Package: adductData Version: 1.23.0 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: 7c3fda29a209763d33ca930457b3d6ab 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: 48998f4 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/adductData_1.23.0.tar.gz vignettes: vignettes/adductData/inst/doc/adductData.html vignetteTitles: Raw mzXML data using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/adductData/inst/doc/adductData.R dependsOnMe: adductomicsR dependencyCount: 68 Package: affycompData Version: 1.45.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp License: GPL (>= 2) MD5sum: 9b2ee12abf554f76b9fc2d19ccf4632f 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: 7729c80 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/affycompData_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: affycomp dependencyCount: 8 Package: affydata Version: 1.55.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Imports: methods Suggests: hgu95av2cdf, hgu133acdf License: GPL (>= 2) MD5sum: 92b57313a5fb96083eba6758b94c3226 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: 427aebc git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/affydata_1.55.0.tar.gz vignettes: vignettes/affydata/inst/doc/affydata.pdf vignetteTitles: affydata primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/affydata/inst/doc/affydata.R dependsOnMe: affyContam suggestsMe: affy, affycoretools, affyPLM, arrayMvout, Biostrings, gcrma, Harman, mimager, puma, pvac, TurboNorm, vsn, RobLoxBioC dependencyCount: 13 Package: Affyhgu133A2Expr Version: 1.43.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 8eb663f5af869b82a603ff633b0d0564 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: e623480 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/Affyhgu133A2Expr_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: Affyhgu133aExpr Version: 1.45.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 413ed59820f89c43035f28079ea99144 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: 6d4accf git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/Affyhgu133aExpr_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: Affyhgu133Plus2Expr Version: 1.41.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: b1f517ceb3e0c3c8ca2ffb6bd2cdcdea 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: 7438f00 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/Affyhgu133Plus2Expr_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: AffymetrixDataTestFiles Version: 0.45.0 Depends: R (>= 2.5.0) License: LGPL-2.1 MD5sum: 22167d3886548cbb01051922d6075803 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: 0b0e503 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/AffymetrixDataTestFiles_0.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: affxparser, affyILM, aroma.affymetrix dependencyCount: 0 Package: Affymoe4302Expr Version: 1.45.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 11ae625a43916732f22a662779e8c950 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: 65b44bd git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/Affymoe4302Expr_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: airway Version: 1.27.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: knitr, GEOquery, markdown License: LGPL MD5sum: 4622797c45a800033ddb417d10c408a4 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: 7998b50 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/airway_1.27.0.tar.gz vignettes: vignettes/airway/inst/doc/airway.html vignetteTitles: Airway smooth muscle cells hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/airway/inst/doc/airway.R dependsOnMe: rnaseqGene importsMe: consensusDE, NetActivity suggestsMe: apeglm, awst, biobroom, BioCor, BiocSet, CeTF, DelayedArray, DESeq2, EnhancedVolcano, EnrichmentBrowser, ExperimentSubset, funOmics, gg4way, ideal, IHW, InteractiveComplexHeatmap, iSEEde, iSEEpathways, iSEEu, OPWeight, pathwayPCA, pcaExplorer, PCAtools, plyxp, progeny, runibic, Rvisdiff, SummarizedExperiment, TTMap, weitrix, IHWpaper, RegParallel, seqgendiff dependencyCount: 37 Package: ALL Version: 1.49.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Suggests: rpart License: Artistic-2.0 MD5sum: aeef38173f89b14b31ba10d37eb45c02 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: d1302d6 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/ALL_1.49.0.tar.gz vignettes: vignettes/ALL/inst/doc/ALLintro.pdf vignetteTitles: ALL data intro hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ALL/inst/doc/ALLintro.R importsMe: ConsensusClusterPlus, dGAselID, scRNAtools suggestsMe: a4, a4Base, a4Classif, a4Preproc, Biobase, BioNet, Category, CellMapper, ChromHeatMap, clipper, EnrichmentBrowser, esetVis, genefilter, GeneSelectMMD, GOstats, graphite, GSAR, GSEAlm, MLInterfaces, npGSEA, pathRender, ReportingTools, rScudo, SNAGEE, topGO, SNAGEEdata, MMDvariance, nlcv dependencyCount: 7 Package: ALLMLL Version: 1.47.0 Depends: R (>= 2.10), affy (>= 1.23.4) License: GPL-2 MD5sum: ee37be23dddb7e245d251e6683d21cd0 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: d2c48d9 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/ALLMLL_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQualityMetrics, pvac dependencyCount: 13 Package: AmpAffyExample Version: 1.47.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Suggests: hgu133acdf License: LGPL (>= 2) MD5sum: 8a3d112a64ba1d21e7844ae7494f118c 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: 57ead8d git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/AmpAffyExample_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: AffyRNADegradation dependencyCount: 13 Package: AneuFinderData Version: 1.35.0 Depends: R (>= 3.3) License: file LICENSE MD5sum: cb2987562f572d62cd53bcd90b193819 NeedsCompilation: no Title: WGSCS Data for Demonstration Purposes Description: Whole-genome single cell sequencing data for demonstration purposes in the AneuFinder package. biocViews: CopyNumberVariationData, LungCancerData, Homo_sapiens_Data, SequencingData Author: Aaron Taudt Maintainer: Aaron Taudt git_url: https://git.bioconductor.org/packages/AneuFinderData git_branch: devel git_last_commit: 1556b6e git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/AneuFinderData_1.35.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: AneuFinder dependencyCount: 0 Package: antiProfilesData Version: 1.43.0 Depends: Biobase, Suggests: frma, GEOquery, GEOmetadb License: Artistic-2.0 MD5sum: 7c5f04abda2f7100cc43731cc4056a50 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: 895bc5f git_last_commit_date: 2024-10-29 Date/Publication: 2024-12-12 source.ver: src/contrib/antiProfilesData_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: antiProfiles, epivizr, epivizrChart, messina dependencyCount: 7 Package: aracne.networks Version: 1.33.0 Depends: R (>= 3.3), viper License: file LICENSE MD5sum: 9ae6dd1e430206d0c935de4eba1097d4 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: 4fe2d27 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/aracne.networks_1.33.0.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: 90 Package: ARRmData Version: 1.43.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: dae21074fd4d1908a91db701697c9898 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: 2b2b55f git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/ARRmData_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ARRmNormalization dependencyCount: 0 Package: AshkenazimSonChr21 Version: 1.37.0 Suggests: knitr, VariantAnnotation License: Artistic-2.0 MD5sum: edebd72e8acb9990b8e84698fbab7e60 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: 5059288 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/AshkenazimSonChr21_1.37.0.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: 1.27.0 Depends: R (>= 3.5) Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: ba8e2184536efcf081574d0e5b095d48 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: a037125 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/ASICSdata_1.27.0.tar.gz vignettes: vignettes/ASICSdata/inst/doc/ASICSdata.html vignetteTitles: ASICSdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ASICS dependencyCount: 0 Package: bcellViper Version: 1.43.0 Depends: R(>= 2.14.0), Biobase, methods License: GPL (>=2) MD5sum: 919d3bce15dc98d8a297bbd9b6924f5b 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: c81130a git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/bcellViper_1.43.0.tar.gz vignettes: vignettes/bcellViper/inst/doc/bcellViper.pdf vignetteTitles: Using bcellViper hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bcellViper/inst/doc/bcellViper.R importsMe: dorothea suggestsMe: GenomicSuperSignature, pageRank, viper dependencyCount: 7 Package: beadarrayExampleData Version: 1.45.0 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>= 2.0.0) License: GPL-2 MD5sum: 2d73d6fa26271c036091ead18f553539 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: b6c796c git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/beadarrayExampleData_1.45.0.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, RobLoxBioC dependencyCount: 82 Package: BeadArrayUseCases Version: 1.45.1 Imports: beadarray (>= 2.3.18), limma, GEOquery Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db License: GPL-2 MD5sum: c1674d7958615e9c4a6ece3ba081a2d5 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: 99c4a86 git_last_commit_date: 2024-11-13 Date/Publication: 2024-11-14 source.ver: src/contrib/BeadArrayUseCases_1.45.1.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: 112 Package: BeadSorted.Saliva.EPIC Version: 1.15.0 Depends: R (>= 4.1), minfi(>= 1.36.0), ExperimentHub Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 458224f0996425d3a175784df4b9044c 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: 0e7bd40 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/BeadSorted.Saliva.EPIC_1.15.0.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: benchmarkfdrData2019 Version: 1.21.0 Depends: R (>= 3.6.0), SummarizedExperiment, ExperimentHub Imports: utils Suggests: rmarkdown, knitr, BiocStyle, testthat, SummarizedBenchmark, dplyr, ggplot2, rlang License: MIT + file LICENSE MD5sum: e8a3cf73bec26133fe718b1573b0f0c2 NeedsCompilation: no Title: Data and Benchmarking Results from Korthauer and Kimes et al. (2019) Description: Benchmarking results for experimental and simulated data sets used in Korthauer and Kimes et al. (2019) to compare methods for controlling the false discovery rate. biocViews: SingleCellData, ExperimentData, RNASeqData, ExpressionData, ExperimentData, ExperimentHub Author: Stephanie Hicks [aut, cre] (ORCID: ), Keegan Korthauer [aut] (ORCID: ), Patrick Kimes [aut] (ORCID: ) Maintainer: Stephanie Hicks VignetteBuilder: knitr BugReports: https://github.com/stephaniehicks/benchmarkfdrData2019/issues git_url: https://git.bioconductor.org/packages/benchmarkfdrData2019 git_branch: devel git_last_commit: c1f2be4 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/benchmarkfdrData2019_1.21.0.tar.gz vignettes: vignettes/benchmarkfdrData2019/inst/doc/benchmarkfdrData2019.html vignetteTitles: Exploring and updating FDR benchmarking results hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/benchmarkfdrData2019/inst/doc/benchmarkfdrData2019.R dependencyCount: 78 Package: beta7 Version: 1.45.0 Depends: R (>= 2.4.0), marray License: LGPL MD5sum: d0370ca15f86ff0d6a1936cd5de0f2c6 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: b3a8ca7 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/beta7_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 8 Package: BioImageDbs Version: 1.15.0 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: 474b51fd5de62fb3dbfe5d0eaaf665a9 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: fbab23e git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/BioImageDbs_1.15.0.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: 103 Package: BioPlex Version: 1.13.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: BiocFileCache, GenomicRanges, GenomeInfoDb, GEOquery, graph, methods, utils Suggests: AnnotationDbi, AnnotationHub, BiocStyle, DEXSeq, ExperimentHub, GenomicFeatures, S4Vectors, depmap, knitr, rmarkdown License: Artistic-2.0 MD5sum: 08ccaa4557ae81e9032d9b73afe215fd 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: 8762199 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/BioPlex_1.13.0.tar.gz vignettes: vignettes/BioPlex/inst/doc/BasicChecks.html, vignettes/BioPlex/inst/doc/BioPlex.html vignetteTitles: 2. Data checks, 1. Data retrieval hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BioPlex/inst/doc/BasicChecks.R, vignettes/BioPlex/inst/doc/BioPlex.R dependencyCount: 90 Package: biotmleData Version: 1.31.0 Depends: R (>= 3.5.0) Suggests: Biobase, SummarizedExperiment License: file LICENSE MD5sum: 60b693067aa7161ba0b6f88e99074f00 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: 6da33db git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/biotmleData_1.31.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: biotmle dependencyCount: 0 Package: biscuiteerData Version: 1.21.0 Depends: R (>= 4.1.0), ExperimentHub Imports: AnnotationHub, utils, curl, GenomicRanges Suggests: knitr, rmarkdown, markdown License: GPL-3 MD5sum: f17ad6da3bb6db0918cc95cd22ac741f 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: 1a228b9 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/biscuiteerData_1.21.0.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: 68 Package: bladderbatch Version: 1.45.0 Depends: Biobase License: Artistic-2.0 MD5sum: bb8c4f86c24d7312b06d00a81a1c8bdb 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: aefd61a git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/bladderbatch_1.45.0.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: 1.27.0 Depends: R(>= 3.0.0) Suggests: blima, beadarray, illuminaHumanv4.db, BiocStyle License: GPL-3 MD5sum: db5f7d97c7418124e60d4ca2663c40c9 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: 33165d2 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/blimaTestingData_1.27.0.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: 1.27.0 Depends: R (>= 3.5.0) Imports: beeswarm, Biobase, DESeq2, devtools, dplyr, ggdendro, ggplot2, glmnet, graphics, grDevices, grid, gtable, ipflasso, methods, RColorBrewer, reshape2, scales, stats, SummarizedExperiment, survival, tibble Suggests: BiocStyle, knitr, rmarkdown, abind, AnnotationDbi, biomaRt, broom, colorspace, cowplot, dendsort, doParallel, foreach, forestplot, genefilter, ggbeeswarm, ggtern, gridExtra, hexbin, IHW, limma, magrittr, Matrix, maxstat, nat, org.Hs.eg.db, pheatmap, piano, readxl, Rtsne, tidyr, xtable License: LGPL (>= 3) MD5sum: c58e93b59ac5cf985e5a3b775a89772b NeedsCompilation: no Title: "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al. - experimental data and complete analysis Description: The package contains data of the Primary Blood Cancer Encyclopedia (PACE) project together with a complete executable transcript of the statistical analysis and reproduces figures presented in the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) 128(1):427-445. doi:10.1172/JCI93801. biocViews: ExperimentData, ReproducibleResearch, CancerData, LeukemiaCancerData Author: Malgorzata Oles, Sascha Dietrich, Junyan Lu, Britta Velten, Andreas Mock, Vladislav Kim, Wolfgang Huber Maintainer: Malgorzata Oles VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/BloodCancerMultiOmics2017 git_branch: devel git_last_commit: ce612ea git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/BloodCancerMultiOmics2017_1.27.0.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: 162 Package: bodymapRat Version: 1.23.0 Depends: R (>= 3.6.0), SummarizedExperiment, ExperimentHub Imports: utils Suggests: rmarkdown, knitr, BiocStyle, testthat License: CC BY 4.0 MD5sum: 730046afef021ca9fb33451a81bb50ab 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: 3ddf493 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/bodymapRat_1.23.0.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: 78 Package: breakpointRdata Version: 1.25.0 Depends: R (>= 3.5) Suggests: knitr, BiocStyle, License: file LICENSE MD5sum: 5e9b9e7ca462c20210dbf2926dc268a8 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: ff6412b git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/breakpointRdata_1.25.0.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: 1.45.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: f11c1aed0e9d8c10013581c48db6b636 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: a64a6c8 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/breastCancerMAINZ_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: DART, genefu, MineICA dependencyCount: 0 Package: breastCancerNKI Version: 1.45.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: a078cb29485a213a32590fcbcb57a8bc 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: 2efc8ae git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/breastCancerNKI_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, seventyGeneData dependencyCount: 0 Package: breastCancerTRANSBIG Version: 1.45.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: ef545badc356d9f1dd09795be1b79ec1 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: 7cf3145 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/breastCancerTRANSBIG_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, GSgalgoR, MineICA dependencyCount: 0 Package: breastCancerUNT Version: 1.45.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 2bfc0d0214329cbbdc8d93d5f2f99ce3 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: ef06328 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/breastCancerUNT_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu dependencyCount: 0 Package: breastCancerUPP Version: 1.45.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 5ab8f0533e1b1b18f491a54117e98444 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: 534424e git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/breastCancerUPP_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, GSgalgoR, MineICA, safe dependencyCount: 0 Package: breastCancerVDX Version: 1.45.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 464e88fd573fe01e97ffa08e430f2143 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: 70bc691 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/breastCancerVDX_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: BAGS suggestsMe: AIMS, DART, genefu, MineICA dependencyCount: 0 Package: brgedata Version: 1.29.0 Depends: R (>= 3.5.0), Biobase Imports: SummarizedExperiment Suggests: minfi, MultiAssayExperiment, knitr, rmarkdown, rexposome, BiocStyle License: MIT + file LICENSE MD5sum: e0bdaeb30bb39287efefea02216b2b9e NeedsCompilation: no Title: Exposures, Gene Expression and Methylation data for ilustration purpouses Description: This package contains several sets of omics data including Gene Expression (ExpressionSet), Methylation (GenomicRatioSet), Proteome and Exposome (ExposomeSet). This data is used in vignettes and exaples at MEAL, MultiDataSet and omicRexposome. biocViews: ExperimentData,Homo_sapiens_Data,MicroarrayData,MethylationArrayData Author: Dolors Pelegri-Siso [aut, cre], Carlos Ruiz-Arenas [aut], Carles Hernandez-Ferrer [aut], Juan R. Gonzalez [aut] Maintainer: Dolors Pelegri-Siso VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/brgedata git_branch: devel git_last_commit: d7a476a git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/brgedata_1.29.0.tar.gz vignettes: vignettes/brgedata/inst/doc/general_description.html vignetteTitles: brgedata -- data R package with three omic data-set and exposome data-set from the same Spanish pupulation hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/brgedata/inst/doc/general_description.R suggestsMe: MEAL, MultiDataSet, omicRexposome dependencyCount: 37 Package: bronchialIL13 Version: 1.45.0 Depends: R(>= 2.10.0), affy (>= 1.23.4) License: GPL-2 MD5sum: cef99ee377cba3f9afe00d6182b1b767 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: 4e828b9 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/bronchialIL13_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 13 Package: bsseqData Version: 0.45.0 Depends: R (>= 3.5.0), bsseq (>= 1.16.0) License: Artistic-2.0 MD5sum: 9f828c9bec2a12c385ae192664d38ab0 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: 10e54a8 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/bsseqData_0.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: bsseq, methylSig dependencyCount: 90 Package: bugphyzz Version: 1.1.0 Depends: R (>= 4.4) Imports: dplyr, utils, purrr, stringr, tidyr, tidyselect, BiocFileCache, httr2, tools, S4Vectors Suggests: DT, forcats, ggplot2, htmltools, knitr, rmarkdown, sessioninfo, testthat, EnrichmentBrowser, MicrobiomeBenchmarkData, mia, stats, rlang, limma, mgsub, methods, readr, crayon, tibble, magrittr, tidytext, BiocStyle License: Artistic-2.0 MD5sum: 107bd5f87369fe0780a7649ead183564 NeedsCompilation: no Title: A harmonized data resource and software for enrichment analysis of microbial physiologies Description: bugphyzz is an electronic database of standardized microbial annotations. It facilitates the creation of microbial signatures based on shared attributes, which are utilized for bug set enrichment analysis. The data also includes annotations imputed with ancestra state reconstruction methods. biocViews: MicrobiomeData, ReproducibleResearch Author: Samuel Gamboa [aut, cre] (ORCID: ), Levi Waldron [aut] (ORCID: ), Kelly Eckenrode [aut], Jonathan Ye [aut], Jennifer Wokaty [aut] Maintainer: Samuel Gamboa URL: https://github.com/waldronlab/bugphyzz VignetteBuilder: knitr BugReports: https://github.com/waldronlab/bugphyzz/issues git_url: https://git.bioconductor.org/packages/bugphyzz git_branch: devel git_last_commit: 3af6a51 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/bugphyzz_1.1.0.tar.gz vignettes: vignettes/bugphyzz/inst/doc/bugphyzz.html, vignettes/bugphyzz/inst/doc/sources.html vignetteTitles: bugphyzz, Sources hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bugphyzz/inst/doc/bugphyzz.R, vignettes/bugphyzz/inst/doc/sources.R dependencyCount: 51 Package: cancerdata Version: 1.45.0 Depends: R (>= 2.10.1), Biobase License: GPL (>= 2) MD5sum: 804475fdbb4083543a88cd55e3c5bada 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: c458aec git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/cancerdata_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: cancerclass dependencyCount: 7 Package: CardinalWorkflows Version: 1.39.0 Depends: R (>= 2.10), Cardinal, methods Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 38414166f373018e566e5b68bac4a45c 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: 139b08c git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/CardinalWorkflows_1.39.0.tar.gz vignettes: vignettes/CardinalWorkflows/inst/doc/MSI-classification.html, vignettes/CardinalWorkflows/inst/doc/MSI-segmentation.html, vignettes/CardinalWorkflows/inst/doc/MSI-testing.html vignetteTitles: 2. Classification: Supervised analysis workflow, 1. Segmentation: Unsupervised analysis workflow, 3. Class comparision: Statistical testing workflow hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CardinalWorkflows/inst/doc/MSI-classification.R, vignettes/CardinalWorkflows/inst/doc/MSI-segmentation.R, vignettes/CardinalWorkflows/inst/doc/MSI-testing.R dependencyCount: 67 Package: ccdata Version: 1.33.0 Depends: R (>= 3.3) License: MIT + file LICENSE MD5sum: 54c720ce50df40f266f7507bc4ec653a 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: 89747f0 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/ccdata_1.33.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE importsMe: ccmap suggestsMe: retriever dependencyCount: 0 Package: CCl4 Version: 1.45.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), limma License: Artistic-2.0 MD5sum: 9e9c13cc2f2df867fe80dce7ab146f25 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: 29e5787 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/CCl4_1.45.0.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: 1.25.0 Depends: R (>= 3.5.0) Suggests: ExperimentHub, knitr, rmarkdown License: GPL-3 MD5sum: 1449d9b38e46715cb2b8fc8db43d8a34 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: c2e0b19 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/celarefData_1.25.0.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: 1.17.0 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: 91ac3ebd8b290b86c1afe5be62e71254 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: 309c56e git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/celldex_1.17.0.tar.gz vignettes: vignettes/celldex/inst/doc/userguide.html vignetteTitles: Cell type references hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/celldex/inst/doc/userguide.R dependsOnMe: OSCA.workflows, SingleRBook importsMe: singleCellTK suggestsMe: ontoProc, scDiagnostics, SingleR, sketchR, tidySingleCellExperiment dependencyCount: 96 Package: CellMapperData Version: 1.33.0 Depends: ExperimentHub, CellMapper Suggests: BiocStyle License: Artistic-2.0 MD5sum: 05e99280c5c22422b8407061a49623d4 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: e63c2a1 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/CellMapperData_1.33.0.