Package: ABAData Version: 1.22.0 Depends: R (>= 3.2) Suggests: BiocStyle, knitr, ABAEnrichment License: GPL (>= 2) MD5sum: beeedad17e1c7196a6ab263209a4aab9 NeedsCompilation: no Title: Averaged gene expression in human brain regions from Allen Brain Atlas Description: Provides the data for the gene expression enrichment analysis conducted in the package 'ABAEnrichment'. The package includes three datasets which are derived from the Allen Brain Atlas: (1) Gene expression data from Human Brain (adults) averaged across donors, (2) Gene expression data from the Developing Human Brain pooled into five age categories and averaged across donors and (3) a developmental effect score based on the Developing Human Brain expression data. All datasets are restricted to protein coding genes. biocViews: ExpressionData, Homo_sapiens_Data, MicroarrayData, RNASeqData Author: Steffi Grote Maintainer: Steffi Grote VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ABAData git_branch: RELEASE_3_13 git_last_commit: 6fd61eb git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ABAData_1.22.0.tar.gz vignettes: vignettes/ABAData/inst/doc/ABAData.html vignetteTitles: ABAData: gene expression data to use with enrichment analysis package ABAEnrichment hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ABAData/inst/doc/ABAData.R importsMe: ABAEnrichment dependencyCount: 0 Package: adductData Version: 1.8.0 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: c189c7de787608010923b4e26dd96ddb NeedsCompilation: no Title: Data from untargeted MS of modifications to Cys34 of serum albumin Description: mzXML files from Grigoryan et al 2016 (Anal Chem). biocViews: ExperimentData,MassSpectrometryData,ExperimentHub Author: Josie Hayes Maintainer: Josie Hayes VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/adductData git_branch: RELEASE_3_13 git_last_commit: 3b6dc44 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/adductData_1.8.0.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: 89 Package: affycompData Version: 1.30.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp License: GPL (>= 2) MD5sum: 13dd30ab208d584c1f5e92b137c012ae NeedsCompilation: no Title: affycomp data Description: Data needed by the affycomp package. biocViews: MicroarrayData Author: Rafael A. Irizarry and Zhijin Wu with contributions from Simon Cawley Maintainer: Harris Jaffee git_url: https://git.bioconductor.org/packages/affycompData git_branch: RELEASE_3_13 git_last_commit: b8d5d95 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/affycompData_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: affycomp dependencyCount: 8 Package: affydata Version: 1.40.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Imports: methods Suggests: hgu95av2cdf, hgu133acdf License: GPL (>= 2) MD5sum: 5d9a3027ac633d612386cd9a4f47105e NeedsCompilation: no Title: Affymetrix Data for Demonstration Purpose Description: Example datasets of a slightly large size. They represent 'real world examples', unlike the artificial examples included in the package affy. biocViews: ExperimentData, Tissue, MicroarrayData, TissueMicroarrayData Author: Laurent Gautier Maintainer: Harris Jaffee git_url: https://git.bioconductor.org/packages/affydata git_branch: RELEASE_3_13 git_last_commit: 1403d4f git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/affydata_1.40.0.tar.gz vignettes: vignettes/affydata/inst/doc/affydata.pdf vignetteTitles: affydata primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/affydata/inst/doc/affydata.R dependsOnMe: affyContam suggestsMe: affy, affycoretools, affyPara, affyPLM, arrayMvout, bgx, Biostrings, farms, gcrma, Harman, mimager, puma, pvac, RefPlus, RPA, sscore, TurboNorm, vsn, RobLoxBioC dependencyCount: 13 Package: Affyhgu133A2Expr Version: 1.28.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 6604813406ceafe753f7eb8a91077276 NeedsCompilation: no Title: Affymetrix Human Genome U133A 2.0 Array (GPL571) Expression Data Package Description: Contains pre-built human (GPL571) databases of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133A2Expr git_branch: RELEASE_3_13 git_last_commit: 9138715 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/Affyhgu133A2Expr_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: Affyhgu133aExpr Version: 1.30.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: ba1c685fbf46564b0380bd215cfaeb7e NeedsCompilation: no Title: Affymetrix Human hgu133a Array (GPL96) Expression Data Package Description: Contains pre-built human (GPL96) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133aExpr git_branch: RELEASE_3_13 git_last_commit: 5ece18d git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/Affyhgu133aExpr_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: Affyhgu133Plus2Expr Version: 1.26.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 9ce3ce41bc5ca5934b069b61546ddb2b NeedsCompilation: no Title: Affyhgu133Plus2Expr (GPL570) Expression Data Package Description: Contains pre-built human (GPL570) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133Plus2Expr git_branch: RELEASE_3_13 git_last_commit: f266936 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/Affyhgu133Plus2Expr_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: AffymetrixDataTestFiles Version: 0.30.0 Depends: R (>= 2.5.0) License: LGPL-2.1 MD5sum: b830ff6bfdcba200beeaea4cf61d49f4 NeedsCompilation: no Title: Affymetrix data files (CEL, CDF, CHP, EXP, PGF, PSI) for testing Description: This package contains annotation data files and sample data files of Affymetrix file formats. The files originate from the Affymetrix' Fusion SDK distribution and other official sources. biocViews: ExperimentData, MicroarrayData Author: Henrik Bengtsson [aut, cre], James Bullard [aut], Kasper Daniel Hansen [aut] Maintainer: Henrik Bengtsson git_url: https://git.bioconductor.org/packages/AffymetrixDataTestFiles git_branch: RELEASE_3_13 git_last_commit: 1e63448 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/AffymetrixDataTestFiles_0.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: affxparser, affyILM, aroma.affymetrix dependencyCount: 0 Package: Affymoe4302Expr Version: 1.30.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 486f33389fc1860e7b9658b548cd2c1b NeedsCompilation: no Title: Affymetrix Mouse Genome 430 2.0 Array (GPL1261) Expression Data Package Description: Contains pre-built mouse (GPL1261) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Mus_musculus_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affymoe4302Expr git_branch: RELEASE_3_13 git_last_commit: 4b49477 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/Affymoe4302Expr_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: airway Version: 1.12.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: knitr, GEOquery, markdown License: LGPL MD5sum: ddffcaf19692ac091ba694b6251bdcfa NeedsCompilation: no Title: RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014 Description: This package provides a RangedSummarizedExperiment object of read counts in genes for an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. Details on the gene model and read counting procedure are provided in the package vignette. The citation for the experiment is: Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri R Jr, Tantisira KG, Weiss ST, Lu Q. 'RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells.' PLoS One. 2014 Jun 13;9(6):e99625. PMID: 24926665. GEO: GSE52778. biocViews: ExperimentData, SequencingData, RNASeqData, GEO Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/airway git_branch: RELEASE_3_13 git_last_commit: 20eae99 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/airway_1.12.0.tar.gz vignettes: vignettes/airway/inst/doc/airway.html vignetteTitles: Airway smooth muscle cells hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/airway/inst/doc/airway.R dependsOnMe: rnaseqGene importsMe: consensusDE suggestsMe: apeglm, awst, biobroom, BioCor, BiocSet, CeTF, DelayedArray, DESeq2, EnhancedVolcano, EnrichmentBrowser, ExperimentSubset, ideal, IHW, InteractiveComplexHeatmap, iSEEu, OPWeight, pathwayPCA, pcaExplorer, PCAtools, progeny, runibic, SummarizedExperiment, TTMap, weitrix, IHWpaper, RegParallel, seqgendiff dependencyCount: 26 Package: ALL Version: 1.34.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Suggests: rpart License: Artistic-2.0 MD5sum: de3f1ceb6e787628a6a43834deaff796 NeedsCompilation: no Title: A data package Description: Data of T- and B-cell Acute Lymphocytic Leukemia from the Ritz Laboratory at the DFCI (includes Apr 2004 versions) biocViews: ExperimentData, CancerData, LeukemiaCancerData Author: Xiaochun Li Maintainer: Robert Gentleman git_url: https://git.bioconductor.org/packages/ALL git_branch: RELEASE_3_13 git_last_commit: 115420b git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ALL_1.34.0.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, SourceSet dependencyCount: 7 Package: ALLMLL Version: 1.32.0 Depends: R (>= 2.10), affy (>= 1.23.4) License: GPL-2 MD5sum: 7ca670f7d26f360d0add5992201f3554 NeedsCompilation: no Title: A subset of arrays from a large acute lymphoblastic leukemia (ALL) study Description: This package provides probe-level data for 20 HGU133A and 20 HGU133B arrays which are a subset of arrays from a large ALL study. The data is for the MLL arrays. This data was published in Mary E. Ross, Xiaodong Zhou, Guangchun Song, Sheila A. Shurtleff, Kevin Girtman, W. Kent Williams, Hsi-Che Liu, Rami Mahfouz, Susana C. Raimondi, Noel Lenny, Anami Patel, and James R. Downing (2003) Classification of pediatric acute lymphoblastic leukemia by gene expression profiling Blood 102: 2951-2959 biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData Author: B. M. Bolstad git_url: https://git.bioconductor.org/packages/ALLMLL git_branch: RELEASE_3_13 git_last_commit: f3e8a4b git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ALLMLL_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQualityMetrics, pvac dependencyCount: 13 Package: alpineData Version: 1.18.0 Depends: ExperimentHub, GenomicAlignments Imports: utils, AnnotationHub Suggests: GenomicAlignments, knitr, markdown License: GPL (>=2) MD5sum: 09b71ec159d4d29fd1564eb60cb942ec NeedsCompilation: no Title: Data for the alpine package vignette Description: A small subset of paired-end RNA-seq reads from four samples of the GEUVADIS project. biocViews: SequencingData, RNASeqData, ExpressionData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/alpineData git_branch: RELEASE_3_13 git_last_commit: cfe6f00 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/alpineData_1.18.0.tar.gz vignettes: vignettes/alpineData/inst/doc/alpineData.html vignetteTitles: tximport hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/alpineData/inst/doc/alpineData.R suggestsMe: alpine dependencyCount: 106 Package: AmpAffyExample Version: 1.32.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Suggests: hgu133acdf License: LGPL (>= 2) MD5sum: 99a439cc07d938bfb4ced4cd02c61b62 NeedsCompilation: no Title: Example of Amplified Data Description: Six arrays. Three from amplified RNA, three from the typical procedure. biocViews: ExperimentData, MicroarrayData Author: Rafael A. Irizarry Maintainer: Rafael A. Irizarry git_url: https://git.bioconductor.org/packages/AmpAffyExample git_branch: RELEASE_3_13 git_last_commit: 4ad683a git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/AmpAffyExample_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: AffyRNADegradation dependencyCount: 13 Package: AneuFinderData Version: 1.20.0 Depends: R (>= 3.3) License: file LICENSE MD5sum: 60005b993d08598ad43472f528896bb3 NeedsCompilation: no Title: WGSCS Data for Demonstration Purposes Description: Whole-genome single cell sequencing data for demonstration purposes in the AneuFinder package. biocViews: CopyNumberVariationData, LungCancerData, Homo_sapiens_Data, SequencingData Author: Aaron Taudt Maintainer: Aaron Taudt git_url: https://git.bioconductor.org/packages/AneuFinderData git_branch: RELEASE_3_13 git_last_commit: b4cfee5 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/AneuFinderData_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: AneuFinder dependencyCount: 0 Package: antiProfilesData Version: 1.28.0 Depends: Biobase, Suggests: frma, GEOquery, GEOmetadb License: Artistic-2.0 MD5sum: 7c177570c06d14b13e4daf1ad7ff8bfa NeedsCompilation: no Title: Normal colon and cancer preprocessed affy data for antiProfile building. Description: Colon normal tissue and cancer samples used in Corrada Bravo, et al. gene expression anti-profiles paper: BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272. Measurements are z-scores obtained from the GeneExpression Barcode in the 'frma' package biocViews: ExperimentData, MicroarrayData, Tissue, CancerData, ColonCancerData Author: Hector Corrada Bravo, Matthew McCall and Rafael A. Irizarry Maintainer: Hector Corrada Bravo git_url: https://git.bioconductor.org/packages/antiProfilesData git_branch: RELEASE_3_13 git_last_commit: b5db8bc git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/antiProfilesData_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: antiProfiles, epivizr, epivizrChart, messina dependencyCount: 7 Package: aracne.networks Version: 1.18.0 Depends: R (>= 3.3), viper License: file LICENSE MD5sum: 02fa7862776d1dc866b4288a768eb616 NeedsCompilation: no Title: ARACNe-inferred gene networks from TCGA tumor datasets Description: This package contains ARACNe-inferred networks from TCGA tumor datasets. It also contains a function to export them into plain-text format. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData Author: Federico M. Giorgi Maintainer: Federico M. Giorgi , Mariano Alvarez git_url: https://git.bioconductor.org/packages/aracne.networks git_branch: RELEASE_3_13 git_last_commit: cfd17d5 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/aracne.networks_1.18.0.tar.gz vignettes: vignettes/aracne.networks/inst/doc/aracne.networks.pdf vignetteTitles: Using aracne.networks hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/aracne.networks/inst/doc/aracne.networks.R dependencyCount: 22 Package: ARRmData Version: 1.28.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: 4ddd9ae8be788074b5c7170ad2cdb631 NeedsCompilation: no Title: Example dataset for normalization of Illumina 450k Methylation data Description: Raw Beta values from 36 samples across 3 groups from Illumina 450k methylation arrays biocViews: ExperimentData, MethylationArrayData Author: Jean-Philippe Fortin, Celia M.T. Greenwood, Aurelie Labbe Maintainer: Jean-Philippe Fortin git_url: https://git.bioconductor.org/packages/ARRmData git_branch: RELEASE_3_13 git_last_commit: 80e207f git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ARRmData_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ARRmNormalization dependencyCount: 0 Package: AshkenazimSonChr21 Version: 1.22.0 Suggests: knitr, VariantAnnotation License: Artistic-2.0 MD5sum: 04e9b958d21f2aa5b5174742912decc2 NeedsCompilation: no Title: Annotated variants on the chromosome 21, human genome 19, Ashkenazim Trio son sample Description: SonVariantsChr21 is a dataset of annotated genomic variants coming from Complete Genomics whole genome sequencing. Data comes from GIAB project, Ashkenazim Trio, sample HG002 run 1. Both vcf and annotated data frame are provided. biocViews: GenomicVariation, Sequencing, WholeGenome Author: Tomasz Stokowy Maintainer: Who to complain to VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/AshkenazimSonChr21 git_branch: RELEASE_3_13 git_last_commit: 59ade03 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/AshkenazimSonChr21_1.22.0.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: 1.12.0 Depends: R (>= 3.5) Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 9bef1320498e351d5ad9d405430796d8 NeedsCompilation: no Title: Example of 1D NMR spectra data for ASICS package Description: 1D NMR example spectra and additional data for use with the ASICS package. Raw 1D Bruker spectral data files were found in the MetaboLights database (https://www.ebi.ac.uk/metabolights/, study MTBLS1). biocViews: ExperimentData, Homo_sapiens_Data Author: Gaëlle Lefort [aut, cre], Rémi Servien [aut], Nathalie Villa-Vialaneix [aut] Maintainer: Gaëlle Lefort VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ASICSdata git_branch: RELEASE_3_13 git_last_commit: 58502bf git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ASICSdata_1.12.0.tar.gz vignettes: vignettes/ASICSdata/inst/doc/ASICSdata.html vignetteTitles: ASICSdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ASICS dependencyCount: 0 Package: AssessORFData Version: 1.10.0 Depends: R (>= 3.5.0) Imports: DECIPHER, utils Suggests: AssessORF, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: c5643b8526226b5a38906b0880e1529f NeedsCompilation: no Title: Data and Files for the AssessORF Package Description: This package provides access to mapping and results objects generated by the AssessORF package, as well as the genome sequences for the strains corresponding to those objects. biocViews: OrganismData, Bacillus_subtilis_Data, Escherichia_coli_Data, Pseudomonas_aeruginosa_Data, Staphylococcus_aureus_Data, Genome, Proteome, SequencingData Author: Deepank Korandla [aut, cre] Maintainer: Deepank Korandla VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/AssessORFData git_branch: RELEASE_3_13 git_last_commit: 60962ad git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/AssessORFData_1.10.0.tar.gz vignettes: vignettes/AssessORFData/inst/doc/AssessORFDataGuide.pdf vignetteTitles: Using AssessORFData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/AssessORFData/inst/doc/AssessORFDataGuide.R suggestsMe: AssessORF dependencyCount: 35 Package: bcellViper Version: 1.28.0 Depends: R(>= 2.14.0), Biobase, methods License: GPL (>=2) MD5sum: c738c87b45aff33a73b1180111e94e06 NeedsCompilation: no Title: Human B-cell transcriptional interactome and normal human B-cell expression data Description: This package provides a human B-cell context-specific transcriptional regulatory network and a human normal B-cells dataset for the examples in package viper. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData Author: Mariano Javier Alvarez Maintainer: Mariano Javier Alvarez git_url: https://git.bioconductor.org/packages/bcellViper git_branch: RELEASE_3_13 git_last_commit: cdd7233 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/bcellViper_1.28.0.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, iterClust, pageRank, viper dependencyCount: 7 Package: beadarrayExampleData Version: 1.30.0 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>= 2.0.0) License: GPL-2 MD5sum: 78bd38e4588c20d686f5a93af7827809 NeedsCompilation: no Title: Example data for the beadarray package Description: An small dataset that can be used to run examples from the beadarray vignette and examples biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/beadarrayExampleData git_branch: RELEASE_3_13 git_last_commit: d2bee01 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/beadarrayExampleData_1.30.0.tar.gz vignettes: vignettes/beadarrayExampleData/inst/doc/beadarrayExampleData.pdf vignetteTitles: beadarrayExampleData: example data for the beadarray package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/beadarrayExampleData/inst/doc/beadarrayExampleData.R suggestsMe: beadarray, MiRaGE, beadarrayFilter, RobLoxBioC dependencyCount: 83 Package: BeadArrayUseCases Version: 1.30.1 Imports: beadarray (>= 2.3.18), limma, GEOquery Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db License: GPL-2 MD5sum: 6d5417c387a716b7c5984c196abe1d41 NeedsCompilation: no Title: Analysing Illumina BeadArray expression data using Bioconductor Description: Example data files and use cases for processing Illumina BeadArray expression data using Bioconductor biocViews: MicroarrayData Author: Mark Dunning, Wei Shi, Andy Lynch, Mike Smith, Matt Ritchie Maintainer: Mike Smith git_url: https://git.bioconductor.org/packages/BeadArrayUseCases git_branch: RELEASE_3_13 git_last_commit: 17d839e git_last_commit_date: 2021-07-26 Date/Publication: 2021-07-27 source.ver: src/contrib/BeadArrayUseCases_1.30.1.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: 98 Package: BeadSorted.Saliva.EPIC Version: 1.0.0 Depends: R (>= 4.1), minfi(>= 1.36.0), ExperimentHub Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 50eb43855238700598c318024c585893 NeedsCompilation: no Title: Illumina EPIC data on BeadSorted adult saliva cells Description: Raw data objects used to estimate saliva cell proportion estimates in ewastools. The FlowSorted.Saliva.EPIC object is constructed from saples assayed by Lauren Middleton et. al. (2021). biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData, Genome, MethylationArrayData, ExperimentHub Author: Jonah Fisher [aut, cre], Kelly Bakulski [aut], Lauren Middleton [aut] Maintainer: Jonah Fisher VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/BeadSorted.Saliva.EPIC git_branch: RELEASE_3_13 git_last_commit: d79fc75 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/BeadSorted.Saliva.EPIC_1.0.0.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: 161 Package: benchmarkfdrData2019 Version: 1.6.0 Depends: R (>= 3.6.0), SummarizedExperiment, ExperimentHub Imports: utils Suggests: knitr, BiocStyle, testthat, SummarizedBenchmark, dplyr, ggplot2, rlang License: MIT + file LICENSE MD5sum: 17a045441d2311736928ece335450b36 NeedsCompilation: no Title: Data and Benchmarking Results from Korthauer and Kimes et al. (2019) Description: Benchmarking results for experimental and simulated data sets used in Korthauer and Kimes et al. (2019) to compare methods for controlling the false discovery rate. biocViews: SingleCellData, ExperimentData, RNASeqData, ExpressionData, ExperimentData, ExperimentHub Author: Stephanie Hicks [aut, cre] (), Keegan Korthauer [aut] (), Patrick Kimes [aut] () Maintainer: Stephanie Hicks VignetteBuilder: knitr BugReports: https://github.com/stephaniehicks/benchmarkfdrData2019/issues git_url: https://git.bioconductor.org/packages/benchmarkfdrData2019 git_branch: RELEASE_3_13 git_last_commit: a560f98 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/benchmarkfdrData2019_1.6.0.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: 96 Package: beta7 Version: 1.30.0 Depends: R (>= 2.4.0), marray License: LGPL MD5sum: 916c2ed16d1bc32112c4b5f99c979522 NeedsCompilation: no Title: Rodriguez et al. (2004) Differential Gene Expression by Memory/Effector T Helper Cells Bearing the Gut-Homing Receptor Integrin alpha4 beta7. Description: Data from 6 gpr files aims to identify differential expressed genes between the beta 7+ and beta 7- memory T helper cells. biocViews: ExperimentData, Homo_sapiens_Data, CGHData, MicroarrayData Author: Jean Yang Maintainer: Jean Yang git_url: https://git.bioconductor.org/packages/beta7 git_branch: RELEASE_3_13 git_last_commit: 359d030 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/beta7_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: BioImageDbs Version: 1.0.5 Depends: R (>= 4.1.0) Imports: ExperimentHub (>= 1.16.1), markdown, rmarkdown, EBImage, magick, magrittr, filesstrings, animation, einsum Suggests: knitr, BiocStyle, purrr License: Artistic-2.0 MD5sum: 443bd8f6c869ff641dd57f50b1ffdd6d 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] (), Kozo Nishida [aut] () Maintainer: Satoshi Kume URL: https://github.com/kumeS/BioImageDbs VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/BioImageDbs git_branch: RELEASE_3_13 git_last_commit: 6d39648 git_last_commit_date: 2021-09-18 Date/Publication: 2021-09-21 source.ver: src/contrib/BioImageDbs_1.0.5.tar.gz vignettes: vignettes/BioImageDbs/inst/doc/BioImageDbs.html vignetteTitles: Providing Bioimage Dataset for ExperimentHub hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BioImageDbs/inst/doc/BioImageDbs.R dependencyCount: 113 Package: biotmleData Version: 1.16.0 Depends: R (>= 3.0) Suggests: Biobase, SummarizedExperiment License: file LICENSE MD5sum: 7bbc9905d3f9192b549d62a5c67a701d NeedsCompilation: no Title: Example experimental microarray data set for the "biotmle" R package Description: Microarray data (from the Illumina Ref-8 BeadChips platform) and phenotype-level data from an epidemiological investigation of benzene exposure, packaged using "SummarizedExperiemnt", for use as an example with the "biotmle" R package. biocViews: GeneExpression, DifferentialExpression, Sequencing, Microarray, RNASeq Author: Nima Hejazi [aut, cre] Maintainer: Nima Hejazi git_url: https://git.bioconductor.org/packages/biotmleData git_branch: RELEASE_3_13 git_last_commit: a3914be git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/biotmleData_1.16.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: biotmle dependencyCount: 0 Package: biscuiteerData Version: 1.6.0 Depends: R (>= 3.6.0), ExperimentHub Imports: AnnotationHub, utils, curl Suggests: knitr License: GPL-3 MD5sum: 9fadeb6513aacedd38b2640270a22724 NeedsCompilation: no Title: Data Package for Biscuiteer Description: Contains default datasets used by the Bioconductor package biscuiteer. biocViews: ExperimentHub, ExperimentData, Genome, Homo_sapiens_Data Author: Tim Triche, Jr. [aut, cre], Wanding Zhou [aut], Ben Johnson [aut], Jacob Morrison [aut], Lyong Heo [aut] Maintainer: "Jacob Morrison" VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/biscuiteerData git_branch: RELEASE_3_13 git_last_commit: fe02bcf git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/biscuiteerData_1.6.0.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: 88 Package: bladderbatch Version: 1.30.0 Depends: Biobase License: Artistic-2.0 MD5sum: 5c5785ee180dd6dcd0dba223dd41d758 NeedsCompilation: no Title: Bladder gene expression data illustrating batch effects Description: This package contains microarray gene expression data on 57 bladder samples from 5 batches. The data are used as an illustrative example for the sva package. biocViews: ExperimentData, CancerData, MicroarrayData Author: Jeffrey T. Leek Maintainer: Jeffrey T. Leek git_url: https://git.bioconductor.org/packages/bladderbatch git_branch: RELEASE_3_13 git_last_commit: 182ef69 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/bladderbatch_1.30.0.tar.gz vignettes: vignettes/bladderbatch/inst/doc/bladderbatch.pdf vignetteTitles: bladderbatchTutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bladderbatch/inst/doc/bladderbatch.R importsMe: RUVcorr suggestsMe: Harman, sva dependencyCount: 7 Package: blimaTestingData Version: 1.12.0 Depends: R(>= 3.0.0) Suggests: blima, beadarray, illuminaHumanv4.db, BiocStyle License: GPL-3 MD5sum: f162e7eb662e93357bdd1195e53e07bb NeedsCompilation: no Title: Data for testing of the package blima. Description: Experiment data package. The set were prepared using microarray images of human mesenchymal cells treated with various supplements. This package is intended to provide example data to test functionality provided by blima. biocViews: MicroarrayData, ExperimentData, GEO Author: Vojtech Kulvait Maintainer: Vojtech Kulvait URL: https://bitbucket.org/kulvait/blima git_url: https://git.bioconductor.org/packages/blimaTestingData git_branch: RELEASE_3_13 git_last_commit: 24e4e8d git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/blimaTestingData_1.12.0.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: 1.12.0 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: 1401fe153134596371e049ac4e8cd26f NeedsCompilation: no Title: "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al. - experimental data and complete analysis Description: The package contains data of the Primary Blood Cancer Encyclopedia (PACE) project together with a complete executable transcript of the statistical analysis and reproduces figures presented in the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) 128(1):427-445. doi:10.1172/JCI93801. biocViews: ExperimentData, ReproducibleResearch, CancerData, LeukemiaCancerData Author: Malgorzata Oles, Sascha Dietrich, Junyan Lu, Britta Velten, Andreas Mock, Vladislav Kim, Wolfgang Huber Maintainer: Malgorzata Oles VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/BloodCancerMultiOmics2017 git_branch: RELEASE_3_13 git_last_commit: c9862a9 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/BloodCancerMultiOmics2017_1.12.0.