTitles: Creating example MinION summary dataset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/minionSummaryData/inst/doc/creating-Styphi-Dataset.R dependencyCount: 0 Package: miRcompData Version: 1.43.0 Depends: R (>= 3.2), Imports: utils License: GPL-3 | file LICENSE MD5sum: f33d6cf35c7955ab798871036a0b3c70 NeedsCompilation: no Title: Data used in the miRcomp package Description: Raw amplification data from a large microRNA mixture / dilution study. These data are used by the miRcomp package to assess the performance of methods that estimate expression from the amplification curves. biocViews: ExperimentData, ExpressionData, qPCRData, Homo_sapiens_Data Author: Matthew N. McCall Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/miRcompData git_branch: devel git_last_commit: 5e1b94f git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/miRcompData_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: miRcomp dependencyCount: 1 Package: miRNATarget Version: 1.51.0 Depends: R (>= 2.10), Biobase License: GPL MD5sum: e803f7c2857630dd40b9ac410c5582c2 NeedsCompilation: no Title: gene target tabale of miRNA for human/mouse used for MiRaGE package Description: gene target tabale of miRNA for human/mouse used for MiRaGE package biocViews: ExperimentData, Homo_sapiens_Data Author: Y-h. Taguchi Maintainer: Y-h. Taguchi git_url: https://git.bioconductor.org/packages/miRNATarget git_branch: devel git_last_commit: d6b6701 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/miRNATarget_1.51.0.tar.gz vignettes: vignettes/miRNATarget/inst/doc/miRNATarget.pdf vignetteTitles: miRNATargetTutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/miRNATarget/inst/doc/miRNATarget.R suggestsMe: MiRaGE dependencyCount: 7 Package: MMDiffBamSubset Version: 1.49.0 Suggests: MMDiff2 License: LGPL MD5sum: cbe83a74cfb962ae580d2c4ae730ae23 NeedsCompilation: no Title: Example ChIP-Seq data for the MMDiff package Description: Subset of BAM files, including WT_2.bam, Null_2.bam, Resc_2.bam, Input.bam from the "Cfp1" experiment (see Clouaire et al., Genes Dev. 2012). Data is available under ArrayExpress accession numbers E-ERAD-79. Additionally, corresponding subset of peaks called by MACS biocViews: ExperimentData, Genome, StemCell, Mus_musculus_Data, DNASeqData, ChIPSeqData, ArrayExpress Author: Gabriele Schweikert Maintainer: Gabriele Schweikert git_url: https://git.bioconductor.org/packages/MMDiffBamSubset git_branch: devel git_last_commit: e8d5d74 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/MMDiffBamSubset_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MMDiff2 dependencyCount: 0 Package: MOFAdata Version: 1.29.0 Depends: R (>= 3.5) Suggests: knitr, MultiAssayExperiment, rmarkdown, BiocStyle License: LGPL-3 MD5sum: 60088c13df811356515ff7dec2923913 NeedsCompilation: yes Title: Data package for Multi-Omics Factor Analysis (MOFA) Description: A collection of datasets to accompany the R package MOFA and illustrate running and analysing MOFA models. biocViews: ReproducibleResearch Author: Ricard Argelaguet, Britta Velten, Damien Arnol, Florian Buettner, Wolfgang Huber, Oliver Stegle Maintainer: Britta Velten VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MOFAdata git_branch: devel git_last_commit: 08ddbb2 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/MOFAdata_1.29.0.tar.gz vignettes: vignettes/MOFAdata/inst/doc/MOFAdata.html vignetteTitles: MOFAdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MOFAdata/inst/doc/MOFAdata.R importsMe: TDbasedUFE suggestsMe: SUMO dependencyCount: 0 Package: mosaicsExample Version: 1.51.0 Depends: R (>= 2.11.1) License: GPL (>= 2) MD5sum: 21041b25d4fd13732aa8c10a698eeb18 NeedsCompilation: no Title: Example data for the mosaics package, which implements MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data for transcription factor binding and histone modification Description: Data for the mosaics package, consisting of (1) chromosome 22 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding and H3K4me3 modification in MCF7 cell line from ENCODE database (HG19) and (2) chromosome 21 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding, with mappability, GC content, and sequence ambiguity scores of human genome HG18. biocViews: ExperimentData, ChIPseqData, Homo_sapiens Author: Dongjun Chung, Pei Fen Kuan, Rene Welch, Sunduz Keles Maintainer: Dongjun Chung URL: http://groups.google.com/group/mosaics_user_group git_url: https://git.bioconductor.org/packages/mosaicsExample git_branch: devel git_last_commit: 5144fa8 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/mosaicsExample_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: mosaics dependencyCount: 0 Package: mouse4302barcodevecs Version: 1.51.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 9fbf57ddbb7b5b1bff06b8440d390dcd NeedsCompilation: no Title: mouse4302 data for barcode Description: Data used by the barcode package for microarrays of type mouse4302. biocViews: Mus_musculus_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/mouse4302barcodevecs git_branch: devel git_last_commit: ab5a04f git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/mouse4302barcodevecs_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: MouseAgingData Version: 1.9.0 Depends: R (>= 4.4.0), SingleCellExperiment Imports: AnnotationHub, ExperimentHub Suggests: BiocStyle, knitr, rmarkdown, scater License: Artistic-2.0 MD5sum: cc16ffbe5f9b60acfc56002287ff55a7 NeedsCompilation: no Title: Multi-omics data access for studies investigating the effects of aging Description: The MouseAgingData package provides analysis-ready data resources from different studies focused on aging and rejuvenation in mice. The package currently provides two 10x Genomics single-cell RNA-seq datasets. The first study profiled the aging mouse brain measured across 37,089 cells (Ximerakis et al., 2019). The second study investigated parabiosis by profiling a total of 105,329 cells (Ximerakis & Holton et al., 2023). The datasets are provided as SingleCellExperiment objects and provide raw UMI counts and cell metadata. biocViews: ExperimentData, ExpressionData, SequencingData, RNASeqData, SingleCellData, ExperimentHub, PackageTypeData, Mus_musculus_Data Author: Tram Nguyen [aut, cre] (ORCID: ), Kris Holton [aut], Tyrone Lee [aut], Nitesh Turaga [ctb], Ludwig Geistlinger [aut], Robert Gentleman [aut] Maintainer: Tram Nguyen URL: https://github.com/ccb-hms/MouseAgingData VignetteBuilder: knitr BugReports: https://github.com/ccb-hms/MouseAgingData/issues git_url: https://git.bioconductor.org/packages/MouseAgingData git_branch: devel git_last_commit: 7613b51 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/MouseAgingData_1.9.0.tar.gz vignettes: vignettes/MouseAgingData/inst/doc/MouseAgingData_parabiosis_droplet.html vignetteTitles: Accessing and Visualizing Parabiosis Droplet Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MouseAgingData/inst/doc/MouseAgingData_parabiosis_droplet.R dependencyCount: 76 Package: MouseGastrulationData Version: 1.27.0 Depends: R (>= 4.1), SingleCellExperiment, SummarizedExperiment, SpatialExperiment Imports: methods, ExperimentHub, BiocGenerics, S4Vectors, BumpyMatrix Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 667e0bb592eeebf33c501b8ba4669ad5 NeedsCompilation: no Title: Single-Cell -omics Data across Mouse Gastrulation and Early Organogenesis Description: Provides processed and raw count data for single-cell RNA sequencing, single-cell ATAC-seq, and seqFISH (spatial transcriptomic) experiments performed along a timecourse of mouse gastrulation and early organogenesis. biocViews: ExperimentData, ExpressionData, SequencingData, RNASeqData, SingleCellData, ExperimentHub, Mus_musculus_Data Author: Jonathan Griffiths [aut, cre], Aaron Lun [aut] Maintainer: Jonathan Griffiths URL: https://github.com/MarioniLab/MouseGastrulationData VignetteBuilder: knitr BugReports: https://github.com/MarioniLab/MouseGastrulationData/issues git_url: https://git.bioconductor.org/packages/MouseGastrulationData git_branch: devel git_last_commit: 729ee39 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/MouseGastrulationData_1.27.0.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 suggestsMe: Coralysis, miloR dependencyCount: 81 Package: MouseThymusAgeing Version: 1.21.0 Depends: SingleCellExperiment, SummarizedExperiment Imports: ExperimentHub, methods, BiocGenerics, S4Vectors Suggests: knitr, scuttle, rmarkdown, BiocStyle License: GPL-3 MD5sum: c91ac29fabf7783531c5923b3ff4b908 NeedsCompilation: no Title: Single-cell Transcriptomics Data of the Ageing Mouse Thymus Description: This package provides data access to counts matrices and meta-data for single-cell RNA sequencing data of thymic epithlial cells across mouse ageing using SMARTseq2 and 10X Genommics chemistries. Access is provided as a data package via ExperimentHub. It is designed to facilitate the re-use of data from Baran-Gale _et al._ in a consistent format that includes relevant and informative meta-data. biocViews: ExperimentHub, SingleCellData, ExpressionData, ExperimentData Author: Mike Morgan [aut, cre], Jeanette Baran-Gale [aut] Maintainer: Mike Morgan VignetteBuilder: knitr BugReports: https://github.com/MarioniLab/MouseThymusAgeing/issues git_url: https://git.bioconductor.org/packages/MouseThymusAgeing git_branch: devel git_last_commit: 6031ad5 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/MouseThymusAgeing_1.21.0.tar.gz vignettes: vignettes/MouseThymusAgeing/inst/doc/MouseThymusAgeing.html vignetteTitles: Available datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MouseThymusAgeing/inst/doc/MouseThymusAgeing.R suggestsMe: miloR dependencyCount: 76 Package: msd16s Version: 1.33.0 Depends: R (>= 2.10), Biobase, metagenomeSeq, License: Artistic-2.0 MD5sum: fdcd3f82b3deeb458be42ce8ce616344 NeedsCompilation: no Title: Healthy and moderate to severe diarrhea 16S expression data Description: Gut 16S sequencing expression data from 992 healthy and moderate-to-severe diarrhetic samples used in 'Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition'. biocViews: ExperimentData, SequencingData, MicrobiomeData Author: Joseph N. Paulson, Hector Corrada Bravo, Mihai Pop Maintainer: Joseph N. Paulson URL: http://www.cbcb.umd.edu/research/projects/GEMS-pathogen-discovery git_url: https://git.bioconductor.org/packages/msd16s git_branch: devel git_last_commit: a3efc3b git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/msd16s_1.33.0.tar.gz vignettes: vignettes/msd16s/inst/doc/msd16s.pdf vignetteTitles: msd16s hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/msd16s/inst/doc/msd16s.R suggestsMe: scTreeViz dependencyCount: 33 Package: msdata Version: 0.53.0 Depends: R (>= 3.5.0) Suggests: xcms, mzR, MSnbase License: GPL (>= 2) MD5sum: 99a2974b1c80b2652260ab7f2131a2b4 NeedsCompilation: no Title: Various Mass Spectrometry raw data example files Description: Ion Trap positive ionization mode data in mzML file format. Subset from 500-850 m/z and 1190-1310 seconds, incl. MS2 and MS3, intensity threshold 100.000. Extracts from FTICR Apex III, m/z 400-450. Subset of UPLC - Bruker micrOTOFq data, both mzML and mz5. LC-MSMS and MRM files from proteomics experiments. PSI mzIdentML example files for various search engines. biocViews: ExperimentData, MassSpectrometryData Author: Steffen Neumann , Laurent Gatto with contriutions from Johannes Rainer Maintainer: Steffen Neumann , Laurent Gatto git_url: https://git.bioconductor.org/packages/msdata git_branch: devel git_last_commit: 56531dd git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/msdata_0.53.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: Chromatograms, QFeatures, TargetDecoy, RforProteomics dependencyCount: 0 Package: msigdb Version: 1.21.0 Depends: R (>= 4.1) Imports: ExperimentHub, utils, GSEABase, org.Mm.eg.db, org.Hs.eg.db, AnnotationDbi, methods, stats, AnnotationHub Suggests: singscore, vissE, knitr, prettydoc, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocFileCache, GO.db, stringr, limma License: CC BY 4.0 MD5sum: 1fea94a942569a051964f48d1acc5d73 NeedsCompilation: no Title: An ExperimentHub Package for the Molecular Signatures Database (MSigDB) Description: This package provides the Molecular Signatures Database (MSigDB) in a R accessible objects. Signatures are stored in GeneSet class objects form the GSEABase package and the entire database is stored in a GeneSetCollection object. These data are then hosted on the ExperimentHub. Data used in this package was obtained from the MSigDB of the Broad Institute. Metadata for each gene set is stored along with the gene set in the GeneSet class object. biocViews: ExperimentHub, Homo_sapiens_Data, Mus_musculus_Data Author: Dharmesh D. Bhuva [aut, cre] (ORCID: ), Gordon K. Smyth [aut] (ORCID: ), Alexandra Garnham [aut] (ORCID: ) Maintainer: Dharmesh D. Bhuva URL: https://davislaboratory.github.io/msigdb VignetteBuilder: knitr BugReports: https://github.com/DavisLaboratory/msigdb/issues git_url: https://git.bioconductor.org/packages/msigdb git_branch: devel git_last_commit: 1c15606 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/msigdb_1.21.0.tar.gz vignettes: vignettes/msigdb/inst/doc/msigdb.html vignetteTitles: msigdb hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/msigdb/inst/doc/msigdb.R importsMe: mastR, postNet, vissE suggestsMe: epiregulon.extra, escape dependencyCount: 71 Package: MSMB Version: 1.31.0 Depends: R (>= 3.5), tibble Suggests: knitr, BiocStyle License: LGPL MD5sum: 136c317137ac69ede9e3f9396647f4a8 NeedsCompilation: no Title: Data sets for the book 'Modern Statistics for Biology' Description: Data sets for the book 'Modern Statistics for Modern Biology', S.P. Holmes and W. Huber. biocViews: ExperimentData Author: Wolfgang Huber, Andrzej Oles, Mike Smith Maintainer: Wolfgang Huber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MSMB git_branch: devel git_last_commit: 3d1244b git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/MSMB_1.31.0.tar.gz vignettes: vignettes/MSMB/inst/doc/MSMB.html vignetteTitles: Data sets for the book 'Modern Statistics for Biology' hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MSMB/inst/doc/MSMB.R dependencyCount: 12 Package: msPurityData Version: 1.41.0 Suggests: knitr License: GPL (>= 2) MD5sum: 98aa7398f7cd491ed8848ff92cb6404a NeedsCompilation: no Title: Data to test the msPurity package Description: Data to test the msPurity package biocViews: ExperimentData, MassSpectrometryData Author: Thomas N. Lawson Maintainer: Thomas N. Lawson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/msPurityData git_branch: devel git_last_commit: 528853c git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/msPurityData_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: msPurity dependencyCount: 0 Package: msqc1 Version: 1.41.0 Depends: R (>= 3.6), lattice, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, specL (>= 1.2) License: GPL MD5sum: 7e69f5787d1181243bbfdd528bef55a3 NeedsCompilation: no Title: Sigma mix MSQC1 data Description: contains eight technical replicate data set and a three replicate dilution series of the MS Qual/Quant Quality Control Mix standard sample (Sigma-Aldrich, Buchs, Switzerland) measured on five different mass spectrometer platforms at the Functional Genomics Center Zurich. biocViews: ExperimentData, MassSpectrometryData, ReproducibleResearch Author: Tobias Kockmann [aut] (ORCID: ), Christian Trachsel [aut], Christian Panse [aut, cre] (ORCID: ) Maintainer: Christian Panse URL: https://panoramaweb.org/labkey/MSQC1.url, http://fgcz-bfabric.uzh.ch/bfabric/project.html?projectId=1959 VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/msqc1 git_branch: devel git_last_commit: 57ada5f git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/msqc1_1.41.0.tar.gz vignettes: vignettes/msqc1/inst/doc/poster.pdf, vignettes/msqc1/inst/doc/chromatography.html, vignettes/msqc1/inst/doc/msqc1.html vignetteTitles: ASMS 2016 poster (in portrait) abstract ID number: 282492, LC Observations - Retention Time Stability, Introducing msqc1 - A Mass Spec Data set for Targeted Proteomics Performance Evaluation hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/msqc1/inst/doc/chromatography.R, vignettes/msqc1/inst/doc/msqc1.R, vignettes/msqc1/inst/doc/poster.R suggestsMe: CalibraCurve dependencyCount: 6 Package: mtbls2 Version: 1.43.0 Depends: R (>= 2.10) Suggests: MSnbase, xcms (>= 3.13.8), CAMERA, knitr, Heatplus, pcaMethods, sp, rmarkdown, Biobase License: CC0 MD5sum: 977e67a5c88e7d1d3fa8f6136e7efaad NeedsCompilation: no Title: MetaboLights MTBLS2: Comparative LC/MS-based profiling of silver nitrate-treated Arabidopsis thaliana leaves of wild-type and cyp79B2 cyp79B3 double knockout plants. Böttcher et al. (2004) Description: Indole-3-acetaldoxime (IAOx) represents an early intermediate of the biosynthesis of a variety of indolic secondary metabolites including the phytoanticipin indol-3-ylmethyl glucosinolate and the phytoalexin camalexin (3-thiazol-2'-yl-indole). Arabidopsis thaliana cyp79B2 cyp79B3 double knockout plants are completely impaired in the conversion of tryptophan to indole-3-acetaldoxime and do not accumulate IAOx-derived metabolites any longer. Consequently, comparative analysis of wild-type and cyp79B2 cyp79B3 plant lines has the potential to explore the complete range of IAOx-derived indolic secondary metabolites. biocViews: MassSpectrometryData, RepositoryData Author: Steffen Neumann Maintainer: Steffen Neumann URL: http://www.ebi.ac.uk/metabolights/MTBLS2, https://github.com/sneumann/mtbls2 VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mtbls2 git_branch: devel git_last_commit: fe3e459 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/mtbls2_1.43.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: yamss dependencyCount: 0 Package: MUGAExampleData Version: 1.33.0 Depends: R (>= 2.10.0) License: GPL-3 MD5sum: a21ed35422068874d55bab8ac974098e NeedsCompilation: no Title: Example {M}ouse {U}niversal {G}enotyping {A}rray data for genome reconstruction and quantitative trait locus mapping. Description: This package contains example data for the MUGA array that is used by the R package DOQTL. biocViews: ExperimentData, Mus_musculus_Data Author: Daniel Gatti Maintainer: Daniel Gatti git_url: https://git.bioconductor.org/packages/MUGAExampleData git_branch: devel git_last_commit: 2a77652 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/MUGAExampleData_1.33.0.tar.gz vignettes: vignettes/MUGAExampleData/inst/doc/MUGAExampleData.pdf vignetteTitles: User Manual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MUGAExampleData/inst/doc/MUGAExampleData.R dependencyCount: 0 Package: muleaData Version: 1.9.0 Suggests: knitr, rmarkdown, ExperimentHub, dplyr License: MIT + file LICENSE MD5sum: 32242acc6f428426bc8358c4e5f41a0e NeedsCompilation: no Title: Genes Sets for Functional Enrichment Analysis with the 'mulea' R Package Description: ExperimentHubData package for the 'mulea' comprehensive overrepresentation and functional enrichment analyser R package. Here we provide ontologies (gene sets) in a data.frame for 27 different organisms, ranging from Escherichia coli to human, all acquired from publicly available data sources. Each ontology is provided with multiple gene and protein identifiers. Please see the NEWS file for a list of changes in each version. biocViews: ExperimentData, ExperimentHub, Arabidopsis_thaliana_Data, Bacillus_subtilis_Data, Caenorhabditis_elegans_Data, Danio_rerio_Data, Drosophila_melanogaster_Data, Escherichia_coli_Data, Homo_sapiens_Data, Pan_troglodytes_Data, Pseudomonas_aeruginosa_Data, Rattus_norvegicus_Data, Saccharomyces_cerevisiae_Data, Staphylococcus_aureus_Data, ChIPSeqData, DNASeqData, ExpressionData, miRNAData Author: Eszter Ari [aut, cre] (ORCID: ), Márton Ölbei [aut] (ORCID: ), Lejla Gul [aut], Balázs Bohár [aut] (ORCID: ), Tamás Stirling [aut] (ORCID: ) Maintainer: Eszter Ari URL: https://github.com/ELTEbioinformatics/muleaData VignetteBuilder: knitr BugReports: https://support.bioconductor.org/tag/muleaData/issues git_url: https://git.bioconductor.org/packages/muleaData git_branch: devel git_last_commit: 9b71eed git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/muleaData_1.9.0.tar.gz vignettes: vignettes/muleaData/inst/doc/muleaData.html vignetteTitles: muleaData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/muleaData/inst/doc/muleaData.R dependencyCount: 0 Package: multiWGCNAdata Version: 1.11.0 Depends: ExperimentHub Imports: utils Suggests: BiocStyle, knitr, multiWGCNA, rmarkdown, SummarizedExperiment License: Artistic-2.0 MD5sum: 343260dae55d0135931e8fa6ffe00c4f NeedsCompilation: no Title: Data Package for multiWGCNA Description: Stores expression profiling data from experiments compatible with the multiWGCNA R package. This includes human postmortem microarray data from patients and controls (GSE28521), astrocyte Ribotag RNA-seq data from EAE and wildtype mice (GSE100329), and mouse RNA-seq data from tau pathology (rTg4510) and wildtype control mice (GSE125957). These data can be accessed using the ExperimentHub workflow (see multiWGCNA vignettes). biocViews: ExperimentHub, ExpressionData, Homo_sapiens_Data, Mus_musculus_Data, RNASeqData, MicroarrayData Author: Dario Tommasini [aut, cre] (ORCID: ) Maintainer: Dario Tommasini VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/multiWGCNAdata git_branch: devel git_last_commit: c550304 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/multiWGCNAdata_1.11.0.tar.gz vignettes: vignettes/multiWGCNAdata/inst/doc/multiWGCNAdata.html vignetteTitles: Loading data through ExperimentHub hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/multiWGCNAdata/inst/doc/multiWGCNAdata.R dependencyCount: 64 Package: muscData Version: 1.27.0 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: 044e904dfde5ba94a55e9d3038e0520f NeedsCompilation: no Title: Multi-sample multi-group scRNA-seq data Description: Data package containing a collection of multi-sample multi-group scRNA-seq datasets in SingleCellExperiment Bioconductor object format. biocViews: ExperimentHub, ExperimentData, ExpressionData, GEO, Homo_sapiens_Data, ImmunoOncologyData, SingleCellData Author: Helena L. Crowell [aut, cre] Maintainer: Helena L. Crowell URL: https://github.com/HelenaLC/muscData VignetteBuilder: knitr BugReports: https://github.com/HelenaLC/muscData/issues git_url: https://git.bioconductor.org/packages/muscData git_branch: devel git_last_commit: 61f765c git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/muscData_1.27.0.tar.gz vignettes: vignettes/muscData/inst/doc/muscData.html vignetteTitles: Multi-sample multi-group scRNA-seq data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/muscData/inst/doc/muscData.R suggestsMe: glmGamPoi dependencyCount: 76 Package: muSpaData Version: 1.5.0 Depends: R (>= 4.5.0), ExperimentHub Suggests: SpatialExperiment, ggplot2, BiocStyle, knitr, rmarkdown, R.utils License: MIT + file LICENSE MD5sum: 35b844439a8aa5d467e7cc471302234f NeedsCompilation: no Title: Multi-sample multi-group spatially resolved transcriptomic data Description: Data package containing a multi-sample multi-group spatial dataset in SpatialExperiment Bioconductor object format. biocViews: ExperimentHub, ExperimentData, ExpressionData, SpatialData, SingleCellData Author: Peiying Cai [aut, cre] (ORCID: ) Maintainer: Peiying Cai URL: https://github.com/peicai/muSpaData VignetteBuilder: knitr BugReports: https://github.com/peicai/muSpaData/issues git_url: https://git.bioconductor.org/packages/muSpaData git_branch: devel git_last_commit: 0d7cb48 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/muSpaData_1.5.0.tar.gz vignettes: vignettes/muSpaData/inst/doc/muSpaData.html vignetteTitles: Multi-sample multi-group spatial transcriptomics data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/muSpaData/inst/doc/muSpaData.R suggestsMe: DESpace dependencyCount: 64 Package: MutSeqRData Version: 1.1.0 Depends: R (>= 3.5.0) Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 4f61901bcf1536536cfc9a0ea31a1d22 NeedsCompilation: no Title: Experimental Data for MutSeqR Examples Description: Experimental data for use with the MutSeqR vignette and examples. This dataset is taken from LeBlanc et al., 2022. 24 MutaMouse animals were exposed to one of three doses of benzo[a]pyrene or a vehicle control for 28 days by oral gavage. 