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: 68 Package: cfToolsData Version: 1.5.0 Depends: R (>= 4.3.0) Imports: utils, ExperimentHub Suggests: BiocStyle, knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0) License: file LICENSE MD5sum: 13502998525d9a9bd18104993479c222 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: 4c64566 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/cfToolsData_1.5.0.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: 67 Package: ChAMPdata Version: 2.39.0 Depends: R (>= 3.5.0), GenomicRanges (>= 1.22.4), BiocGenerics (>= 0.16.1) License: GPL-3 MD5sum: f94690849e0a6d71a88ff96b0a6108fd 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: c9833d6 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/ChAMPdata_2.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ChAMP, methyLImp2 dependencyCount: 24 Package: ChimpHumanBrainData Version: 1.45.0 Depends: affy,qvalue,limma,hexbin,statmod Suggests: hgu95av2cdf License: MIT MD5sum: e7e7308e16f63f1dbe7d0c16c2f6df49 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: 7f0d81b git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/ChimpHumanBrainData_1.45.0.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: 53 Package: chipenrich.data Version: 2.31.0 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: 9a0bbfa142558e7e2429eb8bdc0a07e2 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: 955d144 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/chipenrich.data_2.31.0.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: 91 Package: ChIPexoQualExample Version: 1.31.0 Depends: R (>= 3.3) Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 953be8dc45b0ce602f6601b1f535bee7 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: 110e304 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/ChIPexoQualExample_1.31.0.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: 1.23.0 Imports: AnnotationHub, ExperimentHub, Rsamtools, S4Vectors Suggests: knitr, BiocStyle, rmarkdown License: CC BY 4.0 MD5sum: 5e30a9507e326b7a122fc0ba0fc8c0c8 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: a864587 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/chipseqDBData_1.23.0.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: 80 Package: ChIPXpressData Version: 1.45.0 Depends: bigmemory License: GPL (>=2) MD5sum: ec4895f6c1c137ee36d713629f9eee4f 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: 14bafc0 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/ChIPXpressData_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ChIPXpress dependencyCount: 7 Package: chromstaRData Version: 1.33.0 Depends: R (>= 3.3) License: GPL-3 MD5sum: b18af07bd1c471bcc25e06f3d0ee6538 NeedsCompilation: no Title: ChIP-seq data for Demonstration Purposes Description: ChIP-seq data for demonstration purposes in the chromstaR package. biocViews: Mus_musculus_Data, StemCell, ChIPSeqData Author: Aaron Taudt Maintainer: Aaron Taudt git_url: https://git.bioconductor.org/packages/chromstaRData git_branch: devel git_last_commit: 1507d6c git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/chromstaRData_1.33.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: epigraHMM dependencyCount: 0 Package: CLL Version: 1.47.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: LGPL MD5sum: 6f7b97f71560d73bda4bd95ef851438d 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: 575d56a git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/CLL_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: phenomis dependencyCount: 13 Package: CLLmethylation Version: 1.27.0 Depends: R (>= 3.5.0) Imports: SummarizedExperiment, ExperimentHub Suggests: BiocStyle, ggplot2, knitr, rmarkdown License: LGPL MD5sum: 26e1fd21d83a007780616776de0f1e93 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: 153157c git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/CLLmethylation_1.27.0.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: 78 Package: CluMSIDdata Version: 1.23.0 Depends: R (>= 3.6) License: MIT + file LICENSE MD5sum: 47a32c14abadc0b99c80caf400611aa9 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: b438586 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/CluMSIDdata_1.23.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: CluMSID dependencyCount: 0 Package: clustifyrdatahub Version: 1.17.0 Depends: R (>= 4.0), ExperimentHub Imports: utils Suggests: clustifyr, Seurat, usethis, rmarkdown, knitr, tidyr, BiocStyle License: MIT + file LICENSE MD5sum: 9e8d75fe0675e869976c7cde09971f5b 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: a9d358f git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/clustifyrdatahub_1.17.0.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: 67 Package: cMap2data Version: 1.43.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 1ec4f261bffc24a4e9a38292393b9aca 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: b1b7acf git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/cMap2data_1.43.0.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: 1.43.0 Depends: R (>= 2.10), cnvGSA License: LGPL MD5sum: d8f97dda6cdb173ef0fa3811f2f38842 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: 11278fe git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/cnvGSAdata_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: cnvGSA dependencyCount: 34 Package: COHCAPanno Version: 1.43.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 462f43024fdfacde4ea49127cc51977d 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: 252f99c git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/COHCAPanno_1.43.0.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: 1.49.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: 86e2150d63c2491883d8bae228c2a1b3 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: caf96fa git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/colonCA_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: clustComp, copa dependencyCount: 7 Package: CONFESSdata Version: 1.35.0 Depends: R (>= 3.3) License: GPL-2 MD5sum: 3fc87b51a3787036bff7d3f477c062d4 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: bf3256d git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/CONFESSdata_1.35.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CONFESS dependencyCount: 0 Package: ConnectivityMap Version: 1.43.0 Depends: R (>= 2.15.1) Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 56fe38a6414592586059ecb438f6637e 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: 8040012 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/ConnectivityMap_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: COPDSexualDimorphism.data Version: 1.43.0 License: LGPL-2.1 MD5sum: 11ab407fd4190e951469714db0ab4242 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: b429d64 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/COPDSexualDimorphism.data_1.43.0.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: 1.39.0 Depends: R (>= 3.5.0) Suggests: BiocStyle License: GPL-2 MD5sum: f37e152e9cb4f74241015c2765960497 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: 8c97a5d git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/CopyhelpeR_1.39.0.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: 1.25.0 Depends: R (>= 3.5.0) Imports: ExperimentHub,Rdpack (>= 0.8) Suggests: BiocStyle,knitr,rmarkdown,minfi,conumee,minfiData License: Artistic-2.0 MD5sum: c990605bd4b5bc9df0cf7d44ae83df39 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: 4d2f0d0 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/CopyNeutralIMA_1.25.0.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: 69 Package: CoSIAdata Version: 1.7.0 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: 6da960fd392d879d7d89cebfc1911881 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: da3c8b1 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/CoSIAdata_1.7.0.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: 67 Package: COSMIC.67 Version: 1.43.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, SummarizedExperiment, VariantAnnotation Suggests: testthat, BiocStyle, knitr License: GPL-3 MD5sum: 5d56b63ceb52989282a2866272065cdf 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: 3a6e079 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/COSMIC.67_1.43.0.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: 80 Package: CRCL18 Version: 1.27.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: a3a479ac281c43fbb9ac8524d3f37e76 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: 7fd1422 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/CRCL18_1.27.0.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: 1.11.0 Depends: ExperimentHub Imports: AnnotationHub, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 4c65046a83e75bc0e4442f8b3a2361cd 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: 35ad90a git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/crisprScoreData_1.11.0.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: 67 Package: curatedAdipoArray Version: 1.19.0 Depends: R (>= 4.0) Suggests: knitr, rmarkdown, ExperimentHub, SummarizedExperiment License: GPL-3 + file LICENSE MD5sum: a1a633dfbde6bf920d0ce3bb68df5a9b 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: 670ef61 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/curatedAdipoArray_1.19.0.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: 1.23.0 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: 2421b9e9e577ef7878f379b9039b63c7 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: 500e25a git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/curatedAdipoChIP_1.23.0.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: 78 Package: curatedAdipoRNA Version: 1.23.0 Depends: R (>= 3.6), SummarizedExperiment Suggests: knitr, rmarkdown, DESeq2, fastqcr, devtools, testthat, readr, dplyr, tidyr, ggplot2, S4Vectors License: GPL-3 MD5sum: 07cbedc1aa76d61db9693d19d748acc9 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: c842dfa git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/curatedAdipoRNA_1.23.0.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: 37 Package: curatedBladderData Version: 1.43.0 Depends: R (>= 2.10.0), affy Suggests: BiocStyle, survival, xtable, sva, genefilter, logging License: Artistic-2.0 MD5sum: c2371f6e83d6dea67548c17bb6d27e2c 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: ed80627 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/curatedBladderData_1.43.0.tar.gz vignettes: vignettes/curatedBladderData/inst/doc/curatedBladderData_vignette.pdf vignetteTitles: curatedBladderData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedBladderData/inst/doc/curatedBladderData_vignette.R suggestsMe: covEB dependencyCount: 13 Package: curatedBreastData Version: 2.35.0 Depends: R (>= 3.0.0), XML, ggplot2, impute, Biobase, BiocStyle Imports: methods, stats License: GPL (>= 2) MD5sum: bb4b8951c5e7158a4374f83f69ad7a2b NeedsCompilation: no Title: Curated breast cancer gene expression data with survival and treatment information Description: Curated human breast cancer tissue S4 ExpresionSet datasets from over 16 clinical trials comprising over 2,000 patients. All datasets contain at least one type of outcomes variable and treatment information (minimum level: whether they had chemotherapy and whether they had hormonal therapy). Includes code to post-process these datasets. biocViews: ExperimentData, ExpressionData, CancerData, Tissue, BreastCancerData, qPCRData, MicroarrayData, TissueMicroarrayData, GEO Author: Katie Planey Maintainer: Katie Planey git_url: https://git.bioconductor.org/packages/curatedBreastData git_branch: devel git_last_commit: a06d1b7 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/curatedBreastData_2.35.0.tar.gz vignettes: vignettes/curatedBreastData/inst/doc/curatedBreastData-manual.pdf vignetteTitles: Manual hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedBreastData/inst/doc/curatedBreastData-manual.R dependencyCount: 65 Package: curatedMetagenomicData Version: 3.15.0 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 License: Artistic-2.0 MD5sum: 6987732e5dd6cf0e3a7976c99b82939e 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] 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: c2fbd63 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/curatedMetagenomicData_3.15.0.tar.gz vignettes: vignettes/curatedMetagenomicData/inst/doc/curatedMetagenomicData.html vignetteTitles: curatedMetagenomicData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedMetagenomicData/inst/doc/curatedMetagenomicData.R suggestsMe: lefser, MMUPHin, OmicsMLRepoR dependencyCount: 198 Package: curatedOvarianData Version: 1.45.0 Depends: R (>= 3.0.0), Biobase Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle License: Artistic-2.0 MD5sum: d62a71ca0f04aa5bcf20b1a25e3caba2 NeedsCompilation: no Title: Clinically Annotated Data for the Ovarian Cancer Transcriptome Description: The curatedOvarianData package provides data for gene expression analysis in patients with ovarian cancer. biocViews: ExperimentData, RNASeqData, CancerData, OvarianCancerData, MicroarrayData Author: Benjamin F. Ganzfried, Markus Riester, Steve Skates, Victoria Wang, Thomas Risch, Benjamin Haibe-Kains, Svitlana Tyekucheva, Jie Ding, Ina Jazic, Michael Birrer, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron Maintainer: Levi Waldron URL: http://bcb.dfci.harvard.edu/ovariancancer git_url: https://git.bioconductor.org/packages/curatedOvarianData git_branch: devel git_last_commit: 010dde7 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/curatedOvarianData_1.45.0.tar.gz vignettes: vignettes/curatedOvarianData/inst/doc/curatedOvarianData_vignette.pdf vignetteTitles: curatedOvarianData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedOvarianData/inst/doc/curatedOvarianData_vignette.R suggestsMe: doppelgangR, TOP dependencyCount: 7 Package: curatedPCaData Version: 1.3.0 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: e017bfd063dbaddbd768bfc630154e08 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: 0f0d29a git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/curatedPCaData_1.3.0.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: 84 Package: curatedTBData Version: 2.3.0 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: 1ae2fc3063ee9eed506645eca0b54a57 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: 03baf5e git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/curatedTBData_2.3.0.tar.gz vignettes: vignettes/curatedTBData/inst/doc/curatedTBData.html vignetteTitles: curatedTBData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/curatedTBData/inst/doc/curatedTBData.R dependencyCount: 80 Package: curatedTCGAData Version: 1.29.2 Depends: R (>= 4.5.0), MultiAssayExperiment Imports: AnnotationHub, ExperimentHub, HDF5Array, methods, S4Vectors, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, RaggedExperiment, readr, rmarkdown, TCGAutils, testthat License: Artistic-2.0 MD5sum: e71966bf6870d491e338c9b63a970f1e NeedsCompilation: no Title: Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects Description: This package provides publicly available data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects. MultiAssayExperiment integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. It also links assay barcodes with patient identifiers, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-'omics experiment. biocViews: Homo_sapiens_Data, ReproducibleResearch, CancerData, ExperimentHub Author: Marcel Ramos [aut, cre] (ORCID: ), Levi Waldron [ctb], Lucas Schiffer [ctb], Ludwig Geistlinger [ctb], Valerie Obenchain [ctb], Martin Morgan [ctb] Maintainer: Marcel Ramos VignetteBuilder: knitr BugReports: https://github.com/waldronlab/curatedTCGAData/issues git_url: https://git.bioconductor.org/packages/curatedTCGAData git_branch: devel git_last_commit: 691d0d7 git_last_commit_date: 2024-11-13 Date/Publication: 2024-11-14 source.ver: src/contrib/curatedTCGAData_1.29.2.tar.gz vignettes: vignettes/curatedTCGAData/inst/doc/curatedTCGAData.html vignetteTitles: curatedTCGAData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedTCGAData/inst/doc/curatedTCGAData.R importsMe: AMARETTO suggestsMe: CNVRanger, dce, glmSparseNet, TCGAutils dependencyCount: 84 Package: CytoMethIC Version: 1.3.1 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: 798fabe895dfcb99dc891d2ca70f5db5 NeedsCompilation: no Title: DNA methylation-based classification and regression Description: This package provides DNA methylation-based prediction of cancer type, molecular signature and clinical outcomes. It provides convenience functions for missing value imputation, probe ID conversion, model interpretation and visualization. The package links to our models on ExperimentHub. The package currently supports HM450, EPIC and EPICv2. 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: 430cc34 git_last_commit_date: 2024-12-18 Date/Publication: 2024-12-19 source.ver: src/contrib/CytoMethIC_1.3.1.tar.gz vignettes: vignettes/CytoMethIC/inst/doc/CytoMethIC.html vignetteTitles: CytoMethIC User Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CytoMethIC/inst/doc/CytoMethIC.R dependencyCount: 115 Package: DAPARdata Version: 1.37.0 Depends: R (>= 4.3.0), MSnbase Imports: utils Suggests: knitr, DAPAR, BiocStyle License: GPL-2 MD5sum: b93b8b803effbe0b5d5f2415adb4f7e1 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/prostarproteomics/DAPARdata/issues git_url: https://git.bioconductor.org/packages/DAPARdata git_branch: devel git_last_commit: 93eb58d git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/DAPARdata_1.37.0.tar.gz vignettes: vignettes/DAPARdata/inst/doc/dapardata.html vignetteTitles: DAPARdata User Manual hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DAPARdata/inst/doc/dapardata.R importsMe: DAPAR, Prostar dependencyCount: 137 Package: davidTiling Version: 1.47.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db License: LGPL MD5sum: 4b487838a69abc10f6b8258a0ac4f423 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: 75e8da3 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/davidTiling_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 89 Package: depmap Version: 1.21.0 Depends: R (>= 3.6), 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: 5364fd87119e6ba138b898c1b708748e 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: 62ae0a7 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/depmap_1.21.0.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: 68 Package: derfinderData Version: 2.25.0 Depends: R (>= 3.5.0) Suggests: sessioninfo, knitr (>= 1.6), RefManageR, rmarkdown (>= 0.3.3), BiocStyle License: Artistic-2.0 MD5sum: 0731a135694ef560a6a138d6b4456940 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: 7add4cd git_last_commit_date: 2024-12-12 Date/Publication: 2024-12-17 source.ver: src/contrib/derfinderData_2.25.0.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: 1.43.0 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: 9744ec7d9535114babd91de67189f101 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: 43ecfae git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/DeSousa2013_1.43.0.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: 127 Package: DExMAdata Version: 1.15.0 Depends: R (>= 4.1) Imports: Biobase Suggests: BiocStyle License: GPL-2 MD5sum: ee673344921f16ede8375717795a72c6 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: b87190c git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/DExMAdata_1.15.0.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: 1.35.0 Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 0566571f354b49b18e5b9c3fdadf5e1e 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: 297e5b3 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/diffloopdata_1.35.0.tar.gz vignettes: vignettes/diffloopdata/inst/doc/diffloopdata.html vignetteTitles: diffloopdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: diggitdata Version: 1.39.0 Depends: R(>= 2.14.0), Biobase, methods Imports: viper License: GPL (>=2) MD5sum: 4d2b33767acfe32cc3109bc4b166997b 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: 9342f26 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/diggitdata_1.39.0.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: 90 Package: DLBCL Version: 1.47.0 Depends: R(>= 2.11.0), Biobase, graph License: GPL (>=2) MD5sum: 24243f7b6d985f0ba00c535532f63607 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: 8f35d6a git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/DLBCL_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: BioNet, mwcsr dependencyCount: 9 Package: DMRcatedata Version: 2.25.0 Depends: R (>= 4.0), ExperimentHub Imports: GenomicFeatures, Gviz, readxl, plyr, rtracklayer, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr License: GPL-3 MD5sum: e788426a4f64aa23b2dfe71dfca81223 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: 20279b9 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/DMRcatedata_2.25.0.tar.gz vignettes: vignettes/DMRcatedata/inst/doc/DMRcatedata.pdf vignetteTitles: The DMRcate package user's guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DMRcatedata/inst/doc/DMRcatedata.R suggestsMe: DMRcate dependencyCount: 208 Package: DNAZooData Version: 1.7.0 Depends: R (>= 4.2), HiCExperiment Imports: BiocFileCache, S4Vectors, rjson, utils, tools Suggests: dplyr, testthat, methods, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: a8b8f64af27129b046bd5cb80cf6c304 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: ca6a74d git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/DNAZooData_1.7.0.tar.gz vignettes: vignettes/DNAZooData/inst/doc/DNAZooData.html vignetteTitles: DNAZooData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/DNAZooData/inst/doc/DNAZooData.R importsMe: OHCA dependencyCount: 91 Package: DonaPLLP2013 Version: 1.45.0 Depends: EBImage, parallel License: Artistic-2.0 MD5sum: 4086e09f55cb07f9199bd75405c17700 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: 1b28c97 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/DonaPLLP2013_1.45.0.tar.gz vignettes: vignettes/DonaPLLP2013/inst/doc/PLLPanalysis.pdf, vignettes/DonaPLLP2013/inst/doc/PLLPstatistics.pdf vignetteTitles: PLLP image analysis, PLLP tissue-scale ratio statistics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DonaPLLP2013/inst/doc/PLLPanalysis.R, vignettes/DonaPLLP2013/inst/doc/PLLPstatistics.R dependencyCount: 47 Package: dorothea Version: 1.19.0 Depends: R (>= 4.0) Imports: dplyr, magrittr, bcellViper, decoupleR, Suggests: Biobase, BiocStyle, OmnipathR, viper, knitr, pheatmap, pkgdown, rmarkdown, Seurat, SingleCellExperiment, SummarizedExperiment, testthat (>= 2.1.0), tibble, tidyr, utils License: GPL-3 + file LICENSE MD5sum: ca00af457c883ff5e80d78ea36155c3f NeedsCompilation: no Title: Collection Of Human And Mouse TF Regulons Description: DoRothEA is a gene regulatory network containing signed transcription factor (TF) - target gene interactions. DoRothEA regulons, the collection of a TF and its transcriptional targets, were curated and collected from different types of evidence for both human and mouse. A confidence level was assigned to each TF-target interaction based on the number of supporting evidence. biocViews: ExperimentData, Homo_sapiens_Data, Mus_musculus_Data Author: Pau Badia-i-Mompel [cre] (ORCID: ), Daniel Dimitrov [aut] (ORCID: ), Christian H. Holland [aut] (ORCID: ), Luz Garcia-Alonso [aut], Alberto Valdeolivas [ctb], Minoo Ashtiani [ctb], Attila Gabor [ctb] Maintainer: Pau Badia-i-Mompel URL: https://saezlab.github.io/dorothea/, https://github.com/saezlab/dorothea VignetteBuilder: knitr BugReports: https://github.com/saezlab/dorothea/issues git_url: https://git.bioconductor.org/packages/dorothea git_branch: devel git_last_commit: 93c8143 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/dorothea_1.19.0.tar.gz vignettes: vignettes/dorothea/inst/doc/dorothea.html vignetteTitles: DoRothEA regulons. hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/dorothea/inst/doc/dorothea.R importsMe: cosmosR, easier suggestsMe: epiregulon.extra, MethReg dependencyCount: 46 Package: dressCheck Version: 0.45.0 Depends: R (>= 2.10.1), methods, Biobase (>= 2.5.5) Suggests: survival, chron License: Artistic-2.0 MD5sum: 50b2b2648612d2a3374bf51e9262b56b 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: 904adfe git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/dressCheck_0.45.0.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: 1.17.0 Imports: utils, ExperimentHub, AnnotationHub, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, testthat, DropletUtils License: GPL-3 MD5sum: 2f542b338ce5108dce23d6318fea8342 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: 974d4e8 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/DropletTestFiles_1.17.0.tar.gz vignettes: vignettes/DropletTestFiles/inst/doc/motivation.html vignetteTitles: Test files for droplet-based single-cell utilities hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DropletTestFiles/inst/doc/motivation.R dependsOnMe: OSCA.intro, OSCA.workflows suggestsMe: DropletUtils, TENxIO dependencyCount: 67 Package: DrugVsDiseasedata Version: 1.43.