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: 151 Package: bodymapRat Version: 1.8.0 Depends: R (>= 3.6.0), SummarizedExperiment, ExperimentHub Imports: utils Suggests: knitr, BiocStyle, testthat License: CC BY 4.0 MD5sum: d6029589dcd0ca98b0b048e83355eba3 NeedsCompilation: no Title: Experimental dataset from the rat BodyMap project Description: This package contains a SummarizedExperiment from the Yu et al. (2013) paper that performed the rat BodyMap across 11 organs and 4 developmental stages. Raw FASTQ files were downloaded and mapped using STAR. Data is available on ExperimentHub as a data package. biocViews: SequencingData, RNASeqData, ExpressionData, ExperimentData, ExperimentHub Author: Stephanie Hicks [aut, cre] (), Kwame Okrah [aut] Maintainer: Stephanie Hicks VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/bodymapRat git_branch: RELEASE_3_13 git_last_commit: e1045ab git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/bodymapRat_1.8.0.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: 96 Package: brainImageRdata Version: 1.10.0 Depends: ExperimentHub Suggests: knitr License: CC BY-SA 4.0 MD5sum: e5d61f7d02a769d3ecabdaa96b4922c0 NeedsCompilation: no Title: Image masks and expression data for use with BrainImageR Description: brainImageRdata contains image masks for the developing human and the adult human brain. These masks can be used in conjunction with the gene expression data to generate spatial gene set enrichment plots. It also contains the expression data for the 15 pcw human brain, the adult human brain, and the developing human brain. biocViews: OrganismData, Homo_sapiens_Data, ExpressionData Author: Sara Linker Maintainer: Sara Linker VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/brainImageRdata git_branch: RELEASE_3_13 git_last_commit: 560e7a9 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/brainImageRdata_1.10.0.tar.gz vignettes: vignettes/brainImageRdata/inst/doc/brainImageRdata.html vignetteTitles: brainImageRdata hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/brainImageRdata/inst/doc/brainImageRdata.R dependencyCount: 88 Package: breakpointRdata Version: 1.10.0 Depends: R (>= 3.5) Suggests: knitr, BiocStyle, License: file LICENSE MD5sum: 68e7f69de17628877f53c0dda279175b NeedsCompilation: no Title: Strand-seq data for demonstration purposes Description: Strand-seq data to demonstrate functionalities of breakpointR package. biocViews: ExperimentData, Homo_sapiens_Data, SequencingData, DNASeqData, Genome, SingleCellData Author: David Porubsky, Aaron Taudt, Ashley Sanders Maintainer: David Porubsky URL: https://github.com/daewoooo/breakpointRdata VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/breakpointRdata git_branch: RELEASE_3_13 git_last_commit: 76cf665 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/breakpointRdata_1.10.0.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: 1.30.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 12ee94f4579f827cbca3ee523d5fe70d NeedsCompilation: no Title: Gene expression dataset published by Schmidt et al. [2008] (MAINZ). Description: Gene expression data from the breast cancer study published by Schmidt et al. in 2008, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerMAINZ git_branch: RELEASE_3_13 git_last_commit: 38ea40c git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/breastCancerMAINZ_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: DART, genefu, MIGSA, MineICA, STROMA4 dependencyCount: 0 Package: breastCancerNKI Version: 1.30.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 214f01f071865619f2718ef6c6f4e0d3 NeedsCompilation: no Title: Genexpression dataset published by van't Veer et al. [2002] and van de Vijver et al. [2002] (NKI). Description: Genexpression data from a breast cancer study published by van't Veer et al. in 2002 and van de Vijver et al. in 2002, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, CGHData, MicroarrayData, OneChannelData, ChipOnChipData Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerNKI git_branch: RELEASE_3_13 git_last_commit: 4007304 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/breastCancerNKI_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, MIGSA, SigCheck, seventyGeneData dependencyCount: 0 Package: breastCancerTRANSBIG Version: 1.30.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 6d5b338f88a05dc2c572fe5ade1f8a2e NeedsCompilation: no Title: Gene expression dataset published by Desmedt et al. [2007] (TRANSBIG). Description: Gene expression data from a breast cancer study published by Desmedt et al. in 2007, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerTRANSBIG git_branch: RELEASE_3_13 git_last_commit: f2bacb0 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/breastCancerTRANSBIG_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, GSgalgoR, MIGSA, MineICA dependencyCount: 0 Package: breastCancerUNT Version: 1.30.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 6eb888e2d9ac5985ed8f4ad0405b803e NeedsCompilation: no Title: Gene expression dataset published by Sotiriou et al. [2007] (UNT). Description: Gene expression data from a breast cancer study published by Sotiriou et al. in 2007, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, TwoChannelData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerUNT git_branch: RELEASE_3_13 git_last_commit: 61813a7 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/breastCancerUNT_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, MIGSA dependencyCount: 0 Package: breastCancerUPP Version: 1.30.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: f92c15179f65888b4ea23a31aec416db NeedsCompilation: no Title: Gene expression dataset published by Miller et al. [2005] (UPP). Description: Gene expression data from a breast cancer study published by Miller et al. in 2005, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerUPP git_branch: RELEASE_3_13 git_last_commit: c59a90a git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/breastCancerUPP_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, GSgalgoR, MIGSA, MineICA, safe dependencyCount: 0 Package: breastCancerVDX Version: 1.30.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: cf9bf421e708df80885e20b8b8ccfbe9 NeedsCompilation: no Title: Gene expression datasets published by Wang et al. [2005] and Minn et al. [2007] (VDX). Description: Gene expression data from a breast cancer study published by Wang et al. in 2005 and Minn et al. in 2007, provided as an eSet. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData, BreastCancerData, LungCancerData, MicroarrayData, OneChannelData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerVDX git_branch: RELEASE_3_13 git_last_commit: 5428327 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/breastCancerVDX_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: BAGS suggestsMe: AIMS, DART, genefu, MIGSA, MineICA dependencyCount: 0 Package: brgedata Version: 1.14.0 Depends: R (>= 3.4), Biobase Imports: SummarizedExperiment Suggests: minfi, MultiAssayExperiment, knitr, rexposome License: MIT + file LICENSE MD5sum: 67be36659c7d587f17c722b0a19b4481 NeedsCompilation: no Title: Exposures, Gene Expression and Methylation data for ilustration purpouses Description: This package contains several sets of omics data including Gene Expression (ExpressionSet), Methylation (GenomicRatioSet), Proteome and Exposome (ExposomeSet). This data is used in vignettes and exaples at MEAL, MultiDataSet and omicRexposome. biocViews: ExperimentData,Homo_sapiens_Data,MicroarrayData,MethylationArrayData Author: Carlos Ruiz-Arenas [aut, cre], Carles Hernandez-Ferrer [aut], Juan R. Gonzalez [aut] Maintainer: Carlos Ruiz-Arenas VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/brgedata git_branch: RELEASE_3_13 git_last_commit: e9ba869 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/brgedata_1.14.0.tar.gz vignettes: vignettes/brgedata/inst/doc/general_description.html vignetteTitles: brgedata -- data R package with three omic data-set and exposome data-set from the same Spanish pupulation hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/brgedata/inst/doc/general_description.R suggestsMe: MEAL, MultiDataSet, omicRexposome dependencyCount: 26 Package: bronchialIL13 Version: 1.30.0 Depends: R(>= 2.10.0), affy (>= 1.23.4) License: GPL-2 MD5sum: 0c6649cfc2a2ba6655068bb0b6be7c2e NeedsCompilation: no Title: time course experiment involving il13 Description: derived from CNMC (pepr.cnmcresearch.org) http://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=95 Human Bronchial Cell line A549 biocViews: ExperimentData, MicroarrayData Author: Vince Carey Maintainer: Vince Carey URL: http://www.biostat.harvard.edu/~carey git_url: https://git.bioconductor.org/packages/bronchialIL13 git_branch: RELEASE_3_13 git_last_commit: 482ff69 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/bronchialIL13_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 13 Package: bsseqData Version: 0.30.0 Depends: R (>= 2.15), bsseq (>= 1.16.0) License: Artistic-2.0 MD5sum: d09fd68c2996eac253b4b4e0f4c7dfb1 NeedsCompilation: no Title: Example whole genome bisulfite data for the bsseq package Description: Example whole genome bisulfite data for the bsseq package biocViews: Genome, CancerData, ColonCancerData, SequencingData Author: Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/bsseqData git_branch: RELEASE_3_13 git_last_commit: d988dc9 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/bsseqData_0.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: bsseq, methylSig dependencyCount: 73 Package: cancerdata Version: 1.30.0 Depends: R (>= 2.10.1), Biobase License: GPL (>= 2) MD5sum: 0664ae0c1510bd3238833227dfb8b485 NeedsCompilation: no Title: Development and validation of diagnostic tests from high-dimensional molecular data: Datasets Description: Dataset for the R package cancerclass biocViews: CancerData, MicroarrayData Author: Jan Budczies, Daniel Kosztyla Maintainer: Daniel Kosztyla git_url: https://git.bioconductor.org/packages/cancerdata git_branch: RELEASE_3_13 git_last_commit: eee347e git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/cancerdata_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: cancerclass dependencyCount: 7 Package: CardinalWorkflows Version: 1.24.0 Depends: R (>= 2.10), Cardinal Suggests: BiocStyle, knitr License: Artistic-2.0 MD5sum: ed08ee33d6ac9b3aa3b570ef7cfdeff3 NeedsCompilation: no Title: Datasets and workflows for the Cardinal mass spectrometry imaging package Description: Datasets and workflows for Cardinal: DESI and MALDI examples including pig fetus, cardinal painting, and human RCC. biocViews: ExperimentData, MassSpectrometryData, ImagingMassSpectrometryData Author: Kylie A. Bemis Maintainer: Kylie A. Bemis VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/CardinalWorkflows git_branch: RELEASE_3_13 git_last_commit: 9b947c4 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/CardinalWorkflows_1.24.0.tar.gz vignettes: vignettes/CardinalWorkflows/inst/doc/MSI-classification.html, vignettes/CardinalWorkflows/inst/doc/MSI-segmentation.html, vignettes/CardinalWorkflows/inst/doc/MSI-testing.html vignetteTitles: 2. Classification: Supervised analysis workflow, 1. Segmentation: Unsupervised analysis workflow, 3. Class comparision: Statistical testing workflow hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CardinalWorkflows/inst/doc/MSI-classification.R, vignettes/CardinalWorkflows/inst/doc/MSI-segmentation.R, vignettes/CardinalWorkflows/inst/doc/MSI-testing.R dependencyCount: 66 Package: ccdata Version: 1.18.0 Depends: R (>= 3.3) License: MIT + file LICENSE MD5sum: e7a56603093a17d4ab69e9236caf9da4 NeedsCompilation: no Title: Data for Combination Connectivity Mapping (ccmap) Package Description: This package contains microarray gene expression data generated from the Connectivity Map build 02 and LINCS l1000. The data are used by the ccmap package to find drugs and drug combinations to mimic or reverse a gene expression signature. biocViews: ExperimentData, MicroarrayData, ExpressionData Author: Alex Pickering Maintainer: Alex Pickering git_url: https://git.bioconductor.org/packages/ccdata git_branch: RELEASE_3_13 git_last_commit: fbea98a git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ccdata_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE importsMe: ccmap suggestsMe: retriever dependencyCount: 0 Package: CCl4 Version: 1.30.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), limma License: Artistic-2.0 MD5sum: 1b3c23329e85445293a0c713c20c65f0 NeedsCompilation: no Title: Carbon Tetrachloride (CCl4) treated hepatocytes Description: NChannelSet for rat hepatocytes treated with Carbon Tetrachloride (CCl4) data from LGC company. biocViews: ExperimentData, Genome, Rattus_norvegicus_Data, MicroarrayData Author: Audrey Kauffmann, Wolfgang Huber Maintainer: Audrey Kauffmann git_url: https://git.bioconductor.org/packages/CCl4 git_branch: RELEASE_3_13 git_last_commit: 7acc90b git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/CCl4_1.30.0.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: 9 Package: ccTutorial Version: 1.30.0 Depends: R (>= 2.10), Ringo(>= 1.9.8), affy(>= 1.23.4), topGO(>= 1.13.1) Imports: Biobase Suggests: biomaRt, Biobase(>= 2.5.5), xtable License: Artistic-2.0 MD5sum: 386675a1dc2b323d0ddb10a237a9490a NeedsCompilation: no Title: Data package for ChIP-chip tutorial Description: This is a data package that accompanies a ChIP-chip tutorial, which has been published in PLoS Computational Biology. The data and source code in this package allow the reader to completely reproduce the steps in the tutorial. biocViews: ExperimentData, Mus_musculus_Data, MicroarrayData, ChipOnChipData Author: Joern Toedling, Wolfgang Huber Maintainer: Joern Toedling git_url: https://git.bioconductor.org/packages/ccTutorial git_branch: RELEASE_3_13 git_last_commit: bf21552 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ccTutorial_1.30.0.tar.gz vignettes: vignettes/ccTutorial/inst/doc/ccTutorial.pdf, vignettes/ccTutorial/inst/doc/ccTutorialSupplement.pdf vignetteTitles: A tutorial on how to analyze ChIP-chip readouts using Bioconductor, Supplement to A tutorial on how to analyze ChIP-chip readouts using Bioconductor hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ccTutorial/inst/doc/ccTutorial.R, vignettes/ccTutorial/inst/doc/ccTutorialSupplement.R dependencyCount: 89 Package: celarefData Version: 1.10.0 Depends: R (>= 3.5.0) Suggests: ExperimentHub, knitr, rmarkdown License: GPL-3 MD5sum: b2636e8b9bc8d42d46ab6f81039bc5ce NeedsCompilation: no Title: Processed scRNA data for celaref Vignette - cell labelling by reference Description: This experiment data contains some processed data used in the celaref package vignette. These are publically available datasets, that have been processed by celaref package, and can be manipulated further with it. biocViews: ExperimentData, SingleCellData, ExperimentHub Author: Sarah Williams [aut, cre] Maintainer: Sarah Williams VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/celarefData git_branch: RELEASE_3_13 git_last_commit: 78e943a git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/celarefData_1.10.0.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: 1.2.0 Depends: SummarizedExperiment Imports: utils, ExperimentHub, AnnotationHub, AnnotationDbi, S4Vectors, DelayedArray, DelayedMatrixStats Suggests: testthat, knitr, rmarkdown, BiocStyle, DT License: GPL-3 MD5sum: 9785f10e84851ba69c458b3594e6876c NeedsCompilation: no Title: Reference Index for Cell Types Description: Provides a collection of reference expression datasets with curated cell type labels, for use in procedures like automated annotation of single-cell data or deconvolution of bulk RNA-seq. biocViews: ExperimentHub, ExperimentData, ExpressionData, SequencingData, RNASeqData Author: Dvir Aran [aut], Aaron Lun [aut, cre, cph], Daniel Bunis [aut], Jared Andrews [aut], Friederike Dündar [aut] Maintainer: Aaron Lun URL: https://github.com/LTLA/celldex VignetteBuilder: knitr BugReports: https://support.bioconductor.org/ git_url: https://git.bioconductor.org/packages/celldex git_branch: RELEASE_3_13 git_last_commit: 4aba059 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/celldex_1.2.0.tar.gz vignettes: vignettes/celldex/inst/doc/userguide.html vignetteTitles: Cell type references hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/celldex/inst/doc/userguide.R importsMe: singleCellTK suggestsMe: ontoProc, SingleR, tidySingleCellExperiment dependencyCount: 98 Package: CellMapperData Version: 1.18.0 Depends: ExperimentHub, CellMapper Suggests: BiocStyle License: Artistic-2.0 MD5sum: fac4e418ca4185b21c95e25eb881b96a NeedsCompilation: no Title: Pre-processed data for use with the CellMapper package Description: Experiment data package. Contains microarray data from several large expression compendia that have been pre-processed for use with the CellMapper package. This pre-processed data is recommended for routine searches using the CellMapper package. biocViews: ExperimentData, MicroarrayData, ExpressionData Author: Brad Nelms Maintainer: Brad Nelms git_url: https://git.bioconductor.org/packages/CellMapperData git_branch: RELEASE_3_13 git_last_commit: c90ec2c git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/CellMapperData_1.18.0.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: 89 Package: ChAMPdata Version: 2.24.0 Depends: GenomicRanges (>= 1.22.4),BiocGenerics(>= 0.16.1),R (>= 3.3) License: GPL-3 MD5sum: 238d4a66ca9639432de4e6c0590a62dd NeedsCompilation: no Title: Data Packages for ChAMP package Description: Provides datasets needed for ChAMP including a test dataset and blood controls for CNA analysis. biocViews: ExperimentData Author: Yuan Tian [ctb,aut], Tiffany Morris [cre,aut], Lee Stirling [ctb] and Andrew Teschendorff [ctb] Maintainer: Yuan Tian git_url: https://git.bioconductor.org/packages/ChAMPdata git_branch: RELEASE_3_13 git_last_commit: ed64648 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ChAMPdata_2.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ChAMP dependencyCount: 17 Package: ChIC.data Version: 1.12.0 Depends: R (>= 3.5), genomeIntervals, randomForest Imports: caret (>= 6.0-78) License: GPL-2 MD5sum: d29e088e6c890b4ca3a8786f9093c69c NeedsCompilation: no Title: ChIC package data Description: This package contains annotation and metagene profile data for the ChIC package. biocViews: ExperimentData, ENCODE Author: Carmen Maria Livi [aut, cre, dtc], Endre Sebestyen [aut] Maintainer: Carmen Maria Livi git_url: https://git.bioconductor.org/packages/ChIC.data git_branch: RELEASE_3_13 git_last_commit: 557c32b git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ChIC.data_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: ChIC dependencyCount: 94 Package: ChimpHumanBrainData Version: 1.30.0 Depends: affy,qvalue,limma,hexbin,statmod License: MIT MD5sum: 946cb74b55b6b084fe335f0c65bc05a0 NeedsCompilation: no Title: Chimp and human brain data package Description: This data package contains chimp and human brain data extracted from the ArrayExpress accession E-AFMX-2. Both human and chimp RNAs were run on human hgu95av2 Affymetrix arrays. It is a useful dataset for tutorials. biocViews: Tissue, Homo_sapiens_Data, Pan_troglodytes_Data, MicroarrayData, TissueMicroarrayData, GEO Author: Roman Jaksik, Naomi Altman, and Sean Davis Maintainer: Sean Davis git_url: https://git.bioconductor.org/packages/ChimpHumanBrainData git_branch: RELEASE_3_13 git_last_commit: 0639228 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ChimpHumanBrainData_1.30.0.tar.gz vignettes: vignettes/ChimpHumanBrainData/inst/doc/DiffExpressVignette.pdf vignetteTitles: DiffExpressVignette.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ChimpHumanBrainData/inst/doc/DiffExpressVignette.R dependencyCount: 56 Package: chipenrich.data Version: 2.16.0 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: d93d22e323cc0e4700572c414eb5e045 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: Raymond G. Cavalcante VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/chipenrich.data git_branch: RELEASE_3_13 git_last_commit: 7bbcf41 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/chipenrich.data_2.16.0.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: 88 Package: ChIPexoQualExample Version: 1.16.1 Depends: R (>= 3.3) Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: e76b73afdb5f75667d9b5b1feaa2ffb5 NeedsCompilation: no Title: Example data for the ChIPexoQual package, which implements a quality control pipeline for ChIP-exo data Description: Data for the ChIPexoQual package, consisting of (3) chromosome 1 aligned reads from a ChIP-exo experiment for FoxA1 in mouse liver cell lines aligned to the mm9 genome. biocViews: ExperimentData, Genome Author: Rene Welch, Dongjun Chung, Sunduz Keles Maintainer: Rene Welch URL: http://www.github.com/keleslab/ChIPexoQualExample VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ChIPexoQualExample git_branch: RELEASE_3_13 git_last_commit: d3e8073 git_last_commit_date: 2021-07-26 Date/Publication: 2021-07-27 source.ver: src/contrib/ChIPexoQualExample_1.16.1.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: 1.8.1 Imports: AnnotationHub, ExperimentHub, Rsamtools, S4Vectors Suggests: knitr, BiocStyle, rmarkdown License: CC BY 4.0 MD5sum: 129c07a8e874b4cb4d3f00859f4a882d NeedsCompilation: no Title: Data for the chipseqDB Workflow Description: Sorted and indexed BAM files for ChIP-seq libraries, for use in the chipseqDB workflow. BAM indices are also included. biocViews: SequencingData, ChIPSeqData, ExperimentHub Author: Aaron Lun [aut, cre] Maintainer: Aaron Lun VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/chipseqDBData git_branch: RELEASE_3_13 git_last_commit: 7c2d372 git_last_commit_date: 2021-06-30 Date/Publication: 2021-07-10 source.ver: src/contrib/chipseqDBData_1.8.1.tar.gz vignettes: vignettes/chipseqDBData/inst/doc/chipseqDBData.html vignetteTitles: File manifest and statistics hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/chipseqDBData/inst/doc/chipseqDBData.R suggestsMe: chipseqDB dependencyCount: 98 Package: ChIPXpressData Version: 1.30.0 Depends: bigmemory License: GPL (>=2) MD5sum: d42d45efba6211d20a70776e03f9c154 NeedsCompilation: no Title: ChIPXpress Pre-built Databases Description: Contains pre-built mouse (GPL1261) and human (GPL570) database of gene expression profiles to be used for ChIPXpress ranking. biocViews: Homo_sapiens_Data, Mus_musculus_Data, GEO Author: George Wu Maintainer: George Wu git_url: https://git.bioconductor.org/packages/ChIPXpressData git_branch: RELEASE_3_13 git_last_commit: b01784f git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ChIPXpressData_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ChIPXpress dependencyCount: 6 Package: chromstaRData Version: 1.18.0 Depends: R (>= 3.3) License: GPL-3 MD5sum: 1c290e4aa8468c12754a46c04943c9c0 NeedsCompilation: no Title: ChIP-seq data for Demonstration Purposes Description: ChIP-seq data for demonstration purposes in the chromstaR package. biocViews: Mus_musculus_Data, StemCell, ChIPSeqData Author: Aaron Taudt Maintainer: Aaron Taudt git_url: https://git.bioconductor.org/packages/chromstaRData git_branch: RELEASE_3_13 git_last_commit: 46bfa44 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/chromstaRData_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: chromstaR suggestsMe: epigraHMM dependencyCount: 0 Package: CLL Version: 1.32.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: LGPL MD5sum: 54117a14479d842849022b2bebf561d5 NeedsCompilation: no Title: A Package for CLL Gene Expression Data Description: The CLL package contains the chronic lymphocytic leukemia (CLL) gene expression data. The CLL data had 24 samples that were either classified as progressive or stable in regards to disease progression. The data came from Dr. Sabina Chiaretti at Division of Hematology, Department of Cellular Biotechnologies and Hematology, University La Sapienza, Rome, Italy and Dr. Jerome Ritz at Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts. biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData Author: Elizabeth Whalen Maintainer: Robert Gentleman git_url: https://git.bioconductor.org/packages/CLL git_branch: RELEASE_3_13 git_last_commit: 0ddb030 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/CLL_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 13 Package: CLLmethylation Version: 1.12.0 Depends: R (>= 3.5.0) Imports: SummarizedExperiment, ExperimentHub Suggests: BiocStyle, ggplot2, knitr, rmarkdown License: LGPL MD5sum: e02486f1f0785ed55d975d1e9670e92b NeedsCompilation: no Title: Methylation data of primary CLL samples in PACE project Description: The package includes DNA methylation data for the primary Chronic Lymphocytic Leukemia samples included in the Primary Blood Cancer Encyclopedia (PACE) project. Raw data from the 450k DNA methylation arrays is stored in the European Genome-Phenome Archive (EGA) under accession number EGAS0000100174. For more information concerning the project please refer to the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) and R/Bioconductor package BloodCancerMultiOmics2017. biocViews: ExperimentData, DiseaseModel, CancerData, LeukemiaCancerData Author: Malgorzata Oles, Andreas Mock Maintainer: Malgorzata Oles , Andreas Mock VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/CLLmethylation git_branch: RELEASE_3_13 git_last_commit: 6d214d4 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/CLLmethylation_1.12.0.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: 96 Package: CluMSIDdata Version: 1.8.0 Depends: R (>= 3.6) License: MIT + file LICENSE MD5sum: ead20ecbd69585f9a65b6e25129e2878 NeedsCompilation: no Title: Data for the CluMSID package Description: This package contains various LC-MS/MS and GC-MS data that is used in vignettes and examples in the CluMSID package. biocViews: ExperimentData, MassSpectrometryData Author: Tobias Depke [aut, cre] Maintainer: Tobias Depke git_url: https://git.bioconductor.org/packages/CluMSIDdata git_branch: RELEASE_3_13 git_last_commit: ee100af git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/CluMSIDdata_1.8.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: CluMSID dependencyCount: 0 Package: clustifyrdatahub Version: 1.2.0 Depends: R (>= 4.0), ExperimentHub Imports: utils Suggests: clustifyr, Seurat, usethis, rmarkdown, knitr, tidyr, BiocStyle License: MIT + file LICENSE MD5sum: c4490ccb8b4a7a4036cacbaa191cb81f NeedsCompilation: no Title: External data sets for clustifyr in ExperimentHub Description: References made from external single-cell mRNA sequencing data sets, stored as average gene expression matrices. For use with clustifyr to assign cell type identities. biocViews: SingleCellData, SequencingData, MicroarrayData, ExperimentHub, RNASeqData, PackageTypeData, ExpressionData Author: Rui Fu [aut, cre] (), Kent Riemondy [aut] (), RNA Bioscience Initiative [fnd], Austin Gillen [ctb] (), Jay Hesselberth [ctb] (), Sidhant Puntambekar [ctb] Maintainer: Rui Fu URL: https://rnabioco.github.io/clustifyrdatahub VignetteBuilder: knitr BugReports: https://github.com/rnabioco/clustifyrdatahub/issues git_url: https://git.bioconductor.org/packages/clustifyrdatahub git_branch: RELEASE_3_13 git_last_commit: 0fce6cd git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/clustifyrdatahub_1.2.0.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: 88 Package: cMap2data Version: 1.28.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 78444008b35cec74a60a66a6cbc43e89 NeedsCompilation: no Title: Connectivity Map (version 2) Data Description: Data package which provides default drug profiles for the DrugVsDisease package as well as associated gene lists and data clusters used by the DrugVsDisease package. biocViews: Homo_sapiens_Data, MicroarrayData, GEO Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/cMap2data git_branch: RELEASE_3_13 git_last_commit: e82c0dd git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/cMap2data_1.28.0.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: 1.28.0 Depends: R (>= 2.10), cnvGSA License: LGPL MD5sum: 3f415214324bb6fd823bcbe84669527c NeedsCompilation: no Title: Data used in the vignette of the cnvGSA package Description: This package contains the data used in the vignette of the cnvGSA package. biocViews: ExperimentData, Genome, CopyNumberVariationData Author: Joseph Lugo Maintainer: Joseph Lugo git_url: https://git.bioconductor.org/packages/cnvGSAdata git_branch: RELEASE_3_13 git_last_commit: 8155088 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/cnvGSAdata_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: cnvGSA dependencyCount: 26 Package: COHCAPanno Version: 1.28.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 9670d8fb7dd3e6e9fd9b04dab5a72129 NeedsCompilation: no Title: Annotations for City of Hope CpG Island Analysis Pipeline Description: Provides genomic location, nearby CpG island and nearby gene information for common Illumina methylation array platforms biocViews: Homo_sapiens_Data, MicroarrayData, MethylationArrayData, CpGIslandData, GEO, ArrayExpress Author: Charles Warden Maintainer: Charles Warden git_url: https://git.bioconductor.org/packages/COHCAPanno git_branch: RELEASE_3_13 git_last_commit: 1c2b0bc git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/COHCAPanno_1.28.0.tar.gz vignettes: vignettes/COHCAPanno/inst/doc/COHCAPanno.pdf vignetteTitles: COHCAPanno Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/COHCAPanno/inst/doc/COHCAPanno.R dependsOnMe: COHCAP dependencyCount: 0 Package: colonCA Version: 1.34.