28 days after the end of the exposure, bone marrow of the femurs was harvested from euthanized animals. DNA extraction was conducted via DNeasy Blood and Tissue kit. DNA samples were sequenced using TwinStrand's Duplex Sequencing on the Mouse Mutagenesis Panel at > 10,000 depth. The Mouse Mutagenesis Panel comprises 20 2.4kb genomic targets with one located on each mouse autosome (two on chromosome 1). Pre-processing of sequence reads was redone since publication using an updated version of TwinStrand's Mutagenesis App (v. 3.20.1) which produced tabular mutation data files for each sample. Data contained herein are only those required for running MutSeqR examples and vignette. biocViews: ExperimentHub, Mus_musculus_Data, Genome, Somatic, SequencingData Author: Annette E. Dodge [aut] (ORCID: ), Andrew Williams [aut] (ORCID: ), Danielle P.M. LeBlanc [aut] (ORCID: ), David M. Schuster [aut] (ORCID: ), Elena Esina [aut] (ORCID: ), Clint C. Valentine [aut], Jesse J. Salk [aut], Alexander Y. Maslov [aut], Christopher Bradley [aut], Carole L. Yauk [aut] (ORCID: ), Francesco Marchetti [aut] (ORCID: ), Matthew J. Meier [aut, cre] (ORCID: ), Geronimo Matteo [ctb] (ORCID: ) Maintainer: Matthew J. Meier URL: https://github.com/EHSRB-BSRSE-Bioinformatics/MutSeqRData/ VignetteBuilder: knitr BugReports: https://github.com/EHSRB-BSRSE-Bioinformatics/MutSeqRData/issues git_url: https://git.bioconductor.org/packages/MutSeqRData git_branch: devel git_last_commit: 3849fd0 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/MutSeqRData_1.1.0.tar.gz vignettes: vignettes/MutSeqRData/inst/doc/Supporting_data_for_MutSeqR.html vignetteTitles: SUpporting data for the MutSeqR package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/MutSeqRData/inst/doc/Supporting_data_for_MutSeqR.R suggestsMe: MutSeqR dependencyCount: 0 Package: mvoutData Version: 1.49.0 Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4), lumi License: Artistic-2.0 MD5sum: 5baeea130f6ae7340bb7e1c49adab77f NeedsCompilation: no Title: affy and illumina raw data for assessing outlier detector performance Description: affy and illumina raw data for assessing outlier detector performance biocViews: ExperimentData, MicroarrayData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/mvoutData git_branch: devel git_last_commit: f4e0aa2 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/mvoutData_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayMvout dependencyCount: 168 Package: NanoporeRNASeq Version: 1.23.0 Depends: R(>= 4.0.0), ExperimentHub (>= 1.15.3) Suggests: knitr, bambu, ggbio, BSgenome.Hsapiens.NCBI.GRCh38, circlize, ComplexHeatmap, apeglm, rlang, rmarkdown, GenomicAlignments, Rsamtools Enhances: parallel License: GPL-3 + file LICENSE MD5sum: ebc15543c0aafdeb7df32c9202e3d2a8 NeedsCompilation: no Title: Nanopore RNA-Seq Example data Description: The NanoporeRNASeq package contains long read RNA-Seq data generated using Oxford Nanopore Sequencing. The data consists of 6 samples from two human cell lines (K562 and MCF7) that were generated by the SG-NEx project. Each of these cell lines has three replicates, with 1 direct RNA sequencing data and 2 cDNA sequencing data. Reads are aligned to chromosome 22 (Grch38) and stored as bam files. The original data is from the SG-NEx project. biocViews: ExperimentHub, ExperimentData, RNASeqData, Genome, SequencingData Author: Jonathan Goeke [aut], Ying Chen [cre], Yuk Kei Wan [aut] Maintainer: Ying Chen URL: https://github.com/GoekeLab/NanoporeRNASeq VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/NanoporeRNASeq git_branch: devel git_last_commit: c122688 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/NanoporeRNASeq_1.23.0.tar.gz vignettes: vignettes/NanoporeRNASeq/inst/doc/NanoporeRNASeq.html vignetteTitles: NanoporeRNASeq hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/NanoporeRNASeq/inst/doc/NanoporeRNASeq.R suggestsMe: bambu dependencyCount: 64 Package: nanotubes Version: 1.29.0 Depends: R (>= 3.6) Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, rtracklayer, CAGEfightR License: GPL-3 MD5sum: 52c7ec502c90bfc8db23f23229d2adbd NeedsCompilation: no Title: Mouse nanotube CAGE data Description: Cap Analysis of Gene Expression (CAGE) data from "Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo" by Bornholdt et al. supplied as CAGE Transcription Start Sites (CTSSs). biocViews: ExperimentData, SequencingData, ExpressionData Author: Malte Thodberg Maintainer: Malte Thodberg URL: https://github.com/MalteThodberg/nanotubes VignetteBuilder: knitr BugReports: https://github.com/MalteThodberg/nanotubes/issues git_url: https://git.bioconductor.org/packages/nanotubes git_branch: devel git_last_commit: 9a00e4f git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/nanotubes_1.29.0.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: 1.49.0 Depends: R (>= 2.10.0) Suggests: Rgraphviz License: GPL-3 MD5sum: 18bd4b0eff98bb8c1a46bcb16d3f1192 NeedsCompilation: no Title: Data for the NCIgraph software package Description: Provides pathways from the NCI Pathways Database as R graph objects biocViews: NCI Author: Laurent Jacob Maintainer: Laurent Jacob git_url: https://git.bioconductor.org/packages/NCIgraphData git_branch: devel git_last_commit: 4deaacd git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/NCIgraphData_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: NestLink Version: 1.29.0 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: e7a9b07a3fefe450b2472e408cc83ece NeedsCompilation: no Title: NestLink an R data package to guide through Engineered Peptide Barcodes for In-Depth Analyzes of Binding Protein Ensembles Description: Provides next-generation sequencing (NGS) and mass spectrometry (MS) sample data, code snippets and replication material used for developing NestLink. The NestLink approach is a protein binder selection and identification technology able to biophysically characterize thousands of library members at once without handling individual clones at any stage of the process. Data were acquired on NGS and MS platforms at the Functional Genomics Center Zurich. biocViews: ExperimentHub, ExperimentData, SequencingData, MassSpectrometryData, ReproducibleResearch Author: Pascal Egloff [aut] (ORCID: ), Iwan Zimmermann [ctb] (ORCID: ), Fabian M. Arnold [ctb], Cedric A.J. Hutter [ctb] (ORCID: ), Lennart Opitz [aut, cre] (ORCID: ), Lucy Poveda [ctb] (ORCID: ), Hans-Anton Keserue [ctb], Christian Panse [aut, ctb] (ORCID: ), Bernd Roschitzki [aut] (ORCID: ), Markus Seeger [aut] (ORCID: ) Maintainer: Lennart Opitz VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/NestLink git_branch: devel git_last_commit: cfc4253 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/NestLink_1.29.0.tar.gz vignettes: vignettes/NestLink/inst/doc/analyze-flycode-detectibilty.html, vignettes/NestLink/inst/doc/compare-predicted-observed-flycodes.html, vignettes/NestLink/inst/doc/link-nanobodies-flycodes.html, vignettes/NestLink/inst/doc/make-data.html, vignettes/NestLink/inst/doc/simulate-flycodes.html, vignettes/NestLink/inst/doc/supplement-note1.html vignetteTitles: 2. Analyze flycode detectability using ESP and SSRC prediction, 3. Compare Predicted and Observed flycodes hydrophobicity values using F255744., 1. Link high quality flycode and nanobody sequences by NGS filtering., 5. make-data, 0. Simulate flycode properties., 4. Control experiment to assess the robustness of protein detection via flycodes (NMETH-A35040 Suppl. notes 1). hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/NestLink/inst/doc/analyze-flycode-detectibilty.R, vignettes/NestLink/inst/doc/compare-predicted-observed-flycodes.R, vignettes/NestLink/inst/doc/link-nanobodies-flycodes.R, vignettes/NestLink/inst/doc/make-data.R, vignettes/NestLink/inst/doc/simulate-flycodes.R, vignettes/NestLink/inst/doc/supplement-note1.R dependencyCount: 105 Package: NetActivityData Version: 1.15.0 Depends: R (>= 4.2.0) Suggests: BiocStyle, knitr License: MIT + file LICENSE MD5sum: d5a08fa73a5629167f5bfc8cbd8bd287 NeedsCompilation: no Title: Data required for getting the gene set scores with NetActivity package Description: This package contains the weights from pre-trained shallow sparsely-connected autoencoders. This data is required for getting the gene set scores with NetActivity package. biocViews: ExperimentData, RepositoryData Author: Carlos Ruiz-Arenas [aut, cre] Maintainer: Carlos Ruiz-Arenas VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/NetActivityData git_branch: devel git_last_commit: 83e92c0 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/NetActivityData_1.15.0.tar.gz vignettes: vignettes/NetActivityData/inst/doc/NetActivityData.html vignetteTitles: "NetActivityData" hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/NetActivityData/inst/doc/NetActivityData.R importsMe: NetActivity dependencyCount: 0 Package: Neve2006 Version: 0.51.0 Depends: R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0), hgu133a.db, annotate License: Artistic-2.0 MD5sum: 82291123e3d2bc8adbdc14eb1d1f8106 NeedsCompilation: no Title: expression and CGH data on breast cancer cell lines Description: Experimental organization of combined expression and CGH data biocViews: ExperimentData, CancerData, BreastCancerData Author: M. Neve et al. in Gray Lab at LBL Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/Neve2006 git_branch: devel git_last_commit: fd1a050 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/Neve2006_0.51.0.tar.gz vignettes: vignettes/Neve2006/inst/doc/neve06notes.pdf vignetteTitles: Neve 2006: combined CGH and expression data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Neve2006/inst/doc/neve06notes.R dependencyCount: 47 Package: NGScopyData Version: 1.33.0 License: GPL (>=2) MD5sum: fabcb442d49a62d70178f515c0fcf978 NeedsCompilation: no Title: Subset of BAM files of human tumor and pooled normal sequencing data (Zhao et al. 2014) for the NGScopy package Description: Subset of BAM files of human lung tumor and pooled normal samples by targeted panel sequencing. [Zhao et al 2014. Targeted Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using the University of North Carolina (UNC) Sequencing Assay Captures Most Previously Described Genetic Aberrations in NSCLC. In preparation.] Each sample is a 10 percent random subsample drawn from the original sequencing data. The pooled normal sample has been rescaled accroding to the total number of normal samples in the "pool". Here provided is the subsampled data on chr6 (hg19). biocViews: ExperimentData, CancerData, LungCancerData, SequencingData Author: Xiaobei Zhao [aut, cre, cph] Maintainer: Xiaobei Zhao URL: http://www.bioconductor.org/packages/release/data/experiment/html/NGScopyData.html git_url: https://git.bioconductor.org/packages/NGScopyData git_branch: devel git_last_commit: d34df7e git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/NGScopyData_1.33.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: nmrdata Version: 1.1.0 Imports: ExperimentHub, Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 91c055089ba6633c10060abb1d5b0d18 NeedsCompilation: no Title: Example 1d NMR Data for Metabolic Profiling Description: Provides example one-dimensional proton NMR spectra of murine urine samples collected before and after bariatric or sham surgery (Roux-en-Y gastric bypass). The data are adapted from Jia V Li et al. (2011), "Metabolic surgery profoundly influences gut microbial-host metabolic cross-talk", Gut, 60(9), 1214–1223. . This package serves as example data for metabolomics analysis and teaching purposes. biocViews: ExperimentHub, ExperimentData Author: Torben Kimhofer [aut, cre] (ORCID: ) Maintainer: Torben Kimhofer URL: https://github.com/tkimhofer/nmrdata VignetteBuilder: knitr BugReports: https://github.com/tkimhofer/nmrdata/issues git_url: https://git.bioconductor.org/packages/nmrdata git_branch: devel git_last_commit: 17a3827 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/nmrdata_1.1.0.tar.gz vignettes: vignettes/nmrdata/inst/doc/nmrdata.html vignetteTitles: nmrdata: Example 1D Proton NMR Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/nmrdata/inst/doc/nmrdata.R dependencyCount: 64 Package: nullrangesData Version: 1.19.0 Depends: R (>= 4.1.0), ExperimentHub, GenomicRanges, InteractionSet Imports: utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 261cc9dd91fd7ddae12744ffe695a088 NeedsCompilation: no Title: ExperimentHub datasets for the nullranges package Description: Provides datasets for the nullranges package vignette, in particular example datasets for DNase hypersensitivity sites (DHS), CTCF binding sites, and CTCF genomic interactions. These are used to demonstrate generation of null hypothesis feature sets, either through block bootstrapping or matching, in the nullranges vignette. For more details, see the data object man pages, and the R scripts for object construction provided within the package. biocViews: ExperimentHub, Homo_sapiens_Data, SequencingData, ChIPSeqData, ENCODE Author: Michael Love [aut, cre] (ORCID: ), Wancen Mu [aut] (ORCID: ), Eric Davis [aut] (ORCID: ), Mikhail Dozmorov [aut] Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/nullrangesData git_branch: devel git_last_commit: 051fe60 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/nullrangesData_1.19.0.tar.gz vignettes: vignettes/nullrangesData/inst/doc/nullrangesData.html vignetteTitles: nullrangesData package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/nullrangesData/inst/doc/nullrangesData.R suggestsMe: iSEEhub, nullranges dependencyCount: 77 Package: NxtIRFdata Version: 1.19.0 Imports: ExperimentHub, BiocFileCache, rtracklayer, R.utils Suggests: testthat (>= 3.0.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: ea2373447fb77e159e8cbe93c78496aa NeedsCompilation: no Title: Data for NxtIRF Description: NxtIRFdata is a companion package for SpliceWiz, an interactive analysis and visualization tool for alternative splicing quantitation (including intron retention) for RNA-seq BAM files. NxtIRFdata contains Mappability files required for the generation of human and mouse references. NxtIRFdata also contains a synthetic genome reference and example BAM files used to demonstrate SpliceWiz's functionality. BAM files are based on 6 samples from the Leucegene dataset provided by NCBI Gene Expression Omnibus under accession number GSE67039. biocViews: ExperimentData, PackageTypeData, Genome, RNASeqData, ExpressionData, ExperimentHub Author: Alex Chit Hei Wong [aut, cre, cph], Ulf Schmitz [ctb] Maintainer: Alex Chit Hei Wong URL: https://github.com/alexchwong/NxtIRFdata VignetteBuilder: knitr BugReports: https://support.bioconductor.org/ git_url: https://git.bioconductor.org/packages/NxtIRFdata git_branch: devel git_last_commit: 590b5e7 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/NxtIRFdata_1.19.0.tar.gz vignettes: vignettes/NxtIRFdata/inst/doc/NxtIRFdata.html vignetteTitles: NxtIRFdata: a data package for NxtIRF hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/NxtIRFdata/inst/doc/NxtIRFdata.R dependencyCount: 98 Package: ObMiTi Version: 1.21.0 Depends: R (>= 4.1), SummarizedExperiment, ExperimentHub Suggests: knitr, rmarkdown, BiocManager, GenomicFeatures, S4Vectors, devtools, testthat License: GPL-3 MD5sum: 2981ca427b8defdaf0ba6e8915491125 NeedsCompilation: no Title: Ob/ob Mice Data on Normal and High Fat Diet Description: The package provide RNA-seq count for 2 strains of mus musclus; Wild type and Ob/Ob. Each strain was divided into two groups, and each group received either chow diet or high fat diet. RNA expression was measured after 20 weeks in 7 tissues. biocViews: ExperimentHub, GEO, RNASeqData Author: Omar Elashkar [aut, cre] (ORCID: ), Mahmoud Ahmed [aut] (ORCID: ) Maintainer: Omar Elashkar URL: https://github.com/OmarElAshkar/ObMiTi VignetteBuilder: knitr BugReports: https://github.com/OmarElAshkar/ObMiTi/issues git_url: https://git.bioconductor.org/packages/ObMiTi git_branch: devel git_last_commit: 38e1c8a git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ObMiTi_1.21.0.tar.gz vignettes: vignettes/ObMiTi/inst/doc/ObMiTi.html vignetteTitles: Using ObMiTi hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ObMiTi/inst/doc/ObMiTi.R dependencyCount: 75 Package: oct4 Version: 1.29.0 Suggests: knitr, markdown License: GPL (>= 2) MD5sum: 317a375f6cf569400dc9c65adeee9d61 NeedsCompilation: no Title: Conditional knockdown of OCT4 in mouse ESCs Description: This package provides the output of running Salmon on a set of 12 RNA-seq samples from King & Klose, "The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells", published in eLIFE, March 2017. For details on version numbers and how the samples were processed see the package vignette. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/oct4 git_branch: devel git_last_commit: 6af36b8 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/oct4_1.29.0.tar.gz vignettes: vignettes/oct4/inst/doc/oct4.html vignetteTitles: Salmon quantifications for condition OCT4 knockdown in mouse ESCs hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/oct4/inst/doc/oct4.R dependencyCount: 0 Package: octad.db Version: 1.15.0 Depends: R (>= 4.2.0), ExperimentHub Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: ac0243a48e15baa98719a4f42a5fde71 NeedsCompilation: no Title: Open Cancer TherApeutic Discovery (OCTAD) database Description: Open Cancer TherApeutic Discovery (OCTAD) package implies sRGES approach for the drug discovery. The essential idea is to identify drugs that reverse the gene expression signature of a disease by tamping down over-expressed genes and stimulating weakly expressed ones. The following package contains all required precomputed data for whole OCTAD pipeline computation. biocViews: ExperimentData, CancerData, ExperimentHub, SequencingData, ExpressionData Author: E. Chekalin [aut, cre], S. Paithankar [aut], B. Zeng [aut], B. Glicksberg [ctb], P. Newbury [ctb], J. Xing [ctb], K. Liu [ctb], A. Wen [ctb], D. Joseph [ctb], B. Chen [aut] Maintainer: E. Chekalin VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/octad.db git_branch: devel git_last_commit: 9bbbb0c git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/octad.db_1.15.0.tar.gz vignettes: vignettes/octad.db/inst/doc/octad.db.html vignetteTitles: octad.db hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/octad.db/inst/doc/octad.db.R dependsOnMe: octad dependencyCount: 64 Package: OMICsPCAdata Version: 1.31.0 Depends: R (>= 3.5.0), MultiAssayExperiment Suggests: knitr, kableExtra, rmarkdown License: GPL-3 MD5sum: ecc2c87029e0f5ad463953bdbf3125a2 NeedsCompilation: no Title: Supporting data for package OMICsPCA Description: Supporting data for package OMICsPCA biocViews: RepositoryData, TechnologyData, ChIPSeqData, SequencingData, ExpressionData, ENCODE Author: Subhadeep Das Maintainer: Subhadeep Das VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/OMICsPCAdata git_branch: devel git_last_commit: b953668 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/OMICsPCAdata_1.31.0.tar.gz vignettes: vignettes/OMICsPCAdata/inst/doc/vignettes.html vignetteTitles: OMICsPCAdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/OMICsPCAdata/inst/doc/vignettes.R dependsOnMe: OMICsPCA dependencyCount: 46 Package: OnassisJavaLibs Version: 1.35.0 Depends: R (>= 3.4) Imports: rJava Suggests: BiocStyle, rmarkdown, knitr License: GPL-2 MD5sum: 415704be3277faf88a98e92e44310451 NeedsCompilation: no Title: OnassisJavaLibs, java libraries to run conceptmapper and semantic similarity Description: A package that contains java libraries to call conceptmapper and compute semnatic similarity from R biocViews: ExperimentData Author: Eugenia Galeota Maintainer: Eugenia Galeota SystemRequirements: Java (>= 1.8) VignetteBuilder: rmarkdown, knitr git_url: https://git.bioconductor.org/packages/OnassisJavaLibs git_branch: devel git_last_commit: 306f806 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/OnassisJavaLibs_1.35.0.tar.gz vignettes: vignettes/OnassisJavaLibs/inst/doc/OnassisJavaLibs.html vignetteTitles: OnassisJavaLibs: Java Libraries to support Onassis,, Ontology Annotation and Semantic Similarity software hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/OnassisJavaLibs/inst/doc/OnassisJavaLibs.R dependencyCount: 2 Package: optimalFlowData Version: 1.25.0 Depends: R (>= 4.0) Suggests: knitr, BiocStyle, rmarkdown, magick License: Artistic-2.0 MD5sum: c8088968b7079c274b9484960214a3d1 NeedsCompilation: no Title: optimalFlowData Description: Data files used as examples and for testing of the software provided in the optimalFlow package. biocViews: ExperimentData, PackageTypeData, ImmunoOncologyData, FlowCytometryData Author: Hristo Inouzhe Maintainer: Hristo Inouzhe VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/optimalFlowData git_branch: devel git_last_commit: f84cdd7 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/optimalFlowData_1.25.0.tar.gz vignettes: vignettes/optimalFlowData/inst/doc/optimalFlowData_vignette.html vignetteTitles: optimalFlow: optimal-transport approach to Flow Cytometry analysis hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/optimalFlowData/inst/doc/optimalFlowData_vignette.R dependsOnMe: optimalFlow dependencyCount: 0 Package: orthosData Version: 1.11.0 Imports: AnnotationHub, BiocFileCache, ExperimentHub, HDF5Array, stringr, SummarizedExperiment Suggests: BiocStyle, ggplot2, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 02bbe38422608168c6545dbe92af4962 NeedsCompilation: no Title: Data for the orthos package Description: `orthosData` is the companion ExperimentData package to the `orthos` R package for mechanistic studies using differential gene expression experiments. It provides functions for retrieval from ExperimentHub and local caching of the models and datasets used internally in orthos. biocViews: ExperimentData, RNASeqData, ExperimentHub Author: Panagiotis Papasaikas [aut, cre] (ORCID: ), Charlotte Soneson [aut] (ORCID: ), Michael Stadler [aut] (ORCID: ), Friedrich Miescher Institute for Biomedical Research [cph] Maintainer: Panagiotis Papasaikas URL: https://github.com/fmicompbio/orthosData VignetteBuilder: knitr BugReports: https://github.com/fmicompbio/orthosData/issues git_url: https://git.bioconductor.org/packages/orthosData git_branch: devel git_last_commit: 3036ade git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/orthosData_1.11.0.tar.gz vignettes: vignettes/orthosData/inst/doc/orthosData.html vignetteTitles: 1. Introduction to orthos hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/orthosData/inst/doc/orthosData.R importsMe: orthos dependencyCount: 82 Package: pasilla Version: 1.41.0 Depends: R (>= 3.5.0), DEXSeq Suggests: rmarkdown, BiocStyle, knitr, roxygen2 License: LGPL MD5sum: 85ebfb8828a02c0d48ba4814fd7378cf NeedsCompilation: no Title: Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011. Description: This package provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in the article "Conservation of an RNA regulatory map between Drosophila and mammals" by Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR, Genome Res. 2011 Feb;21(2):193-202, Epub 2010 Oct 4, PMID: 20921232. The experiment studied the effect of RNAi knockdown of Pasilla, the Drosophila melanogaster ortholog of mammalian NOVA1 and NOVA2, on the transcriptome. The package vignette describes how the data provided here were derived from the RNA-Seq read sequence data that are provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. biocViews: ExperimentData, Genome, Drosophila_melanogaster_Data, RNASeqData Author: Wolfgang Huber, Alejandro Reyes Maintainer: Alejandro Reyes VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/pasilla git_branch: devel git_last_commit: 3c91e8d git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/pasilla_1.41.0.tar.gz vignettes: vignettes/pasilla/inst/doc/create_objects.html vignetteTitles: "Data preprocessing and creation of the data objects pasillaGenes and pasillaExons" hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pasilla/inst/doc/create_objects.R importsMe: blacksheepr suggestsMe: BADER, DEXSeq, EnhancedVolcano, gsean, regionReport, tidybulk, tidyprint, pasillaBamSubset dependencyCount: 109 Package: pasillaBamSubset Version: 0.51.0 Suggests: pasilla License: LGPL MD5sum: be6f55d9411a792d9317b726b79f6f27 NeedsCompilation: no Title: Subset of BAM files from "Pasilla" experiment Description: Subset of BAM files untreated1.bam (single-end reads) and untreated3.bam (paired-end reads) from "Pasilla" experiment (Pasilla knock-down by Brooks et al., Genome Research 2011). See the vignette in the pasilla data package for how BAM files untreated1.bam and untreated3.bam were obtained from the RNA-Seq read sequence data that is provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. Also contains the DNA sequence for fly chromosome 4 to which the reads can be mapped. biocViews: ExperimentData, Genome, DNASeqData, RNASeqData Author: Hervé Pagès Maintainer: Hervé Pagès git_url: https://git.bioconductor.org/packages/pasillaBamSubset git_branch: devel git_last_commit: 07bfe23 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/pasillaBamSubset_0.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: DEXSeq, DOTSeq, GenomicAlignments, GenomicFeatures, GenomicRanges, gmoviz, IRanges, plyranges dependencyCount: 0 Package: PasillaTranscriptExpr Version: 1.41.0 Depends: R (>= 3.3.0) Suggests: rtracklayer, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: 7fae8dca86cb53ee076fd7a32bf009e2 NeedsCompilation: no Title: Data package with transcript expression obtained with kallisto from pasilla knock-down RNA-Seq data from Brooks et al. Description: Provides kallisto workflow and transcript expression of RNA-Seq data from Brooks et al. biocViews: Drosophila_melanogaster_Data, Genome, RNASeqData, ExperimentData, SequencingData, ExpressionData, GEO Author: Malgorzata Nowicka [aut, cre] Maintainer: Malgorzata Nowicka VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/PasillaTranscriptExpr git_branch: devel git_last_commit: 76ba8e4 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/PasillaTranscriptExpr_1.41.0.