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: bbe789c9f594a12599b2213a21c62595 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: 49b8b8b git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/DrugVsDiseasedata_1.43.0.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: 1.25.0 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: bdbf0d6cf0e495d405b6aab38b512e25 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: 86c6bd0 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/DuoClustering2018_1.25.0.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: 91 Package: DvDdata Version: 1.43.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 59d719183e596df0fe1387fb1b279857 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: cbbeefc git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/DvDdata_1.43.0.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: 1.47.0 Depends: R (>= 1.4.1), marray, GEOquery Suggests: dyebias, convert, Biobase License: GPL-3 MD5sum: 747a23e424b69ac3f0359ee76ed823de 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: f85f08e git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/dyebiasexamples_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: dyebias dependencyCount: 80 Package: easierData Version: 1.13.0 Depends: R (>= 4.1.0) Imports: ExperimentHub, AnnotationHub, utils, SummarizedExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: d4bf80b66188706621cce8858229415f 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: b9800ba git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/easierData_1.13.0.tar.gz vignettes: vignettes/easierData/inst/doc/easierData.html vignetteTitles: easier data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/easierData/inst/doc/easierData.R importsMe: easier dependencyCount: 78 Package: EatonEtAlChIPseq Version: 0.45.0 Depends: GenomicRanges (>= 1.5.42), ShortRead, rtracklayer License: Artistic 2.0 MD5sum: a92709db92c6837a170fe443bca63d8b 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: 920e16b git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/EatonEtAlChIPseq_0.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 71 Package: ecoliLeucine Version: 1.47.0 Depends: R (>= 1.9.0), affy (>= 1.23.4), ecolicdf License: GPL (>= 2) MD5sum: b8325611d99d65a7c400bd5d5271ffef 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: fdbf15e git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/ecoliLeucine_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ecolitk dependencyCount: 51 Package: EGSEAdata Version: 1.35.0 Depends: R (>= 3.4) Suggests: EGSEA License: file LICENSE MD5sum: cfd8ac3c07b9faa06f3a212a912459da 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: 55e5483 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/EGSEAdata_1.35.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE importsMe: EGSEA dependencyCount: 0 Package: ELMER.data Version: 2.31.0 Depends: R (>= 3.5.0) Imports: GenomicRanges Suggests: BiocStyle, knitr, dplyr, devtools, DT, rmarkdown License: GPL-3 MD5sum: 99dc057bf14f31d0189a8c250a21f547 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: c160a58 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/ELMER.data_2.31.0.tar.gz vignettes: vignettes/ELMER.data/inst/doc/vignettes.html vignetteTitles: ELMER.data: Supporting data for the ELMER package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ELMER.data/inst/doc/vignettes.R dependsOnMe: ELMER importsMe: EpiMix dependencyCount: 24 Package: emtdata Version: 1.15.0 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: 921ec0eb306f02f95594a6511914b2e8 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: 89bf5e9 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/emtdata_1.15.0.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: 82 Package: eoPredData Version: 1.1.0 Depends: ExperimentHub Suggests: BiocStyle, knitr, rmarkdown, RefManageR, planet, mixOmics License: MIT + file LICENSE MD5sum: efc7ac924572d3f15c9ba420f6124724 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: 7e81091 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/eoPredData_1.1.0.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: 67 Package: EpiMix.data Version: 1.9.0 Depends: R (>= 4.2.0), ExperimentHub (>= 0.99.6) Suggests: rmarkdown, knitr License: GPL-3 MD5sum: 2c9884c0af8e9189ea448ecaf2e128ae 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: 5f1fdb2 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/EpiMix.data_1.9.0.tar.gz vignettes: vignettes/EpiMix.data/inst/doc/RetrieveData.html vignetteTitles: vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/EpiMix.data/inst/doc/RetrieveData.R dependsOnMe: EpiMix dependencyCount: 67 Package: epimutacionsData Version: 1.11.0 Depends: R (>= 4.2.0) Suggests: rmarkdown, BiocStyle, knitr, ExperimentHub, minfi License: MIT + file LICENSE MD5sum: 0cdceb985192a6b91203ccbce721d6cf 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: 426c7cb git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/epimutacionsData_1.11.0.tar.gz vignettes: vignettes/epimutacionsData/inst/doc/epimutacionsData.html vignetteTitles: data repository for epimutacions package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/epimutacionsData/inst/doc/epimutacionsData.R dependsOnMe: epimutacions dependencyCount: 0 Package: EpipwR.data Version: 1.1.0 Imports: ExperimentHub Suggests: knitr, rmarkdown, sessioninfo License: Artistic-2.0 MD5sum: 06666b3e053001d4335f3766878ee582 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: e549033 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/EpipwR.data_1.1.0.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: 67 Package: estrogen Version: 1.53.0 Suggests: affy, hgu95av2.db, hgu95av2cdf, vsn, knitr, genefilter License: LGPL MD5sum: 3260b3bd5c114accbc4f5300ae4da3ed 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: f287b25 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/estrogen_1.53.0.tar.gz vignettes: vignettes/estrogen/inst/doc/estrogen.pdf vignetteTitles: estrogen hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/estrogen/inst/doc/estrogen.R suggestsMe: categoryCompare dependencyCount: 0 Package: etec16s Version: 1.35.0 Depends: R (>= 3.3), Biobase, metagenomeSeq(>= 1.12.0) License: Artistic-2.0 MD5sum: 1108f137a6e2b0b2ff462666f49b7e27 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: aa405c6 git_last_commit_date: 2024-10-29 Date/Publication: 2024-12-19 source.ver: src/contrib/etec16s_1.35.0.tar.gz vignettes: vignettes/etec16s/inst/doc/etec16s.pdf vignetteTitles: etec16s hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/etec16s/inst/doc/etec16s.R Package: ewceData Version: 1.15.0 Depends: R (>= 4.1), ExperimentHub Suggests: knitr, BiocStyle, ggplot2, cowplot, rmarkdown, markdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: fdf6dd847e74944c90008035dfe4c2da NeedsCompilation: no Title: The ewceData package provides reference data required for ewce Description: This package provides reference data required for ewce. Expression Weighted Celltype Enrichment (EWCE) is used to determine which cell types are enriched within gene lists. The package provides tools for testing enrichments within simple gene lists (such as human disease associated genes) and those resulting from differential expression studies. The package does not depend upon any particular Single Cell Transcriptome dataset and user defined datasets can be loaded in and used in the analyses. biocViews: ExperimentData, ExperimentHub, ExpressionData, Genome, Proteome, MicroarrayData, SequencingData, SingleCellData, RNASeqData Author: Alan Murphy [cre] (ORCID: ), Nathan Skene [aut] (ORCID: ) Maintainer: Alan Murphy URL: https://github.com/neurogenomics/ewceData VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ewceData git_branch: devel git_last_commit: 02a367f git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/ewceData_1.15.0.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: 67 Package: faahKO Version: 1.47.1 Depends: R (>= 2.10) Imports: xcms (>= 3.4.0) License: LGPL MD5sum: cab66e5e56e52603b9a37c4e7b9d8679 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: c264d11 git_last_commit_date: 2024-11-13 Date/Publication: 2024-11-14 source.ver: src/contrib/faahKO_1.47.1.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: cosmiq suggestsMe: CAMERA, IPO, MAIT, peakPantheR, xcms dependencyCount: 147 Package: fabiaData Version: 1.45.0 Depends: R (>= 2.10.0), Biobase Imports: utils Suggests: fabia License: LGPL (>= 2.1) MD5sum: da600b9baae69e1588616ca97815121d 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: b26d49e git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/fabiaData_1.45.0.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: 1.43.0 Depends: R (>= 2.15.0) License: GPL-3 MD5sum: 0f2cff347578a6c0af8be3647a816895 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: d6688f7 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/FANTOM3and4CAGE_1.43.0.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: 1.45.0 Depends: R (>= 2.10.0), lumi Suggests: genefilter, affy License: GPL (>2) MD5sum: d98e4ca5730b0555c679be2de845b166 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: 822a820 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/ffpeExampleData_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ffpe dependencyCount: 166 Package: fibroEset Version: 1.49.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: c22996234831b3b42ac279cf0688a14b 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: ce679ab git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/fibroEset_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: biocGraph, clusterStab, geneplotter dependencyCount: 7 Package: FieldEffectCrc Version: 1.17.0 Depends: utils Imports: BiocStyle, RUnit, SummarizedExperiment, ExperimentHub (>= 0.99.6), AnnotationHub, DESeq2 Suggests: knitr, rmarkdown, BiocGenerics, sva, BiocManager License: Artistic-2.0 MD5sum: 27f698347392d2c62789052742b9b922 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: c0c5b3d git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/FieldEffectCrc_1.17.0.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: 122 Package: FIs Version: 1.35.0 Depends: R (>= 3.3) License: GPL-3 MD5sum: 1e3bfb92bd574ee6c9b042c0dce24880 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: 27330f4 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/FIs_1.35.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: splineTimeR dependencyCount: 0 Package: fission Version: 1.27.0 Depends: R (>= 2.10), SummarizedExperiment Suggests: knitr, markdown License: LGPL MD5sum: fa8a1cabb321f6bb56fa5345ff291305 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: 3874601 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/fission_1.27.0.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: 37 Package: Fletcher2013a Version: 1.43.0 Depends: R (>= 2.15), limma Imports: Biobase ,VennDiagram, gplots,grid License: GPL (>= 2) MD5sum: 81995cbaabeea4f9c9374a34c1edbce6 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: 4185843 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/Fletcher2013a_1.43.0.tar.gz vignettes: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.pdf vignetteTitles: Main vignette:Fletcher2013a hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.R dependsOnMe: Fletcher2013b suggestsMe: NetActivity dependencyCount: 21 Package: Fletcher2013b Version: 1.43.0 Depends: R (>= 2.15), Fletcher2013a, RTN (>= 1.1.2), RedeR (>= 1.8.1), igraph Imports: RColorBrewer License: GPL (>= 2) MD5sum: 31ef35f09051acffcdcc700eebd28d9e NeedsCompilation: no Title: Master regulators of FGFR2 signalling and breast cancer risk Description: This package reproduces the systems biology analysis for the data in package Fletcher2013a using RTN. biocViews: ExperimentData, ChIPSeqData, CancerData, BreastCancerData, SNPData Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin Meyer. Maintainer: Mauro Castro URL: http://dx.doi.org/10.1038/ncomms3464 git_url: https://git.bioconductor.org/packages/Fletcher2013b git_branch: devel git_last_commit: ba647dd git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/Fletcher2013b_1.43.0.tar.gz vignettes: vignettes/Fletcher2013b/inst/doc/Fletcher2013b.pdf vignetteTitles: Main vignette:Fletcher2013b hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Fletcher2013b/inst/doc/Fletcher2013b.R suggestsMe: geneplast, RTNsurvival dependencyCount: 148 Package: flowPloidyData Version: 1.33.0 Suggests: knitr, rmarkdown, flowCore License: GPL-3 MD5sum: 1ccd1874ff262281a53608805b23f024 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: e7df8ff git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/flowPloidyData_1.33.0.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: 1.45.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 2e18acbc34d4a11a0e58896a188eb5fd 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: 6a7bb27 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/FlowSorted.Blood.450k_1.45.0.tar.gz vignettes: vignettes/FlowSorted.Blood.450k/inst/doc/FlowSorted.Blood.450k.pdf vignetteTitles: FlowSorted Blood 450k Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.Blood.450k/inst/doc/FlowSorted.Blood.450k.R dependsOnMe: methylCC, methylationArrayAnalysis suggestsMe: mCSEA, minfi, wateRmelon, FlowSorted.Blood.EPIC dependencyCount: 145 Package: FlowSorted.Blood.EPIC Version: 2.11.0 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: 906a2af807aa5a3c27f260eb086da5b6 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: e72ce80 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/FlowSorted.Blood.EPIC_2.11.0.tar.gz vignettes: vignettes/FlowSorted.Blood.EPIC/inst/doc/FlowSorted.Blood.EPIC.html vignetteTitles: FlowSorted.Blood.EPIC hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.Blood.EPIC/inst/doc/FlowSorted.Blood.EPIC.R importsMe: HiBED suggestsMe: DMRcate, wateRmelon, FlowSorted.CordBloodCombined.450k dependencyCount: 152 Package: FlowSorted.CordBlood.450k Version: 1.35.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 25c88457aeb69b11560d52e384c8a668 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: f883994 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/FlowSorted.CordBlood.450k_1.35.0.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: 145 Package: FlowSorted.CordBloodCombined.450k Version: 1.23.0 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: ee26f24c7753a958be414c5c16889a17 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: 949d3b6 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/FlowSorted.CordBloodCombined.450k_1.23.0.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: 1.33.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 7335c6eee8b87be806a806af44ec1377 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: ebb63d0 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/FlowSorted.CordBloodNorway.450k_1.33.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 145 Package: FlowSorted.DLPFC.450k Version: 1.43.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: ac4b1c4a6ed2c17b0d68ae54a1fbaa07 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: 73856a3 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/FlowSorted.DLPFC.450k_1.43.0.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: 145 Package: flowWorkspaceData Version: 3.19.0 License: GPL-2 MD5sum: a556e7057ded4654afbe6fe20279abb4 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: 66aca9f git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/flowWorkspaceData_3.19.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: COMPASS, CytoML, flowClust, flowCore, flowWorkspace, ggcyto, openCyto dependencyCount: 0 Package: fourDNData Version: 1.7.0 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: e5d3255c0846cbe28c2b11ab0dc90017 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: 7a26779 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/fourDNData_1.7.0.tar.gz vignettes: vignettes/fourDNData/inst/doc/fourDNData.html vignetteTitles: fourDNData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/fourDNData/inst/doc/fourDNData.R importsMe: OHCA dependencyCount: 90 Package: frmaExampleData Version: 1.43.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: cb1004e89b4341d5f62a8b5414fa8df1 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: b40420e git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/frmaExampleData_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: frma, frmaTools dependencyCount: 0 Package: furrowSeg Version: 1.35.0 Depends: R (>= 3.3), EBImage Imports: abind, dplyr, locfit, tiff Suggests: BiocStyle, ggplot2, knitr License: Artistic-2.0 MD5sum: a99403187d4cfa12536db623c0f03266 NeedsCompilation: no Title: Furrow Segmentation Description: Image feature data and analysis codes for the Guglielmi, Barry et al. paper describing the application of an optogenetics tools to disrupt Drosophila embryo furrowing. biocViews: ExperimentData, Drosophila_melanogaster_Data, Tissue, ReproducibleResearch Author: Joseph Barry Maintainer: Joseph Barry VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/furrowSeg git_branch: devel git_last_commit: d3f9cdf git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/furrowSeg_1.35.0.tar.gz vignettes: vignettes/furrowSeg/inst/doc/exampleFurrowSegmentation.pdf, vignettes/furrowSeg/inst/doc/genPaperFigures.pdf vignetteTitles: Supplementary Methods - Example furrow segmentation, Supplementary Methods - Automatic generation of paper figures hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/furrowSeg/inst/doc/exampleFurrowSegmentation.R, vignettes/furrowSeg/inst/doc/genPaperFigures.R dependencyCount: 56 Package: gageData Version: 2.45.0 Depends: R (>= 2.10) Suggests: gage, pathview, genefilter License: GPL (>=2.0) MD5sum: d2320501dbc3fe23b4673ad20efa0d5b 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: ebfd714 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/gageData_2.45.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: gage dependencyCount: 0 Package: gaschYHS Version: 1.45.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 1372f2a25f3061f5f50028be79bce6b6 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: 06aa4e8 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/gaschYHS_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: gcspikelite Version: 1.45.0 Depends: R (>= 2.5.0) License: LGPL MD5sum: f602a5fa01e871baf97e878ff9c176c4 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: 91d2de3 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/gcspikelite_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: flagme suggestsMe: erah dependencyCount: 0 Package: gDNAinRNAseqData Version: 1.7.0 Depends: R (>= 4.3) Imports: RCurl, XML, ExperimentHub, BiocGenerics, Rsamtools Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 0cee068e7214e365bbeb67c244365a8d 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: 19dee43 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/gDNAinRNAseqData_1.7.0.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: 82 Package: gDRtestData Version: 1.5.1 Depends: R (>= 4.2) Imports: checkmate, data.table Suggests: BiocStyle, gDRstyle (>= 1.1.5), knitr, qs, reshape2, rmarkdown, SummarizedExperiment, testthat, yaml License: Artistic-2.0 MD5sum: 1a0e6d7562dfe0d0a26643514de7c94d NeedsCompilation: no Title: gDRtestData - R data package with testing dose response data Description: R package with internal dose-response test data. Package provides functions to generate input testing data that can be used as the input for gDR pipeline. It also contains qs files with MAE data processed by gDR. biocViews: ExperimentData, TechnologyData Author: Aleksander Chlebowski [aut], Bartosz Czech [aut] (ORCID: ), Arkadiusz Gladki [cre, aut] (ORCID: ), Marc Hafner [aut] (ORCID: ), Marcin Kamianowski [aut], Sergiu Mocanu [aut], Natalia Potocka [aut], Dariusz Scigocki [aut], Janina Smola [aut], Allison Voung [aut] Maintainer: Arkadiusz Gladki URL: https://github.com/gdrplatform/gDRtestData, https://gdrplatform.github.io/gDRtestData/ VignetteBuilder: knitr BugReports: https://github.com/gdrplatform/gDRtestData/issues git_url: https://git.bioconductor.org/packages/gDRtestData git_branch: devel git_last_commit: 8be652c git_last_commit_date: 2024-11-06 Date/Publication: 2024-11-07 source.ver: src/contrib/gDRtestData_1.5.1.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: 1.43.0 Depends: R (>= 2.11.0) Imports: utils, rtracklayer, GenomicFeatures, txdbmaker License: LGPL (>= 2) MD5sum: 857e8dec4ff574038a5a6a35b82b7fb5 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: 9a7cf99 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/geneLenDataBase_1.43.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: goseq importsMe: SMITE dependencyCount: 102 Package: genomationData Version: 1.39.0 Suggests: knitr License: GPL-3 MD5sum: 97f9a7f83c20dc3deb540ab2cfe52426 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: 5db5cb0 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/genomationData_1.39.0.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: 1.15.0 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: 9b2b92e76368d52d1346721db0d1d534 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: b1554ea git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/GenomicDistributionsData_1.15.0.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: 1.35.0 Depends: R (>= 3.5.0) Suggests: limma, rtracklayer, GenomicRanges, Rsamtools, VariantAnnotation, tools, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: fb27d85bf003b79edcafd8bf6baf7d78 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: 04f54b8 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/GeuvadisTranscriptExpr_1.35.0.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: 1.25.0 Depends: R (>= 3.5) Suggests: GIGSEA, knitr, rmarkdown License: LGPL-3 MD5sum: 1ed57e5fdb625eb0006b61c1e916e390 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: a06c838 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/GIGSEAdata_1.25.0.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: 1.49.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: LGPL MD5sum: 95e90f02b19e175839f3a177885aefa2 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: cc2a249 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/golubEsets_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: adSplit, Biobase, biosigner, GlobalAncova, globaltest, idiogram, MLInterfaces, pvca, RDRToolbox, twilight dependencyCount: 7 Package: gpaExample Version: 1.19.0 Depends: R (>= 4.0.0) License: GPL (>= 2) MD5sum: f1aa8e9859b3c309541d71b4d9da31d4 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: 9621c7d git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/gpaExample_1.19.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GPA dependencyCount: 0 Package: grndata Version: 1.39.0 Depends: R (>= 2.10) Suggests: RUnit, BiocGenerics, knitr License: GPL-3 MD5sum: d7fecb31f32dee8934e525e586fa971e 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: be59265 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/grndata_1.39.0.tar.gz vignettes: vignettes/grndata/inst/doc/grndata.html vignetteTitles: GRNdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: GSBenchMark Version: 1.27.0 Depends: R (>= 2.13.1) License: GPL-2 MD5sum: e6514ac226b692d45105d01401270405 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: babaab4 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/GSBenchMark_1.27.0.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: 1.13.0 Depends: Biobase, GEOquery Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown, SummarizedExperiment, SingleCellExperiment License: Artistic-2.0 MD5sum: 3e12466e72c0aaba50c534fcfb5225b6 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: 52ecc8a git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/GSE103322_1.13.0.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: 79 Package: GSE13015 Version: 1.15.0 Depends: Biobase, GEOquery Imports: preprocessCore, SummarizedExperiment, GEOquery, Biobase Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown License: MIT License MD5sum: 55694ec046ee98a3e071e55a293bfe05 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: 64535cb git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/GSE13015_1.15.0.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: 80 Package: GSE159526 Version: 1.13.0 Suggests: ExperimentHub, BiocStyle, RefManageR, knitr, rmarkdown, testthat, minfi, tibble, sessioninfo License: MIT + file LICENSE MD5sum: 3a8bc09158bc78c0f1d45770141a7946 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: 3a02b2d git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/GSE159526_1.13.0.