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: 494d6b66c75c2b7fa93258f95fa88a9b NeedsCompilation: no Title: exprSet for Alon et al. (1999) colon cancer data Description: exprSet for Alon et al. (1999) colon cancer data biocViews: ExperimentData, Tissue, CancerData, ColonCancerData, MicroarrayData, TissueMicroarrayData Author: Sylvia Merk Maintainer: W Sylvia Merk git_url: https://git.bioconductor.org/packages/colonCA git_branch: RELEASE_3_13 git_last_commit: 237f935 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/colonCA_1.34.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: clustComp, copa dependencyCount: 7 Package: CONFESSdata Version: 1.20.0 Depends: R (>= 3.3) License: GPL-2 MD5sum: 4d6cc4d203976adff0fccb7f1402b497 NeedsCompilation: no Title: Example dataset for CONFESS package Description: Example text-converted C01 image files for use in the CONFESS Bioconductor package. biocViews: HighThroughputImagingData,CellCulture,Homo_sapiens_Data,ExpressionData Author: Diana LOW and Efthimios MOTAKIS Maintainer: Diana LOW git_url: https://git.bioconductor.org/packages/CONFESSdata git_branch: RELEASE_3_13 git_last_commit: 62d41be git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/CONFESSdata_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CONFESS dependencyCount: 0 Package: ConnectivityMap Version: 1.28.0 Depends: R (>= 2.15.1) Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 66347ae84512e72eea4f8ccbda348f0c NeedsCompilation: no Title: Functional connections between drugs, genes and diseases as revealed by common gene-expression changes Description: The Broad Institute's Connectivity Map (cmap02) is a "large reference catalogue of gene-expression data from cultured human cells perturbed with many chemicals and genetic reagents", containing more than 7000 gene expression profiles and 1300 small molecules. biocViews: ExperimentData, CancerData, MicroarrayData Author: Paul Shannon Maintainer: Paul Shannon git_url: https://git.bioconductor.org/packages/ConnectivityMap git_branch: RELEASE_3_13 git_last_commit: c11d61d git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ConnectivityMap_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: COPDSexualDimorphism.data Version: 1.28.0 License: LGPL-2.1 MD5sum: 411ed032ce2269e61615ddc800c1ca4f NeedsCompilation: no Title: Data to support sexually dimorphic and COPD differential analysis for gene expression and methylation. Description: Datasets to support COPDSexaulDimorphism Package. biocViews: ExperimentData, Tissue, COPDData Author: J Fah Sathirapongsasuti Maintainer: J Fah Sathirapongsasuti git_url: https://git.bioconductor.org/packages/COPDSexualDimorphism.data git_branch: RELEASE_3_13 git_last_commit: f493f79 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/COPDSexualDimorphism.data_1.28.0.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: 1.24.0 Depends: R(>= 2.10) Suggests: BiocStyle License: GPL-2 MD5sum: 77622bc617c0d4bcbcacbb82079fa5b5 NeedsCompilation: no Title: Helper files for CopywriteR Description: This package contains the helper files that are required to run the Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content and mappability files for the reference genomes hg18, hg19, hg38, mm9 and mm10. In addition, it contains a blacklist filter to remove regions that display CNV. Files are stored as GRanges objects from the GenomicRanges Bioconductor package. biocViews: Homo_sapiens, GenomicSequence Author: Thomas Kuilman Maintainer: Oscar Krijgsman git_url: https://git.bioconductor.org/packages/CopyhelpeR git_branch: RELEASE_3_13 git_last_commit: 50ad5b9 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/CopyhelpeR_1.24.0.tar.gz vignettes: vignettes/CopyhelpeR/inst/doc/CopyhelpeR.pdf vignetteTitles: CopyhelpeR hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CopyhelpeR/inst/doc/CopyhelpeR.R importsMe: CopywriteR dependencyCount: 0 Package: CopyNeutralIMA Version: 1.10.0 Depends: R (>= 3.5.0) Imports: ExperimentHub,Rdpack (>= 0.8) Suggests: BiocStyle,knitr,rmarkdown,minfi,conumee,minfiData License: Artistic-2.0 MD5sum: e09a5f1a24327a8c57cd912130cf6cc9 NeedsCompilation: no Title: Copy Neutral Illumina Methylation Arrays Description: Provides a set of genomic copy neutral samples hybridized using Illumina Methylation arrays (450k and EPIC). biocViews: ExperimentData,Homo_sapiens_Data,MicroarrayData,TwoChannelData,MethylationArrayData,GEO Author: Xavier Pastor Hostench [aut, cre], Moritz Przybilla [aut] Maintainer: Xavier Pastor Hostench VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/CopyNeutralIMA git_branch: RELEASE_3_13 git_last_commit: 8cada07 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/CopyNeutralIMA_1.10.0.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: 90 Package: COSMIC.67 Version: 1.28.0 Depends: R (>= 3.0.2) Imports: GenomicRanges, SummarizedExperiment, VariantAnnotation Suggests: testthat, BiocStyle, knitr License: GPL-3 MD5sum: ecbfd03b86b816d0801bc86e23a4ad23 NeedsCompilation: no Title: COSMIC.67 Description: COSMIC: Catalogue Of Somatic Mutations In Cancer, version 67 (2013-10-24) biocViews: ExperimentData, Genome, CancerData Author: Julian Gehring Maintainer: Julian Gehring VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/COSMIC.67 git_branch: RELEASE_3_13 git_last_commit: ceb9498 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/COSMIC.67_1.28.0.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: 98 Package: CRCL18 Version: 1.12.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: fde2aa9c9280a23b053287120d01b535 NeedsCompilation: no Title: CRC cell line dataset Description: colorectal cancer mRNA and miRNA on 18 cell lines biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/CRCL18 git_branch: RELEASE_3_13 git_last_commit: b04c101 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/CRCL18_1.12.0.tar.gz vignettes: vignettes/CRCL18/inst/doc/CRCL18Vignette.pdf vignetteTitles: CRCL18 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CRCL18/inst/doc/CRCL18Vignette.R dependencyCount: 7 Package: curatedAdipoArray Version: 1.4.0 Depends: R (>= 4.0) Suggests: knitr, rmarkdown, ExperimentHub, SummarizedExperiment License: GPL-3 + file LICENSE MD5sum: 7f1882edee818bf4fc4f551b67f3a132 NeedsCompilation: no Title: A Curated Microarrays Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Under Genetic and Pharmacological Perturbations Description: A curated dataset of Microarrays samples. The samples are MDI- induced pre-adipocytes (3T3-L1) at different time points/stage of differentiation under different types of genetic (knockdown/overexpression) and pharmacological (drug treatment) perturbations. The package documents the data collection and processing. In addition to the documentation, the package contains the scripts that was used to generated the data. biocViews: ExperimentData, ExperimentHub, GEO, MicroarrayData Author: Mahmoud Ahmed [aut, cre] () Maintainer: Mahmoud Ahmed URL: https://github.com/MahShaaban/curatedAdipoArray VignetteBuilder: knitr BugReports: https://github.com/MahShaaban/curatedAdipoArray/issues git_url: https://git.bioconductor.org/packages/curatedAdipoArray git_branch: RELEASE_3_13 git_last_commit: 43f372d git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/curatedAdipoArray_1.4.0.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: 1.8.0 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: ff74ac6b1878ddf7ec17f07e5fff11c7 NeedsCompilation: no Title: A Curated ChIP-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Description: A curated dataset of publicly available ChIP-sequencing of transcription factors, chromatin remodelers and histone modifications in the 3T3-L1 pre-adipocyte cell line. The package document the data collection, pre-processing and processing of the data. In addition to the documentation, the package contains the scripts that was used to generated the data. biocViews: ExperimentData, ExperimentHub, GEO, ChIPSeqData, SequencingData Author: Mahmoud Ahmed [aut, cre] () Maintainer: Mahmoud Ahmed URL: https://github.com/MahShaaban/curatedAdipoChIP VignetteBuilder: knitr BugReports: https://github.com/MahShaaban/curatedAdipoChIP/issues git_url: https://git.bioconductor.org/packages/curatedAdipoChIP git_branch: RELEASE_3_13 git_last_commit: 23986ca git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/curatedAdipoChIP_1.8.0.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: 96 Package: curatedAdipoRNA Version: 1.8.0 Depends: R (>= 3.6), SummarizedExperiment Suggests: knitr, rmarkdown, DESeq2, fastqcr, devtools, testthat, readr, dplyr, tidyr, ggplot2, S4Vectors License: GPL-3 MD5sum: 207a0a6e8b6e64ed83bb831bbb926342 NeedsCompilation: no Title: A Curated RNA-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Description: A curated dataset of RNA-Seq samples. The samples are MDI-induced pre-phagocytes (3T3-L1) at different time points/stage of differentiation. The package document the data collection, pre-processing and processing. In addition to the documentation, the package contains the scripts that was used to generated the data. biocViews: ExperimentData, GEO, RNASeqData, SequencingData Author: Mahmoud Ahmed [aut, cre] () Maintainer: Mahmoud Ahmed URL: https://github.com/MahShaaban/curatedAdipoRNA VignetteBuilder: knitr BugReports: https://github.com/MahShaaban/curatedAdipoRNA/issues git_url: https://git.bioconductor.org/packages/curatedAdipoRNA git_branch: RELEASE_3_13 git_last_commit: eb7adb8 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/curatedAdipoRNA_1.8.0.tar.gz vignettes: vignettes/curatedAdipoRNA/inst/doc/curatedadiporna_vignette.html vignetteTitles: Using curatedAdipoRNA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedAdipoRNA/inst/doc/curatedadiporna_vignette.R dependencyCount: 26 Package: curatedBladderData Version: 1.28.0 Depends: R (>= 2.10.0), affy Suggests: BiocStyle, survival, xtable, sva, genefilter, logging License: Artistic-2.0 MD5sum: 514e6d1df13abe8d1b58997a2d092ba9 NeedsCompilation: no Title: Bladder Cancer Gene Expression Analysis Description: The curatedBladderData package provides relevant functions and data for gene expression analysis in patients with bladder cancer. biocViews: ExperimentData, CancerData, OvarianCancerData, MicroarrayData, ExpressionData Author: Markus Riester Maintainer: Markus Riester URL: https://github.com/lima1/curatedBladderData git_url: https://git.bioconductor.org/packages/curatedBladderData git_branch: RELEASE_3_13 git_last_commit: 2a341cb git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/curatedBladderData_1.28.0.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: 2.20.0 Depends: R (>= 3.0.0), XML, ggplot2, impute, Biobase, BiocStyle Imports: methods, stats License: GPL (>= 2) MD5sum: f9e154410490cfcafcaaa7864a4d3848 NeedsCompilation: no Title: Curated breast cancer gene expression data with survival and treatment information Description: Curated human breast cancer tissue S4 ExpresionSet datasets from over 16 clinical trials comprising over 2,000 patients. All datasets contain at least one type of outcomes variable and treatment information (minimum level: whether they had chemotherapy and whether they had hormonal therapy). Includes code to post-process these datasets. biocViews: ExperimentData, ExpressionData, CancerData, Tissue, BreastCancerData, qPCRData, MicroarrayData, TissueMicroarrayData, GEO Author: Katie Planey Maintainer: Katie Planey git_url: https://git.bioconductor.org/packages/curatedBreastData git_branch: RELEASE_3_13 git_last_commit: 8bc6965 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/curatedBreastData_2.20.0.tar.gz vignettes: vignettes/curatedBreastData/inst/doc/curatedBreastData-manual.pdf vignetteTitles: Manual hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedBreastData/inst/doc/curatedBreastData-manual.R dependencyCount: 61 Package: curatedCRCData Version: 2.24.0 Depends: R (>= 2.10.0), nlme Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle License: Artistic-2.0 MD5sum: 03fc07c31d91672b759ea673965c9879 NeedsCompilation: no Title: Colorectal Cancer Gene Expression Analysis Description: The curatedCRC package provides relevant functions and data for gene expression analysis in patients with colorectal cancer. biocViews: Colorectal, Cancer, TCGA, ExperimentData, RNAExpressionData Author: Princy Parsana, Markus Riester, Curtis Huttenhower, Levi Waldron Maintainer: Princy Parsana URL: https://bitbucket.org/biobakery/curatedcrcdata git_url: https://git.bioconductor.org/packages/curatedCRCData git_branch: RELEASE_3_13 git_last_commit: db0e2ac git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/curatedCRCData_2.24.0.tar.gz vignettes: vignettes/curatedCRCData/inst/doc/curatedCRCData_vignette.pdf vignetteTitles: curatedCRCData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedCRCData/inst/doc/curatedCRCData_vignette.R dependencyCount: 10 Package: curatedMetagenomicData Version: 3.0.10 Depends: R (>= 4.1.0), SummarizedExperiment, TreeSummarizedExperiment Imports: AnnotationHub, ExperimentHub, S4Vectors, dplyr, magrittr, purrr, rlang, stringr, tibble, tidyr, tidyselect Suggests: BiocStyle, DT, knitr, mia, readr, rmarkdown, scater, testthat, utils, uwot, vegan License: Artistic-2.0 MD5sum: 6af2e752683dfdac49cb63b3a35b1ebb 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] (), 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: RELEASE_3_13 git_last_commit: 17da729 git_last_commit_date: 2021-10-11 Date/Publication: 2021-10-12 source.ver: src/contrib/curatedMetagenomicData_3.0.10.tar.gz vignettes: vignettes/curatedMetagenomicData/inst/doc/curatedMetagenomicData.html vignetteTitles: curatedMetagenomicData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedMetagenomicData/inst/doc/curatedMetagenomicData.R suggestsMe: lefser, metavizr, MMUPHin dependencyCount: 113 Package: curatedOvarianData Version: 1.30.0 Depends: R (>= 2.10.0), affy Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle License: Artistic-2.0 MD5sum: c64f32a8c11e1d6a7be978e4decb6995 NeedsCompilation: no Title: Clinically Annotated Data for the Ovarian Cancer Transcriptome Description: The curatedOvarianData package provides data for gene expression analysis in patients with ovarian cancer. biocViews: ExperimentData, RNASeqData, CancerData, OvarianCancerData, MicroarrayData Author: Benjamin F. Ganzfried, Markus Riester, Steve Skates, Victoria Wang, Thomas Risch, Benjamin Haibe-Kains, Svitlana Tyekucheva, Jie Ding, Ina Jazic, Michael Birrer, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron Maintainer: Levi Waldron URL: http://bcb.dfci.harvard.edu/ovariancancer git_url: https://git.bioconductor.org/packages/curatedOvarianData git_branch: RELEASE_3_13 git_last_commit: efcc631 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/curatedOvarianData_1.30.0.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 dependencyCount: 13 Package: curatedTCGAData Version: 1.14.0 Depends: R (>= 3.5.0), MultiAssayExperiment Imports: AnnotationHub, ExperimentHub, HDF5Array, methods, S4Vectors, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, RaggedExperiment, readr, rmarkdown, TCGAutils, testthat License: Artistic-2.0 MD5sum: 0b778ceffef74bb920e716b2ba8ac6fb NeedsCompilation: no Title: Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects Description: This package provides publicly available data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects. MultiAssayExperiment integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. It also links assay barcodes with patient identifiers, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-'omics experiment. biocViews: Homo_sapiens_Data, ReproducibleResearch, CancerData, ExperimentHub Author: Marcel Ramos [aut, cre], Levi Waldron [ctb], Lucas Schiffer [ctb], Ludwig Geistlinger [ctb], Valerie Obenchain [ctb], Martin Morgan [ctb] Maintainer: Marcel Ramos VignetteBuilder: knitr BugReports: https://github.com/waldronlab/curatedTCGAData/issues git_url: https://git.bioconductor.org/packages/curatedTCGAData git_branch: RELEASE_3_13 git_last_commit: f2d8bd3 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/curatedTCGAData_1.14.0.tar.gz vignettes: vignettes/curatedTCGAData/inst/doc/curatedTCGAData.html vignetteTitles: curatedTCGAData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedTCGAData/inst/doc/curatedTCGAData.R importsMe: AMARETTO, BiocOncoTK suggestsMe: CNVRanger, dce, deco, glmSparseNet, netDx, TCGAutils dependencyCount: 103 Package: DAPARdata Version: 1.22.2 Depends: R (>= 4.1.0) Imports: utils, knitr, MSnbase Suggests: DAPAR (>= 1.24) License: GPL-2 MD5sum: 7e0ef69848f1547f0004e3ad3f9f512f NeedsCompilation: no Title: Data accompanying the DAPAR and Prostar packages Description: Mass-spectrometry based UPS proteomics data sets from Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssie D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianferani S, Ferro M, Dorssaeler AV, Burlet-Schiltz O, Schaeffer C, Coute Y, Gonzalez de Peredo A. Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods. Data Brief. 2015 Dec 17;6:286-94 and Giai Gianetto, Q., Combes, F., Ramus, C., Bruley, C., Coute, Y., Burger, T. (2016). Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments. Proteomics, 16(1), 29-32. biocViews: ExperimentData, MassSpectrometryData Author: Samuel Wieczorek and Florence Combes Maintainer: Samuel Wieczorek git_url: https://git.bioconductor.org/packages/DAPARdata git_branch: RELEASE_3_13 git_last_commit: 227ecc9 git_last_commit_date: 2021-06-24 Date/Publication: 2021-06-24 source.ver: src/contrib/DAPARdata_1.22.2.tar.gz vignettes: vignettes/DAPARdata/inst/doc/Exp1_R2_pept.pdf, vignettes/DAPARdata/inst/doc/Exp1_R2_prot.pdf, vignettes/DAPARdata/inst/doc/Exp1_R25_pept.pdf, vignettes/DAPARdata/inst/doc/Exp1_R25_prot.pdf, vignettes/DAPARdata/inst/doc/Exp2_R10_pept.pdf, vignettes/DAPARdata/inst/doc/Exp2_R10_prot.pdf, vignettes/DAPARdata/inst/doc/Exp2_R100_pept.pdf, vignettes/DAPARdata/inst/doc/Exp2_R100_prot.pdf, vignettes/DAPARdata/inst/doc/Exp2_R2_pept.pdf, vignettes/DAPARdata/inst/doc/Exp2_R2_prot.pdf vignetteTitles: Exp1_R2_pept.pdf, Exp1_R2_prot.pdf, Exp1_R25_pept.pdf, Exp1_R25_prot.pdf, Exp2_R10_pept.pdf, Exp2_R10_prot.pdf, Exp2_R100_pept.pdf, Exp2_R100_prot.pdf, Exp2_R2_pept.pdf, Exp2_R2_prot.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: DAPAR, Prostar dependencyCount: 85 Package: davidTiling Version: 1.32.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db License: LGPL MD5sum: a9db2e7050bf14f8fbbded27eb8f5c6f NeedsCompilation: no Title: Data and analysis scripts for David, Huber et al. yeast tiling array paper Description: This package contains the data for the paper by L. David et al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix genechips, an ExpressionSet object with the raw feature data, a probe annotation data structure for the chip and the yeast genome annotation (GFF file) that was used. In addition, some custom-written analysis functions are provided, as well as R scripts in the scripts directory. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, MicroarrayData, ReproducibleResearch Author: Wolfgang Huber , Joern Toedling Maintainer: Wolfgang Huber URL: http://www.ebi.ac.uk/huber git_url: https://git.bioconductor.org/packages/davidTiling git_branch: RELEASE_3_13 git_last_commit: 675412a git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/davidTiling_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 89 Package: depmap Version: 1.6.0 Depends: R (>= 3.6), methods, dplyr Imports: utils, ExperimentHub, AnnotationHub Suggests: knitr, rmarkdown, BiocStyle, viridis, gridExtra, ggplot2, readr, tibble, stringr, tidyr License: Artistic-2.0 MD5sum: b269f7a12ecc345a33e5c90753c2f3f9 NeedsCompilation: no Title: Cancer Dependency Map Data Package Description: The depmap package is a data package that accesses datsets from the Broad Institute DepMap cancer dependency study using ExperimentHub. Datasets from the most current release are available, including RNAI and CRISPR-Cas9 gene knockout screens quantifying the genetic dependency for select cancer cell lines. Additional datasets are also available pertaining to the log copy number of genes for select cell lines, protein expression of cell lines as measured by reverse phase protein lysate microarray (RPPA), 'Transcript Per Million' (TPM) data, as well as supplementary datasets which contain metadata and mutation calls for the other datasets found in the current release. The 19Q3 release adds the drug_dependency dataset, that contains cancer cell line dependency data with respect to drug and drug-candidate compounds. The 20Q2 release adds the proteomic dataset that contains quantitative profiling of proteins via mass spectrometry. This package will be updated on a quarterly basis to incorporate the latest Broad Institute DepMap Public cancer dependency datasets. All data made available in this package was generated by the Broad Institute DepMap for research purposes and not intended for clinical use. This data is distributed under the Creative Commons license (Attribution 4.0 International (CC BY 4.0)). biocViews: ExperimentHub, ExperimentData, ReproducibleResearch, RepositoryData, AssayDomainData, CopyNumberVariationData, DiseaseModel, CancerData, BreastCancerData, ColonCancerData, KidneyCancerData, LeukemiaCancerData, LungCancerData, OvarianCancerData, ProstateCancerData, OrganismData, Homo_sapiens_Data, PackageTypeData, SpecimenSource, CellCulture, Genome, Proteome, StemCell, Tissue Author: Laurent Gatto [cre, aut], Theo Killian [aut] Maintainer: Laurent Gatto VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/depmap git_branch: RELEASE_3_13 git_last_commit: 69104af git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/depmap_1.6.0.tar.gz vignettes: vignettes/depmap/inst/doc/depmap.html, vignettes/depmap/inst/doc/using_depmap.html vignetteTitles: depmap, depmap use cases hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/depmap/inst/doc/depmap.R, vignettes/depmap/inst/doc/using_depmap.R dependencyCount: 88 Package: derfinderData Version: 2.10.0 Depends: R(>= 3.1.1) Suggests: sessioninfo, knitr (>= 1.6), RefManageR, rmarkdown (>= 0.3.3), BiocStyle License: Artistic-2.0 MD5sum: 47aa4075b382f87105b5323a462f54f7 NeedsCompilation: no Title: Processed BigWigs from BrainSpan for examples Description: Processed 22 samples from BrainSpan keeping only the information for chromosome 21. Data is stored in the BigWig format and is used for examples in other packages. biocViews: ExperimentData, Homo_sapiens_Data, RNASeqData Author: Leonardo Collado-Torres [aut, cre] (), Andrew Jaffe [aut] (), Jeffrey Leek [aut, ths] () Maintainer: Leonardo Collado-Torres URL: https://github.com/leekgroup/derfinderData VignetteBuilder: knitr BugReports: https://github.com/leekgroup/derfinderData/issues git_url: https://git.bioconductor.org/packages/derfinderData git_branch: RELEASE_3_13 git_last_commit: 4459056 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/derfinderData_2.10.0.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: 1.28.0 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: dbd01320474db595c34599f57e31c53a NeedsCompilation: no Title: Poor prognosis colon cancer is defined by a molecularly distinct subtype and precursor lesion Description: This package reproduces the main pipeline to analyze the AMC-AJCCII-90 microarray data set in De Sousa et al. accepted by Nature Medicine in 2013. biocViews: CancerData, ColonCancerData, MicroarrayData Author: Xin Wang Maintainer: Xin Wang git_url: https://git.bioconductor.org/packages/DeSousa2013 git_branch: RELEASE_3_13 git_last_commit: c9dc4c4 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/DeSousa2013_1.28.0.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: 117 Package: DExMAdata Version: 1.0.0 Depends: R (>= 4.1) Imports: Biobase Suggests: BiocStyle License: GPL-2 MD5sum: b91e379770438a5e4afe6f9ff0babc73 NeedsCompilation: no Title: Data package for DExMA package Description: Data objects needed to allSameID() function of DExMA package. There are also some objects that are necessary to be able to apply the examples of the DExMA package, which illustrate package functionality. biocViews: ExperimentData, OrganismData, MicroarrayData Author: Juan Antonio Villatoro-García [aut, cre], Pedro Carmona-Sáez [aut] Maintainer: Juan Antonio Villatoro-García git_url: https://git.bioconductor.org/packages/DExMAdata git_branch: RELEASE_3_13 git_last_commit: a33f8dc git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/DExMAdata_1.0.0.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: 1.20.0 Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 1689e4bcce4277efcd825c4cee461d44 NeedsCompilation: no Title: Example ChIA-PET Datasets for the diffloop Package Description: ChIA-PET example datasets and additional data for use with the diffloop package. biocViews: ExperimentData, SequencingData Author: Caleb Lareau [aut], Martin Aryee [aut, cre] Maintainer: Caleb Lareau VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/diffloopdata git_branch: RELEASE_3_13 git_last_commit: 731ad76 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/diffloopdata_1.20.0.tar.gz vignettes: vignettes/diffloopdata/inst/doc/diffloopdata.html vignetteTitles: diffloopdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: diffloop dependencyCount: 0 Package: diggitdata Version: 1.24.0 Depends: R(>= 2.14.0), Biobase, methods Imports: viper License: GPL (>=2) MD5sum: ed39d4ad5901a4b5d9bbbe420591b800 NeedsCompilation: no Title: Example data for the diggit package Description: This package provides expression profile and CNV data for glioblastoma from TCGA, and transcriptional and post-translational regulatory networks assembled with the ARACNe and MINDy algorithms, respectively. biocViews: ExperimentData, Cancer Author: Mariano Javier Alvarez Maintainer: Mariano Javier Alvarez git_url: https://git.bioconductor.org/packages/diggitdata git_branch: RELEASE_3_13 git_last_commit: 4e8b8fa git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/diggitdata_1.24.0.tar.gz vignettes: vignettes/diggitdata/inst/doc/diggitdata.pdf vignetteTitles: Using bcellViper hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/diggitdata/inst/doc/diggitdata.R suggestsMe: diggit dependencyCount: 22 Package: DLBCL Version: 1.32.0 Depends: R(>= 2.11.0), Biobase License: GPL (>=2) MD5sum: 5a8ea6626bb4828b296dc5c0066ad569 NeedsCompilation: no Title: Diffuse large B-cell lymphoma expression data Description: This package provides additional expression data on diffuse large B-cell lymphomas for the BioNet package. biocViews: ExperimentData, CancerData, MicroarrayData, ChipOnChipData Author: Marcus Dittrich and Daniela Beisser Maintainer: Marcus Dittrich URL: http://bionet.bioapps.biozentrum.uni-wuerzburg.de/ git_url: https://git.bioconductor.org/packages/DLBCL git_branch: RELEASE_3_13 git_last_commit: c9430c6 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/DLBCL_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: BioNet, SANTA dependencyCount: 7 Package: DmelSGI Version: 1.24.0 Depends: R (>= 3.0) Imports: grid, TSP, limma, rhdf5, knitr, abind, gplots, igraph, grDevices, graphics, stats Suggests: BiocStyle, EBImage, RColorBrewer, RNAinteractMAPK, RSVGTipsDevice, cgdsr, hwriter, xtable, beeswarm License: Artistic-2.0 MD5sum: d8c83f889758cadf10c588980601b1eb NeedsCompilation: no Title: Experimental data and documented source code for the paper "A Map of Directional Genetic Interactions in a Metazoan Cell" Description: The package contains the experimental data and documented source code of the manuscript "Fischer et al., A Map of Directional Genetic Interactions in a Metazoan Cell, eLife, 2015, in Press.". The vignette code generates all figures in the paper. biocViews: MicrotitrePlateAssayData, CellCulture, HighthroughputImagingData, Drosophila_melanogaster_Data, ExperimentData, HighThroughputImagingData, ReproducibleResearch Author: Bernd Fischer [aut], Wolfgang Huber [ctb], Mike Smith [cre] Maintainer: Mike Smith VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DmelSGI git_branch: RELEASE_3_13 git_last_commit: df09a68 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/DmelSGI_1.24.0.tar.gz vignettes: vignettes/DmelSGI/inst/doc/DmelSGI.pdf vignetteTitles: DmelSGI hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DmelSGI/inst/doc/DmelSGI.R dependencyCount: 34 Package: DMRcatedata Version: 2.10.0 Depends: R (>= 3.6), ExperimentHub Imports: GenomicFeatures, Gviz, readxl, plyr, rtracklayer, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr License: GPL-3 MD5sum: e2859c2b230cff802527a4d28e72e737 NeedsCompilation: no Title: Data Package for DMRcate Description: This package contains 9 data objects supporting functionality and examples of the Bioconductor package DMRcate. biocViews: ExperimentHub, ExperimentData, SNPData, Homo_sapiens_Data, Mus_musculus_Data, SequencingData, MicroarrayData, Genome Author: Tim Peters Maintainer: Tim Peters VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DMRcatedata git_branch: RELEASE_3_13 git_last_commit: 7b93458 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/DMRcatedata_2.10.0.tar.gz vignettes: vignettes/DMRcatedata/inst/doc/DMRcatedata.pdf vignetteTitles: The DMRcate package user's guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DMRcatedata/inst/doc/DMRcatedata.R dependencyCount: 202 Package: DonaPLLP2013 Version: 1.30.0 Depends: EBImage, parallel License: Artistic-2.0 MD5sum: c5c94f2ace331e3cbb8436f760bf2f51 NeedsCompilation: no Title: Supplementary data package for Dona et al. (2013) containing example images and tables Description: An experiment data package associated with the publication Dona et al. (2013). Package contains runnable vignettes showing an example image segmentation for one posterior lateral line primordium, and also the data table and code used to analyze tissue-scale lifetime-ratio statistics. biocViews: ExperimentData, Tissue Author: Erika Dona, Joseph D. Barry, Guillaume Valentin, Charlotte Quirin, Anton Khmelinskii, Andreas Kunze, Sevi Durdu, Lionel R. Newton, Ana Fernandez-Minan, Wolfgang Huber, Michael Knop, Darren Gilmour Maintainer: Joseph D. Barry git_url: https://git.bioconductor.org/packages/DonaPLLP2013 git_branch: RELEASE_3_13 git_last_commit: 3d2c063 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/DonaPLLP2013_1.30.0.