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: 1.49.0 Depends: R (>= 1.14.0) License: GPL-3 MD5sum: c9cb6d2147b11cc6726447603805d717 NeedsCompilation: no Title: Experimental data for the PathNet package Description: This package contains the data employed in the vignette of the PathNet package. These data belong to the following publication: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J., Source Code for Biology and Medicine 2012 Sep 24;7(1):10. biocViews: ExperimentData, PathwayInteractionDatabase Author: Bhaskar Dutta , Anders Wallqvist , and Jaques Reifman Maintainer: Ludwig Geistlinger git_url: https://git.bioconductor.org/packages/PathNetData git_branch: devel git_last_commit: 5b6d6f2 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/PathNetData_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PathNet dependencyCount: 0 Package: PCHiCdata Version: 1.41.0 Depends: R (>= 3.2), Chicago Suggests: testthat, BiocStyle, knitr License: Artistic-2.0 MD5sum: 3c109dbc147458efc26ea388fb5806e5 NeedsCompilation: no Title: Promoter Capture Hi-C data Description: Subsets of Promoter Capture Hi-C data conveniently packaged for Chicago users. Data includes interactions detected for chromosomes 20 and 21 in GM12878 cells and for chromosomes 18 and 19 in mESC. biocViews: ExperimentData, SequencingData, Homo_sapiens_Data, Mus_musculus_Data, StemCell Author: Paula Freire-Pritchett, Jonathan Cairns, Steven Wingett, Mikhail Spivakov Maintainer: Mikhail Spivakov VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/PCHiCdata git_branch: devel git_last_commit: 4674ddf git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/PCHiCdata_1.41.0.tar.gz vignettes: vignettes/PCHiCdata/inst/doc/PCHiCdata.html vignetteTitles: PCHiCdata Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/PCHiCdata/inst/doc/PCHiCdata.R suggestsMe: Chicago dependencyCount: 67 Package: pd.atdschip.tiling Version: 0.51.0 Depends: R (>= 3.5.0), methods, RSQLite (>= 0.10.0), oligoClasses (>= 1.15.58), oligo (>= 1.17.3), DBI Imports: Biostrings (>= 2.21.11), IRanges (>= 1.11.31), S4Vectors License: Artistic-2.0 MD5sum: d6a074bd902d5403c1d8812d6be6b7b6 NeedsCompilation: no Title: Platform Design Info for Affymetrix Atdschip_tiling Description: Platform Design Info for Affymetrix Atdschip_tiling biocViews: Arabidopsis_thaliana_Data, MicroarrayData, SNPData Author: Kristof De Beuf Maintainer: Kristof De Beuf git_url: https://git.bioconductor.org/packages/pd.atdschip.tiling git_branch: devel git_last_commit: 147c455 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/pd.atdschip.tiling_0.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 53 Package: pepDat Version: 1.33.0 Depends: R (>= 3.5.0) Imports: GenomicRanges Suggests: knitr License: Artistic-2.0 MD5sum: cab2f145eb5305aabe95ccffd378514f NeedsCompilation: no Title: Peptide microarray data package Description: Provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV. biocViews: MicroarrayData Author: Renan Sauteraud, Raphael Gottardo Maintainer: Renan Sauteraud VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/pepDat git_branch: devel git_last_commit: 0dd8646 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/pepDat_1.33.0.tar.gz vignettes: vignettes/pepDat/inst/doc/pepDat.pdf vignetteTitles: The pepDat users guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pepDat/inst/doc/pepDat.R suggestsMe: pepStat, Pviz dependencyCount: 11 Package: PepsNMRData Version: 1.31.0 Depends: R (>= 3.5) Suggests: knitr, markdown, rmarkdown, BiocStyle License: GPL-2 | file LICENSE MD5sum: 88950281603f0797ec8011244b2cfac3 NeedsCompilation: no Title: Datasets for the PepsNMR package Description: This package contains all the datasets used in the PepsNMR package. biocViews: ExperimentData, OrganismData, Homo_sapiens_Data Author: Manon Martin [aut, cre], Bernadette Govaerts [aut, ths], Pascal de Tullio [dtc] Maintainer: Manon Martin BugReports: https://github.com/ManonMartin/PepsNMRData/issues git_url: https://git.bioconductor.org/packages/PepsNMRData git_branch: devel git_last_commit: df7046b git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/PepsNMRData_1.31.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: PepsNMR dependencyCount: 0 Package: PhyloProfileData Version: 1.27.0 Depends: R (>= 4.5.0) Imports: ExperimentHub, Biostrings, BiocStyle Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 9a8b9521f49f8b97abc595b8e73029d5 NeedsCompilation: yes Title: Data package for phylogenetic profile analysis using PhyloProfile tool Description: Two experimental datasets to illustrate running and analysing phylogenetic profiles with PhyloProfile package. biocViews: ExperimentData, ReproducibleResearch, ExperimentHub Author: Vinh Tran [aut, cre] (ORCID: ), Ingo Ebersberger [aut], Hannah Mülbaier [ctb], Arpit Jain [ctb] Maintainer: Vinh Tran URL: https://github.com/BIONF/PhyloProfileData VignetteBuilder: knitr BugReports: https://github.com/trvinh/PhyloProfileData/issues git_url: https://git.bioconductor.org/packages/PhyloProfileData git_branch: devel git_last_commit: 34489b4 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/PhyloProfileData_1.27.0.tar.gz vignettes: vignettes/PhyloProfileData/inst/doc/PhyloProfileData.html vignetteTitles: PhyloProfileData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/PhyloProfileData/inst/doc/PhyloProfileData.R dependencyCount: 80 Package: plotgardenerData Version: 1.19.0 Depends: R (>= 4.1.0) Suggests: rmarkdown, knitr License: MIT + file LICENSE MD5sum: ddc654ccdacf5667f24bbd840d711382 NeedsCompilation: no Title: Datasets and test data files for the plotgardener package Description: This is a supplemental data package for the plotgardener package. Includes example datasets used in plotgardener vignettes and example raw data files. For details on how to use these datasets, see the plotgardener package vignettes. biocViews: ExperimentData, Homo_sapiens_Data, ExpressionData, Genome, ChIPSeqData, ENCODE Author: Nicole Kramer [aut, cre] (ORCID: ) Maintainer: Nicole Kramer URL: https://github.com/PhanstielLab/plotgardenerData, https://phanstiellab.github.io/plotgardener VignetteBuilder: knitr BugReports: https://github.com/PhanstielLab/plotgardenerData/issues git_url: https://git.bioconductor.org/packages/plotgardenerData git_branch: devel git_last_commit: cfb9c5b git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/plotgardenerData_1.19.0.tar.gz vignettes: vignettes/plotgardenerData/inst/doc/plotgardenerData.html vignetteTitles: plotgardenerData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/plotgardenerData/inst/doc/plotgardenerData.R suggestsMe: plotgardener dependencyCount: 0 Package: prebsdata Version: 1.49.0 Depends: R (>= 2.14.0) License: Artistic-2.0 MD5sum: 6866fad21aa27d9d296028da8e9a1961 NeedsCompilation: no Title: Data for 'prebs' package Description: This package contains data required to run examples in 'prebs' package. The data files include: 1) Small sample bam files for demonstration purposes 2) Probe sequence mappings for Custom CDF (taken from http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp) 3) Probe sequence mappings for manufacturer's CDF (manually created using bowtie) biocViews: ExperimentData, SequencingData, RNASeqData Author: Karolis Uziela and Antti Honkela Maintainer: Karolis Uziela git_url: https://git.bioconductor.org/packages/prebsdata git_branch: devel git_last_commit: 6279431 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/prebsdata_1.49.0.tar.gz vignettes: vignettes/prebsdata/inst/doc/prebsdata.pdf vignetteTitles: prebsdata User Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: prebs dependencyCount: 0 Package: preciseTADhub Version: 1.21.0 Depends: R (>= 4.1) Imports: ExperimentHub Suggests: knitr, rmarkdown, markdown, BiocStyle, preciseTAD License: MIT + file LICENSE MD5sum: 9bc8f0b628a6cc6501162a788cfb0f9d NeedsCompilation: no Title: Pre-trained random forest models obtained using preciseTAD Description: An experimentdata package to supplement the preciseTAD package containing pre-trained models and the variable importances of each genomic annotation used to build the model parsed into list objects and available in ExperimentHub. In total, preciseTADhub provides access to n=84 random forest classification models optimized to predict TAD/chromatin loop boundary regions and stored as .RDS files. The value, n, comes from the fact that we considered l=2 cell lines {GM12878, K562}, g=2 ground truth boundaries {Arrowhead, Peakachu}, and c=21 autosomal chromosomes {CHR1, CHR2, ..., CHR22} (omitting CHR9). Furthermore, each object is itself a two-item list containing: (1) the model object, and (2) the variable importances for CTCF, RAD21, SMC3, and ZNF143 used to predict boundary regions. Each model is trained via a "holdout" strategy, in which data from chromosomes {CHR1, CHR2, ..., CHRi-1, CHRi+1, ..., CHR22} were used to build the model and the ith chromosome was reserved for testing. See https://doi.org/10.1101/2020.09.03.282186 for more detail on the model building strategy. biocViews: ExperimentData, PackageTypeData, ExperimentHub, Genome Author: Spiro Stilianoudakis [aut], Mikhail Dozmorov [aut, cre] Maintainer: Mikhail Dozmorov URL: https://github.com/dozmorovlab/preciseTADhub VignetteBuilder: knitr BugReports: https://github.com/dozmorovlab/preciseTADhub/issues git_url: https://git.bioconductor.org/packages/preciseTADhub git_branch: devel git_last_commit: da3b1bf git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/preciseTADhub_1.21.0.tar.gz vignettes: vignettes/preciseTADhub/inst/doc/preciseTADhub.html vignetteTitles: preciseTADhub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/preciseTADhub/inst/doc/preciseTADhub.R dependencyCount: 64 Package: PREDAsampledata Version: 0.53.0 Depends: R (>= 2.10.0), methods, PREDA, Biobase, affy, annotate Suggests: hgu133plus2.db, hgu133plus2cdf License: Artistic-2.0 MD5sum: 9fa20b9085e6906ab326a6cc5b3c55b7 NeedsCompilation: no Title: expression and copy number data on clear cell renal carcinoma samples Description: Sample data for PREDA package. (annotations objects synchronized with GeneAnnot custom CDFs version 2.2.0) biocViews: ExperimentData, Tissue, CancerData, KidneyCancerData, MicroarrayData, TissueMicroarrayData, ArrayExpress Author: I. Cifola et al. in Cristina Battaglia Lab, University of Milan Maintainer: Francesco Ferrari git_url: https://git.bioconductor.org/packages/PREDAsampledata git_branch: devel git_last_commit: 11f1d9b git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/PREDAsampledata_0.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PREDA dependencyCount: 59 Package: ProData Version: 1.51.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL MD5sum: 5d70873f59fe733fd478bf3bcd7638d2 NeedsCompilation: no Title: SELDI-TOF data of Breast cancer samples Description: A data package of SELDI-TOF protein mass spectrometry data of 167 breast cancer and normal samples. biocViews: ExperimentData, CancerData, BreastCancerData, MassSpectrometryData, NCI Author: Xiaochun Li Maintainer: Xiaochun Li git_url: https://git.bioconductor.org/packages/ProData git_branch: devel git_last_commit: fc00031 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ProData_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CorrectedFDR dependencyCount: 7 Package: pRolocdata Version: 1.49.0 Depends: R (>= 3.6.3), MSnbase Imports: Biobase, utils Suggests: pRoloc (>= 1.13.8), testthat, SummarizedExperiment License: GPL-2 MD5sum: a13debfb13492951cad6c2a4c2ff5ec1 NeedsCompilation: no Title: Data accompanying the pRoloc package Description: Mass-spectrometry based spatial proteomics data sets and protein complex separation data. Also contains the time course expression experiment from Mulvey et al. 2015. biocViews: ExperimentData, Homo_sapiens_Data, MassSpectrometryData, Arabidopsis_thaliana_Data, Drosophila_melanogaster_Data, Mus_musculus_Data, StemCell, Proteome Author: Laurent Gatto [aut] (ORCID: ), Oliver Crook [aut] (ORCID: ), Lisa Breckels [cre, aut] (ORCID: ) Maintainer: Lisa Breckels URL: https://github.com/lgatto/pRolocdata BugReports: https://github.com/lgatto/pRolocdata/issues git_url: https://git.bioconductor.org/packages/pRolocdata git_branch: devel git_last_commit: ffa71ae git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/pRolocdata_1.49.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics dependencyCount: 8 Package: prostateCancerCamcap Version: 1.41.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 021d0763c12ddd1966db533fa78c4e8c NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Ross-Adams (2015) Prostate Cancer dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerCamcap git_branch: devel git_last_commit: 178101c git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/prostateCancerCamcap_1.41.0.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: 1.41.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 8a5401f13ea43649f1e3b0d7a851245b NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Grasso (2012) Prostate Cancer dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerGrasso git_branch: devel git_last_commit: d568d9a git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/prostateCancerGrasso_1.41.0.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: 1.41.0 Depends: Biobase , R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: d4dc20edcd595321733aabbe642d2b32 NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Stockholm dataset biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerStockholm git_branch: devel git_last_commit: 3a2dbb3 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/prostateCancerStockholm_1.41.0.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: 1.41.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery, org.Hs.eg.db License: Artistic-2.0 MD5sum: e93f8cf049b1c72df9afb3b918a1f9b9 NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Taylor et al (2010) dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerTaylor git_branch: devel git_last_commit: c35677b git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/prostateCancerTaylor_1.41.0.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: 1.41.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 01dc074a6fc1acfec1fc06373e44147f NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Varambally dataset biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerVarambally git_branch: devel git_last_commit: 45cbbbf git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/prostateCancerVarambally_1.41.0.tar.gz vignettes: vignettes/prostateCancerVarambally/inst/doc/prostateCancerVarambally.pdf vignetteTitles: prostateCancerVarambally hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/prostateCancerVarambally/inst/doc/prostateCancerVarambally.R dependencyCount: 7 Package: ProteinGymR Version: 1.7.0 Depends: R (>= 4.4.0) Imports: ExperimentHub, AnnotationHub, dplyr, purrr, queryup, spdl, tidyr, tidyselect, stringr, lifecycle, rlang, htmltools Suggests: tibble, BiocStyle, knitr, testthat (>= 3.0.0), ComplexHeatmap, circlize, pals, ggplot2 (>= 3.5.0), grDevices, ggExtra, bio3d, r3dmol, forcats, ggdist (>= 3.3.0) License: Artistic-2.0 MD5sum: 38f1eb7f13976aabc2a223d655cf01cc NeedsCompilation: no Title: Programmatic access to ProteinGym datasets in R/Bioconductor Description: The ProteinGymR package provides analysis-ready data resources from ProteinGym, generated by Notin et al., 2023, as well as built-in functionality to visualize the data. ProteinGym comprises a collection of benchmarks for evaluating the performance of models predicting the effect of point mutations. This package provides access to 1. deep mutational scanning (DMS) scores from 217 assays measuring the impact of all possible amino acid substitutions across 186 proteins, 2. model performance metrics and prediction scores from 79 variant prediction models in the zero-shot setting and 12 models in the semi-supervised setting. biocViews: ExperimentData, ExperimentHub, PackageTypeData, Homo_sapiens_Data, ReproducibleResearch, CellCulture, SequencingData, Proteome Author: Tram Nguyen [aut, cre] (ORCID: ), Pascal Notin [aut], Aaron Kollasch [aut], Debora Marks [aut], Ludwig Geistlinger [aut] Maintainer: Tram Nguyen URL: https://github.com/ccb-hms/ProteinGymR VignetteBuilder: knitr BugReports: https://github.com/ccb-hms/ProteinGymR/issues git_url: https://git.bioconductor.org/packages/ProteinGymR git_branch: devel git_last_commit: c3b8833 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ProteinGymR_1.7.0.tar.gz vignettes: vignettes/ProteinGymR/inst/doc/data_import_and_representation.html, vignettes/ProteinGymR/inst/doc/visualization_exploration.html vignetteTitles: Data access and representation, Visualization and exploration" hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ProteinGymR/inst/doc/data_import_and_representation.R, vignettes/ProteinGymR/inst/doc/visualization_exploration.R dependencyCount: 71 Package: ptairData Version: 1.21.0 Imports: rhdf5, signal, stats, graphics Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 7b51bdc0757fe78af9bd657c97df1406 NeedsCompilation: no Title: PTR-TOF-MS volatolomics raw datasets from exhaled air and cell culture headspace Description: The package ptairData contains two raw datasets from Proton-Transfer-Reaction Time-of-Flight mass spectrometer acquisitions (PTR-TOF-MS), in the HDF5 format. One from the exhaled air of two volunteer healthy individuals with three replicates, and one from the cell culture headspace from two mycobacteria species and one control (culture medium only) with two replicates. Those datasets are used in the examples and in the vignette of the ptairMS package (PTR-TOF-MS data pre-processing). There are also used to gererate the ptrSet in the ptairMS data : exhaledPtrset and mycobacteriaSet biocViews: ExperimentData, MassSpectrometryData, CellCulture Author: camille Roquencourt [aut, cre] Maintainer: camille Roquencourt VignetteBuilder: knitr BugReports: https://github.com/camilleroquencourt/ptairData/issues git_url: https://git.bioconductor.org/packages/ptairData git_branch: devel git_last_commit: 2658f49 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/ptairData_1.21.0.tar.gz vignettes: vignettes/ptairData/inst/doc/ptairData_vignette.html vignetteTitles: PTR-TOF-MS dataset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ptairData/inst/doc/ptairData_vignette.R dependencyCount: 14 Package: PtH2O2lipids Version: 1.37.0 Depends: R (>= 3.3), xcms, CAMERA, LOBSTAHS, methods, utils Suggests: gplots, RColorBrewer, cluster, vegan License: MIT + file LICENSE MD5sum: 775230e20538eab19bb3a9a057ac16b7 NeedsCompilation: no Title: P. tricornutum HPLC-ESI-MS Lipid Data from van Creveld et al. (2015) Description: Annotated HPLC-ESI-MS lipid data in positive ionization mode from an experiment in which cultures of the marine diatom Phaeodactylum tricornutum were treated with various concentrations of hydrogen peroxide (H2O2) to induce oxidative stress. The experiment is described in Graff van Creveld, et al., 2015, "Early perturbation in mitochondria redox homeostasis in response to environmental stress predicts cell fate in diatoms," ISME Journal 9:385-395. PtH2O2lipids consists of two objects: A CAMERA xsAnnotate object (ptH2O2lipids$xsAnnotate) and LOBSTAHS LOBSet object (ptH2O2lipids$xsAnnotate$LOBSet). The LOBSet includes putative compound assignments from the default LOBSTAHS database. Isomer annotation is recorded in three other LOBSet slots. biocViews: ReproducibleResearch, CellCulture, MassSpectrometryData, Phaeodactylum_tricornutum_data Author: Shiri Graff van Creveld [aut], Shilo Rosenwasser [aut], Daniella Schatz [aut], Ilan Koren [aut], Assaf Vardi [aut], James Collins [cre] Maintainer: James Collins URL: http://dx.doi.org/10.1038/ismej.2014.136, https://github.com/vanmooylipidomics/PtH2O2lipids, http://www.whoi.edu/page.do?pid=133616&tid=282&cid=192529 BugReports: https://github.com/vanmooylipidomics/PtH2O2lipids/issues/new git_url: https://git.bioconductor.org/packages/PtH2O2lipids git_branch: devel git_last_commit: 2258fc0 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/PtH2O2lipids_1.37.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 5 Package: pumadata Version: 2.49.0 Depends: R (>= 3.2.0), Biobase (>= 2.5.5),puma, oligo(>= 1.32.0) License: LGPL MD5sum: b5d9da68a24103b0e960ab7827d06c91 NeedsCompilation: no Title: Various data sets for use with the puma package Description: This is a simple data package including various data sets derived from the estrogen data for use with the puma (Propagating Uncertainty in Microarray Analysis) package. biocViews: ExperimentData, MicroarrayData, SNPData Author: Richard Pearson Maintainer: Xuejun liu URL: http://umber.sbs.man.ac.uk/resources/puma git_url: https://git.bioconductor.org/packages/pumadata git_branch: devel git_last_commit: 04da526 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/pumadata_2.49.0.tar.gz vignettes: vignettes/pumadata/inst/doc/pumadata.pdf vignetteTitles: pumadata User Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pumadata/inst/doc/pumadata.R suggestsMe: puma dependencyCount: 56 Package: PWMEnrich.Dmelanogaster.background Version: 4.47.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: c7c640e80349d3f115dd5c72af460d44 NeedsCompilation: no Title: D. melanogaster background for PWMEnrich Description: PWMEnrich pre-compiled background objects for Drosophila melanogaster and MotifDb D. melanogaster motifs. biocViews: Drosophila_melanogaster_Data Author: Robert Stojnic Maintainer: Diego Diez git_url: https://git.bioconductor.org/packages/PWMEnrich.Dmelanogaster.background git_branch: devel git_last_commit: 719f04c git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/PWMEnrich.Dmelanogaster.background_4.47.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 21 Package: PWMEnrich.Hsapiens.background Version: 4.47.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: a9bc11aa719cf5a2556ca8710cfdb0af NeedsCompilation: no Title: H. sapiens background for PWMEnrich Description: PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs. biocViews: Homo_sapiens_Data, CGHData Author: Robert Stojnic Maintainer: Diego Diez git_url: https://git.bioconductor.org/packages/PWMEnrich.Hsapiens.background git_branch: devel git_last_commit: 67038e8 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/PWMEnrich.Hsapiens.background_4.47.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 21 Package: PWMEnrich.Mmusculus.background Version: 4.47.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: 441944e8018b4ffd575923b19ae73652 NeedsCompilation: no Title: M. musculus background for PWMEnrich Description: PWMEnrich pre-compiled background objects for M.musculus (mouse) and MotifDb M. musculus motifs. biocViews: Mus_musculus_Data Author: Robert Stojnic Maintainer: Diego Diez git_url: https://git.bioconductor.org/packages/PWMEnrich.Mmusculus.background git_branch: devel git_last_commit: 649b8b3 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/PWMEnrich.Mmusculus.background_4.47.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 21 Package: QDNAseq.hg19 Version: 1.43.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: 1c95c481b2064a4148a637bdf7a220cc NeedsCompilation: no Title: QDNAseq bin annotation for hg19 Description: This package provides QDNAseq bin annotations for the human genome build hg19. biocViews: ExperimentData, OrganismData, Homo_sapiens_Data Author: Daoud Sie [aut, cre] Maintainer: Daoud Sie URL: https://github.com/tgac-vumc/QDNAseq.hg19 BugReports: https://github.com/tgac-vumc/QDNAseq.hg19/issues git_url: https://git.bioconductor.org/packages/QDNAseq.hg19 git_branch: devel git_last_commit: dd3ed01 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/QDNAseq.hg19_1.43.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: biscuiteer, QDNAseq dependencyCount: 49 Package: QDNAseq.mm10 Version: 1.43.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: fd6198d93252b3972b83f01c0f66fa80 NeedsCompilation: no Title: Bin annotation mm10 Description: This package provides QDNAseq bin annotations for the mouse genome build mm10. biocViews: ExperimentData, OrganismData, Mus_musculus_Data Author: Daoud Sie [aut, cre] Maintainer: Daoud Sie URL: https://github.com/tgac-vumc/QDNAseq.mm10 BugReports: https://github.com/tgac-vumc/QDNAseq.mm10/issues git_url: https://git.bioconductor.org/packages/QDNAseq.mm10 git_branch: devel git_last_commit: a11ed88 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/QDNAseq.mm10_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: biscuiteer, QDNAseq dependencyCount: 49 Package: QUBICdata Version: 1.41.0 Depends: R (>= 3.1) Suggests: knitr, rmarkdown License: Unlimited | file LICENSE MD5sum: fa749644d875a8c33450bf481fe48220 NeedsCompilation: no Title: Data employed in the vignette of the QUBIC package Description: The data employed in the vignette of the QUBIC package. These data belong to Many Microbe Microarrays Database and STRING v10. biocViews: Escherichia_coli_Data, OrganismData, ExperimentData Author: Yu Zhang [aut, cre], Qin Ma [aut] Maintainer: Yu Zhang URL: http://github.com/zy26/QUBICdata VignetteBuilder: knitr BugReports: http://github.com/zy26/QUBICdata/issues git_url: https://git.bioconductor.org/packages/QUBICdata git_branch: devel git_last_commit: 9f02ff2 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/QUBICdata_1.41.0.tar.gz vignettes: vignettes/QUBICdata/inst/doc/qubic_data_vignette.pdf vignetteTitles: QUBIC Data Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/QUBICdata/inst/doc/qubic_data_vignette.R suggestsMe: QUBIC dependencyCount: 0 Package: raerdata Version: 1.11.0 Imports: ExperimentHub, Rsamtools, BiocGenerics, rtracklayer, SingleCellExperiment Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 460a20146217bddad62d7af70db8a7de NeedsCompilation: no Title: A collection of datasets for use with raer package Description: raerdata is an ExperimentHub package that provides a collection of files useful for demostrating functionality in the raer package. Datasets include 10x genomics scRNA-seq, bulk RNA-seq, and paired whole-genome and RNA-seq data. Additionally databases of human and mouse RNA editing sites are provided. biocViews: SingleCellData, SequencingData, RNASeqData, ExperimentHub, PackageTypeData, ExpressionData Author: Kent Riemondy [aut, cre] (ORCID: ) Maintainer: Kent Riemondy URL: https://github.com/rnabioco/raerdata VignetteBuilder: knitr BugReports: https://github.com/rnabioco/raerdata/issues git_url: https://git.bioconductor.org/packages/raerdata git_branch: devel git_last_commit: b689017 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/raerdata_1.11.0.tar.gz vignettes: vignettes/raerdata/inst/doc/raerdata.html vignetteTitles: raerdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/raerdata/inst/doc/raerdata.R suggestsMe: raer dependencyCount: 96 Package: rcellminerData Version: 2.35.0 Depends: R (>= 3.5.0), Biobase Suggests: knitr, testthat, BiocStyle, rcellminer, rmarkdown License: LGPL-3 + file LICENSE MD5sum: c44d1cdc6265259b6d4a5680d4916efb NeedsCompilation: no Title: rcellminerData: Molecular Profiles and Drug Response for the NCI-60 Cell Lines Description: The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data. biocViews: CancerData, CopyNumberVariationData, ExpressionData, SNPData, NCI, MicroarrayData, miRNAData Author: Augustin Luna, Vinodh Rajapakse, Fabricio Sousa Maintainer: Augustin Luna , Vinodh Rajapakse , Fathi Elloumi VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/rcellminerData git_branch: devel git_last_commit: 6bda806 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/rcellminerData_2.35.0.