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: 1.35.0 Depends: Biobase, GEOquery Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown, DESeq2 License: Artistic-2.0 MD5sum: 425aff7b5bdb8819b15931359c291c57 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: 70fe03e git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/GSE62944_1.35.0.tar.gz vignettes: vignettes/GSE62944/inst/doc/GSE62944.html vignetteTitles: Raw TCGA data using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GSE62944/inst/doc/GSE62944.R suggestsMe: GSEABenchmarkeR dependencyCount: 79 Package: GSVAdata Version: 1.43.0 Depends: R (>= 3.5), Biobase, GSEABase, hgu95a.db, SummarizedExperiment License: Artistic-2.0 MD5sum: f15ad29db0aeba7d16180518a4e4ead6 NeedsCompilation: no Title: Data employed in the vignette of the GSVA package Description: This package stores the data employed in the vignette of the GSVA package. These data belong to the following publications: Armstrong et al. Nat Genet 30:41-47, 2002; Cahoy et al. J Neurosci 28:264-278, 2008; Carrel and Willard, Nature, 434:400-404, 2005; Huang et al. PNAS, 104:9758-9763, 2007; Pickrell et al. Nature, 464:768-722, 2010; Skaletsky et al. Nature, 423:825-837; Verhaak et al. Cancer Cell 17:98-110, 2010; Costa et al. FEBS J, 288:2311-2331, 2021. biocViews: ExperimentData, RNASeqData, Homo_sapiens_Data, CancerData, LeukemiaCancerData Author: Robert Castelo Maintainer: Robert Castelo git_url: https://git.bioconductor.org/packages/GSVAdata git_branch: devel git_last_commit: 6104579 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/GSVAdata_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: singleCellTK, RVA suggestsMe: GSAR, GSVA dependencyCount: 64 Package: GWASdata Version: 1.45.0 Depends: GWASTools Suggests: ncdf4 License: Artistic-2.0 MD5sum: 4b5912cff6f99143eea61c5231ecebe7 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: 835f885 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/GWASdata_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GENESIS, GWASTools dependencyCount: 94 Package: h5vcData Version: 2.27.0 Suggests: h5vc License: GPL (>= 3) MD5sum: b325582b7fdb9e078aa8ef8b250403ae 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: 17a9d32 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/h5vcData_2.27.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: h5vc suggestsMe: HDF5Array dependencyCount: 0 Package: hapmap100khind Version: 1.49.0 Suggests: oligo License: GPL MD5sum: 4ead88e41b92eb29e31af3103a9d1b3a 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: 34ea9c8 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/hapmap100khind_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmap100kxba Version: 1.49.0 Suggests: oligo License: GPL MD5sum: a85be7942e3cfe803b10fbae60349e4c 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: 66f08ce git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/hapmap100kxba_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligo dependencyCount: 0 Package: hapmap500knsp Version: 1.49.0 Suggests: oligo License: GPL MD5sum: 900f6ee4bc29830c0b52d6da8ac7ffc6 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: e67b508 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/hapmap500knsp_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmap500ksty Version: 1.49.0 Suggests: oligo License: GPL MD5sum: 5d9bfe3d6fe1d604818ca56a90ef9c9c 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: 645be9f git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/hapmap500ksty_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmapsnp5 Version: 1.49.0 Suggests: oligo License: GPL MD5sum: 223bff5f9d7229b39e735bc5fa14fa51 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: 16fff35 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/hapmapsnp5_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligoClasses dependencyCount: 0 Package: hapmapsnp6 Version: 1.49.0 Depends: R (>= 2.15) Suggests: oligo, oligoClasses License: GPL MD5sum: 8a0f4ae9e0505d7a8be34f8390a38d8b 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: f7414a9 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/hapmapsnp6_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: crlmm, oligoClasses dependencyCount: 0 Package: harbChIP Version: 1.45.0 Depends: R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5), Biostrings Imports: methods, stats License: Artistic-2.0 MD5sum: 57a78b99cdfecc782e5495f1523f9bd4 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: c0bed2b git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/harbChIP_1.45.0.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: 27 Package: HarmanData Version: 1.35.0 Depends: R (>= 3.5.0) Suggests: BiocGenerics, BiocStyle, knitr, rmarkdown, Harman (>= 1.23.3) License: GPL-3 MD5sum: bb0c27ab7b7bc89f76ea4657d94dbe96 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: 26e5db0 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/HarmanData_1.35.0.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: 1.29.0 Depends: R (>= 3.4.0) Imports: ExperimentHub Suggests: AnnotationHub, knitr, rmarkdown, igraph, survival, ANF, stats, testthat License: GPL-3 MD5sum: 74bc68952a44e5bb1eab63b4e753248f 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: 25a5913 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/HarmonizedTCGAData_1.29.0.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: 67 Package: HCAData Version: 1.23.0 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: 0d253830ff0f8799c189bbad82f5709c 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: a083531 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/HCAData_1.23.0.tar.gz vignettes: vignettes/HCAData/inst/doc/hcadata.html vignetteTitles: Accessing the Human Cell Atlas datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HCAData/inst/doc/hcadata.R dependsOnMe: OSCA.workflows dependencyCount: 83 Package: HCATonsilData Version: 1.5.0 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: 98e841257f36220047d04dcd4a8297ea 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: 484d5f5 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/HCATonsilData_1.5.0.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: 1.47.0 Depends: R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots, limma, vcd, LSD,EBImage Suggests: BiocStyle License: Artistic-2.0 MD5sum: 9af2cc4fd2f66d2e5ca4bc5ab23ed3c2 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: 41addaf git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/HD2013SGI_1.47.0.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: 91 Package: HDCytoData Version: 1.27.0 Depends: ExperimentHub, SummarizedExperiment, flowCore Imports: utils, methods Suggests: BiocStyle, knitr, rmarkdown, Rtsne, umap, ggplot2, FlowSOM, mclust License: MIT + file LICENSE MD5sum: c8be143ecee474d717fce5105836c673 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: e1fdd81 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/HDCytoData_1.27.0.tar.gz vignettes: vignettes/HDCytoData/inst/doc/Contribution_guidelines.html, vignettes/HDCytoData/inst/doc/Examples_and_use_cases.html, vignettes/HDCytoData/inst/doc/HDCytoData_package.html vignetteTitles: 3. Contribution guidelines, 2. Examples and use cases, 1. HDCytoData package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HDCytoData/inst/doc/Contribution_guidelines.R, vignettes/HDCytoData/inst/doc/Examples_and_use_cases.R, vignettes/HDCytoData/inst/doc/HDCytoData_package.R dependsOnMe: cytofWorkflow suggestsMe: CytoMDS, diffcyt, tidyFlowCore, tidytof dependencyCount: 84 Package: healthyControlsPresenceChecker Version: 1.11.0 Depends: R (>= 4.0.0) Imports: xml2, GEOquery, geneExpressionFromGEO, magrittr Suggests: RUnit, BiocGenerics, markdown, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 22be8bd842dd6f40bc6e1e93d1580edf 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: cc1dedc git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/healthyControlsPresenceChecker_1.11.0.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: 97 Package: healthyFlowData Version: 1.45.0 Depends: R (>= 2.15.0), flowCore Imports: methods License: Artistic-2.0 MD5sum: 91533ddc6dec56be9f5e777a72f1e083 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: a06821f git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/healthyFlowData_1.45.0.tar.gz vignettes: vignettes/healthyFlowData/inst/doc/healthyFlowData.pdf vignetteTitles: healthyFlowData: A healthy dataset with 20 flow cytometry samples used by the flowMatch package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/healthyFlowData/inst/doc/healthyFlowData.R suggestsMe: flowMatch dependencyCount: 18 Package: HEEBOdata Version: 1.45.0 License: LGPL MD5sum: 06c2c4ac34dddb361c03464296d9037f 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: 7f7ee54 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/HEEBOdata_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQuality dependencyCount: 0 Package: HelloRangesData Version: 1.33.0 Suggests: BiocStyle License: GPL (>= 2) MD5sum: 4ac6d0a71272561a469c1e5b27e213a2 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: b837d27 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/HelloRangesData_1.33.0.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: 1.45.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 7585e5c0ff61bdb1d2aeb2e46574241d 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: 7ac6a9c git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/hgu133abarcodevecs_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hgu133plus2barcodevecs Version: 1.45.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: a1480646acc592099df36c8afa6d3ce9 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: 68c860a git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/hgu133plus2barcodevecs_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hgu133plus2CellScore Version: 1.27.0 Depends: R (>= 3.5.0) Imports: Biobase (>= 2.39.1) Suggests: knitr License: GPL-3 MD5sum: e8a80eaba27316745e44e690c774b9ac 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: 9cecb7f git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/hgu133plus2CellScore_1.27.0.tar.gz vignettes: vignettes/hgu133plus2CellScore/inst/doc/hgu133plus2Vignette.pdf vignetteTitles: R packages: hgu133plus2CellScore hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/hgu133plus2CellScore/inst/doc/hgu133plus2Vignette.R suggestsMe: CellScore dependencyCount: 7 Package: hgu2beta7 Version: 1.47.0 Depends: R (>= 2.0.0) License: Artistic-2.0 MD5sum: 2201e246ace0696334cab5924d901932 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: 0dced82 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/hgu2beta7_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: HiBED Version: 1.5.0 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: 1f7be11a275230e26a07e65ffc8a5062 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: 5e16340 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/HiBED_1.5.0.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: 1.27.0 Depends: R (>= 3.5.0) Suggests: HiTC, BiocStyle License: GPL-3 MD5sum: f8310db23256fcf69db6790fb21bcec7 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: 204f8c8 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/HiCDataHumanIMR90_1.27.0.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: 1.43.0 Suggests: ShortRead License: GPL-3 MD5sum: 94a3d16d1a8495a5f2b7f3bb04606bc6 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: d2a3a4c git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/HiCDataLymphoblast_1.43.0.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: 1.9.0 Depends: ExperimentHub Imports: BiocFileCache, AnnotationHub Suggests: testthat, methods, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: a22fd270d31a1921e7cfb34d54512c99 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: e5c0452 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/HiContactsData_1.9.0.tar.gz vignettes: vignettes/HiContactsData/inst/doc/HiContactsData.html vignetteTitles: HiContactsData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HiContactsData/inst/doc/HiContactsData.R importsMe: OHCA suggestsMe: HiCExperiment, HiContacts, HiCool, plyinteractions dependencyCount: 67 Package: HighlyReplicatedRNASeq Version: 1.19.0 Depends: SummarizedExperiment, ExperimentHub Imports: S4Vectors Suggests: BiocStyle, BiocFileCache, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 55f8dfeaedc44377c4eab6f25741696f 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: 202c6b5 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/HighlyReplicatedRNASeq_1.19.0.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: 78 Package: HIVcDNAvantWout03 Version: 1.47.0 License: GPL (>= 2) MD5sum: a3e37736c84dd9f3b91d1dbf0f2b217f 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: 62640dc git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/HIVcDNAvantWout03_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: HMP16SData Version: 1.27.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: AnnotationHub, ExperimentHub, S4Vectors, assertthat, dplyr, kableExtra, knitr, magrittr, methods, readr, stringr, tibble, utils Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, circlize, cowplot, dendextend, devtools, ggplot2, gridExtra, haven, phyloseq, rmarkdown, roxygen2, stats, testthat, tidyr License: Artistic-2.0 MD5sum: 90c3f4ec475d843cf073aa60ee38f703 NeedsCompilation: no Title: 16S rRNA Sequencing Data from the Human Microbiome Project Description: HMP16SData is a Bioconductor ExperimentData package of the Human Microbiome Project (HMP) 16S rRNA sequencing data for variable regions 1–3 and 3–5. Raw data files are provided in the package as downloaded from the HMP Data Analysis and Coordination Center. Processed data is provided as SummarizedExperiment class objects via ExperimentHub. biocViews: ExperimentData, ExperimentHub, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch, SequencingData Author: Lucas schiffer [aut, cre] (ORCID: ), Rimsha Azhar [aut], Marcel Ramos [ctb], Ludwig Geistlinger [ctb], Levi Waldron [aut] Maintainer: Lucas schiffer URL: https://github.com/waldronlab/HMP16SData VignetteBuilder: knitr BugReports: https://github.com/waldronlab/HMP16SData/issues git_url: https://git.bioconductor.org/packages/HMP16SData git_branch: devel git_last_commit: 60c5af9 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/HMP16SData_1.27.0.tar.gz vignettes: vignettes/HMP16SData/inst/doc/HMP16SData.html vignetteTitles: HMP16SData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HMP16SData/inst/doc/HMP16SData.R dependencyCount: 112 Package: homosapienDEE2CellScore Version: 1.3.0 Imports: Rtsne (>= 0.15), utils(>= 3.5.0), ExperimentHub, BiocGenerics, DESeq2, S4Vectors, SummarizedExperiment, getDEE2, MatrixGenerics Suggests: knitr, rmarkdown, devtools, Biobase (>= 2.39.1), BiocManager, AnnotationHubData, ExperimentHubData, AnnotationHub, CellScore (>= 1.21.4) License: GPL (>= 3) MD5sum: c1ffa32ac30802ee5939429159c894d8 NeedsCompilation: no Title: Example Data Package for CellScore Description: This is a data package for normalised homosapien data downloaded from DEE2. The package both downloads, normalises, and filters the data, and provides a way to access the data from a canonical store without needing local processing. This package was built as a way to generate and store canonical test data for CellScore. biocViews: RNASeqData, Genome, ExperimentHub, ExpressionData Author: Justin Marsh [aut, cre] Maintainer: Justin Marsh VignetteBuilder: knitr BugReports: https://github.com/flaviusb/homosapienDEE2CellScore/issues git_url: https://git.bioconductor.org/packages/homosapienDEE2CellScore git_branch: devel git_last_commit: abf369d git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/homosapienDEE2CellScore_1.3.0.tar.gz vignettes: vignettes/homosapienDEE2CellScore/inst/doc/use-data-package.html vignetteTitles: Use the Data in this Data Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/homosapienDEE2CellScore/inst/doc/use-data-package.R dependencyCount: 108 Package: HSMMSingleCell Version: 1.27.0 Depends: R (>= 2.10) License: Artistic-2.0 MD5sum: 343997e9cd408fb1366a8e6bcd92646c 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: e89a55f git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/HSMMSingleCell_1.27.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: monocle dependencyCount: 0 Package: HumanAffyData Version: 1.33.0 Depends: ExperimentHub, Biobase, R (>= 3.3) Suggests: BiocStyle License: Artistic-2.0 MD5sum: 3452b585a398df3e91a839e9259832c4 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: 9b19888 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/HumanAffyData_1.33.0.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: 67 Package: humanHippocampus2024 Version: 0.99.5 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: 2235732b89c6334176c822ffc84c8aae 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: c10cf0c git_last_commit_date: 2024-12-02 Date/Publication: 2024-12-05 source.ver: src/contrib/humanHippocampus2024_0.99.5.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: 83 Package: humanStemCell Version: 0.47.0 Depends: Biobase (>= 2.5.5), hgu133plus2.db License: Artistic-2.0 MD5sum: 59eeea16f798202b4b613a2c36da3d43 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: 3ce2c8b git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/humanStemCell_0.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MiRaGE, rtracklayer dependencyCount: 48 Package: IHWpaper Version: 1.35.0 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: 3f77fb5857a8e8f2831ad4fd044c8588 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: 82f41c4 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/IHWpaper_1.35.0.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: 107 Package: Illumina450ProbeVariants.db Version: 1.43.0 Depends: R (>= 3.0.1) License: GPL-3 MD5sum: 8d1c640b3372b5f091de68738f5b5700 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: ed7a63c git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/Illumina450ProbeVariants.db_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: IlluminaDataTestFiles Version: 1.45.0 License: Artistic-2.0 MD5sum: cb2602c728e5c5d11305800a552ad615 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: ea4fa10 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/IlluminaDataTestFiles_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: illuminaio dependencyCount: 0 Package: imcdatasets Version: 1.15.0 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: 709602f0e52d04cbc79e9fb1479f5af1 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: b01a12c git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/imcdatasets_1.15.0.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: 153 Package: ITALICSData Version: 2.45.0 Depends: R (>= 2.0.0) License: GPL MD5sum: e3addce38f913a0ad74de622a0d7af50 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: 910eb87 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/ITALICSData_2.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ITALICS dependencyCount: 0 Package: Iyer517 Version: 1.49.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 4adb1201bbb62105c884d085dcafd502 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: 08a18a0 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/Iyer517_1.49.0.tar.gz vignettes: vignettes/Iyer517/inst/doc/Iyer517.pdf vignetteTitles: Iyer517 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Iyer517/inst/doc/Iyer517.R dependencyCount: 7 Package: JASPAR2014 Version: 1.43.0 Depends: R (>= 3.0.1), methods, Biostrings (>= 2.29.19) License: GPL-2 MD5sum: ccd94d24199e308fa9469337374a057f 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: 296956b git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/JASPAR2014_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MatrixRider, TFBSTools dependencyCount: 26 Package: JASPAR2016 Version: 1.35.0 Depends: R (>= 3.2.2), methods License: GPL-2 MD5sum: 73faf7ffe379ad6547e5050e2381ba54 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: 2417343 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/JASPAR2016_1.35.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: chromVAR, TFBSTools, CAGEWorkflow dependencyCount: 1 Package: JohnsonKinaseData Version: 1.3.0 Imports: ExperimentHub, BiocParallel, checkmate, dplyr, stats, stringr, tidyr, purrr, utils Suggests: knitr, BiocStyle, ExperimentHubData, testthat (>= 3.0.0), rmarkdown License: MIT + file LICENSE MD5sum: 72b935490c56c2958ae8ba1bd3ee7b07 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: 3df4d66 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/JohnsonKinaseData_1.3.0.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: 78 Package: KEGGandMetacoreDzPathwaysGEO Version: 1.27.0 Depends: R (>= 2.15.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: 04b3fade06e6d7fafbe3568a16abbd43 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: 6fb99b8 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/KEGGandMetacoreDzPathwaysGEO_1.27.0.tar.gz vignettes: vignettes/KEGGandMetacoreDzPathwaysGEO/inst/doc/KEGGandMetacoreDzPathwaysGEO.pdf vignetteTitles: KEGGandMetacoreDzPathwaysGEO Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/KEGGandMetacoreDzPathwaysGEO/inst/doc/KEGGandMetacoreDzPathwaysGEO.R importsMe: GSEABenchmarkeR dependencyCount: 7 Package: KEGGdzPathwaysGEO Version: 1.45.0 Depends: R (>= 2.13.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: 93bf1c879e1a7e03ac105d779883383b 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: 4e8f0d5 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/KEGGdzPathwaysGEO_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: PADOG importsMe: GSEABenchmarkeR dependencyCount: 7 Package: kidpack Version: 1.49.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5) License: GPL-2 MD5sum: ebcad422420821db5754023d83d42b68 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: a62f14c git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/kidpack_1.49.0.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: 1.33.0 Depends: R (>= 3.3.0) License: MIT + file LICENSE MD5sum: 55e0d89d745072f7cb3f1df235d0a7b9 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: f20344e git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/KOdata_1.33.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: KEGGlincs dependencyCount: 0 Package: leeBamViews Version: 1.43.0 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: 09ca3ed3dbc98798e3a0c160d94f3be6 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: 4eb8993 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/leeBamViews_1.43.0.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: 60 Package: LegATo Version: 1.1.0 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: ab92663b4f2045f53baee22217c828b7 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: c1cbe1a git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/LegATo_1.1.0.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: 194 Package: leukemiasEset Version: 1.43.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 26854b6814d90473c5159930fd4b7121 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: 6515172 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/leukemiasEset_1.43.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: geNetClassifier, mCSEA, multiclassPairs dependencyCount: 7 Package: LiebermanAidenHiC2009 Version: 0.45.0 Depends: KernSmooth, IRanges License: LGPL MD5sum: 6286e60c57fcedf4e624a5004986d8ae 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: e7e4856 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/LiebermanAidenHiC2009_0.45.0.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: 1.39.0 Depends: R (>= 3.1.1), methylPipe Suggests: BSgenome.Hsapiens.UCSC.hg18 License: Artistic 2.0 MD5sum: 3c356881eb720d2b13fc4e286f5b94f9 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: a794ead git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/ListerEtAlBSseq_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 165 Package: LRcellTypeMarkers Version: 1.15.0 Depends: R (>= 4.1) Imports: ExperimentHub Suggests: LRcell, BiocStyle, knitr, rmarkdown, roxygen2, testthat License: MIT + file LICENSE MD5sum: b15ed8db883d3b6c591c9ef522fb9be3 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: 6219718 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/LRcellTypeMarkers_1.15.0.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: 67 Package: lumiBarnes Version: 1.47.0 Depends: R (>= 2.0), Biobase (>= 2.5.5), lumi (>= 1.1.0) License: LGPL MD5sum: 54e02d6d0e8f09af8932b3a8bca42055 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: 07d4351 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/lumiBarnes_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayMvout, lumi dependencyCount: 166 Package: LungCancerACvsSCCGEO Version: 1.43.0 Depends: R (>= 2.15.0) License: GPL-2 MD5sum: a315826ee55830249ce90b6688c25579 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: 475e218 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/LungCancerACvsSCCGEO_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: LungCancerLines Version: 0.45.0 Imports: Rsamtools License: Artistic-2.0 MD5sum: 0ba92304ae08546516c10880522a3701 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: b631993 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/LungCancerLines_0.