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: 26 Package: dorothea Version: 1.4.2 Depends: R (>= 4.0) Imports: dplyr, magrittr, bcellViper, viper Suggests: Biobase, BiocStyle, knitr, pheatmap, pkgdown, rmarkdown, Seurat, SingleCellExperiment, SummarizedExperiment, testthat (>= 2.1.0), tibble, tidyr, utils License: GPL-3 + file LICENSE MD5sum: d4bb09bd45e6ba6198dbf74b6255569c NeedsCompilation: no Title: Collection Of Human And Mouse TF Regulons Description: This package contains human and mouse TF regulons. The human regulons were curated and collected from different types of evidence such as literature curated resources, ChIP-seq peaks, TF binding site motifs and interactions inferred directly from gene expression. The mouse regulons were constructed by mapping the human gene symbols to their orthologs in mice. Those regulons can be coupled with any statistical method that aims to analyse gene sets to infer TF activity from gene expression data. Preferably the statistical method viper is used. biocViews: ExperimentData, Homo_sapiens_Data, Mus_musculus_Data Author: Christian H. Holland [cre, aut] (), Luz Garcia-Alonso [aut], Alberto Valdeolivas [ctb], Minoo Ashtiani [ctb], Attila Gabor [ctb] Maintainer: Christian H. Holland URL: https://saezlab.github.io/dorothea/, https://github.com/saezlab/dorothea VignetteBuilder: knitr BugReports: https://github.com/saezlab/dorothea/issues git_url: https://git.bioconductor.org/packages/dorothea git_branch: RELEASE_3_13 git_last_commit: cd0c31d git_last_commit_date: 2021-10-08 Date/Publication: 2021-10-09 source.ver: src/contrib/dorothea_1.4.2.tar.gz vignettes: vignettes/dorothea/inst/doc/bulk_vignette.html, vignettes/dorothea/inst/doc/single_cell_vignette.html vignetteTitles: TF activity inference from bulk transcriptomic data with DoRothEA as regulon resource., TF activity inference from scRNA-seq data with DoRothEA as regulon resource. hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/dorothea/inst/doc/bulk_vignette.R, vignettes/dorothea/inst/doc/single_cell_vignette.R importsMe: cosmosR suggestsMe: MethReg dependencyCount: 41 Package: DREAM4 Version: 1.28.0 Depends: R (>= 2.15.1), SummarizedExperiment Suggests: RUnit, networkBMA License: GPL MD5sum: b283d42017420bbd6bbb69a009231886 NeedsCompilation: no Title: Synthetic Expression Data for Gene Regulatory Network Inference from the 2009 DREAM4 challenge Description: Simulated expression data for five 10-node, and five 100-node networks, with associated data (including solutions) from the 2009 DREAM4 challenge. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, SequencingData Author: Paul Shannon Maintainer: Paul Shannon git_url: https://git.bioconductor.org/packages/DREAM4 git_branch: RELEASE_3_13 git_last_commit: 6bb2a25 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/DREAM4_1.28.0.tar.gz vignettes: vignettes/DREAM4/inst/doc/DREAM4_InSilico_Description.pdf, vignettes/DREAM4/inst/doc/DREAM4.pdf vignetteTitles: DREAM4_InSilico_Description.pdf, DREAM4 Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DREAM4/inst/doc/DREAM4.R dependencyCount: 26 Package: dressCheck Version: 0.30.0 Depends: R (>= 2.10.1), methods, Biobase (>= 2.5.5) Suggests: survival, chron License: Artistic-2.0 MD5sum: f921f44b84fe8d85b1561049698222a8 NeedsCompilation: no Title: data and software for checking Dressman JCO 25(5) 2007 Description: data and software for checking Dressman JCO 25(5) 2007 biocViews: ExperimentData, Genome Author: Vincent Carey Maintainer: Vincent Carey git_url: https://git.bioconductor.org/packages/dressCheck git_branch: RELEASE_3_13 git_last_commit: f716c5e git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/dressCheck_0.30.0.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: 1.2.0 Imports: utils, ExperimentHub, AnnotationHub, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, testthat, DropletUtils License: GPL-3 MD5sum: 88bb2d6c714a8250df75b00143421ae5 NeedsCompilation: no Title: Test Files for Single-Cell Droplet Utilities Description: Assorted files generated from droplet-based single-cell protocols, to be used for testing functions in DropletUtils. Primarily intended for storing files that directly come out of processing pipelines like 10X Genomics' CellRanger software, prior to the formation of a SingleCellExperiment object. Unlike other packages, this is not designed to provide objects that are immediately ready for analysis. biocViews: ExperimentHub, ExperimentData, ExpressionData, SequencingData, RNASeqData, SingleCellData Author: Aaron Lun [ctb, cre] Maintainer: Aaron Lun VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DropletTestFiles git_branch: RELEASE_3_13 git_last_commit: a90422b git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/DropletTestFiles_1.2.0.tar.gz vignettes: vignettes/DropletTestFiles/inst/doc/motivation.html vignetteTitles: Test files for droplet-based single-cell utilities hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DropletTestFiles/inst/doc/motivation.R suggestsMe: DropletUtils dependencyCount: 88 Package: DrugVsDiseasedata Version: 1.28.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: ad491fc82db8803e6ff4f23b22c62737 NeedsCompilation: no Title: Drug versus Disease Data Description: Data package which provides default disease expression profiles, clusters and annotation information for use with the DrugVsDisease package. biocViews: Homo_sapiens_Data, MicroarrayData Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/DrugVsDiseasedata git_branch: RELEASE_3_13 git_last_commit: 3f561ee git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/DrugVsDiseasedata_1.28.0.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: 1.10.0 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: 7d6d85ea0319f884ab5f23f900eeffee NeedsCompilation: no Title: Data, Clustering Results and Visualization Functions From Duò et al (2018) Description: Preprocessed experimental and simulated scRNA-seq data sets used for evaluation of clustering methods for scRNA-seq data in Duò et al (2018). Also contains results from applying several clustering methods to each of the data sets, and functions for plotting method performance. biocViews: SingleCellData, ExperimentData Author: Angelo Duò, Charlotte Soneson Maintainer: Angelo Duò VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DuoClustering2018 git_branch: RELEASE_3_13 git_last_commit: 0da984d git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/DuoClustering2018_1.10.0.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: 115 Package: DvDdata Version: 1.28.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 564a994af6a6316482edecaf008fbd60 NeedsCompilation: no Title: Drug versus Disease Data Description: Data package which provides default drug and disease expression profiles for the DvD package. biocViews: GEO Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/DvDdata git_branch: RELEASE_3_13 git_last_commit: 2718d24 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/DvDdata_1.28.0.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: 1.32.0 Depends: R (>= 1.4.1), marray, GEOquery Suggests: dyebias, convert, Biobase License: GPL-3 MD5sum: 3b318cf5600367bf33f7ca40f918c6a9 NeedsCompilation: no Title: Example data for the dyebias package, which implements the GASSCO method. Description: Data for the dyebias package, consisting of 4 self-self hybrizations of self-spotted yeast slides, as well as data from Array Express accession E-MTAB-32 biocViews: ExperimentData, SAGEData, CGHData, MicroarrayData, TwoChannelData, ArrayExpress Author: Philip Lijnzaad and Thanasis Margaritis Maintainer: Philip Lijnzaad URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad git_url: https://git.bioconductor.org/packages/dyebiasexamples git_branch: RELEASE_3_13 git_last_commit: 555102e git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/dyebiasexamples_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: dyebias dependencyCount: 50 Package: EatonEtAlChIPseq Version: 0.30.0 Depends: GenomicRanges (>= 1.5.42), ShortRead, rtracklayer License: Artistic 2.0 MD5sum: e4939cc45e1a546cd484aaa71f86cd75 NeedsCompilation: no Title: ChIP-seq data of ORC-binding sites in Yeast excerpted from Eaton et al. 2010 Description: ChIP-seq analysis subset from "Conserved nucleosome positioning defines replication origins" (PMID 20351051) biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, ChIPSeqData, GEO Author: Patrick Aboyoun Maintainer: Patrick Aboyoun git_url: https://git.bioconductor.org/packages/EatonEtAlChIPseq git_branch: RELEASE_3_13 git_last_commit: cbcae63 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/EatonEtAlChIPseq_0.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 50 Package: ecoliLeucine Version: 1.32.0 Depends: R (>= 1.9.0), affy (>= 1.23.4), ecolicdf License: GPL (>= 2) MD5sum: 11fae96f527b44af3679a56399bb0e07 NeedsCompilation: no Title: Experimental data with Affymetrix E. coli chips Description: Experimental data with Affymetrix E. coli chips, as reported in She-pin Hung, Pierre Baldi, and G. Wesley Hatfield, J. Biol. Chem., Vol. 277, Issue 43, 40309-40323, October 25, 2002 biocViews: ExperimentData, MicroarrayData Author: Laurent Gautier Maintainer: Laurent Gautier git_url: https://git.bioconductor.org/packages/ecoliLeucine git_branch: RELEASE_3_13 git_last_commit: 1936456 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ecoliLeucine_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ecolitk dependencyCount: 51 Package: EGSEAdata Version: 1.20.0 Depends: R (>= 3.4) Suggests: EGSEA License: file LICENSE MD5sum: dfa02a1518275c98e0e927cce4bc8b86 NeedsCompilation: no Title: Gene set collections for the EGSEA package Description: This package includes gene set collections that are used for the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. It includes Human and Mouse versions of the MSidDB (Subramanian, et al. (2005) PNAS, 102(43):15545-15550) and GeneSetDB (Araki, et al. (2012) FEBS Open Bio, 2:76-82) collections. biocViews: ExperimentData, Homo_sapiens_Data, Mus_musculus_Data, Rattus_norvegicus_Data Author: Monther Alhamdoosh, Yifang Hu and Gordon K. Smyth Maintainer: Monther Alhamdoosh git_url: https://git.bioconductor.org/packages/EGSEAdata git_branch: RELEASE_3_13 git_last_commit: 0eec869 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/EGSEAdata_1.20.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE importsMe: EGSEA dependencyCount: 0 Package: ELMER.data Version: 2.16.0 Depends: R (>= 3.5.0) Imports: GenomicRanges Suggests: BiocStyle, knitr, dplyr, devtools, DT License: GPL-3 MD5sum: 65c68d66e2a9da59a6f57c45a4dd382d NeedsCompilation: no Title: Data for the ELMER package Description: Supporting data for the ELMER package. It includes: - elmer.data.example.promoter: mae.promoter - elmer.data.example: data - EPIC.hg38.manifest - EPIC.hg19.manifest - hm450.hg38.manifest - hm450.hg19.manifest - hocomoco.table - human.TF - LUSC_meth_refined: Meth - LUSC_RNA_refined: GeneExp - Probes.motif.hg19.450K - Probes.motif.hg19.EPIC - Probes.motif.hg38.450K - Probes.motif.hg38.EPIC - TF.family - TF.subfamily - Human_genes__GRCh37_p13 - Human_genes__GRCh38_p12 - Human_genes__GRCh37_p13__tss - Human_genes__GRCh38_p12__tss biocViews: AssayDomainData, TechnologyData, OrganismData Author: Tiago Chedraoui Silva, Lijing Yao Simon Coetzee, Benjamin P. Berman Maintainer: Tiago Chedraoui Silva VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ELMER.data git_branch: RELEASE_3_13 git_last_commit: 906c201 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ELMER.data_2.16.0.tar.gz vignettes: vignettes/ELMER.data/inst/doc/vignettes.html vignetteTitles: ELMER.data: Supporting data for the ELMER package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ELMER.data/inst/doc/vignettes.R dependsOnMe: ELMER dependencyCount: 17 Package: emtdata Version: 1.0.0 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: 9bf3cd18ad273d22eda455702ba9586a 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] (), Chin Wee Tan [aut] (), Dharmesh D. Bhuva [aut] () 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: RELEASE_3_13 git_last_commit: 3bf711c git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/emtdata_1.0.0.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: 99 Package: estrogen Version: 1.38.0 Suggests: affy, hgu95av2, hgu95av2cdf, vsn, knitr License: LGPL MD5sum: 8663e105ed56a1ac87219ace0511c233 NeedsCompilation: no Title: Microarray dataset that can be used as example for 2x2 factorial designs Description: Data from 8 Affymetrix genechips, looking at a 2x2 factorial design (with 2 repeats per level). biocViews: ExperimentData, MicroarrayData Author: Wolfgang Huber, Robert Gentleman Maintainer: Wolfgang Huber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/estrogen git_branch: RELEASE_3_13 git_last_commit: 33544ca git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/estrogen_1.38.0.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: 1.20.0 Depends: R (>= 3.3), Biobase, metagenomeSeq(>= 1.12.0) License: Artistic-2.0 MD5sum: de72a8a4a4e422597413abec2a932799 NeedsCompilation: no Title: Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment Description: 16S rRNA gene sequencing data to study changes in the faecal microbiota of 12 volunteers during a human challenge study with ETEC (H10407) and subsequent treatment with ciprofloxacin. biocViews: ExperimentData, SequencingData, MicrobiomeData Author: Joseph N. Paulson Maintainer: Joseph N. Paulson git_url: https://git.bioconductor.org/packages/etec16s git_branch: RELEASE_3_13 git_last_commit: cfca736 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/etec16s_1.20.0.tar.gz vignettes: vignettes/etec16s/inst/doc/etec16s.pdf vignetteTitles: etec16s hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/etec16s/inst/doc/etec16s.R suggestsMe: metavizr dependencyCount: 29 Package: ewceData Version: 1.0.0 Depends: R (>= 4.1), ExperimentHub Suggests: knitr, BiocStyle, ggplot2, cowplot, rmarkdown, markdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: cd88e5016169bbbc875c574a11aa9618 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] (), Nathan Skene [aut] () Maintainer: Alan Murphy URL: https://github.com/neurogenomics/ewceData VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ewceData git_branch: RELEASE_3_13 git_last_commit: 71b6577 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ewceData_1.0.0.tar.gz vignettes: vignettes/ewceData/inst/doc/ewceData.html vignetteTitles: Data package for Expression Weighted Celltype Enrichment EWCE hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ewceData/inst/doc/ewceData.R importsMe: EWCE dependencyCount: 88 Package: faahKO Version: 1.32.0 Depends: R (>= 2.10), xcms (>= 3.4.0) License: LGPL MD5sum: b12383b1bbf0a73e1f2771f973520be0 NeedsCompilation: no Title: Saghatelian et al. (2004) FAAH knockout LC/MS data Description: Positive ionization mode data in NetCDF file format. Centroided subset from 200-600 m/z and 2500-4500 seconds. Data originally reported in "Assignment of Endogenous Substrates to Enzymes by Global Metabolite Profiling" Biochemistry; 2004; 43(45). Also includes detected peaks in an xcmsSet. biocViews: ExperimentData, MassSpectrometryData Author: Colin A. Smith Maintainer: Steffen Neumann URL: http://dx.doi.org/10.1021/bi0480335 git_url: https://git.bioconductor.org/packages/faahKO git_branch: RELEASE_3_13 git_last_commit: 0eb0fb1 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/faahKO_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: cosmiq suggestsMe: CAMERA, IPO, MAIT, peakPantheR, Risa, xcms dependencyCount: 94 Package: fabiaData Version: 1.30.0 Depends: R (>= 2.10.0), Biobase Imports: utils Suggests: fabia License: LGPL (>= 2.1) MD5sum: bc22163a6aaa36ddd5787b7eca918daf NeedsCompilation: no Title: Data sets for FABIA (Factor Analysis for Bicluster Acquisition) Description: Supplying gene expression data sets for the demos of the biclustering method "Factor Analysis for Bicluster Acquisition" (FABIA). The following three data sets are provided: A) breast cancer (van't Veer, Nature, 2002), B) multiple tissues (Su, PNAS, 2002), and C) diffuse large-B-cell lymphoma (Rosenwald, N Engl J Med, 2002). biocViews: CancerData, BreastCancerData, MicroarrayData Author: Sepp Hochreiter Maintainer: Sepp Hochreiter URL: http://www.bioinf.jku.at/software/fabia/fabia.html git_url: https://git.bioconductor.org/packages/fabiaData git_branch: RELEASE_3_13 git_last_commit: e8d998e git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/fabiaData_1.30.0.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: 1.28.0 Depends: R (>= 2.15.0) License: GPL-3 MD5sum: 4da1cff3ca4a9d3072d970a45c355da1 NeedsCompilation: no Title: CAGE data from FANTOM3 and FANTOM4 projects Description: CAGE (Cap Analysis Gene Expression) data from FANTOM3 and FANTOM4 projects produced by RIKEN Omics Science Center. biocViews: ExperimentData, Tissue Author: Vanja Haberle, Department of Biology, University of Bergen, Norway Maintainer: Vanja Haberle git_url: https://git.bioconductor.org/packages/FANTOM3and4CAGE git_branch: RELEASE_3_13 git_last_commit: d4f6281 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/FANTOM3and4CAGE_1.28.0.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: 1.30.0 Depends: R (>= 2.10.0), lumi Suggests: genefilter, affy License: GPL (>2) MD5sum: 948ea26f0d4beef776bc2c3daafeca87 NeedsCompilation: no Title: Illumina DASL example microarray data Description: A subset of GSE17565 (April et al. 2009) containing 32 FFPE samples of Burkitts Lymphoma and Breast Adenocarcinoma, with a dilution series in technical duplicate. biocViews: Tissue, Genome, MicroarrayData, TissueMicroarrayData, GEO Author: Levi Waldron Maintainer: Levi Waldron git_url: https://git.bioconductor.org/packages/ffpeExampleData git_branch: RELEASE_3_13 git_last_commit: 2176b60 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ffpeExampleData_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ffpe dependencyCount: 160 Package: fibroEset Version: 1.34.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: b989ea280895f1d9abe39a8d04a2a878 NeedsCompilation: no Title: exprSet for Karaman et al. (2003) fibroblasts data Description: exprSet for Karaman et al. (2003) human, bonobo and gorilla fibroblasts data biocViews: ExperimentData, Genome, Homo_sapiens_Data, MicroarrayData, ChipOnChipData Author: Sylvia Merk Maintainer: Sylvia Merk git_url: https://git.bioconductor.org/packages/fibroEset git_branch: RELEASE_3_13 git_last_commit: 2e0718b git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/fibroEset_1.34.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: biocGraph, clusterStab, geneplotter dependencyCount: 7 Package: FieldEffectCrc Version: 1.2.0 Depends: utils Imports: BiocStyle, RUnit, SummarizedExperiment, ExperimentHub (>= 0.99.6), AnnotationHub, DESeq2 Suggests: knitr, rmarkdown, BiocGenerics, sva, BiocManager License: Artistic-2.0 MD5sum: 8886c9a614fa7db289f5816c53c719bd NeedsCompilation: no Title: Tumor, tumor-adjacent normal, and healthy colorectal transcriptomes as SummarizedExperiment objects Description: Processed RNA-seq data for 1,139 human primary colorectal tissue samples across three phenotypes, including tumor, normal adjacent-to-tumor, and healthy, available as Synapse ID syn22237139 on synapse.org. Data have been parsed into SummarizedExperiment objects available via ExperimentHub to facilitate reproducibility and extension of results from Dampier et al. (PMCID: PMC7386360, PMID: 32764205). biocViews: ExperimentData, ReproducibleResearch, Tissue, Homo_sapiens_Data, ColonCancerData, RNASeqData, ExpressionData, ExperimentHub, SequencingData Author: Christopher Dampier [aut, cre] (), Bioconductor Package Maintainer [ctb] Maintainer: Christopher Dampier URL: http://bioconductor.org/packages/release/bioc/html/FieldEffectCrc.html VignetteBuilder: knitr BugReports: https://github.com/Bioconductor/FieldEffectCrc/ git_url: https://git.bioconductor.org/packages/FieldEffectCrc git_branch: RELEASE_3_13 git_last_commit: 43fa92c git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/FieldEffectCrc_1.2.0.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: 136 Package: FIs Version: 1.20.0 Depends: R (>= 3.3) License: GPL-3 MD5sum: 424f5f627ca78583a9d85042f123677c NeedsCompilation: no Title: Human Functional Interactions (FIs) for splineTimeR package Description: Data set containing two complete lists of identified functional interaction partners in Human. Data are derived from Reactome and BioGRID databases. biocViews: PathwayInteractionDatabase, Homo_sapiens_Data Author: Agata Michna Maintainer: Herbert Braselmann , Martin Selmansberger git_url: https://git.bioconductor.org/packages/FIs git_branch: RELEASE_3_13 git_last_commit: 1da3086 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/FIs_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: splineTimeR dependencyCount: 0 Package: fission Version: 1.12.0 Depends: R (>= 2.10), SummarizedExperiment Suggests: knitr, markdown License: LGPL MD5sum: 30384475923d69b93a3696bd5fe7eca6 NeedsCompilation: no Title: RangedSummarizedExperiment for time course RNA-Seq of fission yeast in response to stress, by Leong et al., Nat Commun 2014. Description: This package provides a RangedSummarizedExperiment object of read counts in genes for a time course RNA-Seq experiment of fission yeast (Schizosaccharomyces pombe) in response to oxidative stress (1M sorbitol treatment) at 0, 15, 30, 60, 120 and 180 mins. The samples are further divided between a wild-type group and a group with deletion of atf21. The read count matrix was prepared and provided by the author of the study: Leong HS, Dawson K, Wirth C, Li Y, Connolly Y, Smith DL, Wilkinson CR, Miller CJ. "A global non-coding RNA system modulates fission yeast protein levels in response to stress". Nat Commun 2014 May 23;5:3947. PMID: 24853205. GEO: GSE56761. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData, GEO Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/fission git_branch: RELEASE_3_13 git_last_commit: 30ac716 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/fission_1.12.0.tar.gz vignettes: vignettes/fission/inst/doc/fission.html vignetteTitles: Fission yeast time course hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/fission/inst/doc/fission.R dependsOnMe: ROCpAI, rnaseqGene dependencyCount: 26 Package: Fletcher2013a Version: 1.28.0 Depends: R (>= 2.15), limma Imports: Biobase ,VennDiagram, gplots,grid License: GPL (>= 2) MD5sum: b312f90f9cdcf2159a3b5a58e847e814 NeedsCompilation: no Title: Gene expression data from breast cancer cells under FGFR2 signalling perturbation Description: The package Fletcher2013a contains time-course gene expression data from MCF-7 cells treated under different experimental systems in order to perturb FGFR2 signalling. The data comes from Fletcher et al. (Nature Comms 4:2464, 2013) where further details about the background and the experimental design of the study can be found. biocViews: ExperimentData, ExpressionData, CancerData, BreastCancerData, MicroarrayData Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin Meyer. Maintainer: Mauro Castro URL: http://dx.doi.org/10.1038/ncomms3464 git_url: https://git.bioconductor.org/packages/Fletcher2013a git_branch: RELEASE_3_13 git_last_commit: 2b5d201 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/Fletcher2013a_1.28.0.tar.gz vignettes: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.pdf vignetteTitles: Main vignette:Fletcher2013a hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.R dependsOnMe: Fletcher2013b dependencyCount: 20 Package: Fletcher2013b Version: 1.28.0 Depends: R (>= 2.15), Fletcher2013a, RTN (>= 1.1.2), RedeR (>= 1.8.1), igraph Imports: RColorBrewer License: GPL (>= 2) MD5sum: c07f32d424023030efe2dcf31d34feb9 NeedsCompilation: no Title: Master regulators of FGFR2 signalling and breast cancer risk Description: This package reproduces the systems biology analysis for the data in package Fletcher2013a using RTN. biocViews: ExperimentData, ChIPSeqData, CancerData, BreastCancerData, SNPData Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin Meyer. Maintainer: Mauro Castro URL: http://dx.doi.org/10.1038/ncomms3464 git_url: https://git.bioconductor.org/packages/Fletcher2013b git_branch: RELEASE_3_13 git_last_commit: 4adc123 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/Fletcher2013b_1.28.0.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: 134 Package: flowPloidyData Version: 1.18.0 Suggests: knitr, rmarkdown, flowCore License: GPL-3 MD5sum: 086c967fb403e15de5a467b6cdd7dc3b NeedsCompilation: no Title: Example Flow Cytometry Data Description: A collection of raw flow cytometry data for use in vignettes for the flowPloidy package. biocViews: FlowCytometryData Author: Tyler Smith Maintainer: Tyler Smith VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/flowPloidyData git_branch: RELEASE_3_13 git_last_commit: 08c6dfa git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/flowPloidyData_1.18.0.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: 1.30.0 Depends: R (>= 2.13.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: d7fa02fcd0979bef8fadff9bb3714a5f NeedsCompilation: no Title: Illumina HumanMethylation data on sorted blood cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays, and an object depicting which CpGs on the array are associated with cell type. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Andrew E Jaffe Maintainer: Andrew E Jaffe git_url: https://git.bioconductor.org/packages/FlowSorted.Blood.450k git_branch: RELEASE_3_13 git_last_commit: fd1d5f2 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/FlowSorted.Blood.450k_1.30.0.tar.gz vignettes: vignettes/FlowSorted.Blood.450k/inst/doc/FlowSorted.Blood.450k.pdf vignetteTitles: FlowSorted Blood 450k Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.Blood.450k/inst/doc/FlowSorted.Blood.450k.R dependsOnMe: methylCC, methylationArrayAnalysis suggestsMe: mCSEA, minfi, sesame, FlowSorted.Blood.EPIC dependencyCount: 139 Package: FlowSorted.Blood.EPIC Version: 1.10.1 Depends: R (>= 3.5), minfi (>= 1.21.2), SummarizedExperiment, genefilter, quadprog, nlme, S4Vectors, graphics, stats, utils, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, ExperimentHub Suggests: knitr, rmarkdown, EpiDISH, FlowSorted.CordBloodCombined.450k, FlowSorted.Blood.450k(>= 1.0.1), FlowSorted.CordBlood.450k, FlowSorted.CordBloodNorway.450k, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: GPL-3 MD5sum: bd58a8ff6cd51c95952e5a8d8df5492e NeedsCompilation: no Title: Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells Description: Raw data objects to be used for blood cell proportion estimation in minfi and similar packages. The FlowSorted.Blood.EPIC object is based in samples assayed by Brock Christensen and colleagues; for details see Salas et al. 2018. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, Genome, TissueMicroarrayData, MethylationArrayData Author: Lucas A. Salas [cre, aut], Devin C. Koestler [aut], Rondi A. Butler [ctb], Helen M. Hansen [ctb], John K. Wiencke [ctb], Karl T. Kelsey [ctb], Brock C. Christensen [ctb], Kasper Daniel Hansen [ctb] (author and maintainer of the original minfi estimateCellCounts and internal functions), Jean-Philippe Fortin [ctb] (contributor in the original minfi estimateCellCounts and internal functions), Shan V. Andrews [ctb] (contributor in the original minfi estimateCellCounts and internal functions), E. Andres Houseman [ctb] (author of the original quadratic programming function used for cell projection), Andrew E Jaffe [ctb] (author of the original estimateCellCounts and internal functions within minfi) Maintainer: Lucas A. Salas URL: https://github.com/immunomethylomics/FlowSorted.Blood.EPIC VignetteBuilder: knitr BugReports: https://github.com/immunomethylomics/FlowSorted.Blood.EPIC/issues. git_url: https://git.bioconductor.org/packages/FlowSorted.Blood.EPIC git_branch: RELEASE_3_13 git_last_commit: b2e3e91 git_last_commit_date: 2021-07-08 Date/Publication: 2021-07-10 source.ver: src/contrib/FlowSorted.Blood.EPIC_1.10.1.tar.gz vignettes: vignettes/FlowSorted.Blood.EPIC/inst/doc/FlowSorted.Blood.EPIC.html vignetteTitles: FlowSorted.Blood.EPIC hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.Blood.EPIC/inst/doc/FlowSorted.Blood.EPIC.R dependsOnMe: FlowSorted.CordBloodCombined.450k dependencyCount: 162 Package: FlowSorted.CordBlood.450k Version: 1.20.0 Depends: R (>= 3.2.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 770b6297079adaf803e9d13573c096f4 NeedsCompilation: no Title: Illumina 450k data on sorted cord blood cells Description: Raw data objects to be used for cord blood cell proportion estimation in minfi. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Shan V. Andrews [cre, aut], Kelly M. Bakulski [aut] Maintainer: Shan V. Andrews git_url: https://git.bioconductor.org/packages/FlowSorted.CordBlood.450k git_branch: RELEASE_3_13 git_last_commit: 6d082ff git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/FlowSorted.CordBlood.450k_1.20.0.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: 139 Package: FlowSorted.CordBloodCombined.450k Version: 1.8.0 Depends: R (>= 3.6), minfi (>= 1.21.2), SummarizedExperiment, IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b4.hg19, ExperimentHub(>= 1.9.1), FlowSorted.Blood.EPIC, utils Suggests: knitr, rmarkdown, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: GPL-3 MD5sum: c4c11925fba95ed5b6704d473de931a4 NeedsCompilation: no Title: Illumina 450k/EPIC data on FACS and MACS umbilical blood cells Description: Raw data objects to be used for umbilical cord blood cell proportion estimation in minfi and similar packages. The FlowSorted.CordBloodCombined.450k object is based in samples assayed by Bakulski et al, Gervin et al., de Goede et al., and Lin et al. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, Genome, TissueMicroarrayData, MethylationArrayData, ExperimentHub Author: Lucas A. Salas [cre, aut], Kristina Gervin [aut], Meaghan C. Jones [aut], Kelly M. Bakulski [ctb], Devin C. Koestler [ctb], John K. Wiencke [ctb], Karl T. Kelsey [ctb], Robert Lyle [ctb], Brock C. Christensen [ctb], Janine Felix [ctb] Maintainer: Lucas A. Salas URL: https://github.com/immunomethylomics/FlowSorted.CordBloodCombined.450k VignetteBuilder: knitr BugReports: https://github.com/immunomethylomics/FlowSorted.CordBloodCombined.450k/issues. git_url: https://git.bioconductor.org/packages/FlowSorted.CordBloodCombined.450k git_branch: RELEASE_3_13 git_last_commit: a892991 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/FlowSorted.CordBloodCombined.450k_1.8.0.tar.gz vignettes: vignettes/FlowSorted.CordBloodCombined.450k/inst/doc/FlowSorted.CordBloodCombined.450k.html vignetteTitles: FlowSorted.CordBloodCombined.450k hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.CordBloodCombined.450k/inst/doc/FlowSorted.CordBloodCombined.450k.R suggestsMe: FlowSorted.Blood.EPIC dependencyCount: 164 Package: FlowSorted.CordBloodNorway.450k Version: 1.18.0 Depends: R (>= 3.2.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: e40044ab4e5116d2007ec968c384892d NeedsCompilation: no Title: Illumina HumanMethylation data on sorted cord blood cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays, for cell type composition estimation. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: kristina gervin [cre, aut], Kasper Daniel Hansen [aut] Maintainer: kristina gervin URL: https://bitbucket.com/kasperdanielhansen/Illumina_CordBlood git_url: https://git.bioconductor.org/packages/FlowSorted.CordBloodNorway.450k git_branch: RELEASE_3_13 git_last_commit: e67cf07 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/FlowSorted.CordBloodNorway.450k_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: sesame, FlowSorted.Blood.EPIC dependencyCount: 139 Package: FlowSorted.DLPFC.450k Version: 1.28.0 Depends: R (>= 2.13.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 27988a648d68cdb7a2472d9135cf869e NeedsCompilation: no Title: Illumina HumanMethylation data on sorted frontal cortex cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Andrew E Jaffe, Zachary A. Kaminsky Maintainer: Andrew E Jaffe git_url: https://git.bioconductor.org/packages/FlowSorted.DLPFC.450k git_branch: RELEASE_3_13 git_last_commit: d0208dc git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/FlowSorted.DLPFC.450k_1.28.0.tar.gz vignettes: vignettes/FlowSorted.DLPFC.450k/inst/doc/FlowSorted.DLPFC.450k.pdf vignetteTitles: FlowSorted DLPFC 450k Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.DLPFC.450k/inst/doc/FlowSorted.DLPFC.450k.R dependencyCount: 139 Package: flowWorkspaceData Version: 3.4.0 License: GPL-2 MD5sum: 29884f512dab9966890eee1d32d8d598 NeedsCompilation: no Title: A data package containing two flowJo, one diva xml workspace and the associated fcs files as well as three GatingSets for testing the flowWorkspace, openCyto and CytoML packages. Description: The necessary external data to run the flowWorkspace and openCyto vignette is found in this package. biocViews: ExperimentData, FlowCytometryData Author: Greg Finak Maintainer: Mike Jiang git_url: https://git.bioconductor.org/packages/flowWorkspaceData git_branch: RELEASE_3_13 git_last_commit: f1bc899 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/flowWorkspaceData_3.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: COMPASS, CytoML, flowClust, flowCore, flowWorkspace, ggcyto, openCyto dependencyCount: 0 Package: frmaExampleData Version: 1.28.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 3f67126d1b6278083cce7eae2d9e7626 NeedsCompilation: no Title: Frma Example Data Description: Data files used by the examples in frma and frmaTools packages biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/frmaExampleData git_branch: RELEASE_3_13 git_last_commit: c1e4896 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/frmaExampleData_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: frma, frmaTools dependencyCount: 0 Package: furrowSeg Version: 1.20.0 Depends: R (>= 3.3), EBImage Imports: abind, dplyr, locfit, tiff Suggests: BiocStyle, ggplot2, knitr License: Artistic-2.0 MD5sum: 0f5d2499fe87912ff1f8b0b505e31ec5 NeedsCompilation: no Title: Furrow Segmentation Description: Image feature data and analysis codes for the Guglielmi, Barry et al. paper describing the application of an optogenetics tools to disrupt Drosophila embryo furrowing. biocViews: ExperimentData, Drosophila_melanogaster_Data, Tissue, ReproducibleResearch Author: Joseph Barry Maintainer: Joseph Barry VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/furrowSeg git_branch: RELEASE_3_13 git_last_commit: 5645886 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/furrowSeg_1.20.0.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: 43 Package: gageData Version: 2.30.0 Depends: R (>= 2.10) Suggests: gage, pathview, genefilter License: GPL (>=2.0) MD5sum: 7e12bf6f734b4466095d1b18f11f5239 NeedsCompilation: no Title: Auxillary data for gage package Description: This is a supportive data package for the software package, gage. However, the data supplied here are also useful for gene set or pathway analysis or microarray data analysis in general. In this package, we provide two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and BMP6 (originally published as an demo dataset for GAGE, also registered as GSE13604 in GEO). This package also includes commonly used gene set data based on KEGG pathways and GO terms for major research species, including human, mouse, rat and budding yeast. Mapping data between common gene IDs for budding yeast are also included. biocViews: ExperimentData, StemCell, CancerData, BreastCancerData, MicroarrayData, GEO Author: Weijun Luo Maintainer: Weijun Luo git_url: https://git.bioconductor.org/packages/gageData git_branch: RELEASE_3_13 git_last_commit: 2229c65 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/gageData_2.30.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: gage dependencyCount: 0 Package: gaschYHS Version: 1.30.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: e55109aa4f2ebda9d2b60e971dfab92f NeedsCompilation: no Title: ExpressionSet for response of yeast to heat shock and other environmental stresses Description: Data from PMID 11102521 biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data Author: Audrey Gasch and colleagues Maintainer: Vince Carey URL: http://genome-www.stanford.edu/yeast_stress/data/rawdata/complete_dataset.txt git_url: https://git.bioconductor.org/packages/gaschYHS git_branch: RELEASE_3_13 git_last_commit: a31f9c8 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/gaschYHS_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: gatingMLData Version: 2.32.0 Depends: R (>= 1.9.0) Suggests: flowUtils License: GPL MD5sum: bf532f78699284e986ee9c796d23139b NeedsCompilation: no Title: Data and XML files for Gating-ML Test suite Description: Test data and XML files for testing compliance of the flowUtils/flowCore packages with Gating-ML (1.5 and 2.0) standards. biocViews: ExperimentData, FlowCytometryData Author: J. Spidlen, N. Gopalakrishnan Maintainer: J. Spidlen git_url: https://git.bioconductor.org/packages/gatingMLData git_branch: RELEASE_3_13 git_last_commit: 34c65fb git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/gatingMLData_2.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: flowUtils dependencyCount: 0 Package: gcspikelite Version: 1.30.0 Depends: R (>= 2.5.0) License: LGPL MD5sum: 938993ea973fd8eefd492b58717c2dcf NeedsCompilation: no Title: Spike-in data for GC/MS data and methods within flagme Description: Spike-in data for GC/MS data and methods within flagme biocViews: MassSpectrometryData Author: Mark Robinson Maintainer: Mark Robinson git_url: https://git.bioconductor.org/packages/gcspikelite git_branch: RELEASE_3_13 git_last_commit: a8d1340 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/gcspikelite_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: flagme dependencyCount: 0 Package: geneLenDataBase Version: 1.28.0 Depends: R (>= 2.11.0) Imports: utils, rtracklayer, GenomicFeatures (>= 1.3.15) License: LGPL (>= 2) MD5sum: 936ef3844d12172a521a7e4af75b339a NeedsCompilation: no Title: Lengths of mRNA transcripts for a number of genomes Description: Length of mRNA transcripts for a number of genomes and gene ID formats, largely based on UCSC table browser biocViews: ExperimentData, Genome Author: Matthew Young Maintainer: Matthew Young , Nadia Davidson git_url: https://git.bioconductor.org/packages/geneLenDataBase git_branch: RELEASE_3_13 git_last_commit: 7f14bbc git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/geneLenDataBase_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: goseq importsMe: SMITE dependencyCount: 96 Package: genomationData Version: 1.24.0 Suggests: knitr License: GPL-3 MD5sum: 8f1e2d75ac207771c68763c51fb34153 NeedsCompilation: no Title: Experimental data for showing functionalities of the genomation package Description: The package contains Chip Seq, Methylation and Cage data, downloaded from Encode biocViews: ExperimentData, Genome, StemCell, SequencingData, ChIPSeqData, ChipOnChipData, ENCODE Author: Altuna Akalin, Vedran Franke Maintainer: Vedran Franke VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/genomationData git_branch: RELEASE_3_13 git_last_commit: 4c7afae git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/genomationData_1.24.0.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: 1.0.0 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: 5e62b73b85779aa68118b3a178b857f1 NeedsCompilation: no Title: Reference data for GenomicDistributions package Description: This package provides ready to use reference data for GenomicDistributions package. Raw data was obtained from ensembldb and processed with helper functions. Data files are available for the following genome assemblies: hg19, hg38, mm9 and mm10. biocViews: ExperimentHub, ExperimentData, Genome Author: Michal Stolarczyk [aut], Kristyna Kupkova [aut, cre], Jose Verdezoto [aut], John Lawson [ctb], Jason Smith [ctb], Nathan C. Sheffield [ctb] Maintainer: Kristyna Kupkova VignetteBuilder: knitr BugReports: http://github.com/databio/GenomicDistributionsData git_url: https://git.bioconductor.org/packages/GenomicDistributionsData git_branch: RELEASE_3_13 git_last_commit: ad9d50c git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/GenomicDistributionsData_1.0.0.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 dependencyCount: 124 Package: GeuvadisTranscriptExpr Version: 1.20.0 Depends: R (>= 3.3.0) Suggests: limma, rtracklayer, GenomicRanges, Rsamtools, VariantAnnotation, tools, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: 6dc8c28bdfa0a5382d9533f55c94682c NeedsCompilation: no Title: Data package with transcript expression and bi-allelic genotypes from the GEUVADIS project Description: Provides transcript expression and bi-allelic genotypes corresponding to the chromosome 19 for CEU individuals from the GEUVADIS project, Lappalainen et al. biocViews: Homo_sapiens_Data, SNPData, Genome, RNASeqData, SequencingData, ExpressionData Author: Malgorzata Nowicka [aut, cre] Maintainer: Malgorzata Nowicka VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GeuvadisTranscriptExpr git_branch: RELEASE_3_13 git_last_commit: 9984524 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/GeuvadisTranscriptExpr_1.20.0.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: 1.10.0 Depends: R (>= 3.5) Suggests: GIGSEA, knitr, rmarkdown License: LGPL-3 MD5sum: 058d1c354f513a169fcd390cbd2b7e65 NeedsCompilation: no Title: Gene set collections for the GIGSEA package Description: The gene set collection used for the GIGSEA package. biocViews: ExperimentData, Homo_sapiens_Data Author: Shijia Zhu Maintainer: Shijia Zhu VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GIGSEAdata git_branch: RELEASE_3_13 git_last_commit: 2439522 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/GIGSEAdata_1.10.0.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: 1.34.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: LGPL MD5sum: c0e41897e54cd1edda3aefac97e64ff2 NeedsCompilation: no Title: exprSets for golub leukemia data Description: representation of public golub data with some covariate data of provenance unknown to the maintainer at present; now employs ExpressionSet format biocViews: ExperimentData, Genome, CancerData, LeukemiaCancerData Author: Todd Golub Maintainer: Vince Carey git_url: https://git.bioconductor.org/packages/golubEsets git_branch: RELEASE_3_13 git_last_commit: 3b0c2a9 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/golubEsets_1.34.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: adSplit, Biobase, biosigner, GlobalAncova, globaltest, idiogram, MLInterfaces, pvca, RDRToolbox, twilight, rknn dependencyCount: 7 Package: gpaExample Version: 1.4.0 Depends: R (>= 4.0.0) License: GPL (>= 2) MD5sum: f21529df389f64c0bb42507f5352cc1f NeedsCompilation: no Title: Example data for the GPA package (Genetic analysis incorporating Pleiotropy and Annotation) Description: Example data for the GPA package, consisting of the p-values of 1,219,805 SNPs for five psychiatric disorder GWAS from the psychiatric GWAS consortium (PGC), with the annotation data using genes preferentially expressed in the central nervous system (CNS). biocViews: ExperimentData, Homo_sapiens_Data, SNPData Author: Dongjun Chung, Carter Allen Maintainer: Dongjun Chung URL: http://dongjunchung.github.io/GPA/ git_url: https://git.bioconductor.org/packages/gpaExample git_branch: RELEASE_3_13 git_last_commit: ed68366 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/gpaExample_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GPA dependencyCount: 0 Package: grndata Version: 1.24.0 Depends: R (>= 2.10) Suggests: RUnit, BiocGenerics, knitr License: GPL-3 MD5sum: 19d1d92e6c28d991015b8982e0a89fe6 NeedsCompilation: no Title: Synthetic Expression Data for Gene Regulatory Network Inference Description: Simulated expression data for five large Gene Regulatory Networks from different simulators biocViews: ExperimentData, NetworkInference, GeneExpression, Microarray, GeneRegulation, Network Author: Pau Bellot, Catharina Olsen, Patrick E Meyer Maintainer: Pau Bellot VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/grndata git_branch: RELEASE_3_13 git_last_commit: 0a1641c git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/grndata_1.24.0.tar.gz vignettes: vignettes/grndata/inst/doc/grndata.html vignetteTitles: GRNdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: GSBenchMark Version: 1.12.0 Depends: R (>= 2.13.1) License: GPL-2 MD5sum: 29b10b4b05f2d91006b040e2465cb188 NeedsCompilation: no Title: Gene Set Benchmark Description: Benchmarks for Machine Learning Analysis of the Gene Sets. The package contains a list of pathways and gene expression data sets used in "Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)" (2010) by Eddy et al. biocViews: MicroarrayData Author: Bahman Afsari , Elana J. Fertig Maintainer: Bahman Afsari git_url: https://git.bioconductor.org/packages/GSBenchMark git_branch: RELEASE_3_13 git_last_commit: 378467f git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/GSBenchMark_1.12.0.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: GSE13015 Version: 1.0.0 Depends: Biobase, GEOquery Imports: preprocessCore, SummarizedExperiment, GEOquery, Biobase Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown License: MIT License MD5sum: 478e8aa0a79a4d6c85b8b4eec4f22cbd 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] () Maintainer: Darawan Rinchai VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GSE13015 git_branch: RELEASE_3_13 git_last_commit: b494fdd git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/GSE13015_1.0.0.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: 67 Package: GSE62944 Version: 1.20.0 Depends: Biobase, GEOquery Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle License: Artistic-2.0 MD5sum: 294dfa4306bcc8547ec2328a790c5921 NeedsCompilation: no Title: GEO accession data GSE62944 as a SummarizedExperiment Description: TCGA processed RNA-Seq data for 9264 tumor and 741 normal samples across 24 cancer types and made them available as GEO accession [GSE62944](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944). GSE62944 data have been parsed into a SummarizedExperiment object available in ExperimentHub. biocViews: ExperimentData, Genome, DNASeqData, RNASeqData Author: Sonali Arora Maintainer: Bioconductor Package Maintainer URL: http://bioconductor.org/packages/release/bioc/html/GSE62944.html VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GSE62944 git_branch: RELEASE_3_13 git_last_commit: 1a55588 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/GSE62944_1.20.0.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: 49 Package: GSVAdata Version: 1.28.0 Depends: R (>= 3.5), Biobase, GSEABase, hgu95a.db License: Artistic-2.0 MD5sum: 0b265b9254a117890a7dbe736e44276e NeedsCompilation: no Title: Data employed in the vignette of the GSVA package Description: This package stores the data employed in the vignette of the GSVA package. These data belong to the following publications: Armstrong et al. Nat Genet 30:41-47, 2002; Cahoy et al. J Neurosci 28:264-278, 2008; Carrel and Willard, Nature, 434:400-404, 2005; Huang et al. PNAS, 104:9758-9763, 2007; Pickrell et al. Nature, 464:768-722, 2010; Skaletsky et al. Nature, 423:825-837; Verhaak et al. Cancer Cell 17:98-110, 2010 biocViews: ExperimentData, RNASeqData, Homo_sapiens_Data, CancerData, LeukemiaCancerData Author: Robert Castelo Maintainer: Robert Castelo git_url: https://git.bioconductor.org/packages/GSVAdata git_branch: RELEASE_3_13 git_last_commit: be356f4 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/GSVAdata_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: singleCellTK, RVA suggestsMe: GSAR, GSVA dependencyCount: 53 Package: GWASdata Version: 1.30.0 Depends: GWASTools License: Artistic-2.0 MD5sum: 7b076893b77f246246a32ff1c19d368e NeedsCompilation: no Title: Data used in the examples and vignettes of the GWASTools package Description: Selected Affymetrix and Illlumina SNP data for HapMap subjects. Data provided by the Center for Inherited Disease Research at Johns Hopkins University and the Broad Institute of MIT and Harvard University. biocViews: ExperimentData, MicroarrayData, SNPData, HapMap Author: Stephanie Gogarten Maintainer: Stephanie Gogarten , Adrienne Stilp git_url: https://git.bioconductor.org/packages/GWASdata git_branch: RELEASE_3_13 git_last_commit: 4cdd0a5 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/GWASdata_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GENESIS, GWASTools dependencyCount: 69 Package: h5vcData Version: 2.12.0 Suggests: h5vc License: GPL (>= 3) MD5sum: 990215a168c158da6a46f811cd3019c8 NeedsCompilation: no Title: Example data for the h5vc package Description: This package contains the data used in the vignettes and examples of the 'h5vc' package biocViews: CancerData Author: Paul Theodor Pyl Maintainer: Paul Theodor Pyl git_url: https://git.bioconductor.org/packages/h5vcData git_branch: RELEASE_3_13 git_last_commit: 3b0ab56 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/h5vcData_2.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: h5vc suggestsMe: HDF5Array dependencyCount: 0 Package: hapmap100khind Version: 1.34.0 Suggests: oligo License: GPL MD5sum: 3afe60783db8df66d18804555d85882d NeedsCompilation: no Title: Sample data - Hapmap 100K HIND Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap100khind git_branch: RELEASE_3_13 git_last_commit: 670799e git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/hapmap100khind_1.34.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmap100kxba Version: 1.34.0 Suggests: oligo License: GPL MD5sum: 6a465da182b7a9661717d742a8854c0c NeedsCompilation: no Title: Sample data - Hapmap 100K XBA Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap100kxba git_branch: RELEASE_3_13 git_last_commit: 4a90daf git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/hapmap100kxba_1.34.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligo dependencyCount: 0 Package: hapmap500knsp Version: 1.34.0 Suggests: oligo License: GPL MD5sum: ddeb04d99ab048893e598ad25afa1648 NeedsCompilation: no Title: Sample data - Hapmap 500K NSP Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap500knsp git_branch: RELEASE_3_13 git_last_commit: b7e2fea git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/hapmap500knsp_1.34.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmap500ksty Version: 1.34.0 Suggests: oligo License: GPL MD5sum: c8c2972df2a1d9d0868349595776ea52 NeedsCompilation: no Title: Sample data - Hapmap 500K STY Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap500ksty git_branch: RELEASE_3_13 git_last_commit: 696b758 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/hapmap500ksty_1.34.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmapsnp5 Version: 1.34.0 Suggests: oligo License: GPL MD5sum: 4151ec01bb8f30081d547bd1ddfab708 NeedsCompilation: no Title: Sample data - Hapmap SNP 5.0 Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData, SNPData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmapsnp5 git_branch: RELEASE_3_13 git_last_commit: c5edc95 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/hapmapsnp5_1.34.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligoClasses dependencyCount: 0 Package: hapmapsnp6 Version: 1.34.0 Depends: R (>= 2.15) Suggests: oligo, oligoClasses License: GPL MD5sum: de42250f1992b21f5275d1923958d52a NeedsCompilation: no Title: Sample data - Hapmap SNP 6.0 Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, SNPData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmapsnp6 git_branch: RELEASE_3_13 git_last_commit: e196c16 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/hapmapsnp6_1.34.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: crlmm, oligoClasses dependencyCount: 0 Package: harbChIP Version: 1.30.0 Depends: R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5), Biostrings Imports: methods, stats License: Artistic-2.0 MD5sum: 1374c193ba70065c6f3e3ea633fcd622 NeedsCompilation: no Title: Experimental Data Package: harbChIP Description: data from a yeast ChIP-chip experiment biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/harbChIP git_branch: RELEASE_3_13 git_last_commit: ffbc8f0 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/harbChIP_1.30.0.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: 20 Package: HarmanData Version: 1.20.0 Depends: R (>= 3.2.3) Suggests: BiocGenerics, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 8c2c0e9091dfac89e9a9d1c10a03eeaf NeedsCompilation: no Title: Data for the Harman package Description: Datasets of accompany Harman, a PCA and constrained optimisation based technique. Contains three datasets: IMR90, Human lung fibroblast cells exposed to nitric oxide; NPM, an experiment to test skin penetration of metal oxide nanoparticles following topical application of sunscreens in non-pregnant mice; OLF; an experiment to gauge the response of human olfactory neurosphere-derived (hONS) cells to ZnO nanoparticles. biocViews: ExpressionData, MicroarrayData, ExperimentData, Homo_sapiens_Data, Mus_musculus_Data Author: Josh Bowden [aut], Jason Ross [aut, cre], Yalchin Oytam [aut] Maintainer: Jason Ross URL: http://www.bioinformatics.csiro.au/harman/ VignetteBuilder: knitr BugReports: https://github.com/JasonR055/Harman/issues git_url: https://git.bioconductor.org/packages/HarmanData git_branch: RELEASE_3_13 git_last_commit: 2080f4d git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/HarmanData_1.20.0.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: 1.14.0 Depends: R (>= 3.4.0) Imports: ExperimentHub Suggests: AnnotationHub, knitr, rmarkdown, igraph, survival, ANF, stats, testthat License: GPL-3 MD5sum: 9c7feff83083046f8874e9df49dd5830 NeedsCompilation: no Title: Processed Harmonized TCGA Data of Five Selected Cancer Types Description: This package contains the processed harmonized TCGA data of five cancer types used in "Tianle Ma and Aidong Zhang, Integrate Multi-omic Data Using Affinity Network Fusion (ANF) for Cancer Patient Clustering". biocViews: CancerData, ReproducibleResearch Author: Tianle Ma Maintainer: Tianle Ma VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/HarmonizedTCGAData git_branch: RELEASE_3_13 git_last_commit: ad9dc06 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/HarmonizedTCGAData_1.14.0.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: 88 Package: HCAData Version: 1.8.0 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: 585c488e8cabbbc903fb2d242bf34f76 NeedsCompilation: no Title: Accessing The Datasets Of The Human Cell Atlas in R/Bioconductor Description: This package allows a direct access to the dataset generated by the Human Cell Atlas project for further processing in R and Bioconductor, in the comfortable format of SingleCellExperiment objects (available in other formats here: http://preview.data.humancellatlas.org/). biocViews: RNASeqData, SingleCellData, ExperimentData, ExpressionData, ExperimentHub Author: Federico Marini [aut, cre] () Maintainer: Federico Marini URL: https://github.com/federicomarini/HCAData VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/HCAData git_branch: RELEASE_3_13 git_last_commit: 30ddca7 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/HCAData_1.8.0.tar.gz vignettes: vignettes/HCAData/inst/doc/hcadata.html vignetteTitles: Accessing the Human Cell Atlas datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HCAData/inst/doc/hcadata.R dependencyCount: 101 Package: HD2013SGI Version: 1.32.0 Depends: R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots, limma, vcd, LSD,EBImage Suggests: BiocStyle License: Artistic-2.0 MD5sum: d97c0c63be4c86afacbe62e80e62edfd NeedsCompilation: no Title: Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping Description: This package contains the experimental data and a complete executable transcript (vignette) of the analysis of the HCT116 genetic interaction matrix presented in the paper "Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping" by C. Laufer, B. Fischer, M. Billmann, W. Huber, M. Boutros; Nature Methods (2013) 10:427-31. doi: 10.1038/nmeth.2436. biocViews: ExperimentData, CancerData, ColonCancerData, MicrotitrePlateAssayData, CellCulture, Homo_sapiens_Data, HighThroughputImagingData Author: Bernd Fischer Maintainer: Mike Smith SystemRequirements: GNU make git_url: https://git.bioconductor.org/packages/HD2013SGI git_branch: RELEASE_3_13 git_last_commit: fa17585 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/HD2013SGI_1.32.0.