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: 1.33.0 Depends: R (>= 3.3) Imports: data.table License: GPL-3 MD5sum: a82f9671b7d4f4c37ad81faea6a96aab NeedsCompilation: no Title: RcisTarget motif databases for human (hg19) - Subset of 4.6k motifs Description: RcisTarget databases: Gene-based motif rankings and annotation to transcription factors. This package contains a subset of 4.6k motifs (cisbp motifs), scored only within 500bp upstream and the TSS. See RcisTarget tutorial to download the full databases, containing 20k motifs and search space up to 10kbp around the TSS. biocViews: Homo_sapiens_Data Author: Sara Aibar, Gert Hulselmans, Stein Aerts. Laboratory of Computational Biology, KU Leuven Center for Human Genetics. Leuven, Belgium. Maintainer: Sara Aibar URL: http://scenic.aertslab.org git_url: https://git.bioconductor.org/packages/RcisTarget.hg19.motifDBs.cisbpOnly.500bp git_branch: devel git_last_commit: 8cab38a git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.33.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 2 Package: ReactomeGSA.data Version: 1.25.0 Depends: R (>= 3.6), limma, edgeR, ReactomeGSA, Seurat License: Artistic-2.0 MD5sum: 832e084299756d9ed07ab97c1113f54a NeedsCompilation: no Title: Companion data package for the ReactomeGSA package Description: Companion data sets to showcase the functionality of the ReactomeGSA package. This package contains proteomics and RNA-seq data of the melanoma B-cell induction study by Griss et al. and scRNA-seq data from Jerby-Arnon et al. biocViews: ExpressionData, RNASeqData, Proteome, Homo_sapiens_Data Author: Johannes Griss [aut, cre] (ORCID: ) Maintainer: Johannes Griss URL: https://github.com/reactome/ReactomeGSA.data/issues BugReports: https://github.com/reactome/ReactomeGSA.data git_url: https://git.bioconductor.org/packages/ReactomeGSA.data git_branch: devel git_last_commit: a2a3132 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/ReactomeGSA.data_1.25.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 156 Package: RegParallel Version: 1.31.0 Depends: doParallel, foreach, parallel, iterators, data.table, stringr, survival, arm, stats, utils, methods Suggests: RUnit, BiocGenerics, knitr, DESeq2, airway, magrittr, Biobase, GEOquery, biomaRt, survminer, survey, rmarkdown License: GPL-3 MD5sum: f6ac8e97d6c63ec9aa6e3885c70e9614 NeedsCompilation: no Title: Standard regression functions in R enabled for parallel processing over large data-frames Description: In many analyses, a large amount of variables have to be tested independently against the trait/endpoint of interest, and also adjusted for covariates and confounding factors at the same time. The major bottleneck in these is the amount of time that it takes to complete these analyses. With RegParallel, a large number of tests can be performed simultaneously. On a 12-core system, 144 variables can be tested simultaneously, with 1000s of variables processed in a matter of seconds via 'nested' parallel processing. Works for logistic regression, linear regression, conditional logistic regression, Cox proportional hazards and survival models, and Bayesian logistic regression. Also caters for generalised linear models that utilise survey weights created by the 'survey' CRAN package and that utilise 'survey::svyglm'. biocViews: DiseaseModel Author: Kevin Blighe [aut, cre], Sarega Gurudas [ctb], Jessica Lasky-Su [aut] Maintainer: Kevin Blighe URL: https://github.com/kevinblighe/RegParallel VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RegParallel git_branch: devel git_last_commit: 9402c75 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/RegParallel_1.31.0.tar.gz vignettes: vignettes/RegParallel/inst/doc/RegParallel.html vignetteTitles: Standard regression functions in R enabled for parallel processing over large data-frames hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RegParallel/inst/doc/RegParallel.R dependencyCount: 39 Package: RforProteomics Version: 1.49.0 Depends: R (>= 3.5), MSnbase (>= 2.35.2) Imports: R.utils, biocViews, BiocManager Suggests: AnnotationDbi, rpx (>= 2.0.3), DT, knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, MALDIquant (>= 1.12), MALDIquantForeign, readBrukerFlexData, Rdisop, OrgMassSpecR, SummarizedExperiment, BRAIN, rols, hpar, GO.db, org.Hs.eg.db, e1071, biomaRt, RColorBrewer, ggplot2, reshape2, xtable, lattice, mzID, pRoloc, pRolocdata, MSnID, msmsTests, msmsEDA, corrplot, beanplot, Heatplus, gplots, VennDiagram, protViz, genefilter, plotly, gridExtra, dplyr, lubridate, magick, cleaver License: Artistic-2.0 MD5sum: 8fb20d910f7e31b285981ded7e9413ff NeedsCompilation: no Title: Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication Description: This package contains code to illustrate the 'Using R and Bioconductor for proteomics data analysis' and 'Visualisation of proteomics data using R and Bioconductor' manuscripts. The vignettes describe the code and data needed to reproduce the examples and figures described in the paper and functionality for proteomics visualisation. It also contain various function to discover R software for mass spectrometry and proteomics. biocViews: ExperimentData, MassSpectrometryData, ReproducibleResearch Author: Laurent Gatto [aut, cre], Sebastian Gibb [ctb], Vlad Petyuk [ctb], Thomas Pedersen Lin [ctb] Maintainer: Laurent Gatto URL: http://lgatto.github.com/RforProteomics/ VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RforProteomics git_branch: devel git_last_commit: bd10592 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RforProteomics_1.49.0.tar.gz vignettes: vignettes/RforProteomics/inst/doc/RforProteomics.html, vignettes/RforProteomics/inst/doc/RProtVis.html vignetteTitles: Using R for proteomics data analysis, Visualisation of proteomics data using R and Bioconductor hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RforProteomics/inst/doc/RforProteomics.R, vignettes/RforProteomics/inst/doc/RProtVis.R dependencyCount: 22 Package: rheumaticConditionWOLLBOLD Version: 1.51.0 Depends: R (>= 2.10.0) Suggests: genefilter, Biobase, hgu133plus2.db License: Artistic-2.0 MD5sum: 854f4042fd29cfc0abfa1aa137b63a39 NeedsCompilation: no Title: Normalized gene expression dataset published by Wollbold et al. [2009] (WOLLBOLD). Description: Normalized gene expression data from rheumatic diseases from study published by Wollbold et al. in 2009, provided as an eSet. biocViews: ExperimentData, Tissue, MicroarrayData, MultiChannelData, ChipOnChipData, TissueMicroarrayData, GEO, ArrayExpress Author: Alejandro Quiroz-Zarate, John Quackenbush Maintainer: Alejandro Quiroz-Zarate URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/rheumaticConditionWOLLBOLD git_branch: devel git_last_commit: 4585d1a git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/rheumaticConditionWOLLBOLD_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: RITANdata Version: 1.37.0 Depends: R (>= 4.2) Suggests: knitr License: file LICENSE MD5sum: 19d721c4adb353296ff0b9326567853d NeedsCompilation: no Title: This package contains reference annotation and network data sets Description: Data such as is contained in the two R data files in this package are required for the RITAN package examples. Users are highly encouraged to use their own or additional resources in conjunction with RITANdata. See the RITAN vignettes and RITAN.md for more information, such as gathering more up-to-date annotation data. biocViews: AnnotationData, Homo_sapiens Author: Michael Zimmermann [aut, cre] Maintainer: Michael Zimmermann VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RITANdata git_branch: devel git_last_commit: 78df026 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/RITANdata_1.37.0.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: 1.51.0 Suggests: RMassBank License: Artistic-2.0 MD5sum: 5a59f29123a451c67b6c1b49a6b7cdd0 NeedsCompilation: no Title: Test dataset for RMassBank Description: Example spectra, example compound list(s) and an example annotation list for a narcotics dataset; required to test RMassBank. The package is described in the man page for RMassBankData. Includes new XCMS test data. biocViews: ExperimentData, MassSpectrometryData Author: Michael Stravs, Emma Schymanski, Steffen Neumann Maintainer: Michael Stravs, Emma Schymanski git_url: https://git.bioconductor.org/packages/RMassBankData git_branch: devel git_last_commit: 91b1f9c git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/RMassBankData_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: RNAmodR.Data Version: 1.27.0 Depends: R (>= 3.6), ExperimentHub, ExperimentHubData (>= 1.9.2) Imports: utils Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, sessioninfo, testthat License: Artistic-2.0 MD5sum: 36eca61f8cb6f87f0120708717e9f506 NeedsCompilation: no Title: Example data for the RNAmodR package Description: RNAmodR.Data contains example data, which is used for vignettes and example workflows in the RNAmodR and dependent packages. biocViews: ExperimentData, SequencingData, RNASeqData Author: Felix G.M. Ernst [aut, cre], Denis L.J. Lafontaine [ctb, fnd] Maintainer: Felix G.M. Ernst URL: https://github.com/FelixErnst/RNAmodR.Data VignetteBuilder: knitr BugReports: https://github.com/FelixErnst/RNAmodR.Data/issues git_url: https://git.bioconductor.org/packages/RNAmodR.Data git_branch: devel git_last_commit: d2ae61d git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/RNAmodR.Data_1.27.0.tar.gz vignettes: vignettes/RNAmodR.Data/inst/doc/RNAmodR.Data.html vignetteTitles: RNAmodR.Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RNAmodR.Data/inst/doc/RNAmodR.Data.R suggestsMe: RNAmodR, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq dependencyCount: 119 Package: RNAseqData.HNRNPC.bam.chr14 Version: 0.51.0 Suggests: GenomicAlignments, BiocManager License: LGPL MD5sum: 34d777658d3f0bfb30ca84b805bef8e0 NeedsCompilation: no Title: Aligned reads from RNAseq experiment: Transcription profiling by high throughput sequencing of HNRNPC knockdown and control HeLa cells Description: The package contains 8 BAM files, 1 per sequencing run. Each BAM file was obtained by (1) aligning the reads (paired-end) to the full hg19 genome with TopHat2, and then (2) subsetting to keep only alignments on chr14. See accession number E-MTAB-1147 in the ArrayExpress database for details about the experiment, including links to the published study (by Zarnack et al., 2012) and to the FASTQ files. biocViews: ExperimentData, Genome, Homo_sapiens_Data, SequencingData, GEO, NCI, RNASeqData, ArrayExpress Author: Hervé Pagès Maintainer: Hervé Pagès URL: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1147/ git_url: https://git.bioconductor.org/packages/RNAseqData.HNRNPC.bam.chr14 git_branch: devel git_last_commit: dad4f32 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/RNAseqData.HNRNPC.bam.chr14_0.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: sequencing suggestsMe: BiocParallel, cigarillo, GenomicAlignments, GenomicFiles, GenomicRanges, roar, Rsamtools, SplicingGraphs dependencyCount: 0 Package: RnaSeqSampleSizeData Version: 1.45.0 Depends: edgeR,R (>= 2.10) Suggests: BiocStyle, knitr License: GPL (>= 2) MD5sum: 348829b9ab7f00eac0ebabc79d949b59 NeedsCompilation: no Title: RnaSeqSampleSizeData Description: RnaSeqSampleSizeData package provides the read counts and dispersion distribution from real RNA-seq experiments. It can be used by RnaSeqSampleSize package to estimate sample size and power for RNA-seq experiment design. biocViews: ExperimentData, CancerData, RNASeqData Author: Shilin Zhao, Chung-I Li, Yan Guo, Quanhu Sheng, Yu Shyr Maintainer: Shilin Zhao VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RnaSeqSampleSizeData git_branch: devel git_last_commit: ce2c1be git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/RnaSeqSampleSizeData_1.45.0.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: 1.45.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: d5e0bb9d43ab83f32380eaed792d22ee NeedsCompilation: no Title: RnBeads.hg19 Description: Automatically generated RnBeads annotation package for the assembly hg19. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.hg19 git_branch: devel git_last_commit: 284f956 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/RnBeads.hg19_1.45.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: MAGAR suggestsMe: RnBeads dependencyCount: 11 Package: RnBeads.hg38 Version: 1.45.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 4683482d60cc62d05af23b700da9ed24 NeedsCompilation: no Title: RnBeads.hg38 Description: RnBeads annotation package for the assembly hg38. Author: RnBeads Team Maintainer: RnBeads Team git_url: https://git.bioconductor.org/packages/RnBeads.hg38 git_branch: devel git_last_commit: 02f7c22 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/RnBeads.hg38_1.45.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: MAGAR suggestsMe: RnBeads dependencyCount: 11 Package: RnBeads.mm10 Version: 2.21.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: dca764dc3ea054d6ceca37517e9b3bca NeedsCompilation: no Title: RnBeads.mm10 Description: Automatically generated RnBeads annotation package for the assembly mm10. Author: RnBeads Team Maintainer: RnBeads Team git_url: https://git.bioconductor.org/packages/RnBeads.mm10 git_branch: devel git_last_commit: 8c1b1f9 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/RnBeads.mm10_2.21.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 11 Package: RnBeads.mm9 Version: 1.45.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 357fa84550abc1bd863e72d681b03599 NeedsCompilation: no Title: RnBeads.mm9 Description: Automatically generated RnBeads annotation package for the assembly mm9. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.mm9 git_branch: devel git_last_commit: 3d0a9d0 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/RnBeads.mm9_1.45.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RnBeads dependencyCount: 11 Package: RnBeads.rn5 Version: 1.45.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: fbc070d6d2a449b2528d35f8dad399dd NeedsCompilation: no Title: RnBeads.rn5 Description: Automatically generated RnBeads annotation package for the assembly rn5. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.rn5 git_branch: devel git_last_commit: 8e66b32 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/RnBeads.rn5_1.45.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 11 Package: RRBSdata Version: 1.33.0 Depends: R (>= 3.5.0), BiSeq (>= 1.9.2) License: LGPL-3 MD5sum: b169c6d205338a5a333cf9452f0e3aac NeedsCompilation: no Title: An RRBS data set with 12 samples and 10,000 simulated DMRs Description: RRBS data set comprising 12 samples with simulated differentially methylated regions (DMRs). biocViews: ExperimentData, CancerData, SequencingData, CpGIslandData Author: Katja Hebestreit, Hans-Ulrich Klein Maintainer: Katja Hebestreit git_url: https://git.bioconductor.org/packages/RRBSdata git_branch: devel git_last_commit: 5e5af5c git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/RRBSdata_1.33.0.tar.gz vignettes: vignettes/RRBSdata/inst/doc/RRBSdata.pdf vignetteTitles: An RRBS data set with 12 samples and 10,,000 simulated DMRs. hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RRBSdata/inst/doc/RRBSdata.R dependencyCount: 91 Package: RTCGA.clinical Version: 20151101.41.0 Depends: R (>= 3.2.0), RTCGA Suggests: rmarkdown, knitr License: GPL-2 MD5sum: ad0d32fde347f3265e1c1a03a424c76c NeedsCompilation: no Title: Clinical datasets from The Cancer Genome Atlas Project Description: Package provides clinical datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Clinical data format is explained here https://wiki.nci.nih.gov/display/TCGA/Clinical+Data+Overview. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.clinical git_branch: devel git_last_commit: 7ac7064 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RTCGA.clinical_20151101.41.0.tar.gz vignettes: vignettes/RTCGA.clinical/inst/doc/downloading_clinical_datasets.html vignetteTitles: Using RTCGA to download clinical data as included in RTCGA.clinical hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.clinical/inst/doc/downloading_clinical_datasets.R dependencyCount: 1 Package: RTCGA.CNV Version: 1.39.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 7551107ea56e862c1ef544149cf9777c NeedsCompilation: no Title: CNV (Copy-number variation) datasets from The Cancer Genome Atlas Project Description: Package provides CNV (based on Merge snp) datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Retrieving +Data+Using+the+Data+Matrix. Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Przemyslaw Biecek Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.CNV git_branch: devel git_last_commit: d752a3d git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RTCGA.CNV_1.39.0.tar.gz vignettes: vignettes/RTCGA.CNV/inst/doc/downloading_cnv_datasets.html, vignettes/RTCGA.CNV/inst/doc/frequency_of_cnv_for_mdm3.html vignetteTitles: Using RTCGA to download CNV data as included in RTCGA.CNV, Using RTCGA to estimate ratio of MDM2 duplications hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.CNV/inst/doc/downloading_cnv_datasets.R, vignettes/RTCGA.CNV/inst/doc/frequency_of_cnv_for_mdm3.R dependencyCount: 1 Package: RTCGA.methylation Version: 1.39.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: b75414700dec955e14302ab4a5485a20 NeedsCompilation: no Title: Methylation datasets from The Cancer Genome Atlas Project Description: Package provides methylation (humanmethylation27) datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/DNA+methylation Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Marcin Kosinski [aut, cre], Witold Chodor [aut] Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.methylation git_branch: devel git_last_commit: cf22483 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RTCGA.methylation_1.39.0.tar.gz vignettes: vignettes/RTCGA.methylation/inst/doc/downloading_methylation_datasets.html vignetteTitles: Using RTCGA to download methylation data as included in RTCGA.methylation hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.methylation/inst/doc/downloading_methylation_datasets.R dependencyCount: 1 Package: RTCGA.miRNASeq Version: 1.39.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: c2f4b49d77180666e634140654639c34 NeedsCompilation: no Title: miRNASeq datasets from The Cancer Genome Atlas Project Description: Package provides miRNASeq datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/miRNASeq#miRNASeq-DataOverview Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.miRNASeq git_branch: devel git_last_commit: 355ad51 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RTCGA.miRNASeq_1.39.0.tar.gz vignettes: vignettes/RTCGA.miRNASeq/inst/doc/downloading_miRNASeq_datasets.html vignetteTitles: Using RTCGA to download miRNASeq data as included in RTCGA.miRNASeq hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.miRNASeq/inst/doc/downloading_miRNASeq_datasets.R dependencyCount: 1 Package: RTCGA.mRNA Version: 1.39.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 582bb53c2ed34cc47ae10b245b191c79 NeedsCompilation: no Title: mRNA datasets from The Cancer Genome Atlas Project Description: Package provides mRNA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Gene+expression+data Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.mRNA git_branch: devel git_last_commit: b385193 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RTCGA.mRNA_1.39.0.tar.gz vignettes: vignettes/RTCGA.mRNA/inst/doc/downloading_mRNA_datasets.html vignetteTitles: Using RTCGA to download mRNA data as included in RTCGA.mRNA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.mRNA/inst/doc/downloading_mRNA_datasets.R dependencyCount: 1 Package: RTCGA.mutations Version: 20151101.41.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 76c36831488105114e9ac38793cabca5 NeedsCompilation: no Title: Mutations datasets from The Cancer Genome Atlas Project Description: Package provides mutations datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Mutations data format is explained here https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+(MAF)+Specification. There is extra one column with patients' barcodes. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.mutations git_branch: devel git_last_commit: 437eb1f git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RTCGA.mutations_20151101.41.0.tar.gz vignettes: vignettes/RTCGA.mutations/inst/doc/downloading_mutations_datasets.html vignetteTitles: Using RTCGA to download mutations data as included in RTCGA.mutations hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.mutations/inst/doc/downloading_mutations_datasets.R dependencyCount: 1 Package: RTCGA.PANCAN12 Version: 1.39.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 5b142683b33f62ff2088e5853cc9b0b6 NeedsCompilation: no Title: PanCan 12 from Genome Cancer Browser Description: Package provides clinical, expression, cnv and mutation data from Genome Cancer Browser. biocViews: AnnotationData Author: Przemyslaw Biecek Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.PANCAN12 git_branch: devel git_last_commit: 4526368 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RTCGA.PANCAN12_1.39.0.tar.gz vignettes: vignettes/RTCGA.PANCAN12/inst/doc/pancan12.html vignetteTitles: Using RTCGA.PANCAN12 to compare time to death hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.PANCAN12/inst/doc/pancan12.R suggestsMe: GOpro dependencyCount: 1 Package: RTCGA.rnaseq Version: 20151101.41.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 26aae8bbbbff1401fb95d2d6dca310b6 NeedsCompilation: no Title: Rna-seq datasets from The Cancer Genome Atlas Project Description: Package provides rna-seq datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Rna-seq data format is explained here https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2. Data source is illumina hiseq Level 3 RSEM normalized expression data. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.rnaseq git_branch: devel git_last_commit: 80f3b23 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RTCGA.rnaseq_20151101.41.0.tar.gz vignettes: vignettes/RTCGA.rnaseq/inst/doc/downloading_rnaseq_datasets.html vignetteTitles: Using RTCGA to download RNAseq data as included in RTCGA.rnaseq hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.rnaseq/inst/doc/downloading_rnaseq_datasets.R suggestsMe: FSelectorRcpp dependencyCount: 1 Package: RTCGA.RPPA Version: 1.39.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 444f4df85662b6e96d752abe9ff0c3a7 NeedsCompilation: no Title: RPPA datasets from The Cancer Genome Atlas Project Description: Package provides RPPA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Protein+Array +Data+Format+Specification?src=search biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.RPPA git_branch: devel git_last_commit: 165c154 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/RTCGA.RPPA_1.39.0.tar.gz vignettes: vignettes/RTCGA.RPPA/inst/doc/downloading_RPPA_datasets.html vignetteTitles: Using RTCGA to download RPPA data as included in RTCGA.RPPA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.RPPA/inst/doc/downloading_RPPA_datasets.R dependencyCount: 1 Package: RUVnormalizeData Version: 1.33.0 Depends: R (>= 2.10.0), Biobase License: GPL-3 MD5sum: 8e93ca157d8bf1bffac6e784c1af7de0 NeedsCompilation: no Title: Gender data for the RUVnormalize package Description: Microarray gene expression data from the study of Vawter et al., 2004. biocViews: MicroarrayData Author: Laurent Jacob Maintainer: Laurent Jacob git_url: https://git.bioconductor.org/packages/RUVnormalizeData git_branch: devel git_last_commit: 11e2ade git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/RUVnormalizeData_1.33.0.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: 1.37.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: BiocStyle License: Artistic-2.0 MD5sum: 315903973a8bdd77b7b6d520358c24e9 NeedsCompilation: no Title: Pre-processed data for use with the sampleClassifier package Description: This package contains two microarray and two RNA-seq datasets that have been preprocessed for use with the sampleClassifier package. The RNA-seq data are derived from Fagerberg et al. (2014) and the Illumina Body Map 2.0 data. The microarray data are derived from Roth et al. (2006) and Ge et al. (2005). biocViews: ExperimentData, ExpressionData, MicroarrayData, SequencingData, RNASeqData, ArrayExpress Author: Khadija El Amrani Maintainer: Khadija El Amrani git_url: https://git.bioconductor.org/packages/sampleClassifierData git_branch: devel git_last_commit: 665f8e2 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/sampleClassifierData_1.37.0.tar.gz vignettes: vignettes/sampleClassifierData/inst/doc/sampleClassifierData.pdf vignetteTitles: sampleClassifierData Introduction hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/sampleClassifierData/inst/doc/sampleClassifierData.R dependencyCount: 25 Package: SBGNview.data Version: 1.27.0 Depends: R (>= 3.6) Imports: knitr, rmarkdown, bookdown Suggests: SummarizedExperiment License: AGPL-3 MD5sum: 51864cd2a8f055e7aa0c8756c4a583f2 NeedsCompilation: no Title: Supporting datasets for SBGNview package Description: This package contains: 1. A microarray gene expression dataset from a human breast cancer study. 2. A RNA-Seq gene expression dataset from a mouse study on IFNG knockout. 