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: gmapR, VariantTools dependencyCount: 40 Package: lungExpression Version: 0.45.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: b1b7105d0499af56139a6094ddf8d4ab 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: 6571992 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/lungExpression_0.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: globaltest dependencyCount: 7 Package: lydata Version: 1.33.0 License: MIT + file LICENSE MD5sum: 4df8fbc2369d4f602d0912351376d7b5 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: 16233ad git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/lydata_1.33.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: ccmap dependencyCount: 0 Package: M3DExampleData Version: 1.33.0 Depends: R (>= 3.3) License: GPL (>=2) MD5sum: bd637f0112490d459eb7bdfda364df6c 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: ce308ef git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/M3DExampleData_1.33.0.tar.gz hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: celda, M3Drop dependencyCount: 0 Package: macrophage Version: 1.23.0 Depends: R (>= 3.5.0) Suggests: knitr, markdown License: GPL (>= 2) MD5sum: ed076f5958ac63482c3ef435dc0e5fd9 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: dfb4476 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/macrophage_1.23.0.tar.gz vignettes: vignettes/macrophage/inst/doc/macrophage.html vignetteTitles: Salmon quantifications for human macrophage immune response experiment hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/macrophage/inst/doc/macrophage.R suggestsMe: fishpond, GeDi, GeneTonic, mosdef, quantiseqr, fluentGenomics dependencyCount: 0 Package: MACSdata Version: 1.15.0 License: file LICENSE MD5sum: 554b539fd5c1a3aa8e9bab6d2b732a2f 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: dc9f7d7 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/MACSdata_1.15.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: MACSr dependencyCount: 0 Package: mammaPrintData Version: 1.43.0 Depends: R (>= 2.13.0) Suggests: Biobase, readxl, limma License: Artistic-2.0 MD5sum: 1e9aedbd612a649447c7dd059684a764 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: 5b1eb96 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/mammaPrintData_1.43.0.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: 1.51.0 Suggests: oligo, pdInfoBuilder License: GPL MD5sum: 547bef4f0dad262c44e4d1e8db19eeb0 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: 2b1d228 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/maqcExpression4plex_1.51.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligo dependencyCount: 0 Package: MAQCsubset Version: 1.45.0 Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), lumi, methods Suggests: genefilter, codelink License: Artistic-2.0 MD5sum: 9b97c7423a8a9e6c31906f064c3f2fad 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: 194a40b git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/MAQCsubset_1.45.0.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: 166 Package: marinerData Version: 1.7.0 Imports: utils, ExperimentHub Suggests: knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0) License: GPL-3 MD5sum: 2bc23a83b3e59e69154a9c0b19248e49 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: 0859c76 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/marinerData_1.7.0.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: 67 Package: mCSEAdata Version: 1.27.1 Depends: R (>= 3.5) Imports: GenomicRanges Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 7543f5b3b5b59e72d020af126a4667b8 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: bba21e6 git_last_commit_date: 2024-11-27 Date/Publication: 2024-11-28 source.ver: src/contrib/mCSEAdata_1.27.1.tar.gz vignettes: vignettes/mCSEAdata/inst/doc/mCSEAdata.html vignetteTitles: Data for mCSEA package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mCSEAdata/inst/doc/mCSEAdata.R dependsOnMe: mCSEA dependencyCount: 24 Package: mcsurvdata Version: 1.25.0 Depends: R (>= 3.5), ExperimentHub Imports: AnnotationHub, Biobase Suggests: BiocStyle, knitr License: GPL (>=2) MD5sum: f3c7824a48f58b150337e3477c0e3ee1 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: 2babc74 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/mcsurvdata_1.25.0.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: 67 Package: MEDIPSData Version: 1.43.0 Depends: R (>= 3.5.0) License: GPL (>= 2) MD5sum: 23fb8fd989068977d88ee750ccd4ca9c 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: 13378c9 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/MEDIPSData_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MEDIPS, qsea dependencyCount: 0 Package: MEEBOdata Version: 1.45.0 License: LGPL MD5sum: ed356592a098d90494e523ad71ad3bfc 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: 5840615 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/MEEBOdata_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQuality dependencyCount: 0 Package: MerfishData Version: 1.9.0 Depends: R (>= 4.2.0), EBImage, SpatialExperiment Imports: grDevices, AnnotationHub, BumpyMatrix, ExperimentHub, S4Vectors, SingleCellExperiment, SummarizedExperiment, HDF5Array Suggests: grid, ggplot2, ggpubr, knitr, rmarkdown, scater, scattermore, terra, testthat, BiocStyle, DropletUtils License: Artistic-2.0 MD5sum: 7284ee634003f5bf8032835123701439 NeedsCompilation: no Title: Collection of public MERFISH datasets Description: MerfishData is an ExperimentHub package that serves publicly available datasets obtained with Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH). MERFISH is a massively multiplexed single-molecule imaging technology capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells. The scope of the package is to provide MERFISH data for benchmarking and analysis. biocViews: ExperimentHub, ExpressionData, HighThroughputImagingData, Mus_musculus_Data, SingleCellData, SpatialData Author: Ludwig Geistlinger [aut, cre] (ORCID: ), Tyrone Lee [ctb], Helena Crowell [ctb] (ORCID: ), Daniela Corbetta [ctb], Jeffrey Moffitt [aut], Robert Gentleman [aut] Maintainer: Ludwig Geistlinger URL: https://github.com/ccb-hms/MerfishData VignetteBuilder: knitr BugReports: https://github.com/ccb-hms/MerfishData/issues git_url: https://git.bioconductor.org/packages/MerfishData git_branch: devel git_last_commit: 5d260f7 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/MerfishData_1.9.0.tar.gz vignettes: vignettes/MerfishData/inst/doc/Merfish_mouse_colon_ibd.html, vignettes/MerfishData/inst/doc/Merfish_mouse_hypothalamus.html, vignettes/MerfishData/inst/doc/Merfish_mouse_ileum.html vignetteTitles: Mouse colon ibd, Mouse hypothalamus, Mouse ileum hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MerfishData/inst/doc/Merfish_mouse_colon_ibd.R, vignettes/MerfishData/inst/doc/Merfish_mouse_hypothalamus.R, vignettes/MerfishData/inst/doc/Merfish_mouse_ileum.R dependencyCount: 110 Package: MetaGxBreast Version: 1.27.0 Depends: R (>= 3.6.0), Biobase, AnnotationHub, ExperimentHub Imports: stats, lattice, impute, SummarizedExperiment Suggests: testthat, xtable, tinytex License: Apache License (>= 2) MD5sum: e2c5aaf06f104b0b799777c27601d61b 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: 9b2ebf1 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/MetaGxBreast_1.27.0.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: 79 Package: MetaGxOvarian Version: 1.27.0 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: 3d7c5942d51d8c83bb8ecc7a211cf333 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: 7e4535f git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/MetaGxOvarian_1.27.0.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: 79 Package: MetaGxPancreas Version: 1.27.0 Depends: SummarizedExperiment, ExperimentHub, R (>= 3.6.0) Imports: stats, impute, S4Vectors, AnnotationHub Suggests: testthat, knitr, BiocStyle, rmarkdown, markdown License: Artistic-2.0 MD5sum: 37020dd05baabd91369f73ba0cfec062 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], 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: 2c5d902 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/MetaGxPancreas_1.27.0.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: 79 Package: metaMSdata Version: 1.43.0 License: GPL (>= 2) MD5sum: 1c751a2f07676afa2d8fe8484d47b525 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: c14c992 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/metaMSdata_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CluMSID, metaMS dependencyCount: 0 Package: MethylAidData Version: 1.39.0 Depends: MethylAid, R (>= 3.2) Suggests: BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC License: GPL (>= 2) MD5sum: 594ac3de513bcbd9526a30683f6f3c27 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: 13cb1da git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/MethylAidData_1.39.0.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: 1.15.0 Imports: ExperimentHubData, ExperimentHub, utils Suggests: knitr, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: 421a94c04116c029edebe320dca0a982 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: 0dcda1a git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/methylclockData_1.15.0.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: 126 Package: MethylSeqData Version: 1.17.0 Depends: SummarizedExperiment Imports: ExperimentHub, HDF5Array, rhdf5, GenomeInfoDb, S4Vectors, GenomicRanges, stats, IRanges, utils Suggests: BiocFileCache, BiocStyle, data.table, knitr, rmarkdown License: CC0 MD5sum: c1524fefa38884d7cb98a7a1b5821ef1 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: 8aef307 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/MethylSeqData_1.17.0.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: 82 Package: MicrobiomeBenchmarkData Version: 1.9.0 Depends: R (>= 4.2), SummarizedExperiment, TreeSummarizedExperiment Imports: BiocFileCache, tools, S4Vectors, ape, utils Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0), mia, ggplot2, tidyr, dplyr, magrittr, tibble, purrr License: Artistic-2.0 MD5sum: cd31bdc7d9939c50cc6424ba66d1b199 NeedsCompilation: no Title: Datasets for benchmarking in microbiome research Description: The MicrobiomeBenchmarkData package provides functionality to access microbiome datasets suitable for benchmarking. These datasets have some biological truth, which allows to have expected results for comparison. The datasets come from various published sources and are provided as TreeSummarizedExperiment objects. Currently, only datasets suitable for benchmarking differential abundance methods are available. biocViews: ExperimentData, MicrobiomeData, ReproducibleResearch, SequencingData Author: Samuel Gamboa [aut, cre] (ORCID: ), Levi Waldron [aut] (ORCID: ), Marcel Ramos [ctb] Maintainer: Samuel Gamboa URL: https://github.com/waldronlab/MicrobiomeBenchmarkData, http://waldronlab.io/MicrobiomeBenchmarkData/ VignetteBuilder: knitr BugReports: https://github.com/waldronlab/MicrobiomeBenchmarkData/issues git_url: https://git.bioconductor.org/packages/MicrobiomeBenchmarkData git_branch: devel git_last_commit: d9e18a4 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/MicrobiomeBenchmarkData_1.9.0.tar.gz vignettes: vignettes/MicrobiomeBenchmarkData/inst/doc/datasets.html, vignettes/MicrobiomeBenchmarkData/inst/doc/MicrobiomeBenchmarkData.html, vignettes/MicrobiomeBenchmarkData/inst/doc/recalibrare_spikein_data.html vignetteTitles: Datasets in MicrobiomeBenchmarkData, MicrobiomeBenchmarkData, Recalibration of the Stammler_2016_16S_spikein dataset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MicrobiomeBenchmarkData/inst/doc/datasets.R, vignettes/MicrobiomeBenchmarkData/inst/doc/MicrobiomeBenchmarkData.R, vignettes/MicrobiomeBenchmarkData/inst/doc/recalibrare_spikein_data.R suggestsMe: bugphyzz dependencyCount: 89 Package: microbiomeDataSets Version: 1.15.0 Depends: R (>= 4.1), SummarizedExperiment, TreeSummarizedExperiment, MultiAssayExperiment Imports: methods, utils, BiocGenerics, ExperimentHub, Biostrings, ape Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, testthat License: CC0 MD5sum: f743d1fd7af34aff90c60af48657bada 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: 9225d57 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/microbiomeDataSets_1.15.0.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: 100 Package: microRNAome Version: 1.29.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: BiocGenerics, RUnit License: GPL (>= 2) MD5sum: f39002dfbb4daeea3ce82655fcbd69e3 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: 8a2e59a git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/microRNAome_1.29.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 37 Package: minfiData Version: 0.53.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2), IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 License: Artistic-2.0 MD5sum: 45ab287008077657127d77d91ee4c0a2 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: a085a06 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/minfiData_0.53.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: methylationArrayAnalysis suggestsMe: bigmelon, conumee, ENmix, funtooNorm, Harman, mCSEA, MEAL, MethylAid, minfi, missMethyl, MultiDataSet, recountmethylation, regionalpcs, shinyepico, shinyMethyl, skewr, MethylAidData dependencyCount: 147 Package: minfiDataEPIC Version: 1.33.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2), IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: Artistic-2.0 MD5sum: 23f487ca90524754c8e9551e649e8c93 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: 274bea6 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/minfiDataEPIC_1.33.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MethylAid, minfi, recountmethylation, REMP, MethylAidData dependencyCount: 147 Package: minionSummaryData Version: 1.37.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: e11a6b1b98b4a755ca7a553900963e97 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: 9ddf066 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/minionSummaryData_1.37.0.tar.gz vignettes: vignettes/minionSummaryData/inst/doc/creating-Styphi-Dataset.html vignetteTitles: Creating example MinION summary dataset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/minionSummaryData/inst/doc/creating-Styphi-Dataset.R suggestsMe: IONiseR dependencyCount: 0 Package: miRcompData Version: 1.37.0 Depends: R (>= 3.2), Imports: utils License: GPL-3 | file LICENSE MD5sum: e099deeef2ecc9e060642345116fe70e 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: 3f97c85 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/miRcompData_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: miRcomp dependencyCount: 1 Package: miRNATarget Version: 1.45.0 Depends: R (>= 2.10), Biobase License: GPL MD5sum: 89a19e3e63099f3fa7b63a5b80efc0a4 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: fd195d7 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/miRNATarget_1.45.0.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: 1.43.0 Suggests: MMDiff2 License: LGPL MD5sum: 6fbaabe8f46d043759184151efd2fb91 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: 90b7967 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/MMDiffBamSubset_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MMDiff2 dependencyCount: 0 Package: MOFAdata Version: 1.23.0 Depends: R (>= 3.5) Suggests: knitr, MultiAssayExperiment, rmarkdown, BiocStyle License: LGPL-3 MD5sum: 78c98d6e9e6e90540b6e7501a414dad8 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: d64eaf9 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/MOFAdata_1.23.0.tar.gz vignettes: vignettes/MOFAdata/inst/doc/MOFAdata.html vignetteTitles: MOFAdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MOFAdata/inst/doc/MOFAdata.R importsMe: TDbasedUFE suggestsMe: TDbasedUFEadv dependencyCount: 0 Package: mosaicsExample Version: 1.45.0 Depends: R (>= 2.11.1) License: GPL (>= 2) MD5sum: b728a2881490a2409081a55664bb63d1 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: f4e445c git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/mosaicsExample_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: mosaics dependencyCount: 0 Package: mouse4302barcodevecs Version: 1.45.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 36f7707206007c674a0546b8ea2e60e2 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: 48ac16f git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/mouse4302barcodevecs_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: MouseAgingData Version: 1.3.0 Depends: R (>= 4.4.0), SingleCellExperiment Imports: AnnotationHub, ExperimentHub Suggests: BiocStyle, knitr, rmarkdown, scater License: Artistic-2.0 MD5sum: 8afb26f662806c600293290439a41482 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: dba112c git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/MouseAgingData_1.3.0.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: 79 Package: MouseGastrulationData Version: 1.21.0 Depends: R (>= 4.1), SingleCellExperiment, SummarizedExperiment, SpatialExperiment Imports: methods, ExperimentHub, BiocGenerics, S4Vectors, BumpyMatrix Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 08f95cc3314e7cde81b41439f6099c99 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: 83f3743 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/MouseGastrulationData_1.21.0.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: miloR dependencyCount: 84 Package: MouseThymusAgeing Version: 1.15.0 Depends: SingleCellExperiment, SummarizedExperiment Imports: ExperimentHub, methods, BiocGenerics, S4Vectors Suggests: knitr, scuttle, rmarkdown, BiocStyle License: GPL-3 MD5sum: 7401a49d22607155d366062a05336b2f 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: 1aab95d git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/MouseThymusAgeing_1.15.0.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: 79 Package: msd16s Version: 1.27.0 Depends: R (>= 2.10), Biobase, metagenomeSeq, License: Artistic-2.0 MD5sum: 28a932e1d86e39d2d0f46f1f87839334 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: 07e57c4 git_last_commit_date: 2024-10-29 Date/Publication: 2024-12-19 source.ver: src/contrib/msd16s_1.27.0.tar.gz vignettes: vignettes/msd16s/inst/doc/msd16s.pdf vignetteTitles: msd16s hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/msd16s/inst/doc/msd16s.R Package: msdata Version: 0.47.0 Depends: R (>= 3.5.0) Suggests: xcms, mzR, MSnbase License: GPL (>= 2) MD5sum: 86c401841dcd4ad988a367c4f1a18518 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: bb50ac0 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/msdata_0.47.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: MsQuality suggestsMe: IPO, koinar, MetaboAnnotation, MsBackendSql, MsExperiment, MSnbase, msqrob2, mzR, peakPantheR, PSMatch, QFeatures, Spectra, SpectraQL, TargetDecoy, xcms, RforProteomics dependencyCount: 0 Package: msigdb Version: 1.15.0 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: da8dfffb360b9840cbe808f361a27dd1 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: 399bc34 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/msigdb_1.15.0.tar.gz vignettes: vignettes/msigdb/inst/doc/msigdb.html vignetteTitles: msigdb hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/msigdb/inst/doc/msigdb.R importsMe: mastR, vissE dependencyCount: 74 Package: MSMB Version: 1.25.0 Depends: R (>= 3.5), tibble Suggests: knitr, BiocStyle License: LGPL MD5sum: aa20a85a252104472ce4a7ecf4ca3925 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: 9ce5218 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/MSMB_1.25.0.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: 14 Package: msPurityData Version: 1.35.0 Suggests: knitr License: GPL (>= 2) MD5sum: c000017e8f806c57ecdfe1d48185936f NeedsCompilation: no Title: Fragmentation spectral libraries and data to test the msPurity package Description: Fragmentation spectral libraries and data to test the msPurity package biocViews: ExperimentData, MassSpectrometryData Author: Thomas N. Lawson Maintainer: Thomas N. Lawson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/msPurityData git_branch: devel git_last_commit: 57e60b3 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/msPurityData_1.35.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: msPurity dependencyCount: 0 Package: msqc1 Version: 1.35.0 Depends: R (>= 3.6), lattice, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, specL (>= 1.2) License: GPL MD5sum: 225c08b22b1432fd5cc1c574231c4076 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: 3b41b6f git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/msqc1_1.35.0.tar.gz vignettes: vignettes/msqc1/inst/doc/poster.pdf, vignettes/msqc1/inst/doc/chromatography.html, vignettes/msqc1/inst/doc/msqc1.html vignetteTitles: ASMS 2016 poster (in portrait) abstract ID number: 282492, LC Observations - Retention Time Stability, Introducing msqc1 - A Mass Spec Data set for Targeted Proteomics Performance Evaluation hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/msqc1/inst/doc/chromatography.R, vignettes/msqc1/inst/doc/msqc1.R, vignettes/msqc1/inst/doc/poster.R dependencyCount: 6 Package: mtbls2 Version: 1.37.0 Depends: R (>= 2.10) Suggests: xcms (>= 3.13.8), CAMERA, Risa (>= 1.0.0), knitr, Heatplus, pcaMethods, sp, rmarkdown License: CC0 MD5sum: 8169cded15f702d4bdf53c199018f1e9 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: 84dc6ea git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/mtbls2_1.37.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: IPO, yamss dependencyCount: 0 Package: MUGAExampleData Version: 1.27.0 Depends: R (>= 2.10.0) License: GPL-3 MD5sum: 9b5bd023dce0fe2a8f996457a772e24c 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: 500af0a git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/MUGAExampleData_1.27.0.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: 1.3.0 Suggests: knitr, rmarkdown, ExperimentHub, dplyr License: MIT + file LICENSE MD5sum: d2b72833d9e81dd67a22260b323c5d0a 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: 62f936c git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/muleaData_1.3.0.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: 1.5.0 Depends: ExperimentHub Imports: utils Suggests: BiocStyle, knitr, multiWGCNA, rmarkdown, SummarizedExperiment License: Artistic-2.0 MD5sum: 30a800a6eb7952ad92cde86ad45ab975 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: 8baeb94 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/multiWGCNAdata_1.5.0.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: 67 Package: muscData Version: 1.21.0 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: fa457ee660a175462536916864923c80 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: d80b62f git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/muscData_1.21.0.tar.gz vignettes: vignettes/muscData/inst/doc/muscData.html vignetteTitles: Multi-sample multi-group scRNA-seq data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/muscData/inst/doc/muscData.R suggestsMe: dreamlet, glmGamPoi dependencyCount: 79 Package: mvoutData Version: 1.43.0 Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4), lumi License: Artistic-2.0 MD5sum: ba12711ca175e34e0487f8ee3eea7e73 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: f2afe67 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/mvoutData_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayMvout dependencyCount: 166 Package: NanoporeRNASeq Version: 1.17.0 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: 8fda164de0ce84ab40f2d5dee74a4ec6 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: ebbaeef git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/NanoporeRNASeq_1.17.0.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: 67 Package: nanotubes Version: 1.23.0 Depends: R (>= 3.6) Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, rtracklayer, CAGEfightR License: GPL-3 MD5sum: 9a2a2fc42352ea7c7f469871bc5da4ba 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: a1c33d6 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/nanotubes_1.23.0.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: 1.43.0 Depends: R (>= 2.10.0) Suggests: Rgraphviz License: GPL-3 MD5sum: 92063fb2fda80d7bd4f431a0a17852d2 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: bd6c652 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/NCIgraphData_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: NestLink Version: 1.23.0 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: 82edebe20453692cd06f6583cd6a5a44 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: fd7862e git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/NestLink_1.23.0.