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: 76 Package: HDCytoData Version: 1.12.0 Depends: ExperimentHub, SummarizedExperiment, flowCore Imports: utils, methods Suggests: BiocStyle, knitr, rmarkdown, Rtsne, umap, ggplot2, FlowSOM, mclust License: MIT + file LICENSE MD5sum: 46997fd96c715fd833abba44bfafc91c NeedsCompilation: no Title: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats Description: Data package containing a set of publicly available high-dimensional cytometry benchmark datasets, formatted into SummarizedExperiment and flowSet Bioconductor object formats, including all required metadata. Row metadata includes sample IDs, group IDs, patient IDs, reference cell population or cluster labels (where available), and labels identifying 'spiked in' cells (where available). Column metadata includes channel names, protein marker names, and protein marker classes (cell type or cell state). biocViews: ExperimentHub, ExperimentData, ExpressionData, FlowCytometryData, SingleCellData, Homo_sapiens_Data, ImmunoOncologyData Author: Lukas M. Weber [aut, cre], Charlotte Soneson [aut] Maintainer: Lukas M. Weber URL: https://github.com/lmweber/HDCytoData VignetteBuilder: knitr BugReports: https://github.com/lmweber/HDCytoData/issues git_url: https://git.bioconductor.org/packages/HDCytoData git_branch: RELEASE_3_13 git_last_commit: f74624b git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/HDCytoData_1.12.0.tar.gz vignettes: vignettes/HDCytoData/inst/doc/Contribution_guidelines.html, vignettes/HDCytoData/inst/doc/Examples_and_use_cases.html, vignettes/HDCytoData/inst/doc/HDCytoData_package.html vignetteTitles: 3. Contribution guidelines, 2. Examples and use cases, 1. HDCytoData package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HDCytoData/inst/doc/Contribution_guidelines.R, vignettes/HDCytoData/inst/doc/Examples_and_use_cases.R, vignettes/HDCytoData/inst/doc/HDCytoData_package.R dependsOnMe: cytofWorkflow suggestsMe: diffcyt dependencyCount: 103 Package: healthyFlowData Version: 1.30.0 Depends: R (>= 2.15.0), flowCore Imports: methods License: Artistic-2.0 MD5sum: 0fb4f400624f0c1644f0bdff9882b079 NeedsCompilation: no Title: Healthy dataset used by the flowMatch package Description: A healthy dataset with 20 flow cytometry samples used by the flowMatch package. biocViews: FlowCytometryData Author: Ariful Azad Maintainer: Ariful Azad git_url: https://git.bioconductor.org/packages/healthyFlowData git_branch: RELEASE_3_13 git_last_commit: 17e0450 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/healthyFlowData_1.30.0.tar.gz vignettes: vignettes/healthyFlowData/inst/doc/healthyFlowData.pdf vignetteTitles: healthyFlowData: A healthy dataset with 20 flow cytometry samples used by the flowMatch package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/healthyFlowData/inst/doc/healthyFlowData.R suggestsMe: flowMatch dependencyCount: 19 Package: HEEBOdata Version: 1.30.0 License: LGPL MD5sum: e4d9642f9dd893f6b2d521b7c36544f5 NeedsCompilation: no Title: HEEBO set and HEEBO controls. Description: R objects describing the HEEBO oligo set. biocViews: ExperimentData Author: Agnes Paquet Maintainer: Agnes Paquet URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/ git_url: https://git.bioconductor.org/packages/HEEBOdata git_branch: RELEASE_3_13 git_last_commit: 416e3a5 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/HEEBOdata_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQuality dependencyCount: 0 Package: HelloRangesData Version: 1.18.0 Suggests: BiocStyle License: GPL (>= 2) MD5sum: 4ec0a904bf79093a521d65e5c1a7c4ac NeedsCompilation: no Title: Data for the HelloRanges tutorial vignette Description: Provides the data that were used in the bedtools tutorial by Aaron Quinlan (http://quinlanlab.org/tutorials/bedtools/bedtools.html). Includes a subset of the DnaseI hypersensitivity data from "Maurano et al. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA. Science. 2012. Vol. 337 no. 6099 pp. 1190-1195." The rest of the tracks were originally downloaded from the UCSC table browser. See the HelloRanges vignette for a port of the bedtools tutorial to R. biocViews: ExperimentData, SequencingData Author: Michael Lawrence Maintainer: Michael Lawrence git_url: https://git.bioconductor.org/packages/HelloRangesData git_branch: RELEASE_3_13 git_last_commit: 3657376 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/HelloRangesData_1.18.0.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: 1.30.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 3e1960770cdcbb824e1e7f757439e75b NeedsCompilation: no Title: hgu133a data for barcode Description: Data used by the barcode package for microarrays of type hgu133a. biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/hgu133abarcodevecs git_branch: RELEASE_3_13 git_last_commit: 9dce8cc git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/hgu133abarcodevecs_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hgu133plus2barcodevecs Version: 1.30.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: b2d4d9304b79ba334a3f8c947e715101 NeedsCompilation: no Title: hgu133plus2 data for barcode Description: Data used by the barcode package for microarrays of type hgu133plus2. biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/hgu133plus2barcodevecs git_branch: RELEASE_3_13 git_last_commit: 29b65d6 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/hgu133plus2barcodevecs_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hgu133plus2CellScore Version: 1.12.0 Depends: R (>= 3.5.0) Imports: Biobase (>= 2.39.1) Suggests: knitr License: GPL-3 MD5sum: 0ee7bbbdb72a5e8385e3807f801f29dd NeedsCompilation: no Title: CellScore Standard Cell Types Expression Dataset [hgu133plus2] Description: The CellScore Standard Dataset contains expression data from a wide variety of human cells and tissues, which should be used as standard cell types in the calculation of the CellScore. All data was curated from public databases such as Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) or ArrayExpress (https://www.ebi.ac.uk/arrayexpress/). This standard dataset only contains data from the Affymetrix GeneChip Human Genome U133 Plus 2.0 microarrays. Samples were manually annotated using the database information or consulting the publications in which the datasets originated. The sample annotations are stored in the phenoData slot of the expressionSet object. Raw data (CEL files) were processed with the affy package to generate present/absent calls (mas5calls) and background-subtracted values, which were then normalized by the R-package yugene to yield the final expression values for the standard expression matrix. The annotation table for the microarray was retrieved from the BioC annotation package hgu133plus2. All data are stored in an expressionSet object. biocViews: ExpressionData, MicroarrayData, GEO, ExperimentData, Homo_sapiens_Data, Genome, ArrayExpress Author: Nancy Mah, Katerina Taskova Maintainer: Nancy Mah VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/hgu133plus2CellScore git_branch: RELEASE_3_13 git_last_commit: b92d197 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/hgu133plus2CellScore_1.12.0.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: 1.32.0 Depends: R (>= 2.0.0) License: Artistic-2.0 MD5sum: 7316d54753fc636ca37bd805d43c943b NeedsCompilation: no Title: A data package containing annotation data for hgu2beta7 Description: Annotation data file for hgu2beta7 assembled using data from public data repositories biocViews: Genome Author: Chenwei Lin Maintainer: Bioconductor Package Maintainer git_url: https://git.bioconductor.org/packages/hgu2beta7 git_branch: RELEASE_3_13 git_last_commit: b851149 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/hgu2beta7_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: HiCDataHumanIMR90 Version: 1.12.0 Depends: R (>= 2.10) Suggests: HiTC License: GPL-3 MD5sum: 9f44cd5335a03f05f5b0e2b42ddda6f1 NeedsCompilation: no Title: Human IMR90 Fibroblast HiC data from Dixon et al. 2012 Description: The HiC data from Human Fibroblast IMR90 cell line (HindIII restriction) was retrieved from the GEO website, accession number GSE35156 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35156). The raw reads were processed as explained in Dixon et al. (Nature 2012). biocViews: ExperimentData, Genome, Homo_sapiens_Data, GEO Author: Nicolas Servant Maintainer: Nicolas Servant git_url: https://git.bioconductor.org/packages/HiCDataHumanIMR90 git_branch: RELEASE_3_13 git_last_commit: 280887a git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/HiCDataHumanIMR90_1.12.0.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: 1.28.0 Suggests: ShortRead License: GPL-3 MD5sum: a7e7bfe5299d44c44726d2e6b4c34ca4 NeedsCompilation: no Title: Human lymphoblastoid HiC data from Lieberman-Aiden et al. 2009 Description: The HiC data from human lymphoblastoid cell line (HindIII restriction) was retrieved from the sequence read archive and two ends of the paired reads were aligned separately with bowtie. biocViews: ExperimentData, Homo_sapiens_Data Author: Borbala Mifsud Maintainer: Borbala Mifsud git_url: https://git.bioconductor.org/packages/HiCDataLymphoblast git_branch: RELEASE_3_13 git_last_commit: c5ae1fe git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/HiCDataLymphoblast_1.28.0.tar.gz vignettes: vignettes/HiCDataLymphoblast/inst/doc/package_vignettes.pdf vignetteTitles: package_vignettes.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HiCDataLymphoblast/inst/doc/package_vignettes.R suggestsMe: GOTHiC dependencyCount: 0 Package: HighlyReplicatedRNASeq Version: 1.4.0 Depends: SummarizedExperiment, ExperimentHub Imports: S4Vectors Suggests: BiocStyle, BiocFileCache, knitr, rmarkdown License: MIT + file LICENSE MD5sum: b084e945a2a34e34fc3ce5a29ce1957b NeedsCompilation: no Title: Collection of Bulk RNA-Seq Experiments With Many Replicates Description: Gene-level count matrix data for bulk RNA-seq dataset with many replicates. The data are provided as easy to use SummarizedExperiment objects. The source data that is made accessible through this package comes from https://github.com/bartongroup/profDGE48. biocViews: ExperimentHub, ExperimentData, ExpressionData, SequencingData, RNASeqData Author: Constantin Ahlmann-Eltze [aut, cre] () Maintainer: Constantin Ahlmann-Eltze URL: https://github.com/const-ae/HighlyReplicatedRNASeq VignetteBuilder: knitr BugReports: https://github.com/const-ae/HighlyReplicatedRNASeq/issues git_url: https://git.bioconductor.org/packages/HighlyReplicatedRNASeq git_branch: RELEASE_3_13 git_last_commit: 94ba1c5 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/HighlyReplicatedRNASeq_1.4.0.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: 96 Package: Hiiragi2013 Version: 1.28.0 Depends: R (>= 3.0.0), affy, Biobase, boot, clue, cluster, genefilter, geneplotter, gplots, gtools, KEGGREST, MASS, mouse4302.db, RColorBrewer, xtable Imports: grid, lattice, latticeExtra Suggests: ArrayExpress, BiocStyle License: Artistic-2.0 MD5sum: 21dc3ca200abf47597c436d75c16a9e9 NeedsCompilation: no Title: Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages Description: This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881." biocViews: ExperimentData, MicroarrayData, qPCRData, ReproducibleResearch Author: Andrzej Oles, Wolfgang Huber Maintainer: Andrzej Oles git_url: https://git.bioconductor.org/packages/Hiiragi2013 git_branch: RELEASE_3_13 git_last_commit: 0897832 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/Hiiragi2013_1.28.0.tar.gz vignettes: vignettes/Hiiragi2013/inst/doc/Hiiragi2013.pdf vignetteTitles: Hiiragi2013 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Hiiragi2013/inst/doc/Hiiragi2013.R dependencyCount: 73 Package: HIVcDNAvantWout03 Version: 1.32.0 License: GPL (>= 2) MD5sum: 167c22c51c0c8f2e0d9b98de95e2c8be NeedsCompilation: no Title: T cell line infections with HIV-1 LAI (BRU) Description: The expression levels of approximately 4600 cellular RNA transcripts were assessed in CD4+ T cell lines at different times after infection with HIV-1BRU using DNA microarrays. This data corresponds to the first block of a 12 block array image (001030_08_1.GEL) in the first data set (2000095918 A) in the first experiment (CEM LAI vs HI-LAI 24hr). There are two data sets, which are part of a dye-swap experiment with replicates, representing the Cy3 (green) absorption intensities for channel 1 (hiv1raw) and the Cy5 (red) absorption intensities for channel 2 (hiv2raw). biocViews: ExperimentData, MicroarrayData, TwoChannelData, HIVData Author: Dr. Angelique van't Wout, Department of Microbiology, University of Washington Maintainer: Chris Fraley URL: http://expression.microslu.washington.edu/expression/vantwoutjvi2002.html git_url: https://git.bioconductor.org/packages/HIVcDNAvantWout03 git_branch: RELEASE_3_13 git_last_commit: b950ec1 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/HIVcDNAvantWout03_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: HMP16SData Version: 1.12.0 Depends: R (>= 4.0.0), SummarizedExperiment Imports: AnnotationHub, assertthat, dplyr, ExperimentHub, kableExtra, knitr, magrittr, methods, readr, S4Vectors, stringr, tibble, utils Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, circlize, covr, cowplot, dendextend, devtools, ggplot2, gridExtra, haven, phyloseq, rmarkdown, roxygen2, stats, testthat, tidyr License: Artistic-2.0 MD5sum: 7d016f91177c87b7e1d76a591e4c2531 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] (), Rimsha Azhar [aut], Marcel Ramos [ctb], Ludwig Geistlinger [ctb], Levi Waldron [aut] Maintainer: Lucas schiffer URL: https://github.com/waldronlab/HMP16SData VignetteBuilder: knitr BugReports: https://github.com/waldronlab/HMP16SData/issues git_url: https://git.bioconductor.org/packages/HMP16SData git_branch: RELEASE_3_13 git_last_commit: a7b4f2a git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/HMP16SData_1.12.0.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: 130 Package: HMP2Data Version: 1.6.0 Depends: R (>= 3.6.0) Imports: AnnotationHub, assertthat, dplyr, ExperimentHub, kableExtra, knitr, magrittr, methods, readr, S4Vectors, SummarizedExperiment, phyloseq, MultiAssayExperiment, data.table Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, cowplot, devtools, ggplot2, gridExtra, haven, rmarkdown, roxygen2, stats, testthat, tibble, UpSetR License: Artistic-2.0 MD5sum: 1e1fa72c16dec81fb7223cedc850faa4 NeedsCompilation: no Title: 16s rRNA sequencing data from the Human Microbiome Project 2 Description: HMP2Data is a Bioconductor package of the Human Microbiome Project 2 (HMP2) 16S rRNA sequencing data. Processed data is provided as phyloseq, SummarizedExperiment, and MultiAssayExperiment class objects. Individual matrices and data.frames used for building these S4 class objects are also provided in the package. biocViews: ExperimentData, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch, SequencingData Author: John Stansfield , Ekaterina Smirnova , Ni Zhao , Jennifer Fettweis , Levi Waldron , Mikhail Dozmorov Maintainer: John Stansfield , Ekaterina Smirnova URL: https://github.com/jstansfield0/HMP2Data VignetteBuilder: knitr BugReports: https://github.com/jstansfield0/HMP2Data/issues git_url: https://git.bioconductor.org/packages/HMP2Data git_branch: RELEASE_3_13 git_last_commit: 1e6fd64 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/HMP2Data_1.6.0.tar.gz vignettes: vignettes/HMP2Data/inst/doc/hmp2data.html vignetteTitles: HMP2Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HMP2Data/inst/doc/hmp2data.R dependencyCount: 160 Package: HSMMSingleCell Version: 1.12.0 Depends: R (>= 2.10) License: Artistic-2.0 MD5sum: 1e44fc2ee63cf922a7c8bb9e318ca0f2 NeedsCompilation: no Title: Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM) Description: Skeletal myoblasts undergo a well-characterized sequence of morphological and transcriptional changes during differentiation. In this experiment, primary human skeletal muscle myoblasts (HSMM) were expanded under high mitogen conditions (GM) and then differentiated by switching to low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several hundred cells taken over a time-course of serum-induced differentiation. Between 49 and 77 cells were captured at each of four time points (0, 24, 48, 72 hours) following serum switch using the Fluidigm C1 microfluidic system. RNA from each cell was isolated and used to construct mRNA-Seq libraries, which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell. biocViews: ExperimentData, RNASeqData Author: Cole Trapnell Maintainer: Cole Trapnell git_url: https://git.bioconductor.org/packages/HSMMSingleCell git_branch: RELEASE_3_13 git_last_commit: a7c3faa git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/HSMMSingleCell_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: ctgGEM, monocle suggestsMe: cellTree dependencyCount: 0 Package: HumanAffyData Version: 1.18.0 Depends: ExperimentHub, Biobase, R (>= 3.3) Suggests: BiocStyle License: Artistic-2.0 MD5sum: e85bc952ec93cfe2b747b5a1b04a7131 NeedsCompilation: no Title: GEO accession GSE64985 and ArrayExpress accession E-MTAB-62 as ExpressionSet objects Description: Re-analysis of human gene expression data generated on the Affymetrix HG_U133PlusV2 (EH176) and Affymetrix HG_U133A (EH177) platforms. The original data were normalized using robust multiarray averaging (RMA) to obtain an integrated gene expression atlas across diverse biological sample types and conditions. The entire compendia comprisee 9395 arrays for EH176 and 5372 arrays for EH177. biocViews: ExperimentData, GEO, ArrayExpress, Homo_sapiens_Data, MicroarrayData, ExpressionData Author: Brad Nelms Maintainer: Brad Nelms git_url: https://git.bioconductor.org/packages/HumanAffyData git_branch: RELEASE_3_13 git_last_commit: 325a5b3 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/HumanAffyData_1.18.0.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: 88 Package: humanStemCell Version: 0.32.0 Depends: Biobase (>= 2.5.5), hgu133plus2.db License: Artistic-2.0 MD5sum: 47842069556f4829b4eabf53dac394f9 NeedsCompilation: no Title: Human Stem Cells time course experiment Description: Affymetrix time course experiment on human stem cells (two time points: undifferentiated and differentiated). biocViews: ExperimentData, Homo_sapiens_Data Author: R. Gentleman, N. Le Meur, M. Tewari Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/humanStemCell git_branch: RELEASE_3_13 git_last_commit: bba7c88 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/humanStemCell_0.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MiRaGE, rtracklayer dependencyCount: 48 Package: IHWpaper Version: 1.20.0 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, ggbio, latex2exp License: Artistic-2.0 MD5sum: 31d778c476d165a0f047ccc503a9edd7 NeedsCompilation: yes Title: Reproduce figures in IHW paper Description: This package conveniently wraps all functions needed to reproduce the figures in the IHW paper (https://www.nature.com/articles/nmeth.3885) and the latest arXiv preprint available under http://arxiv.org/abs/1701.05179. Thus it is a companion package to the Bioconductor IHW package. biocViews: ReproducibleResearch, ExperimentData, RNASeqData, ExpressionData Author: Nikos Ignatiadis [aut, cre] Maintainer: Nikos Ignatiadis VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/IHWpaper git_branch: RELEASE_3_13 git_last_commit: fe59934 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/IHWpaper_1.20.0.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: 1.28.0 Depends: R (>= 3.0.1) License: GPL-3 MD5sum: 97cf07ff6930e9fff6e6eac78206a973 NeedsCompilation: no Title: Annotation Package combining variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes Description: Includes details on variants for each probe on the 450k bead chip for each of the four populations (Asian, American, African and European) biocViews: Homo_sapiens_Data, CancerData, ChipOnChipData, SNPData Author: Lee Butcher Maintainer: Tiffany Morris git_url: https://git.bioconductor.org/packages/Illumina450ProbeVariants.db git_branch: RELEASE_3_13 git_last_commit: 479524f git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/Illumina450ProbeVariants.db_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: IlluminaDataTestFiles Version: 1.30.0 License: Artistic-2.0 MD5sum: 5df0470a51f3c416bec4d487c997e8c1 NeedsCompilation: no Title: Illumina microarray files (IDAT) for testing Description: Example data for Illumina microarray output files, for testing purposes biocViews: MicroarrayData Author: Kasper Daniel Hansen, Mike L. Smith Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/IlluminaDataTestFiles git_branch: RELEASE_3_13 git_last_commit: efeef98 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/IlluminaDataTestFiles_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: illuminaio dependencyCount: 0 Package: imcdatasets Version: 1.0.1 Depends: R (>= 4.1), SingleCellExperiment, cytomapper, Imports: methods, utils, ExperimentHub, S4Vectors, DelayedArray, HDF5Array Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat License: GPL-3 MD5sum: 826a14a36234b56fe6462abe2f69d56a 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: ExperimentHub, SingleCellData, TechnologyData, PackageTypeData, Tissue Author: Nicolas Damond [aut, cre] (), Nils Eling [ctb] (), Fischer Jana [ctb] () Maintainer: Nicolas Damond URL: https://github.com/BodenmillerGroup/imcdatasets VignetteBuilder: knitr BugReports: https://github.com/BodenmillerGroup/imcdatasets/issues git_url: https://git.bioconductor.org/packages/imcdatasets git_branch: RELEASE_3_13 git_last_commit: 886b412 git_last_commit_date: 2021-06-15 Date/Publication: 2021-06-15 source.ver: src/contrib/imcdatasets_1.0.1.tar.gz vignettes: vignettes/imcdatasets/inst/doc/imcdatasets.html vignetteTitles: "Accessing IMC datasets" hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/imcdatasets/inst/doc/imcdatasets.R dependencyCount: 142 Package: ITALICSData Version: 2.30.0 Depends: R (>= 2.0.0) License: GPL MD5sum: 28a04c60d7c92e74f1fa794ff6b5956a NeedsCompilation: no Title: ITALICSData Description: Data needed to use the ITALICS package biocViews: ExperimentData, HapMap Author: Guillem Rigaill Maintainer: Guillem Rigaill URL: http://bioinfo.curie.fr git_url: https://git.bioconductor.org/packages/ITALICSData git_branch: RELEASE_3_13 git_last_commit: d761290 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ITALICSData_2.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ITALICS dependencyCount: 0 Package: Iyer517 Version: 1.34.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: d7f42c68533615e2c25278c4613f1293 NeedsCompilation: no Title: exprSets for Iyer, Eisen et all 1999 Science paper Description: representation of public Iyer data from http://genome-www.stanford.edu/serum/clusters.html biocViews: ExperimentData Author: Vishy Iyer Maintainer: Vince Carey git_url: https://git.bioconductor.org/packages/Iyer517 git_branch: RELEASE_3_13 git_last_commit: fcc25bb git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/Iyer517_1.34.0.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: 1.28.0 Depends: R (>= 3.0.1), methods, Biostrings (>= 2.29.19) License: GPL-2 MD5sum: 84263af860ec81798e14413db58641aa NeedsCompilation: no Title: Data package for JASPAR Description: Data package for JASPAR 2014. To search this databases, please use the package TFBSTools. biocViews: ExperimentData, SequencingData Author: Ge Tan Maintainer: Ge Tan URL: http://jaspar.genereg.net/ git_url: https://git.bioconductor.org/packages/JASPAR2014 git_branch: RELEASE_3_13 git_last_commit: b572d47 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/JASPAR2014_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MatrixRider, TFBSTools dependencyCount: 19 Package: JASPAR2016 Version: 1.20.0 Depends: R (>= 3.2.2), methods License: GPL-2 MD5sum: 0feefec944508fb722eaa473747ac11f NeedsCompilation: no Title: Data package for JASPAR 2016 Description: Data package for JASPAR 2016. To search this databases, please use the package TFBSTools (>= 1.8.1). biocViews: ExperimentData, MotifAnnotation, GeneRegulation Author: Ge Tan Maintainer: Ge Tan URL: http://jaspar.genereg.net/ git_url: https://git.bioconductor.org/packages/JASPAR2016 git_branch: RELEASE_3_13 git_last_commit: b9a46d3 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/JASPAR2016_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: chromVAR, TFBSTools, CAGEWorkflow dependencyCount: 1 Package: KEGGandMetacoreDzPathwaysGEO Version: 1.12.0 Depends: R (>= 2.15.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: ba853a739fb0c2f10bcbc886d9f1320b NeedsCompilation: no Title: Disease Datasets from GEO Description: This is a collection of 18 data sets for which the phenotype is a disease with a corresponding pathway in either KEGG or metacore database.This collection of datasets were used as gold standard in comparing gene set analysis methods. biocViews: ExperimentData, GEO Author: Gaurav Bhatti Maintainer: Gaurav Bhatti git_url: https://git.bioconductor.org/packages/KEGGandMetacoreDzPathwaysGEO git_branch: RELEASE_3_13 git_last_commit: 89c1db5 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/KEGGandMetacoreDzPathwaysGEO_1.12.0.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: 1.30.0 Depends: R (>= 2.13.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: b834e391078b7b9fa3e2cfdc30bb5522 NeedsCompilation: no Title: KEGG Disease Datasets from GEO Description: This is a collection of 24 data sets for which the phenotype is a disease with a corresponding pathway in the KEGG database.This collection of datasets were used as gold standard in comparing gene set analysis methods by the PADOG package. biocViews: MicroarrayData, GEO, ExperimentData Author: Gaurav Bhatti, Adi L. Tarca Maintainer: Gaurav Bhatti git_url: https://git.bioconductor.org/packages/KEGGdzPathwaysGEO git_branch: RELEASE_3_13 git_last_commit: cc8de0e git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/KEGGdzPathwaysGEO_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: PADOG importsMe: GSEABenchmarkeR dependencyCount: 7 Package: kidpack Version: 1.34.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5) License: GPL-2 MD5sum: 286a73600408ee0f95b9039c3112f009 NeedsCompilation: no Title: DKFZ kidney package Description: kidney microarray data biocViews: ExperimentData, CancerData, KidneyCancerData, MicroarrayData, ArrayExpress Author: Wolfgang Huber Maintainer: Wolfgang Huber URL: http://www.dkfz.de/mga git_url: https://git.bioconductor.org/packages/kidpack git_branch: RELEASE_3_13 git_last_commit: 21667d6 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/kidpack_1.34.0.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: 1.18.0 Depends: R (>= 3.3.0) License: MIT + file LICENSE MD5sum: 694118dcfa64d86e21e26fa93380e6e5 NeedsCompilation: no Title: LINCS Knock-Out Data Package Description: Contains consensus genomic signatures (CGS) for experimental cell-line specific gene knock-outs as well as baseline gene expression data for a subset of experimental cell-lines. Intended for use with package KEGGlincs. biocViews: ExpressionData, CancerData, Homo_sapiens_Data Author: Shana White Maintainer: Shana White git_url: https://git.bioconductor.org/packages/KOdata git_branch: RELEASE_3_13 git_last_commit: 2954bde git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/KOdata_1.18.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: KEGGlincs dependencyCount: 0 Package: leeBamViews Version: 1.28.0 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: c40979db95cfb608927e07e1ddfc03c0 NeedsCompilation: no Title: leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009 Description: data from PMID 19096707; prototype for managing multiple NGS samples biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData, SNPData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/leeBamViews git_branch: RELEASE_3_13 git_last_commit: 8ed77ea git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/leeBamViews_1.28.0.