3. ID mapping tables between gene IDs and SBGN-ML file glyph IDs. 4. Percent of orthologs detected in other species of the genes in a pathway. Cutoffs of this percentage for defining if a pathway exists in another species. 5. XML text of SBGN-ML files for all pre-collected pathways. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO, RNASeqData Author: Xiaoxi Dong*, Kovidh Vegesna*, Weijun Luo Maintainer: Weijun Luo VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/SBGNview.data git_branch: devel git_last_commit: fb52644 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/SBGNview.data_1.27.0.tar.gz vignettes: vignettes/SBGNview.data/inst/doc/SBGNview.data.vignette.html vignetteTitles: Supporting Datasets for SBGNview Package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SBGNview.data/inst/doc/SBGNview.data.vignette.R dependsOnMe: SBGNview dependencyCount: 31 Package: scaeData Version: 1.9.0 Depends: R (>= 4.4.0) Imports: ExperimentHub Suggests: knitr, rmarkdown, markdown, SingleCellAlleleExperiment, Matrix, BiocStyle License: MIT + file LICENSE MD5sum: cc66bebf3944a4dde0a98d69b6c149f6 NeedsCompilation: no Title: Data Package for SingleCellAlleleExperiment Description: Contains default datasets used by the Bioconductor package SingleCellAlleleExperiment. The raw FASTQ files were sourced from publicly accessible datasets provided by 10x Genomics. Subsequently, our scIGD snakemake workflow was employed to process these FASTQ files. The resulting output from scIGD constitutes to the contents of this data package. biocViews: ExperimentHub, ExperimentData, Homo_sapiens_Data, SingleCellData Author: Ahmad Al Ajami [aut, cre] (ORCID: ), Jonas Schuck [aut] (ORCID: ), Federico Marini [aut] (ORCID: ), Katharina Imkeller [aut] (ORCID: ) Maintainer: Ahmad Al Ajami URL: https://github.com/AGImkeller/scaeData VignetteBuilder: knitr BugReports: https://github.com/AGImkeller/scIGD/issues git_url: https://git.bioconductor.org/packages/scaeData git_branch: devel git_last_commit: e04b21b git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/scaeData_1.9.0.tar.gz vignettes: vignettes/scaeData/inst/doc/scaeData.html vignetteTitles: scaeData User Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/scaeData/inst/doc/scaeData.R suggestsMe: SingleCellAlleleExperiment dependencyCount: 64 Package: scanMiRData Version: 1.19.0 Depends: R (>= 4.0) Imports: scanMiR, utils Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: fd64d754577c3f74284aeb3c48edfe45 NeedsCompilation: no Title: miRNA Affinity models for the scanMiR package Description: This package contains companion data to the scanMiR package. It contains `KdModel` (miRNA 12-mer binding affinity models) collections corresponding to all human, mouse and rat mirbase miRNAs. See the scanMiR package for details. biocViews: miRNAData, ExperimentData, Homo_sapiens_Data, Mus_musculus_Data, Rattus_norvegicus_Data Author: Pierre-Luc Germain [cre, aut] (ORCID: ), Michael Soutschek [aut], Fridolin Gross [aut] Maintainer: Pierre-Luc Germain VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/scanMiRData git_branch: devel git_last_commit: 6a5e47e git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/scanMiRData_1.19.0.tar.gz vignettes: vignettes/scanMiRData/inst/doc/scanMiRData.html vignetteTitles: scanMiRData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scanMiRData/inst/doc/scanMiRData.R importsMe: scanMiRApp dependencyCount: 49 Package: scATAC.Explorer Version: 1.19.0 Depends: R (>= 4.1), SingleCellExperiment, BiocFileCache, data.table, utils, S4Vectors, zellkonverter Imports: methods, Matrix Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 3308d10ed424a64ccf4d8ff75fdee126 NeedsCompilation: no Title: A Collection of Single-cell ATAC Sequencing Datasets and Corresponding Metadata Description: This package provides a tool to search and download a collection of publicly available single cell ATAC-seq datasets and their metadata. scATAC-Explorer aims to act as a single point of entry for users looking to study single cell ATAC-seq data. Users can quickly search available datasets using the metadata table and download datasets of interest for immediate analysis within R. biocViews: SingleCellData, SequencingData, ExpressionData, GEO, Tissue, Genome, PackageTypeData Author: Arrian Gibson-Khademi [aut], Erik Christensen [aut], Jonathan Wang [aut, cre], Parisa Shooshtari [aut] Maintainer: Jonathan Wang VignetteBuilder: knitr BugReports: https://github.com/shooshtarilab/scATACseq/issues git_url: https://git.bioconductor.org/packages/scATAC.Explorer git_branch: devel git_last_commit: d5db540 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/scATAC.Explorer_1.19.0.tar.gz vignettes: vignettes/scATAC.Explorer/inst/doc/scATAC.Explorer.html vignetteTitles: scATAC.Explorer hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scATAC.Explorer/inst/doc/scATAC.Explorer.R dependencyCount: 74 Package: SCLCBam Version: 1.45.0 Depends: R(>= 2.10) Suggests: BiocStyle License: GPL-2 MD5sum: 976b551b0486c46e5f91ad28c12759b4 NeedsCompilation: no Title: Sequence data from chromosome 4 of a small-cell lung tumor Description: Whole-exome sequencing data from a murine small-cell lung tumor; only contains data of chromosome 4. biocViews: SequencingData, LungCancerData Author: Thomas Kuilman Maintainer: Oscar Krijgsman git_url: https://git.bioconductor.org/packages/SCLCBam git_branch: devel git_last_commit: 83513b0 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/SCLCBam_1.45.0.tar.gz vignettes: vignettes/SCLCBam/inst/doc/SCLCBam.pdf vignetteTitles: SCLCBam hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SCLCBam/inst/doc/SCLCBam.R dependencyCount: 0 Package: scMultiome Version: 1.13.0 Depends: AnnotationHub, ExperimentHub (>= 2.8.1), MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment Imports: AzureStor, GenomicRanges, HDF5Array, S4Vectors, checkmate, methods, rhdf5, alabaster.matrix Suggests: BiocGenerics, IRanges, Matrix, knitr, rmarkdown, rstudioapi, testthat (>= 3.0.0), devtools, BiocStyle, ExperimentHubData License: CC BY-SA 4.0 MD5sum: f92f28b0b44b275deac4dd5b62aee9f7 NeedsCompilation: no Title: Collection of Public Single-Cell Multiome (scATAC + scRNAseq) Datasets Description: Single cell multiome data, containing chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) information analyzed with the ArchR package and presented as MultiAssayExperiment objects. biocViews: PackageTypeData, ExperimentHub, SingleCellData, ExpressionData, SequencingData, Homo_sapiens_Data, CellCulture, Tissue, GEO Author: Xiaosai Yao [cre, aut] (ORCID: ), Aleksander Chlebowski [aut], Aaron Lun [aut], Shiqi Xie [ctb], Tomasz Włodarczyk [aut] Maintainer: Xiaosai Yao VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/scMultiome git_branch: devel git_last_commit: ac21f3c git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/scMultiome_1.13.0.tar.gz vignettes: vignettes/scMultiome/inst/doc/scMultiome.html vignetteTitles: scMultiome tutorial hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scMultiome/inst/doc/scMultiome.R suggestsMe: epiregulon, epiregulon.extra dependencyCount: 101 Package: scpdata Version: 1.21.0 Depends: R (>= 4.2.0), QFeatures, ExperimentHub Imports: utils, AnnotationHub, SingleCellExperiment, S4Vectors Suggests: scp, magrittr, dplyr, knitr, BiocStyle, BiocCheck, rmarkdown, testthat License: GPL-2 MD5sum: c52c35c5a537ff44acfc98183acae92e NeedsCompilation: no Title: Single-Cell Proteomics Data Package Description: The package disseminates mass spectrometry (MS)-based single-cell proteomics (SCP) datasets. The data were collected from published work and formatted using the `scp` data structure. The data sets contain quantitative information at spectrum, peptide and/or protein level for single cells or minute sample amounts. biocViews: ExperimentData, ExpressionData, ExperimentHub, ReproducibleResearch, MassSpectrometryData, Proteome, SingleCellData, PackageTypeData Author: Christophe Vanderaa [aut, cre] (ORCID: ), Laurent Gatto [aut] (ORCID: ), Enes Ayar [dtc] (ORCID: ), Samuel Grégoire [dtc] (ORCID: ) Maintainer: Christophe Vanderaa VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/scpdata git_branch: devel git_last_commit: dec730b git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/scpdata_1.21.0.tar.gz vignettes: vignettes/scpdata/inst/doc/contribution_guidelines.html, vignettes/scpdata/inst/doc/scpdata.html vignetteTitles: Contribution guidelines, Data Package for Single Cell Proteomics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scpdata/inst/doc/contribution_guidelines.R, vignettes/scpdata/inst/doc/scpdata.R Package: scRNAseq Version: 2.27.0 Depends: SingleCellExperiment Imports: utils, methods, Matrix, BiocGenerics, S4Vectors, SparseArray, DelayedArray, GenomicRanges, SummarizedExperiment, ExperimentHub (>= 2.3.4), AnnotationHub (>= 3.3.6), AnnotationDbi, ensembldb, GenomicFeatures, alabaster.base, alabaster.matrix, alabaster.sce, gypsum, jsonlite, DBI, RSQLite Suggests: BiocStyle, knitr, rmarkdown, testthat, jsonvalidate, BiocManager License: CC0 MD5sum: 7a5362dcb84a9816ced784346ead101f NeedsCompilation: no Title: Collection of Public Single-Cell RNA-Seq Datasets Description: Gene-level counts for a collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata. biocViews: ExperimentHub, ExperimentData, ExpressionData, SequencingData, RNASeqData, SingleCellData Author: Davide Risso [aut, cph], Michael Cole [aut], Aaron Lun [ctb, cre], Alan O'Callaghan [ctb], Jens Preussner [ctb], Charlotte Soneson [ctb], Stephany Orjuela [ctb], Daniel Bunis [ctb], Milan Malfait [ctb] Maintainer: Aaron Lun VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/scRNAseq git_branch: devel git_last_commit: 8f1f471 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/scRNAseq_2.27.0.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: APL, BASiCS, batchelor, bluster, ccImpute, CellMentor, ClusterFoldSimilarity, Coralysis, CSOA, destiny, dittoSeq, hammers, iSEE, iSEEfier, iSEEhex, iSEEindex, iSEEu, looking4clusters, miloR, miQC, mumosa, scAnnotatR, scater, scDblFinder, scDiagnostics, scDotPlot, scECODA, scFeatureFilter, scLang, scone, scran, scrapper, scTreeViz, scuttle, SingleCellExperiment, SingleR, SplineDV, UCell, velociraptor, zellkonverter, zinbwave, LISTO, scStability, speakeasyR dependencyCount: 121 Package: scTHI.data Version: 1.25.0 Depends: R (>= 4.0) License: GPL-2 MD5sum: 8bfb998d038ea55979db8209c4cb6a44 NeedsCompilation: no Title: The package contains examples of single cell data used in vignettes and examples of the scTHI package; data contain both tumor cells and immune cells from public dataset of glioma Description: Data for the vignette and tutorial of the package scTHI. biocViews: ExperimentData, SingleCellData Author: Francesca Pia Caruso [aut], Michele Ceccarelli [aut, cre] Maintainer: Michele Ceccarelli git_url: https://git.bioconductor.org/packages/scTHI.data git_branch: devel git_last_commit: ed688a6 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/scTHI.data_1.25.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: scTHI dependencyCount: 0 Package: seq2pathway.data Version: 1.45.0 Depends: R (>= 3.6.2) License: GPL (>= 2) MD5sum: b76d80bebfbd81a3a482a93c13d9e314 NeedsCompilation: no Title: data set for R package seq2pathway Description: Supporting data for the seq2patheway package. Includes modified gene sets from MsigDB and org.Hs.eg.db; gene locus definitions from GENCODE project. biocViews: ExperimentData Author: Bin Wang Maintainer: Arjun Kinstlick git_url: https://git.bioconductor.org/packages/seq2pathway.data git_branch: devel git_last_commit: 9839e96 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/seq2pathway.data_1.45.0.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: 1.47.0 Depends: R (>= 2.10) Imports: utils, Biobase License: GPL-3 MD5sum: 2f99df86fa085920ed22c1a2bbfa6da3 NeedsCompilation: no Title: RNA-seq data generated from SEQC (MAQC-III) study Description: The SEQC/MAQC-III Consortium has produced benchmark RNA-seq data for the assessment of RNA sequencing technologies and data analysis methods (Nat Biotechnol, 2014). Billions of sequence reads have been generated from ten different sequencing sites. This package contains the summarized read count data for ~2000 sequencing libraries. It also includes all the exon-exon junctions discovered from the study. TaqMan RT-PCR data for ~1000 genes and ERCC spike-in sequence data are included in this package as well. biocViews: ExperimentData, RNASeqData, qPCRData, SequencingData Author: Yang Liao and Wei Shi with contributions from Gordon K Smyth and Steve Lianoglou. Maintainer: Yang Liao and Wei Shi URL: http://bioconductor.org/packages/release/data/experiment/html/seqc.html git_url: https://git.bioconductor.org/packages/seqc git_branch: devel git_last_commit: 5c7a89a git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/seqc_1.47.0.tar.gz vignettes: vignettes/seqc/inst/doc/seqc.pdf vignetteTitles: SEQC Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/seqc/inst/doc/seqc.R dependencyCount: 7 Package: serumStimulation Version: 1.49.0 Depends: R (>= 2.10) License: GPL (>= 2) MD5sum: 080caa170fe1cc7b4b0b6f4b7c40ae5a NeedsCompilation: no Title: serumStimulation is a data package which is used by examples in package pcaGoPromoter Description: Contains 13 micro array data results from a serum stimulation experiment biocViews: ExperimentData, MicroarrayData Author: Morten Hansen Maintainer: Morten Hansen, git_url: https://git.bioconductor.org/packages/serumStimulation git_branch: devel git_last_commit: d4a58cc git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/serumStimulation_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: sesameData Version: 1.31.0 Depends: R (>= 4.3.0), ExperimentHub, AnnotationHub Imports: utils, readr, stringr, GenomicRanges (>= 1.61.1), S4Vectors, IRanges, Seqinfo Suggests: BiocGenerics, GenomeInfoDb, sesame, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: 7e6bb193442b063ca7832f3c7e141c14 NeedsCompilation: no Title: Supporting Data for SeSAMe Package Description: Provides supporting annotation and test data for SeSAMe package. This includes chip tango addresses, mapping information, performance annotation, and trained predictor for Infinium array data. This package provides user access to essential annotation data for working with many generations of the Infinium DNA methylation array. Currently we support human array (HM27, HM450, EPIC), mouse array (MM285) and the HorvathMethylChip40 (Mammal40) array. biocViews: ExperimentData, MicroarrayData, Genome, ExperimentHub, MethylationArrayData Author: Wanding Zhou [aut, cre, fnd] (ORCID: ), Hui Shen [aut, fnd], Timothy Triche [ctb] Maintainer: Wanding Zhou URL: https://github.com/zwdzwd/sesame VignetteBuilder: knitr BugReports: https://github.com/zwdzwd/sesame/issues git_url: https://git.bioconductor.org/packages/sesameData git_branch: devel git_last_commit: a97eba8 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/sesameData_1.31.0.tar.gz vignettes: vignettes/sesameData/inst/doc/sesameData.html vignetteTitles: sesameData User Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/sesameData/inst/doc/sesameData.R dependsOnMe: sesame importsMe: knowYourCG, TENET, CytoMethIC suggestsMe: iNETgrate dependencyCount: 72 Package: seventyGeneData Version: 1.49.0 Depends: R (>= 2.13.0) Suggests: Biobase, limma, breastCancerNKI, knitr, rmarkdown, readxl, BiocStyle License: Artistic-2.0 MD5sum: 2ef224116f157a38c9851fe5f30eb791 NeedsCompilation: no Title: ExpressionSets from the van't Veer and Van de Vijver breast cancer studies Description: Gene expression data for the two breast cancer cohorts published by van't Veer and Van de Vijver in 2002. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData Author: Luigi Marchionni [aut, cre] (ORCID: ), Claudio Zanettini [aut, ctb], Lucio Queiroz [aut, ctb] (ORCID: ) Maintainer: Luigi Marchionni URL: https://bioconductor.org/packages/release/data/experiment/html/seventyGeneData.html VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/seventyGeneData git_branch: devel git_last_commit: 5922435 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/seventyGeneData_1.49.0.tar.gz vignettes: vignettes/seventyGeneData/inst/doc/seventyGeneData.html vignetteTitles: 1. Working with the seventyGeneData package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/seventyGeneData/inst/doc/seventyGeneData.R dependencyCount: 0 Package: SFEData Version: 1.15.0 Depends: R (>= 4.1.0) Imports: BiocFileCache, AnnotationHub, ExperimentHub, utils Suggests: BiocStyle, knitr, rmarkdown, SeuratObject, SpatialFeatureExperiment, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: d323876cf747750436159b92e469295f NeedsCompilation: no Title: Example SpatialFeatureExperiment datasets Description: Example spatial transcriptomics datasets with Simple Feature annotations as SpatialFeatureExperiment objects. Technologies include Visium, slide-seq, Nanostring CoxMX, Vizgen MERFISH, and 10X Xenium. Tissues include mouse skeletal muscle, human melanoma metastasis, human lung, breast cancer, and mouse liver. biocViews: ExperimentHub, ExpressionData, Mus_musculus_Data, Homo_sapiens_Data, SpatialData, Tissue, SingleCellData Author: Lambda Moses [aut, cre] (ORCID: ), Alik Huseynov [aut] (ORCID: ), Kayla Jackson [aut] (ORCID: ), Lior Pachter [aut, ths] (ORCID: ) Maintainer: Lambda Moses URL: https://github.com/pachterlab/SFEData VignetteBuilder: knitr BugReports: https://github.com/pachterlab/SFEData/issues git_url: https://git.bioconductor.org/packages/SFEData git_branch: devel git_last_commit: 463951e git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/SFEData_1.15.0.tar.gz vignettes: vignettes/SFEData/inst/doc/SFEData.html vignetteTitles: Example SpatialFeatureExperiment datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SFEData/inst/doc/SFEData.R suggestsMe: alabaster.sfe, concordexR, jazzPanda, SpatialFeatureExperiment, Voyager, xenLite dependencyCount: 64 Package: shinyMethylData Version: 1.33.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: 5cdb74acc40023b5b9f0927bc11eaeee NeedsCompilation: no Title: Example dataset of input data for shinyMethyl Description: Extracted data from 369 TCGA Head and Neck Cancer DNA methylation samples. The extracted data serve as an example dataset for the package shinyMethyl. Original samples are from 450k methylation arrays, and were obtained from The Cancer Genome Atlas (TCGA). 310 samples are from tumor, 50 are matched normals and 9 are technical replicates of a control cell line. biocViews: Genome, CancerData Author: Jean-Philippe Fortin [cre, aut], Kasper Daniel Hansen [aut] Maintainer: Jean-Philippe Fortin git_url: https://git.bioconductor.org/packages/shinyMethylData git_branch: devel git_last_commit: 0f92ea3 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/shinyMethylData_1.33.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: shinyMethyl dependencyCount: 0 Package: signatureSearchData Version: 1.27.0 Depends: R (>= 3.6) Imports: ExperimentHub, utils, affy, limma, Biobase, magrittr, dplyr, R.utils, stats, rhdf5 Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 5f9fbd03cd28e80dbd513dee521a7c2e NeedsCompilation: no Title: Datasets for signatureSearch package Description: CMAP/LINCS hdf5 databases and other annotations used for signatureSearch software package. biocViews: ExperimentHub, ExperimentData, ExpressionData Author: Yuzhu Duan , Brendan Gongol , Thomas Girke Maintainer: Brendan Gongol VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/signatureSearchData git_branch: devel git_last_commit: a88e9f7 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/signatureSearchData_1.27.0.tar.gz vignettes: vignettes/signatureSearchData/inst/doc/signatureSearchData.html vignetteTitles: signatureSearchData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/signatureSearchData/inst/doc/signatureSearchData.R suggestsMe: signatureSearch, DFD dependencyCount: 77 Package: SimBenchData Version: 1.21.0 Depends: ExperimentHub Imports: S4Vectors, utils Suggests: BiocStyle, knitr, rmarkdown, Seurat License: GPL-3 MD5sum: 20582de733fe8b984305d1c17333bf42 NeedsCompilation: no Title: SimBenchData: a collection of 35 single-cell RNA-seq data covering a wide range of data characteristics Description: The SimBenchData package contains a total of 35 single-cell RNA-seq datasets covering a wide range of data characteristics, including major sequencing protocols, multiple tissue types, and both human and mouse sources. biocViews: ExperimentHub, ExperimentData, SingleCellData, RNASeqData, Tissue, SequencingData Author: Yue Cao [aut, cre], Pengyi Yang [aut], Jean Yee Hwa Yang [aut] Maintainer: Yue Cao VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/SimBenchData git_branch: devel git_last_commit: dd890bf git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/SimBenchData_1.21.0.tar.gz vignettes: vignettes/SimBenchData/inst/doc/SimBenchData-vignette.html vignetteTitles: SimBenchData: a collection of single-cell RNA-seq data covering a wide range of data characteristics hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SimBenchData/inst/doc/SimBenchData-vignette.R dependencyCount: 64 Package: simpIntLists Version: 1.49.0 License: GPL (>= 2) MD5sum: af339d6a061fcf92b48e123773c813f5 NeedsCompilation: no Title: The package contains BioGRID interactions for various organisms in a simple format Description: The package contains BioGRID interactions for arabidopsis(thale cress), c.elegans, fruit fly, human, mouse, yeast( budding yeast ) and S.pombe (fission yeast) . Entrez ids, official names and unique ids can be used to find proteins. The format of interactions are lists. For each gene/protein, there is an entry in the list with "name" containing name of the gene/protein and "interactors" containing the list of genes/proteins interacting with it. biocViews: ExperimentData, Arabidopsis_thaliana_Data Author: Kircicegi Korkmaz, Volkan Atalay, Rengul Cetin-Atalay Maintainer: Kircicegi Korkmaz git_url: https://git.bioconductor.org/packages/simpIntLists git_branch: devel git_last_commit: 0a71dbc git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/simpIntLists_1.49.0.tar.gz vignettes: vignettes/simpIntLists/inst/doc/simpIntLists.pdf vignetteTitles: simpIntLists hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/simpIntLists/inst/doc/simpIntLists.R dependsOnMe: ibh dependencyCount: 0 Package: Single.mTEC.Transcriptomes Version: 1.41.0 Depends: R (>= 3.5.0) Suggests: DESeq2, GenomicRanges, GenomicFeatures, genefilter, statmod, gdata, RColorBrewer, ggplot2, gplots, cluster, clue, grid, gridExtra, ggbio, Gviz, geneplotter, matrixStats, pheatmap, BiocStyle, knitr, BiocParallel License: LGPL MD5sum: 53ab07ebdddf695ff05eba4d3f637e7b NeedsCompilation: no Title: Single Cell Transcriptome Data and Analysis of Mouse mTEC cells Description: This data package contains the code used to analyse the single-cell RNA-seq and the bulk ATAC-seq data from the manuscript titled: Single-cell transcriptome analysis reveals coordinated ectopic-gene expression patterns in medullary thymic epithelial cells. This paper was published in Nature Immunology 16,933-941(2015). The data objects provided in this package has been pre-processed: the raw data files can be downloaded from ArrayExpress under the accession identifiers E-MTAB-3346 and E-MTAB-3624. The vignette of this data package provides a documented and reproducible workflow that includes the code that was used to generate each statistic and figure from the manuscript. biocViews: ExperimentData Author: Alejandro Reyes Maintainer: Alejandro Reyes VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/Single.mTEC.Transcriptomes git_branch: devel git_last_commit: f51e1ab git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/Single.mTEC.Transcriptomes_1.41.0.