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: 107 Package: NetActivityData Version: 1.9.0 Depends: R (>= 4.2.0) Suggests: BiocStyle, knitr License: MIT + file LICENSE MD5sum: 90a8875ff5c71986b0ea872014afd01e 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: dc59833 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/NetActivityData_1.9.0.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: 0.45.0 Depends: R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0), hgu133a.db, annotate License: Artistic-2.0 MD5sum: 71f88881946cce0d150634322c0920b5 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: 543bf36 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/Neve2006_0.45.0.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: 51 Package: NGScopyData Version: 1.27.0 License: GPL (>=2) MD5sum: 2460bfe353537005b8cee7c24c58e991 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: b5322b1 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/NGScopyData_1.27.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: nullrangesData Version: 1.13.0 Depends: R (>= 4.1.0), ExperimentHub, GenomicRanges, InteractionSet Imports: utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: ddd603ed678f0dace47900dc51d3752c 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: 3cebd4a git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/nullrangesData_1.13.0.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: 80 Package: NxtIRFdata Version: 1.13.0 Imports: ExperimentHub, BiocFileCache, rtracklayer, R.utils Suggests: testthat (>= 3.0.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: e7ceb4d3818efdbb9b8f75e39d9f8040 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: 2342b1d git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/NxtIRFdata_1.13.0.tar.gz vignettes: vignettes/NxtIRFdata/inst/doc/NxtIRFdata.html vignetteTitles: NxtIRFdata: a data package for NxtIRF hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/NxtIRFdata/inst/doc/NxtIRFdata.R dependsOnMe: SpliceWiz dependencyCount: 100 Package: ObMiTi Version: 1.15.0 Depends: R (>= 4.1), SummarizedExperiment, ExperimentHub Suggests: knitr, rmarkdown, BiocManager, GenomicFeatures, S4Vectors, devtools, testthat License: GPL-3 MD5sum: 235ce561bfeb9467d4e6b508053be89f 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: 78f6179 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/ObMiTi_1.15.0.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: 78 Package: oct4 Version: 1.23.0 Suggests: knitr, markdown License: GPL (>= 2) MD5sum: 904e986df0acab828f5dbbc37303ff26 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: 7fb616b git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/oct4_1.23.0.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: 1.9.0 Depends: R (>= 4.2.0), ExperimentHub Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 7ade6a4786012a1ff49bf74fb62317ed 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: 8170722 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/octad.db_1.9.0.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: 67 Package: OMICsPCAdata Version: 1.25.0 Depends: R (>= 3.5.0), MultiAssayExperiment Suggests: knitr, kableExtra, rmarkdown License: GPL-3 MD5sum: c800da572d7f4d3c02e717403e500473 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: b0b21ae git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/OMICsPCAdata_1.25.0.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: 58 Package: OnassisJavaLibs Version: 1.29.0 Depends: R (>= 3.4) Imports: rJava Suggests: BiocStyle, rmarkdown, knitr License: GPL-2 MD5sum: fe60eb8a03c2082b5e914ffe30d0b929 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: 7a9bb24 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/OnassisJavaLibs_1.29.0.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: 1.19.0 Depends: R (>= 4.0) Suggests: knitr, BiocStyle, rmarkdown, magick License: Artistic-2.0 MD5sum: 589986afdcb87f96a54c8f4fd9f67fa8 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: 780c0d1 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/optimalFlowData_1.19.0.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: 1.5.0 Imports: AnnotationHub, BiocFileCache, ExperimentHub, HDF5Array, stringr, SummarizedExperiment Suggests: BiocStyle, ggplot2, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: e4d1127a1ace2aa5d7fdfe3fe95f7d6a 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: 0bd2f0f git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/orthosData_1.5.0.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: parathyroidSE Version: 1.45.1 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: Rsamtools, GenomicAlignments, GEOquery, SRAdb, GenomicFeatures, BiocStyle License: LGPL MD5sum: f318c0b80d66e11a4d4c7971856d329f NeedsCompilation: no Title: RangedSummarizedExperiment for RNA-Seq of primary cultures of parathyroid tumors by Haglund et al., J Clin Endocrinol Metab 2012. Description: This package provides RangedSummarizedExperiment objects of read counts in genes and exonic parts for paired-end RNA-Seq data from experiments on primary cultures of parathyroid tumors. The data were presented in the article "Evidence of a Functional Estrogen Receptor in Parathyroid Adenomas" by Haglund F, Ma R, Huss M, Sulaiman L, Lu M, Nilsson IL, Hoog A, Juhlin CC, Hartman J, Larsson C, J Clin Endocrinol Metab. jc.2012-2484, Epub 2012 Sep 28, PMID: 23024189. The sequencing was performed on tumor cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control). One control sample was omitted by the paper authors due to low quality. The package vignette describes the creation of the object from raw sequencing data provided by NCBI Gene Expression Omnibus under accession number GSE37211. The gene and exon features are the GRCh37 Ensembl annotations. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love PackageStatus: Deprecated git_url: https://git.bioconductor.org/packages/parathyroidSE git_branch: devel git_last_commit: 5bb9331 git_last_commit_date: 2024-12-11 Date/Publication: 2024-12-12 source.ver: src/contrib/parathyroidSE_1.45.1.tar.gz vignettes: vignettes/parathyroidSE/inst/doc/parathyroidSE.pdf vignetteTitles: parathyroidGenesSE hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/parathyroidSE/inst/doc/parathyroidSE.R suggestsMe: ClassifyR dependencyCount: 37 Package: pasillaBamSubset Version: 0.45.0 Suggests: pasilla License: LGPL MD5sum: 46ea071baa00008801ceef27c6970622 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: 69a929a git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/pasillaBamSubset_0.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: APAlyzer, GenomicAlignments, GenomicFeatures, GenomicRanges, gmoviz, IRanges, karyoploteR, plyranges dependencyCount: 0 Package: PasillaTranscriptExpr Version: 1.35.0 Depends: R (>= 3.3.0) Suggests: rtracklayer, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: 8049e201728bf256e4686866078d37ad 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: 5eff572 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/PasillaTranscriptExpr_1.35.0.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: 1.43.0 Depends: R (>= 1.14.0) License: GPL-3 MD5sum: 40a33764a0d8c51cf93e32b548f06dc9 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: 8f7f9d1 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/PathNetData_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PathNet dependencyCount: 0 Package: PCHiCdata Version: 1.35.0 Depends: R (>= 3.2), Chicago Suggests: testthat, BiocStyle, knitr License: Artistic-2.0 MD5sum: ae73a854686390138b934864dd9572b7 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: bf8d901 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/PCHiCdata_1.35.0.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: 77 Package: pd.atdschip.tiling Version: 0.45.0 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: ccf3864542b988518cd76aaf343a69ee 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: 1766230 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/pd.atdschip.tiling_0.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 65 Package: pepDat Version: 1.27.0 Depends: R (>= 3.5.0) Imports: GenomicRanges Suggests: knitr License: Artistic-2.0 MD5sum: f0c759127176b98cc0f7d1683380e6c8 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: f49c143 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/pepDat_1.27.0.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: 24 Package: PepsNMRData Version: 1.25.0 Depends: R (>= 3.5) Suggests: knitr, markdown, rmarkdown, BiocStyle License: GPL-2 | file LICENSE MD5sum: 294d5c303e5334e3f74b4e416c455aa3 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: ad78a11 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/PepsNMRData_1.25.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: PepsNMR dependencyCount: 0 Package: PhyloProfileData Version: 1.21.0 Depends: R (>= 4.1.0) Imports: ExperimentHub, Biostrings, BiocStyle Suggests: knitr, rmarkdown, markdown License: MIT + file LICENSE MD5sum: 3b0f8100e4ac353488350ac6de53c0a7 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], 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: 73f878c git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/PhyloProfileData_1.21.0.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: 83 Package: plotgardenerData Version: 1.13.0 Depends: R (>= 4.1.0) Suggests: rmarkdown, knitr License: MIT + file LICENSE MD5sum: e73c7af389aa609844988b8ba83373c1 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: e661004 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/plotgardenerData_1.13.0.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: 1.43.0 Depends: R (>= 2.14.0) License: Artistic-2.0 MD5sum: 04a9528c91dacd200be0bdf1308ef8b6 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: cedacac git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/prebsdata_1.43.0.tar.gz vignettes: vignettes/prebsdata/inst/doc/prebsdata.pdf vignetteTitles: prebsdata User Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: SigFuge dependencyCount: 0 Package: preciseTADhub Version: 1.15.0 Depends: R (>= 4.1) Imports: ExperimentHub Suggests: knitr, rmarkdown, markdown, BiocStyle, preciseTAD License: MIT + file LICENSE MD5sum: 59ef06f52eb97c0ca017404825be1b11 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: 25e0ff0 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/preciseTADhub_1.15.0.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: 67 Package: PREDAsampledata Version: 0.47.0 Depends: R (>= 2.10.0), methods, PREDA, Biobase, affy, annotate Suggests: hgu133plus2.db, hgu133plus2cdf License: Artistic-2.0 MD5sum: b0397fabf1e0ad37ed359ee75aee71d4 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: ab924f6 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/PREDAsampledata_0.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PREDA dependencyCount: 63 Package: ProData Version: 1.45.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL MD5sum: fec32c9f465d30df0c2648436890aeed 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: ba2d39b git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/ProData_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CorrectedFDR dependencyCount: 7 Package: pRolocdata Version: 1.45.1 Depends: R (>= 3.6.3), MSnbase Imports: Biobase, utils Suggests: pRoloc (>= 1.13.8), testthat, SummarizedExperiment License: GPL-2 MD5sum: 6a32f53e97272c8a50805deb7ce9bb9e 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: 307dfbc git_last_commit_date: 2024-11-23 Date/Publication: 2024-11-26 source.ver: src/contrib/pRolocdata_1.45.1.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: bandle suggestsMe: MSnbase, pRoloc, pRolocGUI, RforProteomics dependencyCount: 137 Package: prostateCancerCamcap Version: 1.35.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: b07b4e0a0c75b5a7a207ee2af888ccc4 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: fcde1e6 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/prostateCancerCamcap_1.35.0.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: 1.35.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: d0ee0cebbfb7f54fb462d771abbd7eea 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: e0a3be2 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/prostateCancerGrasso_1.35.0.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: 1.35.0 Depends: Biobase , R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 54c3efa7caeaf3cb1bff66690cfc12b8 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: 8d18aa6 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/prostateCancerStockholm_1.35.0.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: 1.35.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery, org.Hs.eg.db License: Artistic-2.0 MD5sum: 8b0513d518858240d1c84b9f0bc932c2 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: 105ed6c git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/prostateCancerTaylor_1.35.0.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: 1.35.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 4e49b22f1c64426321bf19e08f05d581 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: 03b01df git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/prostateCancerVarambally_1.35.0.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: 1.1.1 Depends: R (>= 4.4.0) Imports: ExperimentHub, dplyr, forcats, ggdist, gghalves, ggplot2, purrr, queryup, spdl, tidyr, tidyselect, ComplexHeatmap, stringr Suggests: AnnotationHub, tibble, BiocStyle, knitr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 111f6fc2e74404dc2c0ff707f37b83a8 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. 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. AlphaMissense pathogenicity scores for ~1.6 M substitutions in the ProteinGym DMS data, and 3. five performance metrics for 62 variant prediction models in a zero-shot 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: 1d27e6e git_last_commit_date: 2024-12-03 Date/Publication: 2024-12-05 source.ver: src/contrib/ProteinGymR_1.1.1.tar.gz vignettes: vignettes/ProteinGymR/inst/doc/data_import_and_representation.html vignetteTitles: Data access and visualization hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ProteinGymR/inst/doc/data_import_and_representation.R dependencyCount: 109 Package: ptairData Version: 1.15.0 Imports: rhdf5, signal, stats, graphics Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 32521efa052aab9218d3099220b6c248 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: aad3246 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/ptairData_1.15.0.tar.gz vignettes: vignettes/ptairData/inst/doc/ptairData_vignette.html vignetteTitles: PTR-TOF-MS dataset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ptairData/inst/doc/ptairData_vignette.R suggestsMe: ptairMS dependencyCount: 10 Package: PtH2O2lipids Version: 1.33.0 Depends: R (>= 3.3), xcms, CAMERA, LOBSTAHS, methods, utils Suggests: gplots, RColorBrewer, cluster, vegan License: MIT + file LICENSE MD5sum: 81746a15104fe4a61d95f599bee9aa20 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: ddcbffb git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/PtH2O2lipids_1.33.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: LOBSTAHS dependencyCount: 162 Package: pumadata Version: 2.43.0 Depends: R (>= 3.2.0), Biobase (>= 2.5.5),puma, oligo(>= 1.32.0) License: LGPL MD5sum: 5654e2e275810c9bbbfcc1cd6bda1bf7 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: e859cbf git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/pumadata_2.43.0.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: 68 Package: PWMEnrich.Dmelanogaster.background Version: 4.41.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: d94360ed324b0986123bfb4e699baee6 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: 9a53922 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/PWMEnrich.Dmelanogaster.background_4.41.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 32 Package: PWMEnrich.Hsapiens.background Version: 4.41.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: cb7b53873630930022594a491cc1c492 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: 22a8270 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/PWMEnrich.Hsapiens.background_4.41.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 32 Package: PWMEnrich.Mmusculus.background Version: 4.41.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: 9d5742eab89b98f3cda64917a52a5b56 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: 4505f19 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/PWMEnrich.Mmusculus.background_4.41.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 32 Package: QDNAseq.hg19 Version: 1.37.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: 23819cc33bf521227f48da51a330663a 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: 132925e git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/QDNAseq.hg19_1.37.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: biscuiteer, QDNAseq dependencyCount: 60 Package: QDNAseq.mm10 Version: 1.37.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: 206e00c09060a6080cae271c551b71fa 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: 61887de git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/QDNAseq.mm10_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: biscuiteer, QDNAseq dependencyCount: 60 Package: qPLEXdata Version: 1.25.0 Depends: R (>= 3.5), qPLEXanalyzer Imports: utils, knitr, MSnbase, dplyr Suggests: statmod License: GPL-2 MD5sum: 3ef1f5079a281d2e169bc57ba3fb1e7f NeedsCompilation: no Title: Data accompanying qPLEXanalyzer package Description: qPLEX-RIME and Full proteome TMT mass spectrometry datasets. biocViews: ExperimentData, MassSpectrometryData, Proteome Author: Kamal Kishore Developer [aut, cre] Maintainer: Kamal Kishore Developer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/qPLEXdata git_branch: devel git_last_commit: e6cd495 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/qPLEXdata_1.25.0.tar.gz vignettes: vignettes/qPLEXdata/inst/doc/qPLEXdata.pdf vignetteTitles: qPLEXdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/qPLEXdata/inst/doc/qPLEXdata.R suggestsMe: qPLEXanalyzer dependencyCount: 150 Package: QUBICdata Version: 1.35.0 Depends: R (>= 3.1) Suggests: knitr, rmarkdown License: Unlimited | file LICENSE MD5sum: d4a0e5917c94f9c40e1f3ac39753b223 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: 7dfe72a git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/QUBICdata_1.35.0.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: 1.5.0 Imports: ExperimentHub, Rsamtools, BiocGenerics, rtracklayer, SingleCellExperiment Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 15f0a85a4b985bedf15ff57aed3db0b0 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: 4f82cec git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/raerdata_1.5.0.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: 98 Package: rcellminerData Version: 2.29.0 Depends: R (>= 3.5.0), Biobase Suggests: knitr, testthat, BiocStyle, rcellminer, rmarkdown License: LGPL-3 + file LICENSE MD5sum: aea284133a8858d241e315b404fd2c6f 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: 53bd41d git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/rcellminerData_2.29.0.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: 1.27.0 Depends: R (>= 3.3) Imports: data.table License: GPL-3 MD5sum: a81e3714d19f578b67ca47e9c9490ea2 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: cad57ca git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.27.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RcisTarget dependencyCount: 2 Package: ReactomeGSA.data Version: 1.21.0 Depends: R (>= 3.6), limma, edgeR, ReactomeGSA, Seurat License: Artistic-2.0 MD5sum: ed7e1eba65e3d71531598e9cc75baba4 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: 4430765 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/ReactomeGSA.data_1.21.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ReactomeGSA dependencyCount: 190 Package: RegParallel Version: 1.25.0 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: a1aaa2fcae75da33afec8ea1f7663107 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: 22c2458 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/RegParallel_1.25.0.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: 36 Package: RforProteomics Version: 1.45.0 Depends: R (>= 3.5), MSnbase (>= 2.5.3) 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, DEP, corrplot, beanplot, Heatplus, gplots, VennDiagram, protViz, genefilter, plotly, gridExtra, dplyr, lubridate, magick, cleaver License: Artistic-2.0 MD5sum: 8a466537006191b168a5101d6fc4dc48 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: 0b531a2 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/RforProteomics_1.45.0.tar.gz vignettes: vignettes/RforProteomics/inst/doc/RforProteomics.html, vignettes/RforProteomics/inst/doc/RProtVis.html vignetteTitles: Using R for proteomics data analysis, Visualisation of proteomics data using R and Bioconductor hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RforProteomics/inst/doc/RforProteomics.R, vignettes/RforProteomics/inst/doc/RProtVis.R suggestsMe: MSstatsQC dependencyCount: 146 Package: RGMQLlib Version: 1.27.0 Depends: R(>= 3.4.2) Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 3b54510f73ec622fd7e8bfab35cfb133 NeedsCompilation: no Title: RGMQLlib, java libraries to run GMQL scala API Description: A package that contains scala libraries to call GMQL from R used by RGMQL package. It contains a scalable data management engine written in Scala programming language. biocViews: ExperimentData,RepositoryData Author: Simone Pallotta [aut, cre], Marco Masseroli [aut] Maintainer: Simone Pallotta URL: http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/ VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RGMQLlib git_branch: devel git_last_commit: 8d6400d git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/RGMQLlib_1.27.0.tar.gz vignettes: vignettes/RGMQLlib/inst/doc/RGMQLlib.pdf vignetteTitles: RGMQLlib: scala Libraries to support GMQL hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: rheumaticConditionWOLLBOLD Version: 1.45.0 Depends: R (>= 2.10.0) Suggests: genefilter, Biobase, hgu133plus2.db License: Artistic-2.0 MD5sum: b504132e05055520cf8d371d762925b4 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: 5aedc0d git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/rheumaticConditionWOLLBOLD_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: RITANdata Version: 1.31.0 Depends: R (>= 4.2) Suggests: knitr License: file LICENSE MD5sum: 9f4317c4efcc5ee31b1e63a74cfbf6dc 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: 5ad3cab git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/RITANdata_1.31.0.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: 1.45.0 Suggests: RMassBank License: Artistic-2.0 MD5sum: 29fc6b678be79cdf117c90575a3488a3 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: 98941db git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/RMassBankData_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RMassBank dependencyCount: 0 Package: RNAmodR.Data Version: 1.21.0 Depends: R (>= 3.6), ExperimentHub, ExperimentHubData (>= 1.9.2) Imports: utils Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, sessioninfo, testthat License: Artistic-2.0 MD5sum: a18900b2acb1f10712bb08a87f540285 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: 3a51bd2 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/RNAmodR.Data_1.21.0.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: 126 Package: RNAseqData.HNRNPC.bam.chr14 Version: 0.45.0 Suggests: GenomicAlignments, BiocManager License: LGPL MD5sum: ee3b2de806dee6c7c504d5109b0e10f6 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: f054c01 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/RNAseqData.HNRNPC.bam.chr14_0.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: sequencing suggestsMe: BiocParallel, GenomicAlignments, GenomicFiles, GenomicRanges, roar, Rsamtools, SplicingGraphs dependencyCount: 0 Package: RnaSeqSampleSizeData Version: 1.39.0 Depends: edgeR,R (>= 2.10) Suggests: BiocStyle, knitr License: GPL (>= 2) MD5sum: 65bed1a31bcfdf0fe07a23e0f7b54f7d 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: 550d841 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/RnaSeqSampleSizeData_1.39.0.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: 1.39.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 7e03bfd3e7c6f86a917039a440307275 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: 05665af git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/RnBeads.hg19_1.39.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: MAGAR suggestsMe: RnBeads dependencyCount: 24 Package: RnBeads.hg38 Version: 1.39.