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: 45 Package: leukemiasEset Version: 1.28.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 0e16c1734fc9369646a0c1410f8dfb18 NeedsCompilation: no Title: Leukemia's microarray gene expression data (expressionSet). Description: Expressionset containing gene expresion data from 60 bone marrow samples of patients with one of the four main types of leukemia (ALL, AML, CLL, CML) or non-leukemia. biocViews: Tissue, Genome, Homo_sapiens_Data, CancerData, LeukemiaCancerData, MicroarrayData, ChipOnChipData, TissueMicroarrayData, GEO Author: Sara Aibar, Celia Fontanillo and Javier De Las Rivas. Bioinformatics and Functional Genomics Group. Cancer Research Center (CiC-IBMCC, CSIC/USAL). Salamanca. Spain. Maintainer: Sara Aibar git_url: https://git.bioconductor.org/packages/leukemiasEset git_branch: RELEASE_3_13 git_last_commit: be5a689 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/leukemiasEset_1.28.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: geNetClassifier, mCSEA, multiclassPairs dependencyCount: 7 Package: LiebermanAidenHiC2009 Version: 0.30.0 Depends: KernSmooth, IRanges License: LGPL MD5sum: 2f97c0f44da19bcaf80166bf7a8b7d40 NeedsCompilation: no Title: Selected data from the HiC paper of E. Lieberman-Aiden et al. in Science (2009) Description: This package provides data that were presented in the article "Comprehensive mapping of long-range interactions reveals folding principles of the human genome", Science 2009 Oct 9;326(5950):289-93. PMID: 19815776 biocViews: ExperimentData, Genome, SequencingData, DNASeqData, ChIPSeqData, miRNAData, SmallRNAData, ChipOnChipData, GEO, NCI, ENCODE Author: Wolfgang Huber, Felix Klein Maintainer: Felix Klein git_url: https://git.bioconductor.org/packages/LiebermanAidenHiC2009 git_branch: RELEASE_3_13 git_last_commit: 2466dc4 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/LiebermanAidenHiC2009_0.30.0.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: 1.24.0 Depends: R (>= 3.1.1), methylPipe Suggests: BSgenome.Hsapiens.UCSC.hg18 License: Artistic 2.0 MD5sum: eaaf5019376ade1a010d4f8bb2161d98 NeedsCompilation: no Title: BS-seq data of H1 and IMR90 cell line excerpted from Lister et al. 2009 Description: Base resolution bisulfite sequencing data of Human DNA methylomes biocViews: ExperimentData, Homo_sapiens_Data, SequencingData Author: Kamal Kishore Maintainer: Kamal Kishore git_url: https://git.bioconductor.org/packages/ListerEtAlBSseq git_branch: RELEASE_3_13 git_last_commit: 17422e9 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ListerEtAlBSseq_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 149 Package: LRcellTypeMarkers Version: 1.0.0 Depends: R (>= 4.1) Imports: ExperimentHub Suggests: LRcell, BiocStyle, knitr, rmarkdown, roxygen2, testthat License: MIT + file LICENSE MD5sum: af012f3c288f8b402fdd9fa06ed3d59b 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] () Maintainer: Wenjing Ma VignetteBuilder: knitr BugReports: https://github.com/marvinquiet/LRcellTypeMarkers/issues git_url: https://git.bioconductor.org/packages/LRcellTypeMarkers git_branch: RELEASE_3_13 git_last_commit: 1a87f87 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/LRcellTypeMarkers_1.0.0.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: 88 Package: lumiBarnes Version: 1.32.0 Depends: R (>= 2.0), Biobase (>= 2.5.5), lumi (>= 1.1.0) License: LGPL MD5sum: 46b0ceafafffc64d07846abab24dfb08 NeedsCompilation: no Title: Barnes Benchmark Illumina Tissues Titration Data Description: The Barnes benchmark dataset can be used to evaluate the algorithms for Illumina microarrays. It measured a titration series of two human tissues, blood and placenta, and includes six samples with the titration ratio of blood and placenta as 100:0, 95:5, 75:25, 50:50, 25:75 and 0:100. The samples were hybridized on HumanRef-8 BeadChip (Illumina, Inc) in duplicate. The data is loaded as an LumiBatch Object (see documents in the lumi package). biocViews: ExperimentData, Tissue, MicroarrayData, ChipOnChipData Author: Pan Du Maintainer: Pan Du git_url: https://git.bioconductor.org/packages/lumiBarnes git_branch: RELEASE_3_13 git_last_commit: bf9205b git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/lumiBarnes_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayMvout, lumi dependencyCount: 160 Package: LungCancerACvsSCCGEO Version: 1.28.0 Depends: R (>= 2.15.0) License: GPL-2 MD5sum: 45a8a608e219565ae154488c2bf8bf97 NeedsCompilation: no Title: A lung cancer dataset that can be used with maPredictDSC package for developing outcome prediction models from Affymetrix CEL files. Description: This package contains 30 Affymetrix CEL files for 7 Adenocarcinoma (AC) and 8 Squamous cell carcinoma (SCC) lung cancer samples taken at random from 3 GEO datasets (GSE10245, GSE18842 and GSE2109) and other 15 samples from a dataset produced by the organizers of the IMPROVER Diagnostic Signature Challenge available from GEO (GSE43580). biocViews: CancerData, LungCancerData, MicroarrayData, GEO Author: Adi Laurentiu Tarca Maintainer: Adi Laurentiu Tarca URL: http://bioinformaticsprb.med.wayne.edu/ git_url: https://git.bioconductor.org/packages/LungCancerACvsSCCGEO git_branch: RELEASE_3_13 git_last_commit: b02cc2a git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/LungCancerACvsSCCGEO_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: LungCancerLines Version: 0.30.0 Imports: Rsamtools License: Artistic-2.0 MD5sum: 80054915bf8c53be6242b29a0a458b08 NeedsCompilation: no Title: Reads from Two Lung Cancer Cell Lines Description: Reads from an RNA-seq experiment between two lung cancer cell lines: H1993 (met) and H2073 (primary). The reads are stored as Fastq files and are meant for use with the TP53Genome object in the gmapR package. biocViews: ExperimentData, Genome, CancerData, LungCancerData, RNASeqData Author: Cory Barr, Michael Lawrence Maintainer: Cory Barr git_url: https://git.bioconductor.org/packages/LungCancerLines git_branch: RELEASE_3_13 git_last_commit: 76a4666 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/LungCancerLines_0.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: gmapR, HTSeqGenie, VariantTools dependencyCount: 29 Package: lungExpression Version: 0.30.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: f161520ca421f94f17061bdf2f76d228 NeedsCompilation: no Title: ExpressionSets for Parmigiani et al., 2004 Clinical Cancer Research paper Description: Data from three large lung cancer studies provided as ExpressionSets biocViews: ExperimentData, CancerData, LungCancerData Author: Robert Scharpf , Simens Zhong , Giovanni Parmigiani Maintainer: Robert Scharpf git_url: https://git.bioconductor.org/packages/lungExpression git_branch: RELEASE_3_13 git_last_commit: 04e1d97 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/lungExpression_0.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: globaltest dependencyCount: 7 Package: lydata Version: 1.18.0 License: MIT + file LICENSE MD5sum: 698aaf8fa9335620c5c308295a00056c NeedsCompilation: no Title: Example Dataset for crossmeta Package Description: Raw data downloaded from GEO for the compound LY294002. Raw data is from multiple platforms from Affymetrix and Illumina. This data is used to illustrate the cross-platform meta-analysis of microarray data using the crossmeta package. biocViews: ExperimentData, MicroarrayData Author: Alex Pickering Maintainer: Alex Pickering git_url: https://git.bioconductor.org/packages/lydata git_branch: RELEASE_3_13 git_last_commit: 7baee12 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/lydata_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: ccmap, crossmeta dependencyCount: 0 Package: M3DExampleData Version: 1.18.0 Depends: R (>= 3.3) License: GPL (>=2) MD5sum: 079e5deb1d3c64b79879f06c4006694e NeedsCompilation: no Title: M3Drop Example Data Description: Example data for M3Drop package. biocViews: Mus_musculus_Data, RNASeqData, ExpressionData, GEO, Tissue, ExperimentData Author: Tallulah Andrews Maintainer: Tallulah Andrews git_url: https://git.bioconductor.org/packages/M3DExampleData git_branch: RELEASE_3_13 git_last_commit: 35a1aef git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/M3DExampleData_1.18.0.tar.gz hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: celda, M3Drop dependencyCount: 0 Package: macrophage Version: 1.8.0 Depends: R (>= 3.5.0) Suggests: knitr, markdown License: GPL (>= 2) MD5sum: a180dc530275e7d6f9044b4f2ca06f99 NeedsCompilation: no Title: Human macrophage immune response Description: This package provides the output of running Salmon on a set of 24 RNA-seq samples from Alasoo, et al. "Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response", published in Nature Genetics, January 2018. For details on version numbers and how the samples were processed see the package vignette. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/macrophage git_branch: RELEASE_3_13 git_last_commit: 4e74eec git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/macrophage_1.8.0.tar.gz vignettes: vignettes/macrophage/inst/doc/macrophage.html vignetteTitles: Salmon quantifications for human macrophage immune response experiment hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/macrophage/inst/doc/macrophage.R suggestsMe: fishpond, GeneTonic, quantiseqr, fluentGenomics dependencyCount: 0 Package: MACSdata Version: 1.0.0 License: file LICENSE MD5sum: e1e53806c94c0e3e0593c514eb1a9e6a NeedsCompilation: no Title: Test datasets for the MACSr package Description: Test datasets from the MACS3 test examples are use in the examples of the `MACSr` package. All 9 datasets are uploaded to the `ExperimentHub`. The original data can be found at: https://github.com/macs3-project/MACS/. biocViews: ExperimentHub, ExperimentData, ChIPSeqData Author: Qiang Hu [aut, cre] Maintainer: Qiang Hu git_url: https://git.bioconductor.org/packages/MACSdata git_branch: RELEASE_3_13 git_last_commit: 218fc1a git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/MACSdata_1.0.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: MACSr dependencyCount: 0 Package: mammaPrintData Version: 1.28.0 Depends: R (>= 2.13.0) Suggests: Biobase, gdata, limma License: Artistic-2.0 MD5sum: 436049bf7dd19df500744f880a026d06 NeedsCompilation: no Title: RGLists from the Glas and Buyse breast cancer studies Description: Gene expression data for the two breast cancer cohorts published by Glas and Buyse in 2006. This cohorts were used to implement and validate the mammaPrint breast cancer test. biocViews: ExperimentData, ExpressionData, CancerData, BreastCancerData, MicroarrayData, TwoChannelData Author: Luigi Marchionni Maintainer: Luigi Marchionni URL: http://luigimarchionni.org/breastTSP.html git_url: https://git.bioconductor.org/packages/mammaPrintData git_branch: RELEASE_3_13 git_last_commit: 20aa4a4 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/mammaPrintData_1.28.0.tar.gz vignettes: vignettes/mammaPrintData/inst/doc/mammaPrintData.pdf vignetteTitles: Working with the mammaPrintData package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mammaPrintData/inst/doc/mammaPrintData.R dependencyCount: 0 Package: mAPKLData Version: 1.24.0 Depends: R (>= 3.2.0) Suggests: Biobase License: Artistic-2.0 MD5sum: d35f552df890ff28fa49cea18415339c NeedsCompilation: no Title: Gene expression data for testing of the package mAPKL. Description: Gene expression data from a breast cancer study published by Turashvili et al. in 2007, provided as an eSet. biocViews: ExperimentData, ExpressionData, Cancer, Breast Author: Argiris Sakellariou Maintainer: Argiris Sakellariou git_url: https://git.bioconductor.org/packages/mAPKLData git_branch: RELEASE_3_13 git_last_commit: c6c8840 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/mAPKLData_1.24.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: mAPKL dependencyCount: 0 Package: maqcExpression4plex Version: 1.36.0 Suggests: oligo, pdInfoBuilder License: GPL MD5sum: 7ec57788af8e2e6c7fec58a41886b770 NeedsCompilation: no Title: Sample Expression Data - MAQC / HG18 - NimbleGen Description: Data from human (HG18) 4plex NimbleGen array. It has 24k genes with 3 60mer probes per gene. biocViews: ExperimentData, CancerData Author: NimbleGen Systems Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/maqcExpression4plex git_branch: RELEASE_3_13 git_last_commit: acdc4d6 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/maqcExpression4plex_1.36.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligo dependencyCount: 0 Package: MAQCsubset Version: 1.30.0 Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), lumi, methods Suggests: genefilter, codelink License: Artistic-2.0 MD5sum: 7cde1d383f33daa53099cecec4afb833 NeedsCompilation: no Title: Experimental Data Package: MAQCsubset Description: Data Package automatically created on Sun Nov 19 15:59:29 2006. biocViews: ExperimentData, MicroarrayData, GEO Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/MAQCsubset git_branch: RELEASE_3_13 git_last_commit: e2a8f10 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/MAQCsubset_1.30.0.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: 160 Package: MAQCsubsetAFX Version: 1.30.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 51a486f2cd3df1701fe19920f11e64fd NeedsCompilation: no Title: MAQC data subset for the Affymetrix platform Description: MAQC data subset for the Affymetrix platform biocViews: ExperimentData, Genome, Homo_sapiens_Data, MicroarrayData Author: Laurent Gatto Maintainer: Laurent Gatto PackageStatus: Deprecated git_url: https://git.bioconductor.org/packages/MAQCsubsetAFX git_branch: RELEASE_3_13 git_last_commit: 7521495 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/MAQCsubsetAFX_1.30.0.tar.gz vignettes: vignettes/MAQCsubsetAFX/inst/doc/MAQCsubsetAFX.pdf vignetteTitles: MAQCsubsetAFX: MAQC data subset for the Affymetrix platform hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MAQCsubsetAFX/inst/doc/MAQCsubsetAFX.R dependencyCount: 13 Package: MAQCsubsetILM Version: 1.30.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), lumi License: Artistic-2.0 MD5sum: e206b30ec05ad25c2a479efdbf1601dc NeedsCompilation: no Title: MAQC data subset for the Illumina platform Description: MAQC data subset for the Illumina platform biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData Author: Laurent Gatto Maintainer: Laurent Gatto git_url: https://git.bioconductor.org/packages/MAQCsubsetILM git_branch: RELEASE_3_13 git_last_commit: bb8e755 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/MAQCsubsetILM_1.30.0.tar.gz vignettes: vignettes/MAQCsubsetILM/inst/doc/MAQCsubsetILM.pdf vignetteTitles: MAQCsubsetILM: MAQC data subset for the Illumina platform hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MAQCsubsetILM/inst/doc/MAQCsubsetILM.R dependencyCount: 160 Package: mCSEAdata Version: 1.12.0 Depends: R (>= 3.5) Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 90ec56a61a50599c88dbadae9982560e NeedsCompilation: no Title: Data package for mCSEA package Description: Data objects necessary to some mCSEA package functions. There are also example data objects to illustrate mCSEA package functionality. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData, ExperimentData Author: Jordi Martorell Marugán Maintainer: Jordi Martorell Marugán VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mCSEAdata git_branch: RELEASE_3_13 git_last_commit: 2385817 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/mCSEAdata_1.12.0.tar.gz vignettes: vignettes/mCSEAdata/inst/doc/mCSEAdata.pdf vignetteTitles: Data for mCSEA package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mCSEAdata/inst/doc/mCSEAdata.R dependsOnMe: mCSEA dependencyCount: 0 Package: mcsurvdata Version: 1.10.0 Depends: R (>= 3.5), ExperimentHub Imports: AnnotationHub, Biobase Suggests: knitr License: GPL (>=2) MD5sum: cf8703e68e5aa9540983a131f645070f NeedsCompilation: no Title: Meta cohort survival data Description: This package stores two merged expressionSet objects that contain the gene expression profile and clinical information of -a- six breast cancer cohorts and -b- four colorectal cancer cohorts. Breast cancer data are employed in the vignette of the hrunbiased package for survival analysis of gene signatures. biocViews: ExperimentData, Homo_sapiens_Data, GEO, MicroarrayData Author: Adria Caballe Mestres [aut, cre], Antoni Berenguer Llergo [aut], Camille Stephan-Otto Attolini [aut] Maintainer: Adria Caballe Mestres URL: https://github.com/adricaba/mcsurvdata VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mcsurvdata git_branch: RELEASE_3_13 git_last_commit: 26b157e git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/mcsurvdata_1.10.0.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: 88 Package: MEDIPSData Version: 1.28.0 Depends: R (>= 2.15.0) License: GPL (>= 2) MD5sum: cdeb83db1e64f12b54935bc5600cb63b NeedsCompilation: no Title: Example data for MEDIPS and QSEA packages Description: Example data for MEDIPS and QSEA packages, consisting of chromosome 22 MeDIP and control/Input sample data. Additionally, the package contains MeDIP seq data from 3 NSCLC samples and adjacent normal tissue (chr 20-22). All data has been aligned to human genome hg19. biocViews: ExperimentData, Genome, SequencingData Author: Lukas Chavez Maintainer: Lukas Chavez git_url: https://git.bioconductor.org/packages/MEDIPSData git_branch: RELEASE_3_13 git_last_commit: 9224c0f git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/MEDIPSData_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MEDIPS, qsea dependencyCount: 0 Package: MEEBOdata Version: 1.30.0 License: LGPL MD5sum: 5ae0e9d7f492691596c1063cba917d04 NeedsCompilation: no Title: MEEBO set and MEEBO controls. Description: R objects describing the MEEBO set. biocViews: ExperimentData Author: Agnes Paquet Maintainer: Agnes Paquet URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/ git_url: https://git.bioconductor.org/packages/MEEBOdata git_branch: RELEASE_3_13 git_last_commit: 66d0391 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/MEEBOdata_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQuality dependencyCount: 0 Package: MetaGxBreast Version: 1.12.0 Depends: R (>= 3.6.0), Biobase, AnnotationHub, ExperimentHub Imports: stats, lattice, impute, SummarizedExperiment Suggests: testthat, xtable, tinytex License: Apache License (>= 2) MD5sum: 7dec825d9fd57546df06c0fcc57297ae NeedsCompilation: no Title: Transcriptomic Breast Cancer Datasets Description: A collection of Breast Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium. biocViews: ExpressionData, ExperimentHub, CancerData, Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData, ExperimentData Author: Michael Zon [aut], Deena M.A. Gendoo [aut], Christopher Eeles [ctb], Benjamin Haibe-Kains [aut, cre] Maintainer: Benjamin Haibe-Kains git_url: https://git.bioconductor.org/packages/MetaGxBreast git_branch: RELEASE_3_13 git_last_commit: 632a5f1 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/MetaGxBreast_1.12.0.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: 97 Package: MetaGxOvarian Version: 1.12.0 Depends: Biobase, stats, lattice, impute, AnnotationHub, ExperimentHub, SummarizedExperiment, R (>= 3.6.0) Suggests: testthat, xtable License: Artistic-2.0 MD5sum: 1b905aa8a607d865380784df318ddc4f NeedsCompilation: no Title: Transcriptomic Ovarian Cancer Datasets Description: A collection of Ovarian Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium. biocViews: ExpressionData, ExperimentHub, CancerData, Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData, ExperimentData Author: Michael Zon , Deena M.A. Gendoo , Benjamin Haibe-Kains Maintainer: Michael Zon git_url: https://git.bioconductor.org/packages/MetaGxOvarian git_branch: RELEASE_3_13 git_last_commit: 83cbe19 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/MetaGxOvarian_1.12.0.tar.gz vignettes: vignettes/MetaGxOvarian/inst/doc/MetaGxOvarian.pdf vignetteTitles: MetaGxOvarian: a package for ovarian cancer gene expression analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MetaGxOvarian/inst/doc/MetaGxOvarian.R dependencyCount: 97 Package: MetaGxPancreas Version: 1.12.1 Depends: SummarizedExperiment, ExperimentHub, R (>= 3.6.0) Imports: stats, impute, S4Vectors, AnnotationHub Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: ada87e497f98e65bf75a8adc225208d6 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], Benjamin Haibe-Kains [aut, cre] Maintainer: Benjamin Haibe-Kains VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MetaGxPancreas git_branch: RELEASE_3_13 git_last_commit: 119f129 git_last_commit_date: 2021-06-21 Date/Publication: 2021-06-22 source.ver: src/contrib/MetaGxPancreas_1.12.1.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: 97 Package: metaMSdata Version: 1.28.0 License: GPL (>= 2) MD5sum: 5b378f12060d8c94fbd857a7e3ade6d1 NeedsCompilation: no Title: Example CDF data for the metaMS package Description: Example CDF data for the metaMS package biocViews: ExperimentData, MassSpectrometryData Author: Ron Wehrens [aut, cre], Pietro Franceschi [aut], Georg Weingart [ctb] Maintainer: Yann Guitton git_url: https://git.bioconductor.org/packages/metaMSdata git_branch: RELEASE_3_13 git_last_commit: 7d37424 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/metaMSdata_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CluMSID, metaMS dependencyCount: 0 Package: MethylAidData Version: 1.24.0 Depends: MethylAid, R (>= 3.2) Suggests: BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC License: GPL (>= 2) MD5sum: 881928d56721ca284613af9dc0ad11aa NeedsCompilation: no Title: MethylAid-summarized data for 2800 Illumina 450k array samples and 2620 EPIC array samples Description: A data package containing summarized Illumina 450k array data on 2800 samples and summarized EPIC data for 2620 samples. The data can be use as a background data set in the interactive application. biocViews: ExperimentData, TechnologyData, MicroarrayData, MethylationArrayData Author: Davy Cats, Tyler J. Gorrie-Stone, Bastiaan T. Heijmans, John W. Holloway, BIOS Consortium, Maarten van Iterson, Faisal I. Rezwam, Leonard Schalkwyk Maintainer: M. van Iterson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MethylAidData git_branch: RELEASE_3_13 git_last_commit: 486aa95 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/MethylAidData_1.24.0.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: 165 Package: methylclockData Version: 1.0.9 Imports: ExperimentHubData, ExperimentHub, utils Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 636ad2204e4d0731332c1b7bcaddede4 NeedsCompilation: no Title: Data for methylclock package Description: Collection of 9 datasets, andrews and bakulski cord blood, blood gse35069, blood gse35069 chen, blood gse35069 complete, combined cord blood, cord bloo d gse68456, gervin and lyle cord blood, guintivano dlpfc and saliva gse48472". Data downloaded from [meffil](https://github.com/perishky/meffil/). Data used to estimate cell counts using Extrinsic epigenetic age acceleration (EEAA) method Collection of 12 datasets to use with MethylClock package to estimate chronological and gestational DNA methylationwith estimators to use wit different methylation clocks biocViews: SpecimenSource, ExperimentHub, Tissue, OrganismData, Homo_sapiens_Data Author: Juan R. Gonzalez [aut], Dolors Pelegri-Siso [aut, cre] Maintainer: Dolors Pelegri-Siso URL: https://github.com/isglobal-brge/methylclockData VignetteBuilder: knitr BugReports: https://github.com/isglobal-brge/methylclockData/issues git_url: https://git.bioconductor.org/packages/methylclockData git_branch: RELEASE_3_13 git_last_commit: 736ea9c git_last_commit_date: 2021-06-30 Date/Publication: 2021-07-01 source.ver: src/contrib/methylclockData_1.0.9.tar.gz vignettes: vignettes/methylclockData/inst/doc/methylcockData.html vignetteTitles: References for metilclock using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/methylclockData/inst/doc/methylcockData.R dependencyCount: 136 Package: MethylSeqData Version: 1.2.0 Depends: SummarizedExperiment Imports: ExperimentHub, HDF5Array, rhdf5, GenomeInfoDb, S4Vectors, GenomicRanges, stats, IRanges, utils Suggests: BiocFileCache, BiocStyle, data.table, knitr, rmarkdown License: CC0 MD5sum: e1b910ab4ef4d30e57a481b3bb10c58f NeedsCompilation: no Title: Collection of Public DNA Methylation Sequencing Datasets Description: Base-level (i.e. cytosine-level) counts for a collection of public bisulfite-seq datasets (e.g., WGBS and RRBS), provided as SummarizedExperiment objects with sample- and base-level metadata. biocViews: ExperimentHub, ExperimentData, SequencingData, Homo_sapiens_Data, Mus_musculus_Data, MethylSeqData Author: Peter Hickey [aut, cre] Maintainer: Peter Hickey VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MethylSeqData git_branch: RELEASE_3_13 git_last_commit: 8425fe8 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/MethylSeqData_1.2.0.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: 100 Package: microbiomeDataSets Version: 1.0.1 Depends: R (>= 4.1), SummarizedExperiment, TreeSummarizedExperiment, MultiAssayExperiment Imports: methods, utils, BiocGenerics, ExperimentHub, Biostrings, ape Suggests: knitr, rmarkdown, BiocStyle, testthat License: CC0 MD5sum: eae33adc78d6507f53567a7efb9fc0d3 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] (), Felix G.M. Ernst [aut] (), Sudarshan Shetty [aut] () Maintainer: Leo Lahti VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/microbiomeDataSets git_branch: RELEASE_3_13 git_last_commit: c24e263 git_last_commit_date: 2021-07-24 Date/Publication: 2021-07-27 source.ver: src/contrib/microbiomeDataSets_1.0.1.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, miaViz dependencyCount: 112 Package: microRNAome Version: 1.14.0 Depends: R (>= 3.4), SummarizedExperiment Suggests: BiocGenerics, RUnit License: GPL (>= 2) MD5sum: 320d3b1bd208ca319ac756f879b06880 NeedsCompilation: no Title: SummarizedExperiment for the microRNAome project Description: This package provides a SummarizedExperiment object of read counts for microRNAs across tissues, cell-types, and cancer cell-lines. The read count matrix was prepared and provided by the author of the study: Towards the human cellular microRNAome. biocViews: ExperimentData, CellCulture, CancerData, SequencingData, RNASeqData, miRNAData Author: Matthew N. McCall , Marc K. Halushka Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/microRNAome git_branch: RELEASE_3_13 git_last_commit: bdcfd35 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/microRNAome_1.14.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 26 Package: MIGSAdata Version: 1.16.0 Depends: R (>= 3.4) Suggests: BiocGenerics License: GPL (>= 2) MD5sum: a45f742cbe72b45e6cb1b9b1df647fd3 NeedsCompilation: no Title: MIGSA vignette data Description: MIGSA vignette data. The MIGSAdata package provides several data objects needed by MIGSA package to correctly generate its vignette, and follow it step by step. biocViews: ExperimentData, RepositoryData, ReproducibleResearch, CancerData, BreastCancerData, MicroarrayData Author: Juan C. Rodriguez, Cristobal Fresno, Andrea S. Llera and Elmer A. Fernandez Maintainer: Juan C. Rodriguez URL: http://www.bdmg.com.ar/ git_url: https://git.bioconductor.org/packages/MIGSAdata git_branch: RELEASE_3_13 git_last_commit: 43e243e git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/MIGSAdata_1.16.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MIGSA dependencyCount: 0 Package: minfiData Version: 0.38.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2), IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 License: Artistic-2.0 MD5sum: 856d32d13c769fa2866f0b4299527973 NeedsCompilation: no Title: Example data for the Illumina Methylation 450k array Description: Data from 6 samples across 2 groups from 450k methylation arrays. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData Author: Kasper Daniel Hansen, Martin Aryee, Winston Timp Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/minfiData git_branch: RELEASE_3_13 git_last_commit: 89eea21 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/minfiData_0.38.