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: 1.25.1 Depends: R (>= 4.2.0), MultiAssayExperiment Imports: AnnotationHub, BiocBaseUtils, BiocFileCache, ExperimentHub, graphics, HDF5Array, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, Matrix, methods, utils Suggests: BiocStyle, ggplot2, knitr, RaggedExperiment, rmarkdown, scater, scran, UpSetR, uwot License: Artistic-2.0 MD5sum: a16777b9885ceee1f1deb58b2cc4cb58 NeedsCompilation: no Title: Integrating Multi-modal Single Cell Experiment datasets Description: SingleCellMultiModal is an ExperimentHub package that serves multiple datasets obtained from GEO and other sources and represents them as MultiAssayExperiment objects. We provide several multi-modal datasets including scNMT, 10X Multiome, seqFISH, CITEseq, SCoPE2, and others. The scope of the package is is to provide data for benchmarking and analysis. To cite, use the 'citation' function and see . biocViews: ExperimentData, SingleCellData, ReproducibleResearch, ExperimentHub, GEO Author: Marcel Ramos [aut, cre] (ORCID: ), Ricard Argelaguet [aut], Al Abadi [ctb], Dario Righelli [aut], Christophe Vanderaa [ctb], Kelly Eckenrode [aut], Ludwig Geistlinger [aut], Levi Waldron [aut], NCI [fnd] (GrantNo.: U24CA289073) Maintainer: Marcel Ramos VignetteBuilder: knitr BugReports: https://github.com/waldronlab/SingleCellMultiModal/issues git_url: https://git.bioconductor.org/packages/SingleCellMultiModal git_branch: devel git_last_commit: 9c2ec19 git_last_commit_date: 2026-04-29 Date/Publication: 2026-04-30 source.ver: src/contrib/SingleCellMultiModal_1.25.1.tar.gz vignettes: vignettes/SingleCellMultiModal/inst/doc/CITEseq.html, vignettes/SingleCellMultiModal/inst/doc/ECCITEseq.html, vignettes/SingleCellMultiModal/inst/doc/GTseq.html, vignettes/SingleCellMultiModal/inst/doc/scMultiome.html, vignettes/SingleCellMultiModal/inst/doc/scNMT.html, vignettes/SingleCellMultiModal/inst/doc/SCoPE2.html, vignettes/SingleCellMultiModal/inst/doc/seqFISH.html, vignettes/SingleCellMultiModal/inst/doc/SingleCellMultiModal.html vignetteTitles: CITEseq Cord Blood, ECCITEseq Peripheral Blood, GT-seq Mouse Embryo, scMultiome 10x PBMC, scNMT Mouse Gastrulation, SCoPE2: macrophage vs monocytes, seqFISH Mouse Visual Cortex, SingleCellMultiModal Introduction hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SingleCellMultiModal/inst/doc/CITEseq.R, vignettes/SingleCellMultiModal/inst/doc/ECCITEseq.R, vignettes/SingleCellMultiModal/inst/doc/GTseq.R, vignettes/SingleCellMultiModal/inst/doc/scMultiome.R, vignettes/SingleCellMultiModal/inst/doc/scNMT.R, vignettes/SingleCellMultiModal/inst/doc/SCoPE2.R, vignettes/SingleCellMultiModal/inst/doc/seqFISH.R, vignettes/SingleCellMultiModal/inst/doc/SingleCellMultiModal.R suggestsMe: decontX, MuData, StabMap dependencyCount: 88 Package: SingleMoleculeFootprintingData Version: 1.21.0 Imports: ExperimentHub, utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 3797b33a3b4f1983ed8176d8956a7f3c NeedsCompilation: no Title: Data supporting the SingleMoleculeFootprinting pkg Description: This Data package contains data objcets relevanat for the SingleMoleculeFootprinting package. More specifically, it contains one example of aligned sequencing data (.bam & .bai) necessary to run the SingleMoleculeFootprinting vignette. Additionally, we provide data that are essential for some functions to work correctly such as BaitCapture() and SampleCorrelation(). biocViews: ExperimentHub, ExperimentData, SequencingData Author: Guido Barzaghi [aut, cre] (ORCID: ), Arnaud Krebs [aut] (ORCID: ), Mike Smith [ctb] (ORCID: ) Maintainer: Guido Barzaghi VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/SingleMoleculeFootprintingData git_branch: devel git_last_commit: cfcbcd2 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/SingleMoleculeFootprintingData_1.21.0.tar.gz vignettes: vignettes/SingleMoleculeFootprintingData/inst/doc/SingleMoleculeFootprintingData.html vignetteTitles: SingleMoleculeFootprintingData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/SingleMoleculeFootprintingData/inst/doc/SingleMoleculeFootprintingData.R dependencyCount: 64 Package: smokingMouse Version: 1.11.0 Suggests: AnnotationHubData, BiocStyle, ExperimentHub, ExperimentHubData, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 7484abd05bc416d55d4ee69e63bda8be NeedsCompilation: no Title: Provides access to smokingMouse project data Description: This is an ExperimentHub package that provides access to the data generated and analyzed in the [smoking-nicotine-mouse](https://github.com/LieberInstitute/smoking-nicotine-mouse/) LIBD project. The datasets contain the expression data of mouse genes, transcripts, exons, and exon-exon junctions across 208 samples from pup and adult mouse brain, and adult blood, that were exposed to nicotine, cigarette smoke, or controls. They also contain relevant metadata of these samples and gene expression features, such QC metrics, if they were used after filtering steps and also if the features were differently expressed in the different experiments. biocViews: ExperimentHub, ExpressionData, Mus_musculus_Data, RNASeqData Author: Daianna Gonzalez-Padilla [aut, cre] (ORCID: ) Maintainer: Daianna Gonzalez-Padilla URL: https://github.com/LieberInstitute/smokingMouse VignetteBuilder: knitr BugReports: https://support.bioconductor.org/tag/smokingMouse git_url: https://git.bioconductor.org/packages/smokingMouse git_branch: devel git_last_commit: 9a01d42 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/smokingMouse_1.11.0.tar.gz vignettes: vignettes/smokingMouse/inst/doc/smokingMouse.html vignetteTitles: Introduction to smokingMouse hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/smokingMouse/inst/doc/smokingMouse.R dependencyCount: 0 Package: SNAData Version: 1.59.0 Depends: R (>= 2.4.0), graph Suggests: Rgraphviz License: LGPL MD5sum: ee3db547257aaf4485fe53a045e9023f NeedsCompilation: no Title: Social Networks Analysis Data Examples Description: Data from Wasserman & Faust (1999) "Social Network Analysis" biocViews: ExperimentData Author: Denise Scholtens Maintainer: Denise Scholtens git_url: https://git.bioconductor.org/packages/SNAData git_branch: devel git_last_commit: 5bb2ab5 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/SNAData_1.59.0.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: 1.49.0 Depends: R (>= 2.6.0) Suggests: ALL, hgu95av2.db, SNAGEE License: Artistic-2.0 MD5sum: b451bde6f0c9bd3e37565f63c76a979e NeedsCompilation: no Title: SNAGEE data Description: SNAGEE data - gene list and correlation matrix biocViews: MicroarrayData Author: David Venet Maintainer: David Venet URL: http://fleming.ulb.ac.be/SNAGEE git_url: https://git.bioconductor.org/packages/SNAGEEdata git_branch: devel git_last_commit: 4e6f455 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/SNAGEEdata_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: SNAGEE dependencyCount: 0 Package: SNPhoodData Version: 1.43.0 Depends: R (>= 3.2) Suggests: BiocStyle,knitr,rmarkdown License: LGPL (>= 3) MD5sum: eb748917e602ad5a50858be363c822d3 NeedsCompilation: no Title: Additional and more complex example data for the SNPhood package Description: This companion package for SNPhood provides some example datasets of a larger size than allowed for the SNPhood package. They include full and real-world examples for performing analyses with the SNPhood package. biocViews: ExperimentData Author: Christian Arnold, Judith Zaugg Maintainer: Christian Arnold VignetteBuilder: knitr BugReports: christian.arnold@embl.de git_url: https://git.bioconductor.org/packages/SNPhoodData git_branch: devel git_last_commit: 8a2eac1 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/SNPhoodData_1.43.0.tar.gz vignettes: vignettes/SNPhoodData/inst/doc/SNPhoodData.html vignetteTitles: The *SNPhoodData* package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: SomatiCAData Version: 1.51.0 Depends: R (>= 2.14) License: Artistic-2.0 MD5sum: 2f028a116f89943a7658743ca0d9937c NeedsCompilation: no Title: An example cancer whole genome sequencing data for the SomatiCA package Description: An example cancer whole genome sequencing data for the SomatiCA package biocViews: ExperimentData, Genome, CancerData, SequencingData Author: Mengjie Chen Maintainer: Mengjie Chen git_url: https://git.bioconductor.org/packages/SomatiCAData git_branch: devel git_last_commit: 707adf6 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/SomatiCAData_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: SomaticCancerAlterations Version: 1.49.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, IRanges, S4Vectors Suggests: testthat, ggbio, ggplot2, knitr License: GPL-3 MD5sum: e4cbfcc506d177d47353b7386d4d2dda NeedsCompilation: no Title: Somatic Cancer Alterations Description: Collection of somatic cancer alteration datasets biocViews: ExperimentData, Genome, CancerData, Project1000genomes, NCI Author: Julian Gehring Maintainer: Julian Gehring VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/SomaticCancerAlterations git_branch: devel git_last_commit: c6f9711 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/SomaticCancerAlterations_1.49.0.tar.gz vignettes: vignettes/SomaticCancerAlterations/inst/doc/SomaticCancerAlterations-html.html vignetteTitles: SomaticCancerAlterations - HTML hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SomaticCancerAlterations/inst/doc/SomaticCancerAlterations-html.R suggestsMe: SomaticSignatures dependencyCount: 11 Package: SpatialDatasets Version: 1.11.0 Depends: ExperimentHub, SpatialExperiment, Imports: utils Suggests: BiocStyle, knitr, rmarkdown, cytomapper License: GPL-3 MD5sum: 74fd34ff1c538fc8f4f875097ac3b677 NeedsCompilation: no Title: Collection of spatial omics datasets Description: This is a collection of publically available spatial omics datasets. Where possible we have curated these datasets as either SpatialExperiments, MoleculeExperiments or CytoImageLists and included annotations of the sample characteristics. biocViews: ExperimentData, ExperimentHub, ReproducibleResearch, SingleCellData, SpatialData, Homo_sapiens_Data, Mus_musculus_Data Author: Farhan Ameen [aut], Nick Robertson [aut], Alex Qin [aut], Shreya Rao [aut], Elijah Willie [aut], Ellis Patrick [aut, cre] Maintainer: Ellis Patrick URL: https://github.com/SydneyBioX/SpatialDatasets VignetteBuilder: knitr BugReports: https://github.com/SydneyBioX/SpatialDatasets/issues git_url: https://git.bioconductor.org/packages/SpatialDatasets git_branch: devel git_last_commit: 7861da2 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/SpatialDatasets_1.11.0.tar.gz vignettes: vignettes/SpatialDatasets/inst/doc/SpatialDatasets_overview.html vignetteTitles: The SpatialDataset package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SpatialDatasets/inst/doc/SpatialDatasets_overview.R suggestsMe: lisaClust, spicyR dependencyCount: 80 Package: spatialDmelxsim Version: 1.19.0 Depends: R (>= 4.1), ExperimentHub, SummarizedExperiment Imports: utils Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: b8e9265df1f65b0c1021825cdf827e4f NeedsCompilation: no Title: Spatial allelic expression counts for fly cross embryo Description: Spatial allelic expression counts from Combs & Fraser (2018), compiled into a SummarizedExperiment object. This package contains data of allelic expression counts of spatial slices of a fly embryo, a Drosophila melanogaster x Drosophila simulans cross. See the CITATION file for the data source, and the associated script for how the object was constructed from publicly available data. biocViews: ExperimentHub, SequencingData, RNASeqData, ExpressionData, Drosophila_melanogaster_Data, GEO Author: Michael Love [aut, cre] Maintainer: Michael Love URL: https://github.com/mikelove/spatialDmelxsim VignetteBuilder: knitr BugReports: https://github.com/mikelove/spatialDmelxsim/issues git_url: https://git.bioconductor.org/packages/spatialDmelxsim git_branch: devel git_last_commit: fbba8be git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/spatialDmelxsim_1.19.0.tar.gz vignettes: vignettes/spatialDmelxsim/inst/doc/spatialDmelxsim.html vignetteTitles: spatialDmelxsim hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/spatialDmelxsim/inst/doc/spatialDmelxsim.R dependencyCount: 75 Package: spatialLIBD Version: 1.23.2 Depends: SpatialExperiment (>= 1.3.3), R (>= 4.1) Imports: shiny, golem, ggplot2, cowplot, plotly, viridisLite, shinyWidgets, sessioninfo, grid, grDevices, methods, AnnotationHub, utils, png, scater, DT, ExperimentHub, SummarizedExperiment, stats, graphics, S4Vectors, IRanges, benchmarkme, SingleCellExperiment, BiocFileCache, jsonlite, tibble, rtracklayer, Matrix, BiocGenerics, GenomicRanges, magick, paletteer, scuttle, edgeR, limma, statmod, MatrixGenerics, rlang, dplyr, ComplexHeatmap, circlize Suggests: knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager, lobstr, DropletUtils, RColorBrewer License: Artistic-2.0 MD5sum: 66b831426fc84b98e39356034eb0a295 NeedsCompilation: no Title: spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data Description: Inspect interactively the spatially-resolved transcriptomics data from the 10x Genomics Visium platform as well as data from the Maynard, Collado-Torres et al, Nature Neuroscience, 2021 project analyzed by Lieber Institute for Brain Development (LIBD) researchers and collaborators. biocViews: Homo_sapiens_Data, ExperimentHub, SequencingData, SingleCellData, ExpressionData, Tissue, PackageTypeData, SpatialData Author: Leonardo Collado-Torres [aut, cre] (ORCID: ), Kristen R. Maynard [ctb] (ORCID: ), Andrew E. Jaffe [ctb] (ORCID: ), Brenda Pardo [ctb] (ORCID: ), Abby Spangler [ctb] (ORCID: ), Jesús Vélez Santiago [ctb] (ORCID: ), Lukas M. Weber [ctb] (ORCID: ), Louise Huuki-Myers [ctb] (ORCID: ), Nicholas Eagles [ctb] (ORCID: ) Maintainer: Leonardo Collado-Torres URL: https://github.com/LieberInstitute/spatialLIBD VignetteBuilder: knitr BugReports: https://support.bioconductor.org/tag/spatialLIBD git_url: https://git.bioconductor.org/packages/spatialLIBD git_branch: devel git_last_commit: e4921b4 git_last_commit_date: 2026-03-26 Date/Publication: 2026-04-21 source.ver: src/contrib/spatialLIBD_1.23.2.tar.gz vignettes: vignettes/spatialLIBD/inst/doc/guide_to_spatial_registration.html, vignettes/spatialLIBD/inst/doc/multi_gene_plots.html, vignettes/spatialLIBD/inst/doc/spatialLIBD.html, vignettes/spatialLIBD/inst/doc/TenX_data_download.html vignetteTitles: Guide to Spatial Registration, Guide to Multi-Gene Plots, Introduction to spatialLIBD, Using spatialLIBD with 10x Genomics public datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/spatialLIBD/inst/doc/guide_to_spatial_registration.R, vignettes/spatialLIBD/inst/doc/multi_gene_plots.R, vignettes/spatialLIBD/inst/doc/spatialLIBD.R, vignettes/spatialLIBD/inst/doc/TenX_data_download.R importsMe: DeconvoBuddies, visiumStitched suggestsMe: Banksy, BatchSVG, BayesSpace, DESpace dependencyCount: 197 Package: SpikeIn Version: 1.55.0 Depends: R (>= 2.10), affy (>= 1.23.4) License: Artistic-2.0 MD5sum: 97239f9748359669123b64764c77e191 NeedsCompilation: no Title: Affymetrix Spike-In Experiment Data Description: Contains the HGU133 and HGU95 spikein experiment data. biocViews: ExperimentData, MicroarrayData Author: Rafael Irizarry Maintainer: Robert D Shear URL: https://bioconductor.org/packages/SpikeIn BugReports: https://github.com/rafalab/SpikeIn/issues git_url: https://git.bioconductor.org/packages/SpikeIn git_branch: devel git_last_commit: dd50d94 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/SpikeIn_1.55.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PECA dependencyCount: 12 Package: SpikeInSubset Version: 1.53.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5), affy (>= 1.23.4) License: LGPL MD5sum: 6cb5915c8242ac653a5334d7e8ba16e7 NeedsCompilation: no Title: Part of Affymetrix's Spike-In Experiment Data Description: Includes probe-level and expression data for the HGU133 and HGU95 spike-in experiments biocViews: ExperimentData, MicroarrayData Author: Rafael Irizarry and Zhijin Wu Maintainer: Robert D Shear URL: https://bioconductor.org/packages/SpikeInSubset BugReports: https://github.com/rafalab/SpikeInSubset/issues git_url: https://git.bioconductor.org/packages/SpikeInSubset git_branch: devel git_last_commit: 5f6a18a git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/SpikeInSubset_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 12 Package: spqnData Version: 1.25.0 Depends: R (>= 4.0), SummarizedExperiment License: Artistic-2.0 MD5sum: 643807b44e008ae13a5cda5df4c251f2 NeedsCompilation: no Title: Data for the spqn package Description: Bulk RNA-seq from GTEx on 4,000 randomly selected, expressed genes. Data has been processed for co-expression analysis. biocViews: Homo_sapiens_Data, ExpressionData, Tissue, RNASeqData Author: Yi Wang [cre, aut], Kasper Daniel Hansen [aut] Maintainer: Yi Wang git_url: https://git.bioconductor.org/packages/spqnData git_branch: devel git_last_commit: 191dd6c git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/spqnData_1.25.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: spqn dependencyCount: 25 Package: stemHypoxia Version: 1.49.0 Depends: R (>= 2.14.1) License: GPL (>=2) MD5sum: dc7a58f94e8f94b4e30aaeaf92b273d8 NeedsCompilation: no Title: Differentiation of Human Embryonic Stem Cells under Hypoxia gene expression dataset by Prado-Lopez et al. (2010) Description: Expression profiling using microarray technology to prove if 'Hypoxia Promotes Efficient Differentiation of Human Embryonic Stem Cells to Functional Endothelium' by Prado-Lopez et al. (2010) Stem Cells 28:407-418. Full data available at Gene Expression Omnibus series GSE37761. biocViews: ExperimentData, Tissue, StemCell, Homo_sapiens_Data, CancerData, MicroarrayData, TissueMicroarrayData, GEO Author: Cristobal Fresno and Elmer A. Fernandez Maintainer: Cristobal Fresno URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37761, http://onlinelibrary.wiley.com/doi/10.1002/stem.295/abstract git_url: https://git.bioconductor.org/packages/stemHypoxia git_branch: devel git_last_commit: f214334 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/stemHypoxia_1.49.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: lmdme dependencyCount: 0 Package: STexampleData Version: 1.21.0 Depends: ExperimentHub, SingleCellExperiment, SpatialExperiment Imports: utils Suggests: BiocStyle, knitr, rmarkdown, BumpyMatrix, HDF5Array License: MIT + file LICENSE MD5sum: 95cc23da47a02ebc05579dd76ba5ec73 NeedsCompilation: no Title: Collection of spatial transcriptomics datasets in SpatialExperiment Bioconductor format Description: Collection of spatial transcriptomics datasets stored in SpatialExperiment Bioconductor format, for use in examples, demonstrations, and tutorials. The datasets are from several different platforms and have been sourced from various publicly available sources. Several datasets include images and/or reference annotation labels. biocViews: ExperimentData, ExperimentHub, ReproducibleResearch, ExpressionData, SingleCellData, SpatialData, Homo_sapiens_Data, Mus_musculus_Data Author: Lukas M. Weber [aut, cre] (ORCID: ), Yixing E. Dong [aut] (ORCID: ) Maintainer: Lukas M. Weber URL: https://github.com/lmweber/STexampleData VignetteBuilder: knitr BugReports: https://github.com/lmweber/STexampleData/issues git_url: https://git.bioconductor.org/packages/STexampleData git_branch: devel git_last_commit: 9ad6f4b git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/STexampleData_1.21.0.tar.gz vignettes: vignettes/STexampleData/inst/doc/STexampleData_overview.html vignetteTitles: STexampleData overview hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/STexampleData/inst/doc/STexampleData_overview.R suggestsMe: Battlefield, BulkSignalR, escheR, ggsc, ggspavis, nnSVG, poem, smoothclust, spatialSimGP, spoon, SpotSweeper, SVP, tpSVG dependencyCount: 80 Package: SubcellularSpatialData Version: 1.9.0 Depends: R (>= 4.4) Imports: dplyr, hexbin, Matrix, SpatialExperiment, stats Suggests: BiocStyle, ExperimentHub, ggplot2, knitr, prettydoc, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: 0945859b7f633fa7f51e858ac100acaf NeedsCompilation: no Title: Annotated spatial transcriptomics datasets from 10x Xenium, NanoString CosMx and BGI STOmics. Description: This is a data package that hosts annotated sub-cellular localised datasets from the STOmics, Xenium and CosMx platforms. Specifically, it hosts datasets analysed in the publication Bhuva et. al, 2024 titled "Library size confounds biology in spatial transcriptomics data". Raw transcript detections are hosted and functions to convert them to SpatialExperiment objects have been implemented. biocViews: ExperimentHub, SpatialData, Homo_sapiens_Data, Mus_musculus_Data, LungCancerData Author: Dharmesh D. Bhuva [aut, cre] (ORCID: ) Maintainer: Dharmesh D. Bhuva URL: https://davislaboratory.github.io/SubcellularSpatialData VignetteBuilder: knitr BugReports: https://github.com/DavisLaboratory/SubcellularSpatialData/issues git_url: https://git.bioconductor.org/packages/SubcellularSpatialData git_branch: devel git_last_commit: 7a2f671 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/SubcellularSpatialData_1.9.0.tar.gz vignettes: vignettes/SubcellularSpatialData/inst/doc/SubcellularSpatialData.html vignetteTitles: SubcellularSpatialData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SubcellularSpatialData/inst/doc/SubcellularSpatialData.R dependencyCount: 67 Package: SVM2CRMdata Version: 1.45.0 Depends: R(>= 3.2.0) License: LGPL (>= 2) MD5sum: b06dd5e3f3c0af83d8837bdf9d3bc15c NeedsCompilation: no Title: An example dataset for use with the SVM2CRM package Description: An example dataset for use with the SVM2CRM package. biocViews: ExperimentData, ChIPSeq, HistoneModification, Preprocessing, DataImport Author: Guidantonio Malagoli Tagliazucchi Maintainer: Guidantonio Malagoli Tagliazucchi git_url: https://git.bioconductor.org/packages/SVM2CRMdata git_branch: devel git_last_commit: 2399734 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/SVM2CRMdata_1.45.0.tar.gz vignettes: vignettes/SVM2CRMdata/inst/doc/SVM2CRMdata.pdf vignetteTitles: The \Rpackage{SVM2CRMdata} Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SVM2CRMdata/inst/doc/SVM2CRMdata.R dependencyCount: 0 Package: systemPipeRdata Version: 2.17.0 Depends: R (>= 3.6.0) Imports: methods, Biostrings, BiocGenerics, jsonlite, remotes Suggests: GenomicFeatures, DT, txdbmaker, GenomicRanges, IRanges, Rsamtools, ShortRead, rtracklayer, RUnit, BiocStyle, knitr, rmarkdown, systemPipeR, kableExtra, magrittr, dplyr, gert License: Artistic-2.0 MD5sum: 55dc06dab55a5fd00b942213999b4b5e NeedsCompilation: no Title: systemPipeRdata: Workflow templates and sample data Description: systemPipeRdata complements the systemPipeR workflow management system (WMS) by offering a collection of pre-designed data analysis workflow templates. These templates are easily accessible and can be readily loaded onto a user's system with a single command. Once loaded, the WMS can immediately utilize these templates for efficient end-to-end analysis, serving a wide range of data analysis needs. biocViews: Genetics, Infrastructure, DataImport, Sequencing, RNASeq, ChIPSeq, MethylSeq, SNP, GeneExpression, Coverage, GeneSetEnrichment, Alignment, QualityControl, ImmunoOncology, RiboSeq, WorkflowStep Author: Thomas Girke Maintainer: Thomas Girke URL: https://github.com/tgirke/systemPipeRdata VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/systemPipeRdata git_branch: devel git_last_commit: 5601947 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/systemPipeRdata_2.17.0.tar.gz vignettes: vignettes/systemPipeRdata/inst/doc/new.html, vignettes/systemPipeRdata/inst/doc/SPblast.html, vignettes/systemPipeRdata/inst/doc/SPcheminfo.html, vignettes/systemPipeRdata/inst/doc/SPscrna.html, vignettes/systemPipeRdata/inst/doc/systemPipeChIPseq.html, vignettes/systemPipeRdata/inst/doc/systemPipeRdata.html, vignettes/systemPipeRdata/inst/doc/systemPipeRIBOseq.html, vignettes/systemPipeRdata/inst/doc/systemPipeRNAseq.html, vignettes/systemPipeRdata/inst/doc/systemPipeVARseq.html vignetteTitles: WF: Basic Generic Template, WF: BLAST Template, WF: Cheminformatics Drug Similarity Template, WF: Basic Single Cell Template, WF: ChIP-Seq Workflow Template, systemPipeRdata: Workflow templates and sample data, WF: RIBO-Seq Workflow Template, WF: RNA-Seq Workflow Template, WF: VAR-Seq Template hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/systemPipeRdata/inst/doc/new.R, vignettes/systemPipeRdata/inst/doc/SPblast.R, vignettes/systemPipeRdata/inst/doc/SPcheminfo.R, vignettes/systemPipeRdata/inst/doc/SPscrna.R, vignettes/systemPipeRdata/inst/doc/systemPipeChIPseq.R, vignettes/systemPipeRdata/inst/doc/systemPipeRdata.R, vignettes/systemPipeRdata/inst/doc/systemPipeRIBOseq.R, vignettes/systemPipeRdata/inst/doc/systemPipeRNAseq.R, vignettes/systemPipeRdata/inst/doc/systemPipeVARseq.R suggestsMe: systemPipeR, systemPipeShiny dependencyCount: 17 Package: TabulaMurisData Version: 1.31.0 Depends: R (>= 3.5) Imports: ExperimentHub, utils Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran, scater, iSEE, testthat License: MIT + file LICENSE MD5sum: e6e36e68f43d790001746f87847eb23f NeedsCompilation: no Title: 10x And SmartSeq2 Data From The Tabula Muris Consortium Description: Access to processed 10x (droplet) and SmartSeq2 (on FACS-sorted cells) single-cell RNA-seq data from the Tabula Muris consortium (http://tabula-muris.ds.czbiohub.org/). biocViews: SingleCellData, ExperimentData, RNASeqData Author: Charlotte Soneson [aut, cre] (ORCID: ) Maintainer: Charlotte Soneson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TabulaMurisData git_branch: devel git_last_commit: 16a28d8 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/TabulaMurisData_1.31.0.tar.gz vignettes: vignettes/TabulaMurisData/inst/doc/TabulaMurisData.html vignetteTitles: Tabula Muris data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TabulaMurisData/inst/doc/TabulaMurisData.R dependencyCount: 64 Package: TabulaMurisSenisData Version: 1.19.0 Imports: ExperimentHub, SingleCellExperiment, HDF5Array, SummarizedExperiment, gdata, AnnotationHub Suggests: ggplot2, testthat, knitr, rmarkdown, iSEE, BiocStyle License: MIT + file LICENSE MD5sum: c0e562708daf077fd1951eb921f9299a NeedsCompilation: no Title: Bulk and single-cell RNA-seq data from the Tabula Muris Senis project Description: This package provides access to RNA-seq data generated by the Tabula Muris Senis project via the Bioconductor project. The data is made available without restrictions by the Chan Zuckerberg Biohub. It is provided here without further processing, collected in the form of SingleCellExperiment objects. biocViews: SingleCellData, ExperimentData, RNASeqData, ExperimentHub Author: Charlotte Soneson [aut, cre] (ORCID: ), Dania Machlab [aut] (ORCID: ), Federico Marini [aut] (ORCID: ), Stefania Astrologo [aut] (ORCID: ) Maintainer: Charlotte Soneson URL: https://github.com/fmicompbio/TabulaMurisSenisData VignetteBuilder: knitr BugReports: https://github.com/fmicompbio/TabulaMurisSenisData/issues git_url: https://git.bioconductor.org/packages/TabulaMurisSenisData git_branch: devel git_last_commit: c645a42 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/TabulaMurisSenisData_1.19.0.tar.gz vignettes: vignettes/TabulaMurisSenisData/inst/doc/TabulaMurisSenisData.html vignetteTitles: TabulaMurisSenisData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TabulaMurisSenisData/inst/doc/TabulaMurisSenisData.R suggestsMe: SETA, SPOTlight dependencyCount: 85 Package: TargetScoreData Version: 1.49.0 Suggests: TargetScore, gplots License: GPL-2 MD5sum: da9cedec4b3a7b8ff4a0c57e7b7f30b1 NeedsCompilation: no Title: TargetScoreData Description: Precompiled and processed miRNA-overexpression fold-changes from 84 Gene Expression Omnibus (GEO) series corresponding to 6 platforms, 77 human cells or tissues, and 113 distinct miRNAs. Accompanied with the data, we also included in this package the sequence feature scores from TargetScanHuman 6.1 including the context+ score and the probabilities of conserved targeting for each miRNA-mRNA interaction. Thus, the user can use these static sequence-based scores together with user-supplied tissue/cell-specific fold-change due to miRNA overexpression to predict miRNA targets using the package TargetScore (download separately) biocViews: ExperimentData, RNASeqData, miRNAData Author: Yue Li Maintainer: Yue Li git_url: https://git.bioconductor.org/packages/TargetScoreData git_branch: devel git_last_commit: ea3fb42 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/TargetScoreData_1.49.0.