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 2096c129400789f8162de8b7e9cb1ded NeedsCompilation: no Title: RnBeads.hg38 Description: RnBeads annotation package for genome assembly hg38. Author: RnBeads Team Maintainer: RnBeads Team git_url: https://git.bioconductor.org/packages/RnBeads.hg38 git_branch: devel git_last_commit: 9c8f149 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/RnBeads.hg38_1.39.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: MAGAR suggestsMe: RnBeads dependencyCount: 24 Package: RnBeads.mm10 Version: 2.15.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 8e01e1b7c8fa3898673da4e3c183db5c 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: f501dc3 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/RnBeads.mm10_2.15.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 24 Package: RnBeads.mm9 Version: 1.39.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: f6a64540759cf484ddf53b87389ad8cf 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: b460c6d git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/RnBeads.mm9_1.39.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RnBeads dependencyCount: 24 Package: RnBeads.rn5 Version: 1.39.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 7779f98727eed6501a9154d7ff58dcb1 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: a258c78 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/RnBeads.rn5_1.39.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 24 Package: RRBSdata Version: 1.27.0 Depends: R (>= 3.5.0), BiSeq (>= 1.9.2) License: LGPL-3 MD5sum: 06e4f756d04c8969f63a32575a3cb7a1 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: 7335bdd git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/RRBSdata_1.27.0.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: 93 Package: rRDPData Version: 1.27.0 Depends: rRDP License: GPL-2 MD5sum: 257c9775fb31e60dc113072da8ed2472 NeedsCompilation: no Title: Databases for the Default RDP Classifier Description: The package provides the data for the RDP Classifier 2.14 released in August 2023. It contains the latest bacterial and archaeal taxonomy training set No. 19 as described in Wang Q, Cole JR. 2024. Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification. Microbiol Resour Announc 0:e01063-23. biocViews: SequencingData, MicrobiomeData, RNASeqData Author: Michael Hahsler [aut, cre] (ORCID: ), Nagar Anurag [aut] Maintainer: Michael Hahsler URL: https://github.com/mhahsler/rRDP git_url: https://git.bioconductor.org/packages/rRDPData git_branch: devel git_last_commit: bc56232 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/rRDPData_1.27.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: rRDP dependencyCount: 28 Package: RTCGA.clinical Version: 20151101.37.0 Depends: R (>= 3.2.0), RTCGA Suggests: rmarkdown, knitr License: GPL-2 MD5sum: 6d4b9e37855d50b491fbee1213e6e0cc 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: 706d355 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/RTCGA.clinical_20151101.37.0.tar.gz vignettes: vignettes/RTCGA.clinical/inst/doc/downloading_clinical_datasets.html vignetteTitles: Using RTCGA to download clinical data as included in RTCGA.clinical hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.clinical/inst/doc/downloading_clinical_datasets.R suggestsMe: RTCGA, TDbasedUFEadv dependencyCount: 129 Package: RTCGA.CNV Version: 1.35.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 37f13e72c73cbcbf1daa1011d576cb35 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: 9682326 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/RTCGA.CNV_1.35.0.tar.gz vignettes: vignettes/RTCGA.CNV/inst/doc/downloading_cnv_datasets.html, vignettes/RTCGA.CNV/inst/doc/frequency_of_cnv_for_mdm3.html vignetteTitles: Using RTCGA to download CNV data as included in RTCGA.CNV, Using RTCGA to estimate ratio of MDM2 duplications hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.CNV/inst/doc/downloading_cnv_datasets.R, vignettes/RTCGA.CNV/inst/doc/frequency_of_cnv_for_mdm3.R suggestsMe: RTCGA dependencyCount: 129 Package: RTCGA.methylation Version: 1.35.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 7795701ed0042b9e5be1d14f43259000 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: eaac672 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/RTCGA.methylation_1.35.0.tar.gz vignettes: vignettes/RTCGA.methylation/inst/doc/downloading_methylation_datasets.html vignetteTitles: Using RTCGA to download methylation data as included in RTCGA.methylation hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.methylation/inst/doc/downloading_methylation_datasets.R suggestsMe: RTCGA dependencyCount: 129 Package: RTCGA.miRNASeq Version: 1.35.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: f457ffdf62f6f7ff60c91f4fe9d30267 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: eb001af git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/RTCGA.miRNASeq_1.35.0.tar.gz vignettes: vignettes/RTCGA.miRNASeq/inst/doc/downloading_miRNASeq_datasets.html vignetteTitles: Using RTCGA to download miRNASeq data as included in RTCGA.miRNASeq hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.miRNASeq/inst/doc/downloading_miRNASeq_datasets.R suggestsMe: RTCGA dependencyCount: 129 Package: RTCGA.mRNA Version: 1.35.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 21f856b3b08475faacf5905c0455b164 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: 50b92b0 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/RTCGA.mRNA_1.35.0.tar.gz vignettes: vignettes/RTCGA.mRNA/inst/doc/downloading_mRNA_datasets.html vignetteTitles: Using RTCGA to download mRNA data as included in RTCGA.mRNA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.mRNA/inst/doc/downloading_mRNA_datasets.R suggestsMe: RTCGA dependencyCount: 129 Package: RTCGA.mutations Version: 20151101.37.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: b791059fa97ecfacdf8c1d0ddb893294 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: 15cec69 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/RTCGA.mutations_20151101.37.0.tar.gz vignettes: vignettes/RTCGA.mutations/inst/doc/downloading_mutations_datasets.html vignetteTitles: Using RTCGA to download mutations data as included in RTCGA.mutations hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.mutations/inst/doc/downloading_mutations_datasets.R suggestsMe: RTCGA dependencyCount: 129 Package: RTCGA.PANCAN12 Version: 1.35.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: eee6fba40a9c21dd2939038b16b6eb98 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: 2e0db04 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/RTCGA.PANCAN12_1.35.0.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: 129 Package: RTCGA.rnaseq Version: 20151101.37.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 09691473b4315bd24b84f88d52f54b23 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: 8d36feb git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/RTCGA.rnaseq_20151101.37.0.tar.gz vignettes: vignettes/RTCGA.rnaseq/inst/doc/downloading_rnaseq_datasets.html vignetteTitles: Using RTCGA to download RNAseq data as included in RTCGA.rnaseq hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.rnaseq/inst/doc/downloading_rnaseq_datasets.R suggestsMe: RTCGA, TDbasedUFEadv, FSelectorRcpp dependencyCount: 129 Package: RTCGA.RPPA Version: 1.35.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: fa827334d89b819e00c89e4e32391831 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: c61b94b git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/RTCGA.RPPA_1.35.0.tar.gz vignettes: vignettes/RTCGA.RPPA/inst/doc/downloading_RPPA_datasets.html vignetteTitles: Using RTCGA to download RPPA data as included in RTCGA.RPPA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.RPPA/inst/doc/downloading_RPPA_datasets.R suggestsMe: RTCGA dependencyCount: 129 Package: RUVnormalizeData Version: 1.27.0 Depends: R (>= 2.10.0), Biobase License: GPL-3 MD5sum: 1f14ab47c34557d36bddd84a891d97fb 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: 76a8fa0 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/RUVnormalizeData_1.27.0.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: 1.31.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: BiocStyle License: Artistic-2.0 MD5sum: 7cbbfea26ab52670855d8a49360f158a 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: 2ba9b11 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/sampleClassifierData_1.31.0.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 suggestsMe: sampleClassifier dependencyCount: 37 Package: SBGNview.data Version: 1.21.0 Depends: R (>= 3.6) Imports: knitr, rmarkdown, bookdown Suggests: SummarizedExperiment License: AGPL-3 MD5sum: d32b563e655c8610eab26bf6bfd92ea6 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: 974f78f git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/SBGNview.data_1.21.0.tar.gz vignettes: vignettes/SBGNview.data/inst/doc/SBGNview.data.vignette.html vignetteTitles: Supporting Datasets for SBGNview Package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SBGNview.data/inst/doc/SBGNview.data.vignette.R dependsOnMe: SBGNview dependencyCount: 32 Package: scaeData Version: 1.3.0 Depends: R (>= 4.4.0) Imports: ExperimentHub Suggests: knitr, rmarkdown, markdown, SingleCellAlleleExperiment, Matrix, BiocStyle License: MIT + file LICENSE MD5sum: 6b36819e7a4fba14a5d5a13d61459b5d 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: 562cb07 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/scaeData_1.3.0.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: 67 Package: scanMiRData Version: 1.13.0 Depends: R (>= 4.0) Imports: scanMiR, utils Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 41c5f77807bc6e35df07a635f4317abf 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: 6f31480 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/scanMiRData_1.13.0.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: 72 Package: scATAC.Explorer Version: 1.13.0 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: 19c81a63f0dc197709ecbe8e5ceae759 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, cre], Erik Christensen [aut], Jonathan Wang [aut], Parisa Shooshtari [aut] Maintainer: Arrian Gibson-Khademi VignetteBuilder: knitr BugReports: https://github.com/shooshtarilab/scATACseq/issues git_url: https://git.bioconductor.org/packages/scATAC.Explorer git_branch: devel git_last_commit: b8190d2 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/scATAC.Explorer_1.13.0.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: 82 Package: SCLCBam Version: 1.39.0 Depends: R(>= 2.10) Suggests: BiocStyle License: GPL-2 MD5sum: f59e6632d218659b8be91742a7c16981 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: 045494f git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/SCLCBam_1.39.0.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: 1.7.1 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: b5b88212749c4de5460ca07d343882ed 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: 05759d2 git_last_commit_date: 2024-12-18 Date/Publication: 2024-12-19 source.ver: src/contrib/scMultiome_1.7.1.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 importsMe: epiregulon suggestsMe: epiregulon.extra dependencyCount: 102 Package: scpdata Version: 1.13.0 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: 30146cda4456215c29de894ae2966d76 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: 5c8b368 git_last_commit_date: 2024-04-30 Date/Publication: 2024-10-27 source.ver: src/contrib/scpdata_1.13.0.tar.gz vignettes: vignettes/scpdata/inst/doc/contribution_guidelines.html, vignettes/scpdata/inst/doc/scpdata.html vignetteTitles: Contribution guidelines, Data Package for Single Cell Proteomics hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scpdata/inst/doc/contribution_guidelines.R, vignettes/scpdata/inst/doc/scpdata.R suggestsMe: scp dependencyCount: 126 Package: scRNAseq Version: 2.21.0 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: 870a9e45cb0e8d5675ea96cf60f60ffc 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: e33f182 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-07 source.ver: src/contrib/scRNAseq_2.21.0.tar.gz vignettes: vignettes/scRNAseq/inst/doc/scRNAseq.html vignetteTitles: User's Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scRNAseq/inst/doc/scRNAseq.R dependsOnMe: OSCA.intro, OSCA.workflows, SingleRBook importsMe: singleCellTK suggestsMe: APL, BASiCS, batchelor, bluster, ccImpute, ClusterFoldSimilarity, destiny, dittoSeq, Glimma, iSEE, iSEEfier, iSEEhex, iSEEindex, iSEEu, miloR, miQC, mumosa, ReactomeGSA, scAnnotatR, scater, scDblFinder, scDiagnostics, scDotPlot, scFeatureFilter, scone, scran, scrapper, scTreeViz, scuttle, SingleCellExperiment, SingleR, SplineDV, UCell, velociraptor, zellkonverter, zinbwave, speakeasyR dependencyCount: 119 Package: scTHI.data Version: 1.19.0 Depends: R (>= 4.0) License: GPL-2 MD5sum: f0ec707b8aa4852ddac6166ccfe56fe9 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: ea018df git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/scTHI.data_1.19.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: scTHI dependencyCount: 0 Package: seq2pathway.data Version: 1.39.0 Depends: R (>= 3.6.2) License: GPL (>= 2) MD5sum: de8d51527350fb1862b056b9294a153c 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: 4a799c2 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/seq2pathway.data_1.39.0.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: 1.41.0 Depends: R (>= 2.10) Imports: utils, Biobase License: GPL-3 MD5sum: d5acd487f4f6fffbf2bfd9db8e01fd8f 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: 301ac11 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/seqc_1.41.0.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: 1.43.0 Depends: R (>= 2.10) License: GPL (>= 2) MD5sum: edd42a0e1ef0517d4b9ac75c5166fbaa 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: 73b3f19 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/serumStimulation_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: sesameData Version: 1.25.0 Depends: R (>= 4.2.0), ExperimentHub, AnnotationHub Imports: utils, readr, stringr, GenomicRanges, S4Vectors, IRanges, GenomeInfoDb Suggests: BiocGenerics, sesame, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: bc32b871419ae6e1d05fc141fd624912 NeedsCompilation: no Title: Supporting Data for SeSAMe Package Description: Provides supporting annotation and test data for SeSAMe package. This includes chip tango addresses, mapping information, performance annotation, and trained predictor for Infinium array data. This package provides user access to essential annotation data for working with many generations of the Infinium DNA methylation array. Current we support human array (HM27, HM450, EPIC), mouse array (MM285) and the HorvathMethylChip40 (Mammal40) array. biocViews: ExperimentData, MicroarrayData, Genome, ExperimentHub, MethylationArrayData Author: Wanding Zhou [aut, cre] (ORCID: ), Hui Shen [aut], Timothy Triche [ctb] Maintainer: Wanding Zhou URL: https://github.com/zwdzwd/sesame VignetteBuilder: knitr BugReports: https://github.com/zwdzwd/sesame/issue git_url: https://git.bioconductor.org/packages/sesameData git_branch: devel git_last_commit: a049c9a git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/sesameData_1.25.0.tar.gz vignettes: vignettes/sesameData/inst/doc/sesameData.html vignetteTitles: sesameData User Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/sesameData/inst/doc/sesameData.R dependsOnMe: sesame importsMe: knowYourCG, MethReg, CytoMethIC suggestsMe: ELMER, iNETgrate dependencyCount: 75 Package: seventyGeneData Version: 1.43.0 Depends: R (>= 2.13.0) Suggests: Biobase, limma, breastCancerNKI, knitr, rmarkdown, readxl, BiocStyle License: Artistic-2.0 MD5sum: b7bd0acb551b9915800422d14c258d88 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: 9e86cda git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/seventyGeneData_1.43.0.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: 1.9.1 Imports: BiocFileCache, AnnotationHub, ExperimentHub, utils Suggests: BiocStyle, knitr, rmarkdown, SeuratObject, SpatialFeatureExperiment, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: fb9fa470d592ea10ca8fce67b10ed0fb 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: 41362ac git_last_commit_date: 2024-12-17 Date/Publication: 2024-12-19 source.ver: src/contrib/SFEData_1.9.1.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: concordexR, SpatialFeatureExperiment, Voyager, xenLite dependencyCount: 67 Package: shinyMethylData Version: 1.27.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: df5587c341c1290ec289b01c90ce032b 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: 1baedcf git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/shinyMethylData_1.27.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: shinyMethyl dependencyCount: 0 Package: signatureSearchData Version: 1.21.0 Depends: R (>= 3.6) Imports: ExperimentHub, utils, affy, limma, Biobase, magrittr, dplyr, R.utils, stats, rhdf5 Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 504c442f1656a372f2dcbe1092d53372 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: 4d1195c git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/signatureSearchData_1.21.0.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 importsMe: DFD suggestsMe: signatureSearch dependencyCount: 78 Package: SimBenchData Version: 1.15.0 Depends: ExperimentHub Imports: S4Vectors, utils Suggests: BiocStyle, knitr, rmarkdown, Seurat License: GPL-3 MD5sum: a9da702d09bdca4c4f6f65cb58b29a5b 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: 9215c5a git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/SimBenchData_1.15.0.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: 67 Package: simpIntLists Version: 1.43.0 License: GPL (>= 2) MD5sum: 32afccc3829de0219fd2a7640992a7fb 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: 6724d0e git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/simpIntLists_1.43.0.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: 1.35.0 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: 65d4e50a9700a074e38b5fc888951f68 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: 5995538 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/Single.mTEC.Transcriptomes_1.35.0.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: 1.19.1 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: 52ca241c239b8376046f8ebbc6a84849 NeedsCompilation: no Title: Integrating Multi-modal Single Cell Experiment datasets Description: SingleCellMultiModal is an ExperimentHub package that serves multiple datasets obtained from GEO and other sources and represents them as MultiAssayExperiment objects. We provide several multi-modal datasets including scNMT, 10X Multiome, seqFISH, CITEseq, SCoPE2, and others. The scope of the package is is to provide data for benchmarking and analysis. To cite, use the 'citation' function and see . biocViews: ExperimentData, SingleCellData, ReproducibleResearch, ExperimentHub, GEO Author: Marcel Ramos [aut, cre] (ORCID: ), Ricard Argelaguet [aut], Al Abadi [ctb], Dario Righelli [aut], Christophe Vanderaa [ctb], Kelly Eckenrode [aut], Ludwig Geistlinger [aut], Levi Waldron [aut] Maintainer: Marcel Ramos VignetteBuilder: knitr BugReports: https://github.com/waldronlab/SingleCellMultiModal/issues git_url: https://git.bioconductor.org/packages/SingleCellMultiModal git_branch: devel git_last_commit: 0c4f175 git_last_commit_date: 2024-11-20 Date/Publication: 2024-11-21 source.ver: src/contrib/SingleCellMultiModal_1.19.1.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: 89 Package: SingleMoleculeFootprintingData Version: 1.15.0 Imports: ExperimentHub, utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: ed5ca85afb52efead33d658b02923796 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: 99cb0ef git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/SingleMoleculeFootprintingData_1.15.0.tar.gz vignettes: vignettes/SingleMoleculeFootprintingData/inst/doc/SingleMoleculeFootprintingData.html vignetteTitles: SingleMoleculeFootprintingData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/SingleMoleculeFootprintingData/inst/doc/SingleMoleculeFootprintingData.R suggestsMe: SingleMoleculeFootprinting dependencyCount: 67 Package: smokingMouse Version: 1.5.1 Suggests: AnnotationHubData, BiocStyle, ExperimentHub, ExperimentHubData, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: e035921c33092a2255e5aecc055fa60a 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: 7f4f18b git_last_commit_date: 2024-12-10 Date/Publication: 2024-12-12 source.ver: src/contrib/smokingMouse_1.5.1.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: 1.53.0 Depends: R (>= 2.4.0), graph Suggests: Rgraphviz License: LGPL MD5sum: f78edd0083231de0f45d0351b6011390 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: f583142 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/SNAData_1.53.0.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: 1.43.0 Depends: R (>= 2.6.0) Suggests: ALL, hgu95av2.db, SNAGEE License: Artistic-2.0 MD5sum: e8f25ba86521398bac4662806991e875 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: c460c79 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/SNAGEEdata_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: SNAGEE dependencyCount: 0 Package: SNPhoodData Version: 1.37.0 Depends: R (>= 3.2) Suggests: BiocStyle,knitr,rmarkdown License: LGPL (>= 3) MD5sum: cd0c2d934e935286a85d0bd55d5dbc67 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: 3f50936 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/SNPhoodData_1.37.0.tar.gz vignettes: vignettes/SNPhoodData/inst/doc/SNPhoodData.html vignetteTitles: The *SNPhoodData* package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: SNPhood dependencyCount: 0 Package: SomatiCAData Version: 1.45.0 Depends: R (>= 2.14) License: Artistic-2.0 MD5sum: 185bf924c2f889655e7b10c481d2990a 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: 9292976 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/SomatiCAData_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: SomaticCancerAlterations Version: 1.43.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, IRanges, S4Vectors Suggests: testthat, ggbio, ggplot2, knitr License: GPL-3 MD5sum: e3763d5c33cc5074f2dcfd84323d0991 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: 0a08c2e git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/SomaticCancerAlterations_1.43.0.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: 24 Package: SpatialDatasets Version: 1.5.0 Depends: ExperimentHub, SpatialExperiment, Imports: utils Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: e8a226a1ba2fc632f10ef94b21d64c35 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], 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: 4d2db5a git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/SpatialDatasets_1.5.0.tar.gz vignettes: vignettes/SpatialDatasets/inst/doc/SpatialDatasets_overview.html vignetteTitles: The SpatialDataset package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SpatialDatasets/inst/doc/SpatialDatasets_overview.R suggestsMe: lisaClust, spicyR, spicyWorkflow dependencyCount: 83 Package: spatialDmelxsim Version: 1.13.0 Depends: R (>= 4.1), ExperimentHub, SummarizedExperiment Imports: utils Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 7b9a6a918e490911ea6b6ff4040503dd 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: e8d55bf git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/spatialDmelxsim_1.13.0.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: 78 Package: spatialLIBD Version: 1.19.6 Depends: SpatialExperiment (>= 1.3.3), R (>= 3.6) 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: f6f4f5294ac1b11ab6187a7a89f9e4b3 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: 27db42d git_last_commit_date: 2024-12-16 Date/Publication: 2024-12-17 source.ver: src/contrib/spatialLIBD_1.19.6.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: visiumStitched suggestsMe: Banksy, BayesSpace, DESpace dependencyCount: 202 Package: SpikeIn Version: 1.49.0 Depends: R (>= 2.10), affy (>= 1.23.4) License: Artistic-2.0 MD5sum: 453eab7fae5a13c3a1e82aa3ecf3dc3d 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: 7257c31 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/SpikeIn_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PECA dependencyCount: 13 Package: SpikeInSubset Version: 1.47.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5), affy (>= 1.23.4) License: LGPL MD5sum: 41641756f3e88c32e622ea477b41c96b 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: 6570b1c git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/SpikeInSubset_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 13 Package: spqnData Version: 1.19.0 Depends: R (>= 4.0), SummarizedExperiment License: Artistic-2.0 MD5sum: a168c83344ebfdc15e9ba933e78ab707 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: 672de9e git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/spqnData_1.19.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: spqn dependencyCount: 37 Package: stemHypoxia Version: 1.43.0 Depends: R (>= 2.14.1) License: GPL (>=2) MD5sum: 1aaa320b1dab303cc23a8560296bb0c4 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: 52faab6 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/stemHypoxia_1.43.