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: 1.51.0 License: GPL (>= 2) MD5sum: 192c57d9d1b9021987abbe54aa14c8d5 NeedsCompilation: no Title: Example GC-MS data for TargetSearch Package Description: Example files of GC-MS data for the TargetSearch Package. The package contains raw NetCDF files from a E.coli salt stress experiment, extracted peak lists, and sample metadata required for a GC-MS analysis. The raw data has been restricted for demonstration purposes. biocViews: ExperimentData, Escherichia_coli_Data Author: Alvaro Cuadros-Inostroza [aut, cre], Jan Lisec [aut], Henning Redestig [aut], Matt Hannah [aut] Maintainer: Alvaro Cuadros-Inostroza URL: https://github.com/acinostroza/TargetSearchData BugReports: https://github.com/acinostroza/TargetSearchData/issues git_url: https://git.bioconductor.org/packages/TargetSearchData git_branch: devel git_last_commit: 35ae221 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/TargetSearchData_1.51.0.tar.gz vignettes: vignettes/TargetSearchData/inst/doc/TargetSearchData.pdf vignetteTitles: The TargetSearchData Package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TargetSearchData/inst/doc/TargetSearchData.R suggestsMe: TargetSearch dependencyCount: 0 Package: tartare Version: 1.27.0 Depends: R (>= 4.1), AnnotationHub (>= 2.16), ExperimentHub (>= 1.0) Imports: utils Suggests: BiocStyle, knitr, rmarkdown, testthat, tools License: GPL-3 MD5sum: 95adbb177f9d7d2e0733da531d8c52e4 NeedsCompilation: no Title: Raw ground spectra recorded on Thermo Fisher Scientific mass spectrometers Description: Provides raw files recorded on different Liquid Chromatography Mass Spectrometry (LC-MS) instruments. All included MS instruments are manufactured by Thermo Fisher Scientific and belong to the Orbitrap Tribrid or Q Exactive Orbitrap family of instruments. Despite their common origin and shared hardware components, e.g., Orbitrap mass analyser, the above instruments tend to write data in different "dialects" in a shared binary file format (.raw). The intention behind tartare is to provide complex but slim real-world files that can be used to make code robust with respect to this diversity. In other words, it is intended for enhanced unit testing. The package is considered to be used with the rawrr package and the Spectra MsBackends. biocViews: ExperimentData, MassSpectrometryData, ExperimentHub Author: Christian Panse [aut, cre] (ORCID: ), Tobias Kockmann [aut] (ORCID: ) Maintainer: Christian Panse URL: https://github.com/cpanse/tartare VignetteBuilder: knitr BugReports: https://github.com/cpanse/tartare/issues git_url: https://git.bioconductor.org/packages/tartare git_branch: devel git_last_commit: 037fa12 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/tartare_1.27.0.tar.gz vignettes: vignettes/tartare/inst/doc/tartare.html vignetteTitles: make and use tartare data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tartare/inst/doc/tartare.R suggestsMe: MsBackendRawFileReader, rawDiag, rawrr dependencyCount: 64 Package: TBX20BamSubset Version: 1.49.0 Depends: Rsamtools (>= 1.9.8) Imports: xtable License: LGPL MD5sum: 2130def67b5b3278bbeef13d2b7775f9 NeedsCompilation: no Title: Subset of BAM files from the "TBX20" experiment Description: Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. A subset of the RNA-Seq data. biocViews: ExperimentData, SequencingData, RNASeqData Author: D. Bindreither Maintainer: D. Bindreither git_url: https://git.bioconductor.org/packages/TBX20BamSubset git_branch: devel git_last_commit: 4272689 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/TBX20BamSubset_1.49.0.tar.gz vignettes: vignettes/TBX20BamSubset/inst/doc/TBX20BamSubset.pdf vignetteTitles: TBX20 RNA-Seq data subset hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TBX20BamSubset/inst/doc/TBX20BamSubset.R importsMe: Rmmquant suggestsMe: magpie dependencyCount: 30 Package: TCGAbiolinksGUI.data Version: 1.33.0 Depends: R (>= 3.5.0) Suggests: BiocStyle, knitr, rmarkdown, readr, DT License: GPL-3 MD5sum: 732b48436e4cd5d3180526ae312402da NeedsCompilation: no Title: Data for the TCGAbiolinksGUI package Description: Supporting data for the TCGAbiolinksGUI package. biocViews: AssayDomainData, TechnologyData, OrganismData Author: Tiago Chedraoui Silva Maintainer: Tiago Chedraoui Silva URL: https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data VignetteBuilder: knitr BugReports: https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data/issues git_url: https://git.bioconductor.org/packages/TCGAbiolinksGUI.data git_branch: devel git_last_commit: a2c4747 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/TCGAbiolinksGUI.data_1.33.0.tar.gz vignettes: vignettes/TCGAbiolinksGUI.data/inst/doc/vignettes.html vignetteTitles: Supporting data for the TCGAbiolinksGUI package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TCGAbiolinksGUI.data/inst/doc/vignettes.R importsMe: TCGAbiolinks dependencyCount: 0 Package: TCGAcrcmiRNA Version: 1.33.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 4c65c76a4f464f547ab725896c8d4c75 NeedsCompilation: no Title: TCGA CRC 450 miRNA dataset Description: colorectal cancer miRNA profile provided by TCGA biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/TCGAcrcmiRNA git_branch: devel git_last_commit: a99f8e5 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/TCGAcrcmiRNA_1.33.0.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: 1.33.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 79f8072a8b8f788e357af056584f353b NeedsCompilation: no Title: TCGA CRC 450 mRNA dataset Description: colorectal cancer mRNA profile provided by TCGA biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/TCGAcrcmRNA git_branch: devel git_last_commit: 38edd92 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/TCGAcrcmRNA_1.33.0.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: 1.49.0 License: GPL-2 MD5sum: ed95746f2656ba430f3fea7ef03e248c NeedsCompilation: no Title: The Cancer Genome Atlas Illumina 450k methylation example data Description: The Cancer Genome Atlas (TCGA) is applying genomics technologies to over 20 different types of cancer. This package contains a small set of 450k array data in idat format. biocViews: Genome, CancerData, MethylationArrayData Author: Sean Davis Maintainer: Sean Davis git_url: https://git.bioconductor.org/packages/TCGAMethylation450k git_branch: devel git_last_commit: 18b0057 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/TCGAMethylation450k_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: methylumi dependencyCount: 0 Package: TCGAWorkflowData Version: 1.37.0 Depends: R (>= 3.5.0) Imports: SummarizedExperiment Suggests: knitr, rmarkdown, pander, testthat, BiocStyle License: GPL-3 MD5sum: 7fe6a215024fcedee203ad035be0e0d6 NeedsCompilation: no Title: Data for TCGA Workflow Description: This experimental data package contains 11 data sets necessary to follow the "TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages". biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData, CancerData Author: Tiago Chedraoui Silva Maintainer: Tiago Chedraoui Silva URL: https://f1000research.com/articles/5-1542/v2 VignetteBuilder: knitr BugReports: https://github.com/BioinformaticsFMRP/TCGAWorkflow/issues git_url: https://git.bioconductor.org/packages/TCGAWorkflowData git_branch: devel git_last_commit: 4a3c750 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/TCGAWorkflowData_1.37.0.tar.gz vignettes: vignettes/TCGAWorkflowData/inst/doc/TCGAWorkflowData.html vignetteTitles: 'Example data for TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages' hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TCGAWorkflowData/inst/doc/TCGAWorkflowData.R dependencyCount: 25 Package: TENET.ExperimentHub Version: 1.5.0 Depends: R (>= 4.5), ggplot2 (>= 4.0) Imports: ExperimentHub, SummarizedExperiment, MultiAssayExperiment, GenomicRanges, methods Suggests: TENET, ExperimentHubData, testthat (>= 3.0.0), BiocManager, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 9ccae1a9bf48f0294b37f52feaa49e75 NeedsCompilation: no Title: Experiment data for the TENET package Description: ExperimentHub package containing datasets for use in the TENET package's vignette and function examples. These include a variety of different objects to illustrate different datasets used in TENET functions. Where applicable, all datasets are aligned to the hg38 human genome. biocViews: ExperimentHub, ExperimentData, Homo_sapiens_Data, CancerData, BreastCancerData, MicroarrayData, ExpressionData, RNASeqData, MethylationArrayData, Genome, CellCulture, Tissue Author: Rhie Lab at the University of Southern California [cre], Daniel Mullen [aut] (ORCID: ), Zexun Wu [aut] (ORCID: ), Ethan Nelson-Moore [aut] (ORCID: ), Suhn Rhie [aut] (ORCID: ) Maintainer: Rhie Lab at the University of Southern California URL: https://github.com/rhielab/TENET.ExperimentHub VignetteBuilder: knitr BugReports: https://github.com/rhielab/TENET.ExperimentHub/issues git_url: https://git.bioconductor.org/packages/TENET.ExperimentHub git_branch: devel git_last_commit: 8efd40f git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/TENET.ExperimentHub_1.5.0.tar.gz vignettes: vignettes/TENET.ExperimentHub/inst/doc/TENET.ExperimentHub_vignette.html vignetteTitles: Using the TENET.ExperimentHub datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TENET.ExperimentHub/inst/doc/TENET.ExperimentHub_vignette.R importsMe: TENET dependencyCount: 85 Package: TENxBrainData Version: 1.33.0 Depends: SingleCellExperiment, HDF5Array Imports: AnnotationHub (>= 2.9.22), ExperimentHub Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel, data.table, rmarkdown License: CC BY 4.0 MD5sum: a700aaaf369d9ada0a1ec8c953d53a45 NeedsCompilation: no Title: Data from the 10X 1.3 Million Brain Cell Study Description: Single-cell RNA-seq data for 1.3 million brain cells from E18 mice, generated by 10X Genomics. biocViews: SequencingData, RNASeqData, ExpressionData, SingleCellData Author: Aaron Lun [aut], Martin Morgan [aut], Bioconductor Package Maintainer [cre] Maintainer: Bioconductor Package Maintainer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TENxBrainData git_branch: devel git_last_commit: 3c24246 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/TENxBrainData_1.33.0.tar.gz vignettes: vignettes/TENxBrainData/inst/doc/TENxBrainData.html vignetteTitles: Exploring the 1.3 million brain cell scRNA-seq data from 10X Genomics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TENxBrainData/inst/doc/TENxBrainData.R suggestsMe: h5mread, HDF5Array dependencyCount: 83 Package: TENxBUSData Version: 1.27.0 Imports: ExperimentHub, AnnotationHub, utils, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle License: BSD_2_clause + file LICENSE MD5sum: 3cf9821367a59691b0bc72c482e98a37 NeedsCompilation: no Title: Single cell dataset from 10x in BUS format Description: Download Barcode, UMI, and Set (BUS) format of 10x datasets from within R. This package accompanies the package BUSpaRse, which can load BUS format into R as a sparse matrix, and which has utility functions related to using the C++ command line package bustools. biocViews: SingleCellData, SequencingData, ExperimentHub, ExperimentData, ExpressionData Author: Lambda Moses [aut, cre] (ORCID: ) Maintainer: Lambda Moses URL: https://github.com/BUStools/TENxBUSData VignetteBuilder: knitr BugReports: https://github.com/BUStools/TENxBUSData/issues git_url: https://git.bioconductor.org/packages/TENxBUSData git_branch: devel git_last_commit: a9fdc65 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/TENxBUSData_1.27.0.tar.gz vignettes: vignettes/TENxBUSData/inst/doc/downloading-10x-hgmm-data.html vignetteTitles: Downloading BUS data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TENxBUSData/inst/doc/downloading-10x-hgmm-data.R suggestsMe: BUSpaRse dependencyCount: 64 Package: TENxPBMCData Version: 1.31.0 Depends: SingleCellExperiment, HDF5Array Imports: AnnotationHub, ExperimentHub Suggests: rmarkdown, knitr, BiocStyle, snow, BiocFileCache, BiocParallel License: CC BY 4.0 MD5sum: 90ff8c7c9acfd9a626c11199f3329f88 NeedsCompilation: no Title: PBMC data from 10X Genomics Description: Single-cell RNA-seq data for on PBMC cells, generated by 10X Genomics. biocViews: SequencingData, RNASeqData, ExpressionData, ExperimentHub, ExperimentData, SingleCellData Author: Kasper D. Hansen [aut], Davide Risso [aut], Milan Malfait [ctb], Jeroen Gilis [ctb], Theodore Killian [ctb], Murat Cem Kose [ctb], Chong Tang [ctb], Teun van den Brand [ctb], Dania Machlab [ctb], Stephanie Hicks [aut, cre] Maintainer: Stephanie Hicks VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TENxPBMCData git_branch: devel git_last_commit: 1d4a004 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/TENxPBMCData_1.31.0.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: adverSCarial, ASURAT, celda, concordexR, decontX, ExperimentSubset, glmGamPoi, GSVA, iSEE, mbkmeans, scGraphVerse, schex, scone, scry, Seqtometry, sketchR, transformGamPoi dependencyCount: 83 Package: TENxVisiumData Version: 1.21.0 Depends: ExperimentHub, SpatialExperiment Imports: utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 39a5227893f0caa1a117497214d344fa NeedsCompilation: no Title: Visium spatial gene expression data by 10X Genomics Description: Collection of Visium spatial gene expression datasets by 10X Genomics, formatted into objects of class SpatialExperiment. Data cover various organisms and tissues, and include: single- and multi-section experiments, as well as single sections subjected to both whole transcriptome and targeted panel analysis. Datasets may be used for testing of and as examples in packages, for tutorials and workflow demonstrations, or similar purposes. biocViews: ExperimentHub, ExpressionData, ExperimentData, Homo_sapiens_Data, Mus_musculus_Data, ReproducibleResearch Author: Helena L. Crowell [aut, cre] (ORCID: ) Maintainer: Helena L. Crowell URL: https://github.com/helenalc/TENxVisiumData VignetteBuilder: knitr BugReports: https://github.com/helenalc/TENxVisiumData/issues git_url: https://git.bioconductor.org/packages/TENxVisiumData git_branch: devel git_last_commit: 3fa35d9 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/TENxVisiumData_1.21.0.tar.gz vignettes: vignettes/TENxVisiumData/inst/doc/vignette.html vignetteTitles: TENxVisiumData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TENxVisiumData/inst/doc/vignette.R suggestsMe: GSVA, SPOTlight dependencyCount: 80 Package: TENxXeniumData Version: 1.9.0 Depends: ExperimentHub Imports: SpatialExperiment, SpatialFeatureExperiment, BumpyMatrix, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: e42c66e9fc14d1797facc7ede32fb884 NeedsCompilation: no Title: Collection of Xenium spatial data by 10X genomics Description: Collection of Xenium spatial transcriptomics datasets provided by 10x Genomics, formatted into the Bioconductor classes, the SpatialExperiment or SpatialFeatureExperiment (SFE), to facilitate seamless integration into various applications, including examples, demonstrations, and tutorials. The constructed data objects include gene expression profiles, per-transcript location data, centroid, segmentation boundaries (e.g., cell or nucleus boundaries), and image. biocViews: ExperimentData, ExperimentHub, SpatialData Author: Matineh Rahmatbakhsh [aut, cre], Monica Ge [aut] Maintainer: Matineh Rahmatbakhsh URL: https://github.com/mrbakhsh/TENxXeniumData VignetteBuilder: knitr BugReports: https://github.com/mrbakhsh/TENxXeniumData/issues git_url: https://git.bioconductor.org/packages/TENxXeniumData git_branch: devel git_last_commit: 9b23b60 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/TENxXeniumData_1.9.0.tar.gz vignettes: vignettes/TENxXeniumData/inst/doc/TENxXeniumData.html vignetteTitles: TENxXeniumData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TENxXeniumData/inst/doc/TENxXeniumData.R suggestsMe: jazzPanda dependencyCount: 171 Package: timecoursedata Version: 1.23.0 Depends: R (>= 4.0), SummarizedExperiment Suggests: testthat (>= 1.0.0), knitr, rmarkdown, markdown, covr, BiocStyle License: BSD 3-clause License + file LICENSE MD5sum: 3930670bc98a9e8f140e906af3062267 NeedsCompilation: no Title: A data package for timecourse RNA-seq and microarray gene expression data sets Description: This data package contains timecourse gene expression data sets. The first dataset, from Shoemaker et al, consists of microarray samples from lung tissue of mice exposed to different influenzy strains from 14 timepoints. The two other datasets are leaf and root samples from sorghum crops exposed to pre- and post-flowering drought stress and a control condition, sampled across the plants lifetime. biocViews: ExpressionData, MicroarrayData, RNASeqData Author: Elizabeth Purdom [aut] (ORCID: ), Nelle Varoquaux [aut, cre] (ORCID: ) Maintainer: Nelle Varoquaux VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/timecoursedata git_branch: devel git_last_commit: f238c19 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/timecoursedata_1.23.0.tar.gz vignettes: vignettes/timecoursedata/inst/doc/documentation.html vignetteTitles: timecoursedata: Time course gene expression datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/timecoursedata/inst/doc/documentation.R dependencyCount: 25 Package: tinesath1cdf Version: 1.51.0 License: Artistic-2.0 MD5sum: af03efd9c515fafe3a8a890c6e3352fe NeedsCompilation: no Title: tinesath1cdf Description: A package containing an environment represeting the newcdf/tinesATH1.cdf.cdf file. biocViews: Arabidopsis_thaliana_Data, ChipOnChipData Author: Tine Casneuf Maintainer: Tine Casneuf git_url: https://git.bioconductor.org/packages/tinesath1cdf git_branch: devel git_last_commit: 9d714e1 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/tinesath1cdf_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: XhybCasneuf dependencyCount: 0 Package: tinesath1probe Version: 1.51.0 Depends: R (>= 1.6), AnnotationDbi (>= 1.11.9) License: LGPL MD5sum: 8792099e3630c682283e068080f26096 NeedsCompilation: no Title: Probe sequence data for microarrays of type tinesath1 Description: This package was automatically created by package matchprobes version 1.4.0. The probe sequence data was obtained from http://www.affymetrix.com. biocViews: Arabidopsis_thaliana_Data, SequencingData, MicroarrayData Author: The Bioconductor Project www.bioconductor.org Maintainer: Tine Casneuf git_url: https://git.bioconductor.org/packages/tinesath1probe git_branch: devel git_last_commit: d095549 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/tinesath1probe_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 42 Package: tissueTreg Version: 1.33.0 Depends: R (>= 3.5) Suggests: BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq, SummarizedExperiment, ggplot2, reshape2 License: GPL (>= 2) MD5sum: cbda568d9379b779abbc8518aff9bee3 NeedsCompilation: no Title: TWGBS and RNA-seq data from tissue T regulatory cells from mice Description: The package provides ready to use epigenomes (obtained from TWGBS) and transcriptomes (RNA-seq) from various tissues as obtained in the study (Delacher and Imbusch 2017, PMID: 28783152). Regulatory T cells (Treg cells) perform two distinct functions: they maintain self-tolerance, and they support organ homeostasis by differentiating into specialized tissue Treg cells. The underlying dataset characterises the epigenetic and transcriptomic modifications for specialized tissue Treg cells. biocViews: ExperimentData, Tissue, Mus_musculus_Data, SequencingData, RNASeqData Author: Charles Imbusch [aut, cre], Michael Delacher [aut], Markus Feuerer [aut], Benedikt Brors [aut] Maintainer: Charles Imbusch URL: https://github.com/cimbusch/tissueTreg VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tissueTreg git_branch: devel git_last_commit: c89d03b git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/tissueTreg_1.33.0.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: 1.23.0 Depends: R (>= 4.1), SingleCellExperiment, BiocFileCache Imports: methods, Matrix Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: bcbf2a71b763401c84766d0e689a2c5d NeedsCompilation: no Title: A Collection of Tumour Microenvironment Single-cell RNA Sequencing Datasets and Corresponding Metadata Description: This package provides a tool to search and download a collection of tumour microenvironment single-cell RNA sequencing datasets and their metadata. TMExplorer aims to act as a single point of entry for users looking to study the tumour microenvironment at the single cell level. Users can quickly search available datasets using the metadata table and then download the ones they are interested in for analysis. biocViews: CancerData, SingleCellData, RNASeqData, SequencingData, ExpressionData, GEO, PackageTypeData Author: Erik Christensen [aut, cre], Alaine Naidas [aut], David Chen [aut], Parisa Shooshtari [aut] Maintainer: Erik Christensen VignetteBuilder: knitr BugReports: https://github.com/shooshtarilab/TMExplorer/issues git_url: https://git.bioconductor.org/packages/TMExplorer git_branch: devel git_last_commit: 7bcab7f git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/TMExplorer_1.23.0.tar.gz vignettes: vignettes/TMExplorer/inst/doc/TMExplorer.html vignetteTitles: TMExplorer hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TMExplorer/inst/doc/TMExplorer.R dependencyCount: 62 Package: tofsimsData Version: 1.41.0 Depends: R (>= 3.2.0) Suggests: knitr, rmarkdown, tools License: GPL-3 MD5sum: 9ecbbdbd376a67e68e45b3488878096e NeedsCompilation: no Title: Import, process and analysis of ToF-SIMS imaging data Description: This packages contains data to be used with the 'tofsims' package. biocViews: ExperimentData, MassSpectrometry, ImagingMassSpectrometry, DataImport Author: Lorenz Gerber, Viet Mai Hoang Maintainer: Lorenz Gerber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tofsimsData git_branch: devel git_last_commit: 0a2ebb4 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/tofsimsData_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: topdownrdata Version: 1.33.0 Depends: topdownr License: GPL (>= 3) MD5sum: 13a5cbeb88df2418ef7c9db76a4ee76d NeedsCompilation: no Title: Example Files for the topdownr R Package Description: Example data for the topdownr package generated on a Thermo Orbitrap Fusion Lumos MS device. biocViews: ExperimentData, MassSpectrometryData Author: Sebastian Gibb [aut, cre], Pavel Shliaha [aut], Ole Nørregaard Jensen [aut] Maintainer: Sebastian Gibb URL: https://codeberg.org/sgibb/topdownrdata/ BugReports: https://codeberg.org/sgibb/topdownrdata/issues/ git_url: https://git.bioconductor.org/packages/topdownrdata git_branch: devel git_last_commit: 062bb26 git_last_commit_date: 2025-10-29 Date/Publication: 2026-04-21 source.ver: src/contrib/topdownrdata_1.33.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 1 Package: TransOmicsData Version: 1.9.0 Imports: S4Vectors, utils Suggests: BiocStyle, knitr, rmarkdown, RefManageR, sessioninfo, testthat, ExperimentHub License: GPL-3 + file LICENSE MD5sum: bffca284dbf28b42f83840b0176183ba NeedsCompilation: no Title: A collection of trans-omics datasets across various biological systems Description: Contains a collection of trans-omics datasets generated using various sequencing technologies such as RNA-seq, Mass spectrometry and ChIP-seq. Modalities include the bulk profiling of the phosphoproteome, proteome, transcriptome and epigenome. Data reflects the timecourses of different developmental systems from the mouse or human. biocViews: ExperimentHub, MassSpectrometryData, RNASeqData, ChIPSeqData, Tissue, SequencingData Author: Carissa Chen [aut] (ORCID: ), Di Xiao [aut, cre] (ORCID: ), Pengyi Yang [aut] (ORCID: ) Maintainer: Di Xiao URL: https://github.com/PYangLab/TransOmicsData VignetteBuilder: knitr BugReports: https://support.bioconductor.org/t/TransOmicsData git_url: https://git.bioconductor.org/packages/TransOmicsData git_branch: devel git_last_commit: 2bc8e51 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/TransOmicsData_1.9.0.tar.gz vignettes: vignettes/TransOmicsData/inst/doc/TransOmicsData-vignette.html vignetteTitles: TransOmicsData: A collection of trans-omics datasets across various biological systems hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TransOmicsData/inst/doc/TransOmicsData-vignette.R dependencyCount: 8 Package: tuberculosis Version: 1.19.