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: lmdme dependencyCount: 0 Package: STexampleData Version: 1.15.0 Depends: ExperimentHub, SingleCellExperiment, SpatialExperiment Imports: utils Suggests: BiocStyle, knitr, rmarkdown, BumpyMatrix, HDF5Array License: MIT + file LICENSE MD5sum: 13871e91b97a59a6708db91aad585308 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: 5424966 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/STexampleData_1.15.0.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: escheR, ggsc, ggspavis, nnSVG, smoothclust, spatialSimGP, spoon, SpotSweeper, tpSVG dependencyCount: 83 Package: SubcellularSpatialData Version: 1.3.0 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: 94a8e0ce07274d4866444fb14b3993da 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: 060a422 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/SubcellularSpatialData_1.3.0.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: 74 Package: SVM2CRMdata Version: 1.39.0 Depends: R(>= 3.2.0) License: LGPL (>= 2) MD5sum: e93a872f3e1e1b5ba2b176d80890e1c0 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: bc24b23 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/SVM2CRMdata_1.39.0.tar.gz vignettes: vignettes/SVM2CRMdata/inst/doc/SVM2CRMdata.pdf vignetteTitles: The \Rpackage{SVM2CRMdata} Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SVM2CRMdata/inst/doc/SVM2CRMdata.R dependencyCount: 0 Package: synapterdata Version: 1.45.0 Depends: R (>= 2.10), synapter (>= 1.99.2) Imports: utils License: GPL-2 MD5sum: 6ad5efa56eb7e26aec024cd8207907c9 NeedsCompilation: no Title: Data accompanying the synapter package Description: Data independant acquisition of UPS1 protein mix in an E. coli background obtained on a Waters Synapt G2 instrument. biocViews: ExperimentData, MassSpectrometryData Author: Laurent Gatto, Sebastian Gibb and Pavel V. Shliaha Maintainer: Laurent Gatto git_url: https://git.bioconductor.org/packages/synapterdata git_branch: devel git_last_commit: 6bc3685 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/synapterdata_1.45.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: synapter dependencyCount: 152 Package: systemPipeRdata Version: 2.11.0 Depends: R (>= 3.6.0) Imports: methods, Biostrings, BiocGenerics, jsonlite, remotes Suggests: GenomicFeatures, GenomicRanges, IRanges, Rsamtools, ShortRead, rtracklayer, RUnit, BiocStyle, knitr, rmarkdown, systemPipeR, kableExtra, magrittr, dplyr License: Artistic-2.0 MD5sum: e6471975e5087945824bc3e87e20c358 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, https://systempipe.org/ VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/systemPipeRdata git_branch: devel git_last_commit: f041ddb git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/systemPipeRdata_2.11.0.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: 27 Package: TabulaMurisData Version: 1.25.0 Depends: R (>= 3.5) Imports: ExperimentHub, utils Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran, scater, iSEE, testthat License: MIT + file LICENSE MD5sum: 1a65079ddb3fb50bcbdf5bff5057403c 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: 3ac627b git_last_commit_date: 2024-11-02 Date/Publication: 2024-11-05 source.ver: src/contrib/TabulaMurisData_1.25.0.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: 67 Package: TabulaMurisSenisData Version: 1.13.0 Imports: ExperimentHub, SingleCellExperiment, HDF5Array, SummarizedExperiment, gdata, AnnotationHub Suggests: ggplot2, testthat, knitr, rmarkdown, iSEE, BiocStyle License: MIT + file LICENSE MD5sum: 05f9343a2baf4de2051b1f1f2a5b8ffb 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: f4845ad git_last_commit_date: 2024-11-02 Date/Publication: 2024-11-05 source.ver: src/contrib/TabulaMurisSenisData_1.13.0.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: SPOTlight dependencyCount: 85 Package: TargetScoreData Version: 1.43.0 Suggests: TargetScore, gplots License: GPL-2 MD5sum: 78dfdb9e0ee2f6592dd3fb2d5d41c4f1 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: 94f8d71 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/TargetScoreData_1.43.0.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: 1.45.0 License: GPL (>= 2) MD5sum: c50c91b62be7a02a4b73d3d15f9e20b7 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: 056652e git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/TargetSearchData_1.45.0.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: 1.21.0 Depends: R (>= 4.1), AnnotationHub (>= 2.16), ExperimentHub (>= 1.0) Imports: utils Suggests: BiocStyle, knitr, rmarkdown, testthat, tools License: GPL-3 MD5sum: 48c9942b1eb77de91e814536818c38ad 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: 8cf6c33 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/tartare_1.21.0.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: 67 Package: TBX20BamSubset Version: 1.43.0 Depends: Rsamtools (>= 1.9.8) Imports: xtable License: LGPL MD5sum: 188622195025c2b80d0aeab263fa4b2d 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: bcd0497 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/TBX20BamSubset_1.43.0.tar.gz vignettes: vignettes/TBX20BamSubset/inst/doc/TBX20BamSubset.pdf vignetteTitles: TBX20 RNA-Seq data subset hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TBX20BamSubset/inst/doc/TBX20BamSubset.R importsMe: Rmmquant suggestsMe: APAlyzer, magpie dependencyCount: 41 Package: TCGAbiolinksGUI.data Version: 1.27.0 Depends: R (>= 3.5.0) Suggests: BiocStyle, knitr, rmarkdown, readr, DT License: GPL-3 MD5sum: a6bc79f3e8545071ae79cd196f427067 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: f2fe372 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/TCGAbiolinksGUI.data_1.27.0.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: 1.27.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 6e6d33e52d656403945f6d291c44a259 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: f353de8 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/TCGAcrcmiRNA_1.27.0.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: 1.27.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 010934a7d3a5520bb9f8b72d4ba3bf43 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: cc827ef git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/TCGAcrcmRNA_1.27.0.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: 1.43.0 License: GPL-2 MD5sum: 454b825091aae6a8a3692a95d76464f4 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: 72df838 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/TCGAMethylation450k_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: methylumi dependencyCount: 0 Package: TCGAWorkflowData Version: 1.31.0 Depends: R (>= 3.5.0) Imports: SummarizedExperiment Suggests: knitr, rmarkdown, pander, testthat, BiocStyle License: GPL-3 MD5sum: 974c3c54de6b29c24d0786030035cee4 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: 46a3dbc git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/TCGAWorkflowData_1.31.0.tar.gz vignettes: vignettes/TCGAWorkflowData/inst/doc/TCGAWorkflowData.html vignetteTitles: 'Example data for TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages' hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TCGAWorkflowData/inst/doc/TCGAWorkflowData.R importsMe: TCGAWorkflow dependencyCount: 37 Package: TENxBrainData Version: 1.27.0 Depends: SingleCellExperiment, HDF5Array Imports: AnnotationHub (>= 2.9.22), ExperimentHub Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel, data.table, rmarkdown License: CC BY 4.0 MD5sum: 5424ca26d12f008c9605703f97e4f33e 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: d3ef120 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/TENxBrainData_1.27.0.tar.gz vignettes: vignettes/TENxBrainData/inst/doc/TENxBrainData.html vignetteTitles: Exploring the 1.3 million brain cell scRNA-seq data from 10X Genomics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TENxBrainData/inst/doc/TENxBrainData.R suggestsMe: HDF5Array dependencyCount: 83 Package: TENxBUSData Version: 1.21.0 Imports: ExperimentHub, AnnotationHub, utils, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle License: BSD_2_clause + file LICENSE MD5sum: 2470bb239951b3895d9bd3650ab7d5e9 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: c3090aa git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/TENxBUSData_1.21.0.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: 67 Package: TENxPBMCData Version: 1.25.0 Depends: SingleCellExperiment, HDF5Array Imports: AnnotationHub, ExperimentHub Suggests: rmarkdown, knitr, BiocStyle, snow, BiocFileCache, BiocParallel License: CC BY 4.0 MD5sum: 0c77103f1faf8e9df52f1014456734fd 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: 89cadcb git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/TENxPBMCData_1.25.0.tar.gz vignettes: vignettes/TENxPBMCData/inst/doc/TENxPBMCData.html vignetteTitles: Obtaining scRNA-seq data on PBMCs from 10X Genomics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TENxPBMCData/inst/doc/TENxPBMCData.R dependsOnMe: SingleRBook importsMe: singleCellTK suggestsMe: adverSCarial, ASURAT, celda, concordexR, decontX, ExperimentSubset, glmGamPoi, iSEE, mbkmeans, schex, scone, scry, sketchR, transformGamPoi dependencyCount: 83 Package: TENxVisiumData Version: 1.15.0 Depends: ExperimentHub, SpatialExperiment Imports: utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 27ea9c34d59d03fd8362afbc1f9d3d66 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: a942978 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/TENxVisiumData_1.15.0.tar.gz vignettes: vignettes/TENxVisiumData/inst/doc/vignette.html vignetteTitles: TENxVisiumData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TENxVisiumData/inst/doc/vignette.R suggestsMe: SPOTlight dependencyCount: 83 Package: TENxXeniumData Version: 1.3.0 Depends: ExperimentHub Imports: SpatialExperiment, SpatialFeatureExperiment, BumpyMatrix, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 4f5058a3d9a8463a34c44b23abe5a5ec 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: 0469621 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/TENxXeniumData_1.3.0.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 dependencyCount: 166 Package: timecoursedata Version: 1.17.0 Depends: R (>= 4.0), SummarizedExperiment Suggests: testthat (>= 1.0.0), knitr, rmarkdown, markdown, covr, BiocStyle License: BSD 3-clause License + file LICENSE MD5sum: 02da4ea04181b2b211b79eb63c7f4b6a 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: da93ca5 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/timecoursedata_1.17.0.tar.gz vignettes: vignettes/timecoursedata/inst/doc/documentation.html vignetteTitles: timecoursedata: Time course gene expression datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/timecoursedata/inst/doc/documentation.R suggestsMe: moanin dependencyCount: 37 Package: TimerQuant Version: 1.37.0 Depends: shiny Imports: ggplot2, grid, gridExtra, deSolve, dplyr, locfit Suggests: BiocStyle, reshape2, knitr, shinyBS License: Artistic-2.0 MD5sum: 73957245e90ba9144191c6d52d5cb812 NeedsCompilation: no Title: Timer Quantification Description: Supplementary Data package for tandem timer methods paper by Barry et al. (2015) including TimerQuant shiny applications. biocViews: ExperimentData, Danio_rerio_Data, HighThroughputImagingData, Tissue Author: Joseph Barry Maintainer: Joseph Barry VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TimerQuant git_branch: devel git_last_commit: 3faf043 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/TimerQuant_1.37.0.tar.gz vignettes: vignettes/TimerQuant/inst/doc/genPaperFigures.pdf, vignettes/TimerQuant/inst/doc/mathematicalDerivations.pdf vignetteTitles: Supplementary Methods - automatic generation of paper figures, Supplementary Methods - mathematical derivations hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TimerQuant/inst/doc/genPaperFigures.R, vignettes/TimerQuant/inst/doc/mathematicalDerivations.R dependencyCount: 65 Package: tinesath1cdf Version: 1.45.0 License: Artistic-2.0 MD5sum: 322d8ae91b996730b6530ccdd11ad162 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: c0482da git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/tinesath1cdf_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: XhybCasneuf dependencyCount: 0 Package: tinesath1probe Version: 1.45.0 Depends: R (>= 1.6), AnnotationDbi (>= 1.11.9) License: LGPL MD5sum: b87e21f497804d6c5e5c501e7132c03c 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: 1e7ffd6 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/tinesath1probe_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 46 Package: tissueTreg Version: 1.27.0 Depends: R (>= 3.5) Suggests: BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq, SummarizedExperiment, ggplot2, reshape2 License: GPL (>= 2) MD5sum: a37e11ea97c66f93f5aaf8d70c712aeb 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: 59c6ede git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/tissueTreg_1.27.0.tar.gz vignettes: vignettes/tissueTreg/inst/doc/tissueTreg.html vignetteTitles: tissueTreg hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tissueTreg/inst/doc/tissueTreg.R suggestsMe: DMRcate dependencyCount: 0 Package: TMExplorer Version: 1.17.0 Depends: R (>= 4.1), SingleCellExperiment, BiocFileCache Imports: methods, Matrix Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 22df25c1941b1410790634e6315ee365 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: 9a6c437 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/TMExplorer_1.17.0.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: 69 Package: tofsimsData Version: 1.35.0 Depends: R (>= 3.2.0) Suggests: knitr, rmarkdown, tools License: GPL-3 MD5sum: 992b8d29b479ce62f2874cf1c71b95a0 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: aec79ec git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/tofsimsData_1.35.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: topdownrdata Version: 1.29.0 Depends: topdownr License: GPL (>= 3) MD5sum: 80873f2ff18fb7960a56d11aba44fe62 NeedsCompilation: no Title: Example Files for the topdownr R Package Description: Example data for the topdownr package generated on a Thermo Orbitrap Fusion Lumos MS device. biocViews: ExperimentData, MassSpectrometryData Author: Sebastian Gibb [aut, cre], Pavel Shliaha [aut], Ole Nørregaard Jensen [aut] Maintainer: Sebastian Gibb URL: https://github.com/sgibb/topdownrdata/ BugReports: https://github.com/sgibb/topdownrdata/issues/ git_url: https://git.bioconductor.org/packages/topdownrdata git_branch: devel git_last_commit: c4f7a05 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/topdownrdata_1.29.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: topdownr dependencyCount: 139 Package: TransOmicsData Version: 1.3.0 Imports: S4Vectors, utils Suggests: BiocStyle, knitr, rmarkdown, RefManageR, sessioninfo, testthat, ExperimentHub License: GPL-3 + file LICENSE MD5sum: 0157118d7fa08f14c20cb02eb975ac4c 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: c717e68 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/TransOmicsData_1.3.0.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: 1.13.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: AnnotationHub, ExperimentHub, S4Vectors, dplyr, magrittr, purrr, rlang, stringr, tibble, tidyr Suggests: BiocStyle, ggplot2, hrbrthemes, knitr, readr, rmarkdown, scater, usethis, utils License: Artistic-2.0 MD5sum: 90ed2b232d77c841f4de0cdfd4048134 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: 777ac2e git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/tuberculosis_1.13.0.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: 78 Package: tweeDEseqCountData Version: 1.45.0 Depends: Biobase, R (>= 4.3.0) Suggests: knitr, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: 116162a8ac50938b009116e9531eac72 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: 25ac306 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/tweeDEseqCountData_1.45.0.tar.gz vignettes: vignettes/tweeDEseqCountData/inst/doc/tweeDEseqCountData.html vignetteTitles: RNA-seq count data employed in the vignette of the tweeDEseq package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tweeDEseqCountData/inst/doc/tweeDEseqCountData.R suggestsMe: GSAR, missMethyl, tweeDEseq, zenith dependencyCount: 7 Package: tximportData Version: 1.35.0 Suggests: knitr, markdown License: GPL (>= 2) MD5sum: 122b25cc3651e9ad68d7bb9df35ce9f7 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: 4ffea7a git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/tximportData_1.35.0.tar.gz vignettes: vignettes/tximportData/inst/doc/tximportData.html vignetteTitles: Sample output files for tximport hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tximportData/inst/doc/tximportData.R importsMe: TDbasedUFE suggestsMe: DESeq2, eds, fishpond, tximeta, tximport, variancePartition dependencyCount: 0 Package: VariantToolsData Version: 1.31.0 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: eaefee21b394d87667c42950970f0f8b 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: 2b15fb1 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/VariantToolsData_1.31.0.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: 80 Package: VectraPolarisData Version: 1.11.0 Depends: ExperimentHub, SpatialExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, dplyr License: Artistic-2.0 MD5sum: 7d2ee50d2e8c8d21662653768ef76863 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: 81088b4 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/VectraPolarisData_1.11.0.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: 83 Package: vulcandata Version: 1.29.0 Imports: utils Suggests: viper License: LGPL-3 MD5sum: e32b32a695af0a2f565709a25158de61 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: 5ef67f4 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/vulcandata_1.29.0.tar.gz vignettes: vignettes/vulcandata/inst/doc/vulcandata.pdf vignetteTitles: Vulcan: VirtUaL ChIP-Seq Analysis through Networks,, dummy datasets hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/vulcandata/inst/doc/vulcandata.R suggestsMe: vulcan dependencyCount: 1 Package: WeberDivechaLCdata Version: 1.9.0 Depends: ExperimentHub, SpatialExperiment, SingleCellExperiment Imports: utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 2fd482bcaf0a6a0496463409c9df2580 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: abd3973 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/WeberDivechaLCdata_1.9.0.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: 83 Package: WES.1KG.WUGSC Version: 1.39.0 License: GPL-2 MD5sum: 1adc488a563fb8d28cbb2d7f7a9179b0 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: 1478bdb git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/WES.1KG.WUGSC_1.39.0.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: 1.19.0 Depends: R (>= 3.6.0), GenomicRanges License: GPL-2 MD5sum: b025dcca8b8e81202cb16550060e8986 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: 4daaa9f git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/WGSmapp_1.19.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: SCOPE dependencyCount: 24 Package: xcoredata Version: 1.11.0 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: 291ba974a4311b2682188d0336f267f9 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: c947e34 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/xcoredata_1.11.0.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: 67 Package: XhybCasneuf Version: 1.45.0 Depends: R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf , RColorBrewer , methods, grid License: Artistic-2.0 MD5sum: 8462fe131a0dc6519a7a090404e2bd3a 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: 5573402 git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/XhybCasneuf_1.45.0.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: 54 Package: yeastCC Version: 1.47.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 077fa47da9c0b4fcafd2560bc0486803 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: ce926ae git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/yeastCC_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: LiquidAssociation suggestsMe: fastLiquidAssociation, ibh dependencyCount: 7 Package: yeastExpData Version: 0.53.0 Depends: R (>= 2.4), graph (>= 1.9.26) Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db License: GPL MD5sum: 742723a5506e5ea3eff1f56640f389cf 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: d89aebf git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/yeastExpData_0.53.0.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: 0.45.0 License: Artistic-2.0 MD5sum: c1292ad7dfb67c65e5184c3f04abf2f2 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: c531554 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/yeastGSData_0.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: yeastNagalakshmi Version: 1.43.0 License: Artistic-2.0 MD5sum: 60826e93bf52f5c4161ef7b5683a5dbd 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: 69b6747 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/yeastNagalakshmi_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ShortRead dependencyCount: 0 Package: yeastRNASeq Version: 0.45.0 Depends: R (>= 2.4) Suggests: Biobase, ShortRead, IRanges License: GPL MD5sum: 4f34f88e46c9673b280858e90e83917a 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: 88c46db git_last_commit_date: 2024-10-29 Date/Publication: 2024-11-05 source.ver: src/contrib/yeastRNASeq_0.45.0.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: 1.27.0 Depends: R (>= 2.10) Suggests: BiocStyle, knitr License: GPL MD5sum: cdb2edae2d781eeb9ef5459a467db349 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: 2504652 git_last_commit_date: 2024-10-29 Date/Publication: 2024-10-31 source.ver: src/contrib/zebrafishRNASeq_1.27.0.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: pasilla Version: 1.35.0 Depends: R (>= 3.5.0), DEXSeq Suggests: rmarkdown, BiocStyle, knitr, roxygen2 License: LGPL 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 Package: Hiiragi2013 Version: 1.43.0 Depends: R (>= 3.0.0), affy, Biobase, boot, clue, cluster, genefilter, geneplotter, gplots, gtools, KEGGREST, MASS, mouse4302.db, RColorBrewer, xtable Imports: grid, lattice, latticeExtra Suggests: ArrayExpress, BiocStyle License: Artistic-2.0 Title: Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages Description: This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881." biocViews: ExperimentData, MicroarrayData, qPCRData, ReproducibleResearch Author: Andrzej Oles, Wolfgang Huber Maintainer: Andrzej Oles Package: curatedCRCData Version: 2.39.0 Depends: R (>= 2.10.0), nlme Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle License: Artistic-2.0 Title: Colorectal Cancer Gene Expression Analysis Description: The curatedCRC package provides relevant functions and data for gene expression analysis in patients with colorectal cancer. biocViews: Colorectal, Cancer, TCGA, ExperimentData, RNAExpressionData Author: Princy Parsana, Markus Riester, Curtis Huttenhower, Levi Waldron Maintainer: Princy Parsana URL: https://bitbucket.org/biobakery/curatedcrcdata Package: AssessORFData Version: 1.25.0 Depends: R (>= 3.5.0) Imports: DECIPHER, utils Suggests: AssessORF, BiocStyle, knitr, rmarkdown License: GPL-3 NeedsCompilation: no Title: Data and Files for the AssessORF Package Description: This package provides access to mapping and results objects generated by the AssessORF package, as well as the genome sequences for the strains corresponding to those objects. biocViews: OrganismData, Bacillus_subtilis_Data, Escherichia_coli_Data, Pseudomonas_aeruginosa_Data, Staphylococcus_aureus_Data, Genome, Proteome, SequencingData Author: Deepank Korandla [aut, cre] Maintainer: Deepank Korandla VignetteBuilder: knitr Package: HMP2Data Version: 1.21.0 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: MetaScope Version: 1.7.0 Depends: R (>= 4.4.0) Imports: BiocFileCache, Biostrings, data.table (>= 1.16.2), dplyr, ggplot2, magrittr, Matrix, MultiAssayExperiment, Rbowtie2, readr, rlang, Rsamtools, S4Vectors, stringr, SummarizedExperiment, taxize, tibble, tidyr, tools Suggests: animalcules, BiocStyle, biomformat, GenomicRanges, IRanges, knitr, lintr, plyr, R.utils, rmarkdown, Rsubread, spelling, sys, taxonomizr, testthat, usethis Enhances: BiocParallel License: GPL (>= 3) 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: Aubrey Odom [aut, cre] (ORCID: ), Rahul Varki [aut], W. Evan Johnson [aut] (ORCID: ), Howard Fan [ctb] Maintainer: Aubrey Odom URL: https://github.com/wejlab/metascope https://wejlab.github.io/metascope-docs/ VignetteBuilder: knitr BugReports: https://github.com/wejlab/MetaScope/issues Package: TumourMethData Version: 1.5.0 Depends: R (>= 4.2), SummarizedExperiment Imports: ExperimentHub, GenomicRanges, HDF5Array, R.utils, rhdf5 Suggests: ggplot2, knitr, rmarkdown 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