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: AnnotationHub, ExperimentHub, S4Vectors, dplyr, magrittr, purrr, rlang, stringr, tibble, tidyr Suggests: BiocStyle, ggplot2, knitr, readr, rmarkdown, scater, usethis, utils License: Artistic-2.0 MD5sum: 0753c716893c8fbc5d7b666841143201 NeedsCompilation: no Title: Tuberculosis Gene Expression Data for Machine Learning Description: The tuberculosis R/Bioconductor package features tuberculosis gene expression data for machine learning. All human samples from GEO that did not come from cell lines, were not taken postmortem, and did not feature recombination have been included. The package has more than 10,000 samples from both microarray and sequencing studies that have been processed from raw data through a hyper-standardized, reproducible pipeline. biocViews: ExperimentHub, ExpressionData, Homo_sapiens_Data, MicroarrayData, SequencingData, ReproducibleResearch Author: Lucas Schiffer [aut, cre] (ORCID: ) Maintainer: Lucas Schiffer URL: https://github.com/schifferl/tuberculosis VignetteBuilder: knitr BugReports: https://github.com/schifferl/tuberculosis/issues git_url: https://git.bioconductor.org/packages/tuberculosis git_branch: devel git_last_commit: 2cdbcd3 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/tuberculosis_1.19.0.tar.gz vignettes: vignettes/tuberculosis/inst/doc/tuberculosis.html vignetteTitles: tuberculosis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tuberculosis/inst/doc/tuberculosis.R dependencyCount: 75 Package: tweeDEseqCountData Version: 1.51.0 Depends: Biobase, R (>= 4.3.0) Suggests: knitr, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: 6c9ab785a18d996fffc2ee81a18965db NeedsCompilation: no Title: RNA-seq count data employed in the vignette of the tweeDEseq package Description: RNA-seq count data from Pickrell et al. (2010) employed to illustrate the use of the Poisson-Tweedie family of distributions with the tweeDEseq package. biocViews: Genome, Homo_sapiens_Data, RNASeqData Author: Dolors Pelegri-Siso [aut, cre] (ORCID: ), Juan R. Gonzalez [aut] (ORCID: ), Mikel Esnaola [aut], Robert Castelo [aut] Maintainer: Dolors Pelegri-Siso URL: https://github.com/isglobal-brge/tweeDEseqCountData/ VignetteBuilder: knitr BugReports: https://github.com/isglobal-brge/tweeDEseqCountData/issues git_url: https://git.bioconductor.org/packages/tweeDEseqCountData git_branch: devel git_last_commit: 92081a4 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/tweeDEseqCountData_1.51.0.tar.gz vignettes: vignettes/tweeDEseqCountData/inst/doc/tweeDEseqCountData.html vignetteTitles: RNA-seq count data employed in the vignette of the tweeDEseq package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tweeDEseqCountData/inst/doc/tweeDEseqCountData.R suggestsMe: GSAR, tweeDEseq dependencyCount: 7 Package: tximportData Version: 1.41.0 Suggests: knitr, markdown License: GPL (>= 2) MD5sum: 841de6a141db6031287f0918d9464008 NeedsCompilation: no Title: tximportData Description: This package provides the output of running various transcript abundance quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project. The quantifiers were Cufflinks, RSEM, kallisto, Salmon and Sailfish. alevin example output is also included. Forr details on version numbers, sample information, and details on calls, see the package vignette. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tximportData git_branch: devel git_last_commit: 02887f7 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/tximportData_1.41.0.tar.gz vignettes: vignettes/tximportData/inst/doc/tximportData.html vignetteTitles: Sample output files for tximport hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tximportData/inst/doc/tximportData.R importsMe: TDbasedUFE suggestsMe: DESeq2, eds, fishpond, tximeta, tximport dependencyCount: 0 Package: VariantToolsData Version: 1.37.0 Depends: R (>= 3.5.0), VariantAnnotation (>= 1.7.35) Imports: BiocGenerics, GenomicRanges Suggests: VariantTools (>= 1.3.4), gmapR (>= 1.3.3), BiocStyle License: Artistic-2.0 MD5sum: 5145175ea9841552b5c0682299e45fa5 NeedsCompilation: no Title: Data for the VariantTools tutorial Description: Data from the sequencing of a 50/50 mixture of HapMap trio samples NA12878 (CEU) and NA19240 (YRI), subset to the TP53 region. biocViews: ExperimentData, SequencingData, HapMap, SNPData Author: Michael Lawrence Maintainer: Michael Lawrence git_url: https://git.bioconductor.org/packages/VariantToolsData git_branch: devel git_last_commit: 82a2f41 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/VariantToolsData_1.37.0.tar.gz vignettes: vignettes/VariantToolsData/inst/doc/intro.pdf vignetteTitles: VariantTools Example Data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/VariantToolsData/inst/doc/intro.R dependencyCount: 78 Package: VectraPolarisData Version: 1.17.0 Depends: ExperimentHub, SpatialExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, dplyr License: Artistic-2.0 MD5sum: bae7cd4be39ac70883281f01720bee6e NeedsCompilation: no Title: Vectra Polaris and Vectra 3 multiplex single-cell imaging data Description: Provides two multiplex imaging datasets collected on Vectra instruments at the University of Colorado Anschutz Medical Campus. Data are provided as a Spatial Experiment objects. Data is provided in tabular form and has been segmented and phenotyped using Inform software. Raw .tiff files are not included. biocViews: ExperimentHub, ExperimentData, SpatialData, SingleCellData, Homo_sapiens_Data, ReproducibleResearch Author: Wrobel Julia [aut, cre] (ORCID: ), Tusharkanti Ghosh [aut] Maintainer: Wrobel Julia URL: https://github.com/julia-wrobel/VectraPolarisData VignetteBuilder: knitr BugReports: https://support.bioconductor.org/t/VectraPolarisData git_url: https://git.bioconductor.org/packages/VectraPolarisData git_branch: devel git_last_commit: d5a6d87 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/VectraPolarisData_1.17.0.tar.gz vignettes: vignettes/VectraPolarisData/inst/doc/VectraPolarisData.html vignetteTitles: VectraPolarisData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/VectraPolarisData/inst/doc/VectraPolarisData.R dependencyCount: 80 Package: vulcandata Version: 1.35.0 Imports: utils Suggests: viper License: LGPL-3 MD5sum: 09b62b60e69aef75bfc612fad88ae0ae NeedsCompilation: no Title: VirtUaL ChIP-Seq data Analysis using Networks, dummy dataset Description: This package provides a dummy regulatory network and ChIP-Seq dataset for running examples in the vulcan package biocViews: ExperimentData, Homo_sapiens_Data, CancerData, ChIPSeqData Author: Federico M. Giorgi, Andrew N. Holding, Florian Markowetz Maintainer: Federico M. Giorgi git_url: https://git.bioconductor.org/packages/vulcandata git_branch: devel git_last_commit: c448180 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/vulcandata_1.35.0.tar.gz vignettes: vignettes/vulcandata/inst/doc/vulcandata.pdf vignetteTitles: Vulcan: VirtUaL ChIP-Seq Analysis through Networks,, dummy datasets hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/vulcandata/inst/doc/vulcandata.R dependencyCount: 1 Package: WeberDivechaLCdata Version: 1.15.0 Depends: ExperimentHub, SpatialExperiment, SingleCellExperiment Imports: utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: ee6df1441ee745bcc6df074a1f850e05 NeedsCompilation: no Title: Spatially-resolved transcriptomics and single-nucleus RNA-sequencing data from the locus coeruleus (LC) in postmortem human brain samples Description: Spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from the locus coeruleus (LC) in postmortem human brain samples. Data were generated with the 10x Genomics Visium SRT and 10x Genomics Chromium snRNA-seq platforms. Datasets are stored in SpatialExperiment and SingleCellExperiment formats. biocViews: ExperimentData, ExperimentHub, ReproducibleResearch, ExpressionData, SequencingData, RNASeqData, SingleCellData, SpatialData, Homo_sapiens_Data Author: Lukas M. Weber [aut, cre] (ORCID: ), Heena R. Divecha [aut] (ORCID: ) Maintainer: Lukas M. Weber URL: https://github.com/lmweber/WeberDivechaLCdata VignetteBuilder: knitr BugReports: https://github.com/lmweber/WeberDivechaLCdata/issues git_url: https://git.bioconductor.org/packages/WeberDivechaLCdata git_branch: devel git_last_commit: 4c6a287 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/WeberDivechaLCdata_1.15.0.tar.gz vignettes: vignettes/WeberDivechaLCdata/inst/doc/WeberDivechaLCdata.html vignetteTitles: WeberDivechaLCdata package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/WeberDivechaLCdata/inst/doc/WeberDivechaLCdata.R suggestsMe: nnSVG dependencyCount: 80 Package: WES.1KG.WUGSC Version: 1.45.0 License: GPL-2 MD5sum: de07442e083303ffaa778d0facd3db5e NeedsCompilation: no Title: Whole Exome Sequencing (WES) of chromosome 22 401st to 500th exon from the 1000 Genomes (1KG) Project by the Washington University Genome Sequencing Center (WUGSC). Description: The assembled .bam files of whole exome sequencing data from the 1000 Genomes Project. 46 samples sequenced by the Washington University Genome Sequencing Center are included. biocViews: ExperimentData, Project1000genomes, SequencingData, DNASeqData, Homo_sapiens_Data Author: Yuchao Jiang, Nancy R. Zhang Maintainer: Yuchao Jiang git_url: https://git.bioconductor.org/packages/WES.1KG.WUGSC git_branch: devel git_last_commit: a085f58 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/WES.1KG.WUGSC_1.45.0.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: 1.25.0 Depends: R (>= 3.6.0), GenomicRanges License: GPL-2 MD5sum: 43a71d90645d776a6db351ad64f456da NeedsCompilation: no Title: Mappability tracks of Whole-genome Sequencing from the ENCODE Project Description: This package provides whole-genome mappability tracks on human hg19/hg38 assembly. We employed the 100-mers mappability track from the ENCODE Project and computed weighted average of the mappability scores if multiple ENCODE regions overlap with the same bin. “Blacklist” bins, including segmental duplication regions and gaps in reference assembly from telomere, centromere, and/or heterochromatin regions are included. The dataset consists of three assembled .bam files of single-cell whole genome sequencing from 10X for illustration purposes. biocViews: ExperimentData, SequencingData, DNASeqData, SingleCellData, Homo_sapiens_Data, Genome, ENCODE Author: Rujin Wang Maintainer: Rujin Wang git_url: https://git.bioconductor.org/packages/WGSmapp git_branch: devel git_last_commit: 1f88691 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/WGSmapp_1.25.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: SCOPE dependencyCount: 11 Package: xcoredata Version: 1.17.0 Depends: R (>= 4.2) Imports: ExperimentHub (>= 2.2.0), utils (>= 4.2.0) Suggests: BiocGenerics (>= 0.40.0), data.table (>= 1.14.2), GenomeInfoDb (>= 1.30.0), GenomicRanges (>= 1.46.1), IRanges (>= 2.28.0), knitr (>= 1.37), rmarkdown (>= 2.11), Matrix (>= 1.3.4), stringr (>= 1.4.0), S4Vectors (>= 0.32.3), TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.14.0), xcore License: GPL-2 MD5sum: f8d8d17105b87e1a38c4c8072d2f1004 NeedsCompilation: no Title: data package for xcore Description: Provides data to use with xcore package. biocViews: ExperimentHub, ExperimentData, Homo_sapiens_Data Author: Maciej Migdał [aut, cre] (ORCID: ), Bogumił Kaczkowski [aut] (ORCID: ) Maintainer: Maciej Migdał VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/xcoredata git_branch: devel git_last_commit: e4375ad git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/xcoredata_1.17.0.tar.gz vignettes: vignettes/xcoredata/inst/doc/xcoredata.html vignetteTitles: xcoredata hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/xcoredata/inst/doc/xcoredata.R suggestsMe: xcore dependencyCount: 64 Package: XhybCasneuf Version: 1.51.0 Depends: R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf , RColorBrewer , methods, grid License: Artistic-2.0 MD5sum: c4605cd43e9cb26b279fd0a3a4a50536 NeedsCompilation: no Title: EBI/PSB cross-hybridisation study package Description: Cross-hybridisation study on the ATH1 Affymetrix GeneChip biocViews: ExperimentData, Tissue, MicroarrayData, TissueMicroarrayData Author: Tineke Casneuf Maintainer: Tineke Casneuf git_url: https://git.bioconductor.org/packages/XhybCasneuf git_branch: devel git_last_commit: cd3922e git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/XhybCasneuf_1.51.0.tar.gz vignettes: vignettes/XhybCasneuf/inst/doc/Xhyb.pdf vignetteTitles: Xhyb hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/XhybCasneuf/inst/doc/Xhyb.R dependencyCount: 50 Package: yeastCC Version: 1.53.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: b62eec0e62427118ae0b930847969e48 NeedsCompilation: no Title: Spellman et al. (1998) and Pramila/Breeden (2006) yeast cell cycle microarray data Description: ExpressionSet for Spellman et al. (1998) yeast cell cycle microarray experiment biocViews: ExperimentData, CellCulture, Saccharomyces_cerevisiae_Data, CancerData, MicroarrayData, OneChannelData, GEO Author: Sandrine Dudoit Maintainer: Sandrine Dudoit git_url: https://git.bioconductor.org/packages/yeastCC git_branch: devel git_last_commit: 65a77f0 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/yeastCC_1.53.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: LiquidAssociation suggestsMe: fastLiquidAssociation, ibh dependencyCount: 7 Package: yeastExpData Version: 0.59.0 Depends: R (>= 2.4), graph (>= 1.9.26) Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db License: GPL MD5sum: 9d89c3f535b168904f7821a43e050714 NeedsCompilation: no Title: Yeast Experimental Data Description: A collection of different sets of experimental data from yeast. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data Author: R. Gentleman Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/yeastExpData git_branch: devel git_last_commit: afb1c9a git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/yeastExpData_0.59.0.tar.gz vignettes: vignettes/yeastExpData/inst/doc/yeastExample.pdf vignetteTitles: Yeast PPI Example hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/yeastExpData/inst/doc/yeastExample.R dependsOnMe: PPInfer suggestsMe: ClusterJudge dependencyCount: 8 Package: yeastGSData Version: 0.51.0 License: Artistic-2.0 MD5sum: 17ec02f6cdc481222609499ba36aa757 NeedsCompilation: no Title: Yeast Gold Standard Data Description: A collection of so-called gold (and other) standard data sets biocViews: ExperimentData, Saccharomyces_cerevisiae_Data Author: R. Gentleman Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/yeastGSData git_branch: devel git_last_commit: 120e727 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/yeastGSData_0.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: yeastNagalakshmi Version: 1.49.0 License: Artistic-2.0 MD5sum: f42e611808e630004edd113c4ddcbba4 NeedsCompilation: no Title: Yeast genome RNA sequencing data based on Nagalakshmi et. al. Description: The yeast genome data was retrieved from the sequence read archive, aligned with bwa, and converted to BAM format with samtools. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, SequencingData, BiocViews, ChIPSeqData Author: Martin Morgan Maintainer: Bioconductor Package Maintainer git_url: https://git.bioconductor.org/packages/yeastNagalakshmi git_branch: devel git_last_commit: 48c897f git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/yeastNagalakshmi_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ShortRead dependencyCount: 0 Package: yeastRNASeq Version: 0.51.0 Depends: R (>= 2.4) Suggests: Biobase, ShortRead, IRanges License: GPL MD5sum: 5606d4f2a03d805bd8920338b077f56d NeedsCompilation: no Title: Yeast RNA-Seq Experimental Data from Lee et al. 2008 Description: A selection of RNA-Seq data from a yeast transcriptome experiment. biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData Author: James H. Bullard and Kasper D. Hansen Maintainer: J. Bullard git_url: https://git.bioconductor.org/packages/yeastRNASeq git_branch: devel git_last_commit: f2f505d git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/yeastRNASeq_0.51.0.tar.gz vignettes: vignettes/yeastRNASeq/inst/doc/yeastRNASeq.pdf vignetteTitles: An overview of yeastRNASeq hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/yeastRNASeq/inst/doc/yeastRNASeq.R suggestsMe: EDASeq dependencyCount: 0 Package: zebrafishRNASeq Version: 1.33.0 Depends: R (>= 2.10) Suggests: BiocStyle, knitr License: GPL MD5sum: 4c59a3b1b2686350805b8564d028afcf NeedsCompilation: no Title: Zebrafish RNA-Seq Experimental Data from Ferreira et al. (2014) Description: Gene-level read counts from RNA-Seq for gallein-treated and control zebrafish. biocViews: ExperimentData, Danio_rerio_Data, RNASeqData Author: Davide Risso Maintainer: Davide Risso VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/zebrafishRNASeq git_branch: devel git_last_commit: 2a45047 git_last_commit_date: 2026-04-28 Date/Publication: 2026-04-30 source.ver: src/contrib/zebrafishRNASeq_1.33.0.tar.gz vignettes: vignettes/zebrafishRNASeq/inst/doc/preprocessing.html vignetteTitles: Pre-Processing for the Zebrafish RNA-Seq Gene-Level Counts hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/zebrafishRNASeq/inst/doc/preprocessing.R suggestsMe: RUVSeq, sva dependencyCount: 0 Package: Hiiragi2013 Version: 1.49.0 Depends: R (>= 4.0.0), Biobase Imports: MASS, RColorBrewer, cluster, gplots, grid, lattice, latticeExtra, genefilter Suggests: affy, BiocStyle, boot, clue, geneplotter, gtools, KEGGREST, mouse4302.db, xtable License: Artistic-2.0 Title: Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages Description: This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881." biocViews: ExperimentData, MicroarrayData, qPCRData, ReproducibleResearch Author: Andrzej Oles [aut], Wolfgang Huber [aut, cre] Maintainer: Wolfgang Huber Package: TimerQuant Version: 1.43.0 Depends: shiny Imports: ggplot2, grid, gridExtra, deSolve, dplyr, locfit Suggests: BiocStyle, reshape2, knitr, shinyBS License: Artistic-2.0 NeedsCompilation: no Title: Timer Quantification Description: Supplementary Data package for tandem timer methods paper by Barry et al. (2015) including TimerQuant shiny applications. biocViews: ExperimentData, Danio_rerio_Data, HighThroughputImagingData, Tissue Author: Joseph Barry Maintainer: Joseph Barry VignetteBuilder: knitr Package: furrowSeg Version: 1.41.0 Depends: R (>= 3.3), EBImage Imports: abind, dplyr, locfit, tiff Suggests: BiocStyle, ggplot2, knitr License: Artistic-2.0 NeedsCompilation: no Title: Furrow Segmentation Description: Image feature data and analysis codes for the Guglielmi, Barry et al. paper describing the application of an optogenetics tools to disrupt Drosophila embryo furrowing. biocViews: ExperimentData, Drosophila_melanogaster_Data, Tissue, ReproducibleResearch Author: Joseph Barry Maintainer: Joseph Barry VignetteBuilder: knitr Package: qPLEXdata Version: 1.31.0 Depends: R (>= 3.5), qPLEXanalyzer Imports: utils, knitr, MSnbase, dplyr Suggests: statmod License: GPL-2 NeedsCompilation: no Title: Data accompanying qPLEXanalyzer package Description: qPLEX-RIME and Full proteome TMT mass spectrometry datasets. biocViews: ExperimentData, MassSpectrometryData, Proteome Author: Kamal Kishore Developer [aut, cre] Maintainer: Kamal Kishore Developer VignetteBuilder: knitr Package: HMP2Data Version: 1.27.0 Depends: R (>= 3.6.0) Imports: AnnotationHub, assertthat, dplyr, ExperimentHub, kableExtra, knitr, magrittr, methods, readr, S4Vectors, SummarizedExperiment, phyloseq, MultiAssayExperiment, data.table Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, cowplot, devtools, ggplot2, gridExtra, haven, rmarkdown, roxygen2, stats, testthat, tibble, UpSetR License: Artistic-2.0 Title: 16s rRNA sequencing data from the Human Microbiome Project 2 Description: HMP2Data is a Bioconductor package of the Human Microbiome Project 2 (HMP2) 16S rRNA sequencing data. Processed data is provided as phyloseq, SummarizedExperiment, and MultiAssayExperiment class objects. Individual matrices and data.frames used for building these S4 class objects are also provided in the package. biocViews: ExperimentData, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch, SequencingData Author: John Stansfield , Ekaterina Smirnova , Ni Zhao , Jennifer Fettweis , Levi Waldron , Mikhail Dozmorov Maintainer: John Stansfield , Ekaterina Smirnova URL: https://github.com/jstansfield0/HMP2Data VignetteBuilder: knitr BugReports: https://github.com/jstansfield0/HMP2Data/issues Package: dorothea Version: 1.25.0 Depends: R (>= 4.0) Imports: dplyr, magrittr, bcellViper, decoupleR, Suggests: Biobase, BiocStyle, OmnipathR, viper, knitr, pheatmap, pkgdown, rmarkdown, Seurat, SingleCellExperiment, SummarizedExperiment, testthat (>= 2.1.0), tibble, tidyr, utils License: GPL-3 + file LICENSE Title: Collection Of Human And Mouse TF Regulons Description: DoRothEA is a gene regulatory network containing signed transcription factor (TF) - target gene interactions. DoRothEA regulons, the collection of a TF and its transcriptional targets, were curated and collected from different types of evidence for both human and mouse. A confidence level was assigned to each TF-target interaction based on the number of supporting evidence. biocViews: ExperimentData, Homo_sapiens_Data, Mus_musculus_Data Author: Pau Badia-i-Mompel [cre] (ORCID: ), Daniel Dimitrov [aut] (ORCID: ), Christian H. Holland [aut] (ORCID: ), Luz Garcia-Alonso [aut], Alberto Valdeolivas [ctb], Minoo Ashtiani [ctb], Attila Gabor [ctb] Maintainer: Pau Badia-i-Mompel URL: https://saezlab.github.io/dorothea/, https://github.com/saezlab/dorothea VignetteBuilder: knitr BugReports: https://github.com/saezlab/dorothea/issues Package: brgedata Version: 1.35.0 Depends: R (>= 3.4), Biobase Imports: SummarizedExperiment Suggests: minfi, MultiAssayExperiment, knitr, rmarkdown, rexposome, BiocStyle License: MIT + file LICENSE Title: Exposures, Gene Expression and Methylation data for ilustration purpouses Description: This package contains several sets of omics data including Gene Expression (ExpressionSet), Methylation (GenomicRatioSet), Proteome and Exposome (ExposomeSet). This data is used in vignettes and exaples at MEAL, MultiDataSet and omicRexposome. biocViews: ExperimentData,Homo_sapiens_Data,MicroarrayData,MethylationArrayData Author: Dolors Pelegri-Siso [aut, cre], Carlos Ruiz-Arenas [aut], Carles Hernandez-Ferrer [aut], Juan R. Gonzalez [aut] Maintainer: Dolors Pelegri-Siso VignetteBuilder: knitr Package: MerfishData Version: 1.15.0 Depends: R (>= 4.2.0), EBImage, SpatialExperiment Imports: grDevices, AnnotationHub, BumpyMatrix, ExperimentHub, S4Vectors, SingleCellExperiment, SummarizedExperiment, HDF5Array Suggests: grid, ggplot2, ggpubr, knitr, rmarkdown, scater, scattermore, terra, testthat, BiocStyle, DropletUtils License: Artistic-2.0 Title: Collection of public MERFISH datasets Description: MerfishData is an ExperimentHub package that serves publicly available datasets obtained with Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH). MERFISH is a massively multiplexed single-molecule imaging technology capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells. The scope of the package is to provide MERFISH data for benchmarking and analysis. biocViews: ExperimentHub, ExpressionData, HighThroughputImagingData, Mus_musculus_Data, SingleCellData, SpatialData Author: Ludwig Geistlinger [aut, cre] (ORCID: ), Tyrone Lee [ctb], Helena Crowell [ctb] (ORCID: ), Daniela Corbetta [ctb], Jeffrey Moffitt [aut], Robert Gentleman [aut] Maintainer: Ludwig Geistlinger URL: https://github.com/ccb-hms/MerfishData VignetteBuilder: knitr BugReports: https://github.com/ccb-hms/MerfishData/issues Package: TumourMethData Version: 1.11.0 Depends: R (>= 4.2), SummarizedExperiment Imports: base, BSgenome.Hsapiens.UCSC.hg19, dplyr, ExperimentHub, ExperimentHubData, GenomicRanges, HDF5Array, knitr, methodical, methrix, openxlsx, R.utils, readr, rhdf5, rmarkdown, stringr, TCGAutils, tibble, usethis, xlsx Suggests: ggplot2 License: Artistic-2.0 Title: A Collection of DNA Methylation Datasets for Human Tumour Samples and Matching Normal Samples Description: TumourMethData collects tumour methylation data from a variety of different tumour types (and also matching normal samples where available) and produced with different technologies (e.g. WGBS, RRBS and methylation arrays) and provides them as RangedSummarizedExperiments. This facilitates easy extraction of methylation data for regions of interest across different tumour types and studies. biocViews: ExperimentData, ExperimentHub, MethylSeqData, CancerData, Homo_sapiens_Data, Author: Richard Heery [aut, cre] (ORCID: ) Maintainer: Richard Heery URL: https://github.com/richardheery/TumourMethData VignetteBuilder: knitr BugReports: https://support.bioconductor.org/tag/TumourMethData Package: homosapienDEE2CellScore Version: 1.9.0 Imports: Rtsne (>= 0.15), utils(>= 3.5.0), ExperimentHub, BiocGenerics, DESeq2, S4Vectors, SummarizedExperiment, getDEE2, MatrixGenerics Suggests: knitr, rmarkdown, devtools, Biobase (>= 2.39.1), BiocManager, AnnotationHubData, ExperimentHubData, AnnotationHub, CellScore (>= 1.21.4) License: GPL (>= 3) Title: Example Data Package for CellScore Description: This is a data package for normalised homosapien data downloaded from DEE2. The package both downloads, normalises, and filters the data, and provides a way to access the data from a canonical store without needing local processing. This package was built as a way to generate and store canonical test data for CellScore. biocViews: RNASeqData, Genome, ExperimentHub, ExpressionData Author: Justin Marsh [aut, cre] Maintainer: Justin Marsh VignetteBuilder: knitr BugReports: https://github.com/flaviusb/homosapienDEE2CellScore/issues Package: CENTREprecomputed Version: 1.3.0 Depends: R (>= 4.5.0) Imports: ExperimentHub, RSQLite, DBI, BiocGenerics, methods Suggests: knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 Title: Hub package for the precomputed data of CENTRE and example data Description: Interface and documentation for the Experiment Hub records needed by the CENTRE Bioconductor software package. The Experiment Hub records contains the precomputed fisher combined p-values, CRUP correlations. Additionally, the records hold ChIP-seq and RNA-seq data used for the example of the software package. biocViews: ExperimentData, PackageTypeData, ExperimentHub, RNASeqData, ChIPSeqData, ChipOnChipData Author: Sara Lopez Ruiz de Vargas [aut, cre] (ORCID: ) Maintainer: Sara Lopez Ruiz de Vargas URL: https://github.com/slrvv/CENTREprecomputed VignetteBuilder: knitr BugReports: https://github.com/slrvv/CENTREprecomputed/issues