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: methylationArrayAnalysis suggestsMe: bigmelon, conumee, ENmix, funtooNorm, Harman, mCSEA, MEAL, MethylAid, minfi, missMethyl, MultiDataSet, shinyepico, shinyMethyl, skewr, MethylAidData dependencyCount: 141 Package: minfiDataEPIC Version: 1.18.0 Depends: R (>= 3.3), minfi (>= 1.21.2), IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: Artistic-2.0 MD5sum: 8cab2cdd66090b22b1bce5bffe83afb9 NeedsCompilation: no Title: Example data for the Illumina Methylation EPIC array Description: Data from 3 technical replicates of the cell line GM12878 from the EPIC methylation array. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData Author: Jean-Philippe Fortin, Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/minfiDataEPIC git_branch: RELEASE_3_13 git_last_commit: 4b61f27 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/minfiDataEPIC_1.18.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MethylAid, minfi, REMP, MethylAidData dependencyCount: 141 Package: minionSummaryData Version: 1.22.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 9fc970b840e2ebe6ccef16fa506eae97 NeedsCompilation: no Title: Summarised MinION sequencing data published by Ashton et al. 2015 Description: Summarised MinION sequencing data for Salmonella Typhi published by Ashton et al. in 2015. Three replicate runs are each provided as Fast5Summary objects. biocViews: ExperimentData, SequencingData Author: Mike Smith [aut, cre] Maintainer: Mike Smith VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/minionSummaryData git_branch: RELEASE_3_13 git_last_commit: a1eb1ca git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/minionSummaryData_1.22.0.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: 1.22.0 Depends: R (>= 3.2), Imports: utils License: GPL-3 | file LICENSE MD5sum: 374b8621709a61376e0f303ba0c6ab82 NeedsCompilation: no Title: Data used in the miRcomp package Description: Raw amplification data from a large microRNA mixture / dilution study. These data are used by the miRcomp package to assess the performance of methods that estimate expression from the amplification curves. biocViews: ExperimentData, ExpressionData, qPCRData, Homo_sapiens_Data Author: Matthew N. McCall Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/miRcompData git_branch: RELEASE_3_13 git_last_commit: 1393299 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/miRcompData_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: miRcomp dependencyCount: 1 Package: miRNATarget Version: 1.30.0 Depends: R (>= 2.10), Biobase License: GPL MD5sum: d757eb839684fc90509d9f0a610069f3 NeedsCompilation: no Title: gene target tabale of miRNA for human/mouse used for MiRaGE package Description: gene target tabale of miRNA for human/mouse used for MiRaGE package biocViews: ExperimentData, Homo_sapiens_Data Author: Y-h. Taguchi Maintainer: Y-h. Taguchi git_url: https://git.bioconductor.org/packages/miRNATarget git_branch: RELEASE_3_13 git_last_commit: 2ebdd8e git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/miRNATarget_1.30.0.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: MMAPPR2data Version: 1.6.0 Depends: R (>= 3.6.0) Imports: Rsamtools Suggests: knitr, rmarkdown, BiocStyle, roxygen2, seqinr, readr Enhances: MMAPPR2 License: GPL-3 MD5sum: 396d12d31ee6dc558bf5a66b8bed42a6 NeedsCompilation: no Title: Sample Data for MMAPPR2 Description: Contains data for illustration purposes in the MMAPPR2 package, namely simulated BAM files containing RNA-Seq data for a mutation in the slc24a5 gene, taken from the GRCz11 genome. Also contains reference sequence and annotation files for the region. biocViews: RNASeqData, Danio_rerio_Data, SequencingData, Genome Author: Kyle Johnsen [aut], Jonathon Hill [cre] Maintainer: Jonathon Hill URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3613585/, https://github.com/kjohnsen/MMAPPR2 VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MMAPPR2data git_branch: RELEASE_3_13 git_last_commit: 3560161 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/MMAPPR2data_1.6.0.tar.gz vignettes: vignettes/MMAPPR2data/inst/doc/MMAPPR2data.html vignetteTitles: Using MMAPPR2data Resources hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MMAPPR2data/inst/doc/MMAPPR2data.R suggestsMe: MMAPPR2 dependencyCount: 29 Package: MMDiffBamSubset Version: 1.28.0 Suggests: MMDiff2 License: LGPL MD5sum: d627bea662c8baddd99d606baca149a8 NeedsCompilation: no Title: Example ChIP-Seq data for the MMDiff package Description: Subset of BAM files, including WT_2.bam, Null_2.bam, Resc_2.bam, Input.bam from the "Cfp1" experiment (see Clouaire et al., Genes Dev. 2012). Data is available under ArrayExpress accession numbers E-ERAD-79. Additionally, corresponding subset of peaks called by MACS biocViews: ExperimentData, Genome, StemCell, Mus_musculus_Data, DNASeqData, ChIPSeqData, ArrayExpress Author: Gabriele Schweikert Maintainer: Gabriele Schweikert git_url: https://git.bioconductor.org/packages/MMDiffBamSubset git_branch: RELEASE_3_13 git_last_commit: d2cb3eb git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/MMDiffBamSubset_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MMDiff2 dependencyCount: 0 Package: MOFAdata Version: 1.8.0 Depends: R (>= 3.5) Suggests: knitr, MultiAssayExperiment License: LGPL-3 MD5sum: ab7778dbfb6c294571786475a2da67a7 NeedsCompilation: yes Title: Data package for Multi-Omics Factor Analysis (MOFA) Description: A collection of datasets to accompany the R package MOFA and illustrate running and analysing MOFA models. biocViews: ReproducibleResearch Author: Ricard Argelaguet, Britta Velten, Damien Arnol, Florian Buettner, Wolfgang Huber, Oliver Stegle Maintainer: Britta Velten VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MOFAdata git_branch: RELEASE_3_13 git_last_commit: 8ffc6c6 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/MOFAdata_1.8.0.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 dependencyCount: 0 Package: mosaicsExample Version: 1.30.0 Depends: R (>= 2.11.1) License: GPL (>= 2) MD5sum: b1df94c2fe1e824bee018e8fdb866452 NeedsCompilation: no Title: Example data for the mosaics package, which implements MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data for transcription factor binding and histone modification Description: Data for the mosaics package, consisting of (1) chromosome 22 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding and H3K4me3 modification in MCF7 cell line from ENCODE database (HG19) and (2) chromosome 21 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding, with mappability, GC content, and sequence ambiguity scores of human genome HG18. biocViews: ExperimentData, ChIPseqData, Homo_sapiens Author: Dongjun Chung, Pei Fen Kuan, Rene Welch, Sunduz Keles Maintainer: Dongjun Chung URL: http://groups.google.com/group/mosaics_user_group git_url: https://git.bioconductor.org/packages/mosaicsExample git_branch: RELEASE_3_13 git_last_commit: 6de5929 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/mosaicsExample_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: mosaics dependencyCount: 0 Package: mouse4302barcodevecs Version: 1.30.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 836023a7d2ac8673b5873f5073796199 NeedsCompilation: no Title: mouse4302 data for barcode Description: Data used by the barcode package for microarrays of type mouse4302. biocViews: Mus_musculus_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/mouse4302barcodevecs git_branch: RELEASE_3_13 git_last_commit: 35cfacc git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/mouse4302barcodevecs_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: MouseGastrulationData Version: 1.6.0 Depends: R (>= 4.1), SingleCellExperiment, SummarizedExperiment, SpatialExperiment Imports: methods, ExperimentHub, BiocGenerics, S4Vectors, BumpyMatrix Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 6881df70d5f2a466aeeb9202150ef203 NeedsCompilation: no Title: Single-Cell -omics Data across Mouse Gastrulation and Early Organogenesis Description: Provides processed and raw count data for single-cell RNA sequencing, single-cell ATAC-seq, and seqFISH (spatial transcriptomic) experiments performed along a timecourse of mouse gastrulation and early organogenesis. biocViews: ExperimentData, ExpressionData, SequencingData, RNASeqData, SingleCellData, ExperimentHub, Mus_musculus_Data Author: Jonathan Griffiths [aut, cre], Aaron Lun [aut] Maintainer: Jonathan Griffiths URL: https://github.com/MarioniLab/MouseGastrulationData VignetteBuilder: knitr BugReports: https://github.com/MarioniLab/MouseGastrulationData/issues git_url: https://git.bioconductor.org/packages/MouseGastrulationData git_branch: RELEASE_3_13 git_last_commit: f26215b git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/MouseGastrulationData_1.6.0.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: 125 Package: MouseThymusAgeing Version: 1.0.0 Depends: SingleCellExperiment, SummarizedExperiment Imports: ExperimentHub, methods, BiocGenerics, S4Vectors Suggests: knitr, scuttle, rmarkdown, BiocStyle License: GPL-3 MD5sum: 0d9ab81a7f58e7a49e382a4775d64bd9 NeedsCompilation: no Title: Single-cell Transcriptomics Data of the Ageing Mouse Thymus Description: This package provides data access to counts matrices and meta-data for single-cell RNA sequencing data of thymic epithlial cells across mouse ageing using SMARTseq2 and 10X Genommics chemistries. Access is provided as a data package via ExperimentHub. It is designed to facilitate the re-use of data from Baran-Gale _et al._ in a consistent format that includes relevant and informative meta-data. biocViews: ExperimentHub, SingleCellData, ExpressionData, ExperimentData Author: Mike Morgan [aut, cre], Jeanette Baran-Gale [aut] Maintainer: Mike Morgan VignetteBuilder: knitr BugReports: https://github.com/MarioniLab/MouseThymusAgeing/issues git_url: https://git.bioconductor.org/packages/MouseThymusAgeing git_branch: RELEASE_3_13 git_last_commit: 4ae1ca1 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/MouseThymusAgeing_1.0.0.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 dependencyCount: 97 Package: msd16s Version: 1.12.0 Depends: R (>= 2.10), Biobase, metagenomeSeq, License: Artistic-2.0 MD5sum: 4e39e9f6ea37c1a4efeb1c451a3d9e4f NeedsCompilation: no Title: Healthy and moderate to severe diarrhea 16S expression data Description: Gut 16S sequencing expression data from 992 healthy and moderate-to-severe diarrhetic samples used in 'Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition'. biocViews: ExperimentData, SequencingData, MicrobiomeData Author: Joseph N. Paulson, Hector Corrada Bravo, Mihai Pop Maintainer: Joseph N. Paulson URL: http://www.cbcb.umd.edu/research/projects/GEMS-pathogen-discovery git_url: https://git.bioconductor.org/packages/msd16s git_branch: RELEASE_3_13 git_last_commit: f2d0e1b git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/msd16s_1.12.0.tar.gz vignettes: vignettes/msd16s/inst/doc/msd16s.pdf vignetteTitles: msd16s hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/msd16s/inst/doc/msd16s.R suggestsMe: metavizr dependencyCount: 29 Package: msdata Version: 0.32.0 Depends: R (>= 2.10) Suggests: xcms, mzR, MSnbase License: GPL (>= 2) MD5sum: 64cba6756b2339540648c931e9266741 NeedsCompilation: no Title: Various Mass Spectrometry raw data example files Description: Ion Trap positive ionization mode data in mzData file format. Subset from 500-850 m/z and 1190-1310 seconds, incl. MS2 and MS3, intensity threshold 100.000. Extracts from FTICR Apex III, m/z 400-450. Subset of UPLC - Bruker micrOTOFq data, both mzData, mzML and mz5. LC-MSMS and MRM files from proteomics experiments. PSI mzIdentML example files for various search engines. biocViews: ExperimentData, MassSpectrometryData Author: Steffen Neumann , Laurent Gatto with contriutions from Johannes Rainer Maintainer: Steffen Neumann , Laurent Gatto git_url: https://git.bioconductor.org/packages/msdata git_branch: RELEASE_3_13 git_last_commit: c925f5a git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/msdata_0.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: IPO, MSnbase, msqrob2, mzR, peakPantheR, QFeatures, Spectra, xcms, RforProteomics dependencyCount: 0 Package: msigdb Version: 1.0.0 Depends: R (>= 4.1) Imports: ExperimentHub, utils, GSEABase, org.Mm.eg.db, org.Hs.eg.db, AnnotationDbi, methods, stats Suggests: singscore, vissE, knitr, prettydoc, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocFileCache, GO.db, stringr, limma License: CC BY 4.0 MD5sum: 260abb00c13da2f40d7cc6eda7f73243 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] (), Gordon K. Smyth [aut] (), Alexandra Garnham [aut] () Maintainer: Dharmesh D. Bhuva URL: https://davislaboratory.github.io/msigdb VignetteBuilder: knitr BugReports: https://github.com/DavisLaboratory/msigdb/issues git_url: https://git.bioconductor.org/packages/msigdb git_branch: RELEASE_3_13 git_last_commit: cfd1c7c git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/msigdb_1.0.0.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: vissE dependencyCount: 94 Package: MSMB Version: 1.10.0 Depends: R (>= 2.10) Suggests: knitr, BiocStyle License: LGPL MD5sum: 13b9523ee71397ca41e05e66ceb1a19e NeedsCompilation: no Title: Data sets for the book 'Modern Statistics for Biology' Description: Data sets for the book 'Modern Statistics for Modern Biology', S.P. Holmes and W. Huber. biocViews: ExperimentData, ReproducibleResearch Author: Wolfgang Huber, Andrzej Oles, Mike Smith Maintainer: Wolfgang Huber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MSMB git_branch: RELEASE_3_13 git_last_commit: 2a8dfaf git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/MSMB_1.10.0.tar.gz vignettes: vignettes/MSMB/inst/doc/MSMB.pdf vignetteTitles: Modern Statistics for Modern Biology hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MSMB/inst/doc/MSMB.R dependencyCount: 0 Package: msPurityData Version: 1.20.0 Suggests: knitr License: GPL (>= 2) MD5sum: b07188f6c96da8fef3179159e04087d6 NeedsCompilation: no Title: Fragmentation spectral libraries and data to test the msPurity package Description: Fragmentation spectral libraries and data to test the msPurity package biocViews: ExperimentData, MassSpectrometryData Author: Thomas N. Lawson Maintainer: Thomas N. Lawson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/msPurityData git_branch: RELEASE_3_13 git_last_commit: ea0eb87 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/msPurityData_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: msPurity dependencyCount: 0 Package: msqc1 Version: 1.20.0 Depends: R (>= 3.6), lattice, stats, utils Suggests: BiocStyle, knitr, testthat, specL (>= 1.2) License: GPL MD5sum: 691c20a0e8915634c7866581e62ae214 NeedsCompilation: no Title: Sigma mix MSQC1 data Description: contains eight technical replicate data set and a three replicate dilution series of the MS Qual/Quant Quality Control Mix standard sample (Sigma-Aldrich, Buchs, Switzerland) measured on five different mass spectrometer platforms at the Functional Genomics Center Zurich. biocViews: ExperimentData, MassSpectrometryData, ReproducibleResearch Author: Tobias Kockmann [aut] (), Christian Trachsel [aut], Christian Panse [aut, cre] () Maintainer: Christian Panse URL: https://panoramaweb.org/labkey/MSQC1.url, http://fgcz-bfabric.uzh.ch/bfabric/project.html?projectId=1959 VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/msqc1 git_branch: RELEASE_3_13 git_last_commit: 1d3a3bb git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/msqc1_1.20.0.tar.gz vignettes: vignettes/msqc1/inst/doc/poster.pdf, vignettes/msqc1/inst/doc/chromatography.html, vignettes/msqc1/inst/doc/msqc1.html vignetteTitles: ASMS 2016 poster (in portrait) abstract ID number: 282492, LC Observations - Retention Time Stability, Introducing msqc1 - A Mass Spec Data set for Targeted Proteomics Performance Evaluation hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/msqc1/inst/doc/chromatography.R, vignettes/msqc1/inst/doc/msqc1.R, vignettes/msqc1/inst/doc/poster.R dependencyCount: 6 Package: MSstatsBioData Version: 1.13.0 Depends: R (>= 3.4) Suggests: BiocStyle, knitr, MSstats License: Artistic-2.0 MD5sum: 061e924cf88f01e2e6f29e614e12f30c NeedsCompilation: no Title: Datasets of published biological studies with DDA or SRM experiments Description: Provides the peak intensity data for detecting differentially abundant proteins in seven published biological investigations. biocViews: ExperimentData, MassSpectrometryData, Proteome Author: Meena Choi Maintainer: Meena Choi VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MSstatsBioData git_branch: master git_last_commit: 026711e git_last_commit_date: 2020-10-27 Date/Publication: 2021-03-25 source.ver: src/contrib/MSstatsBioData_1.13.0.tar.gz vignettes: vignettes/MSstatsBioData/inst/doc/MSstatsBioData.html vignetteTitles: MSstatsBioData: Datasets of published biological studies with DDA or SRM experiments hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MSstatsBioData/inst/doc/MSstatsBioData.R suggestsMe: MSstats dependencyCount: 0 Package: mtbls2 Version: 1.22.0 Depends: R (>= 2.10) Suggests: xcms (>= 3.13.8), CAMERA, Risa (>= 1.0.0), knitr, Heatplus, pcaMethods, sp, rmarkdown License: CC0 MD5sum: 35d066f278a7dbfa793e801fa0b737e9 NeedsCompilation: no Title: MetaboLights MTBLS2: Comparative LC/MS-based profiling of silver nitrate-treated Arabidopsis thaliana leaves of wild-type and cyp79B2 cyp79B3 double knockout plants. Böttcher et al. (2004) Description: Indole-3-acetaldoxime (IAOx) represents an early intermediate of the biosynthesis of a variety of indolic secondary metabolites including the phytoanticipin indol-3-ylmethyl glucosinolate and the phytoalexin camalexin (3-thiazol-2'-yl-indole). Arabidopsis thaliana cyp79B2 cyp79B3 double knockout plants are completely impaired in the conversion of tryptophan to indole-3-acetaldoxime and do not accumulate IAOx-derived metabolites any longer. Consequently, comparative analysis of wild-type and cyp79B2 cyp79B3 plant lines has the potential to explore the complete range of IAOx-derived indolic secondary metabolites. biocViews: MassSpectrometryData, RepositoryData Author: Steffen Neumann Maintainer: Steffen Neumann URL: http://www.ebi.ac.uk/metabolights/MTBLS2, https://github.com/sneumann/mtbls2 VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mtbls2 git_branch: RELEASE_3_13 git_last_commit: e1a932b git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/mtbls2_1.22.0.tar.gz vignettes: vignettes/mtbls2/inst/doc/MTBLS2-xcms3.html, vignettes/mtbls2/inst/doc/MTBLS2.html vignetteTitles: MTBLS2 Processing and Analysis with xcms3,, CAMERA and export to MetaboLights, MTBLS2 Processing and Analysis with xcms,, CAMERA and export to MetaboLights hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mtbls2/inst/doc/MTBLS2-xcms3.R, vignettes/mtbls2/inst/doc/MTBLS2.R suggestsMe: Autotuner, IPO, yamss dependencyCount: 0 Package: MUGAExampleData Version: 1.12.0 Depends: R (>= 2.10.0) License: GPL-3 MD5sum: 8ec1d5c8cb7747e5ebaf6b353d3050a8 NeedsCompilation: no Title: Example {M}ouse {U}niversal {G}enotyping {A}rray data for genome reconstruction and quantitative trait locus mapping. Description: This package contains example data for the MUGA array that is used by the R package DOQTL. biocViews: ExperimentData, Mus_musculus_Data Author: Daniel Gatti Maintainer: Daniel Gatti git_url: https://git.bioconductor.org/packages/MUGAExampleData git_branch: RELEASE_3_13 git_last_commit: c599273 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/MUGAExampleData_1.12.0.tar.gz vignettes: vignettes/MUGAExampleData/inst/doc/MUGAExampleData.pdf vignetteTitles: User Manual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MUGAExampleData/inst/doc/MUGAExampleData.R dependencyCount: 0 Package: muscData Version: 1.6.0 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: 5581cdb6ad08c7ccdcc0e78a3073b216 NeedsCompilation: no Title: Multi-sample multi-group scRNA-seq data Description: Data package containing a collection of multi-sample multi-group scRNA-seq datasets in SingleCellExperiment Bioconductor object format. biocViews: ExperimentHub, ExperimentData, ExpressionData, GEO, Homo_sapiens_Data, ImmunoOncologyData, SingleCellData Author: Helena L. Crowell [aut, cre] Maintainer: Helena L. Crowell URL: https://github.com/HelenaLC/muscData VignetteBuilder: knitr BugReports: https://github.com/HelenaLC/muscData/issues git_url: https://git.bioconductor.org/packages/muscData git_branch: RELEASE_3_13 git_last_commit: 57e9161 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/muscData_1.6.0.tar.gz vignettes: vignettes/muscData/inst/doc/muscData.html vignetteTitles: Multi-sample multi-group scRNA-seq data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/muscData/inst/doc/muscData.R suggestsMe: glmGamPoi dependencyCount: 97 Package: mvoutData Version: 1.28.0 Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4), lumi License: Artistic-2.0 MD5sum: 8476aaf7ad4b323c5c35efda3c97b5b2 NeedsCompilation: no Title: affy and illumina raw data for assessing outlier detector performance Description: affy and illumina raw data for assessing outlier detector performance biocViews: ExperimentData, MicroarrayData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/mvoutData git_branch: RELEASE_3_13 git_last_commit: d96b842 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/mvoutData_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayMvout dependencyCount: 160 Package: NanoporeRNASeq Version: 1.2.1 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: 9b1fac0b68ad420da57bafed64451833 NeedsCompilation: no Title: Nanopore RNA-Seq Example data Description: The NanoporeRNASeq package contains long read RNA-Seq data generated using Oxford Nanopore Sequencing. The data consists of 6 samples from two human cell lines (K562 and MCF7) that were generated by the SG-NEx project. Each of these cell lines has three replicates, with 1 direct RNA sequencing data and 2 cDNA sequencing data. Reads are aligned to chromosome 22 (Grch38) and stored as bam files. The original data is from the SG-NEx project. biocViews: ExperimentHub, ExperimentData, RNASeqData, Genome, SequencingData Author: Jonathan Goeke Developer [aut], Ying Chen Developer [cre], Yuk Kei Wan Developer [aut] Maintainer: Ying Chen Developer URL: https://github.com/GoekeLab/NanoporeRNASeq VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/NanoporeRNASeq git_branch: RELEASE_3_13 git_last_commit: 8b3a7a0 git_last_commit_date: 2021-07-03 Date/Publication: 2021-07-06 source.ver: src/contrib/NanoporeRNASeq_1.2.1.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: 88 Package: nanotubes Version: 1.8.0 Depends: R (>= 3.6) Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, rtracklayer, CAGEfightR License: GPL-3 MD5sum: c412bd43bd75d8d69759ff593b44ed9b NeedsCompilation: no Title: Mouse nanotube CAGE data Description: Cap Analysis of Gene Expression (CAGE) data from "Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo" by Bornholdt et al. supplied as CAGE Transcription Start Sites (CTSSs). biocViews: ExperimentData, SequencingData, ExpressionData Author: Malte Thodberg Maintainer: Malte Thodberg URL: https://github.com/MalteThodberg/nanotubes VignetteBuilder: knitr BugReports: https://github.com/MalteThodberg/nanotubes/issues git_url: https://git.bioconductor.org/packages/nanotubes git_branch: RELEASE_3_13 git_last_commit: f92ca90 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/nanotubes_1.8.0.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: 1.28.0 Depends: R (>= 2.10.0) Suggests: Rgraphviz License: GPL-3 MD5sum: 5e2a390ae372976c610793f05c884ee2 NeedsCompilation: no Title: Data for the NCIgraph software package Description: Provides pathways from the NCI Pathways Database as R graph objects biocViews: NCI Author: Laurent Jacob Maintainer: Laurent Jacob git_url: https://git.bioconductor.org/packages/NCIgraphData git_branch: RELEASE_3_13 git_last_commit: 3b4dd42 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/NCIgraphData_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: NestLink Version: 1.8.0 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: 2525f38fadb7aca8f11f730765eb6603 NeedsCompilation: no Title: NestLink an R data package to guide through Engineered Peptide Barcodes for In-Depth Analyzes of Binding Protein Ensembles Description: Provides next-generation sequencing (NGS) and mass spectrometry (MS) sample data, code snippets and replication material used for developing NestLink. The NestLink approach is a protein binder selection and identification technology able to biophysically characterize thousands of library members at once without handling individual clones at any stage of the process. Data were acquired on NGS and MS platforms at the Functional Genomics Center Zurich. biocViews: ExperimentHub, ExperimentData, SequencingData, MassSpectrometryData, ReproducibleResearch Author: Pascal Egloff [aut] (), Iwan Zimmermann [ctb] (), Fabian M. Arnold [ctb], Cedric A.J. Hutter [ctb] (), Lennart Opitz [aut, cre] (), Lucy Poveda [ctb] (), Hans-Anton Keserue [ctb], Christian Panse [aut, ctb] (), Bernd Roschitzki [aut] (), Markus Seeger [aut] () Maintainer: Lennart Opitz VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/NestLink git_branch: RELEASE_3_13 git_last_commit: e3a3aee git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/NestLink_1.8.0.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: 116 Package: Neve2006 Version: 0.30.0 Depends: R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0), hgu133a.db, annotate License: Artistic-2.0 MD5sum: d643125284b67918662218f0e997cafd NeedsCompilation: no Title: expression and CGH data on breast cancer cell lines Description: Experimental organization of combined expression and CGH data biocViews: ExperimentData, CancerData, BreastCancerData Author: M. Neve et al. in Gray Lab at LBL Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/Neve2006 git_branch: RELEASE_3_13 git_last_commit: b141c19 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/Neve2006_0.30.0.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: 1.12.0 License: GPL (>=2) MD5sum: 8cc4c62a16a98fe9ccb543db89b038ec NeedsCompilation: no Title: Subset of BAM files of human tumor and pooled normal sequencing data (Zhao et al. 2014) for the NGScopy package Description: Subset of BAM files of human lung tumor and pooled normal samples by targeted panel sequencing. [Zhao et al 2014. Targeted Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using the University of North Carolina (UNC) Sequencing Assay Captures Most Previously Described Genetic Aberrations in NSCLC. In preparation.] Each sample is a 10 percent random subsample drawn from the original sequencing data. The pooled normal sample has been rescaled accroding to the total number of normal samples in the "pool". Here provided is the subsampled data on chr6 (hg19). biocViews: ExperimentData, CancerData, LungCancerData, SequencingData Author: Xiaobei Zhao [aut, cre, cph] Maintainer: Xiaobei Zhao URL: http://www.bioconductor.org/packages/release/data/experiment/html/NGScopyData.html git_url: https://git.bioconductor.org/packages/NGScopyData git_branch: RELEASE_3_13 git_last_commit: 8b87483 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/NGScopyData_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: ObMiTi Version: 1.0.0 Depends: R (>= 4.1), SummarizedExperiment, ExperimentHub Suggests: knitr, rmarkdown, BiocManager, GenomicFeatures, S4Vectors, devtools, testthat License: GPL-3 MD5sum: c0f2faa296119c8a3b070f991f4ab4f6 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 12 weeks in 7 tissues. biocViews: ExperimentHub, GEO, RNASeqData Author: Omar Elashkar [aut, cre] (), Mahmoud Ahmed [aut] () Maintainer: Omar Elashkar URL: https://github.com/OmarElAshkar/ObMiTi VignetteBuilder: knitr BugReports: https://github.com/OmarElAshkar/ObMiTi/issues git_url: https://git.bioconductor.org/packages/ObMiTi git_branch: RELEASE_3_13 git_last_commit: 917898f git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ObMiTi_1.0.0.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: 96 Package: oct4 Version: 1.8.0 Suggests: knitr, markdown License: GPL (>= 2) MD5sum: 7154d632f42a0690a229964e57103edb NeedsCompilation: no Title: Conditional knockdown of OCT4 in mouse ESCs Description: This package provides the output of running Salmon on a set of 12 RNA-seq samples from King & Klose, "The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells", published in eLIFE, March 2017. For details on version numbers and how the samples were processed see the package vignette. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/oct4 git_branch: RELEASE_3_13 git_last_commit: 4f8be12 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/oct4_1.8.0.tar.gz vignettes: vignettes/oct4/inst/doc/oct4.html vignetteTitles: Salmon quantifications for condition OCT4 knockdown in mouse ESCs hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/oct4/inst/doc/oct4.R dependencyCount: 0 Package: OMICsPCAdata Version: 1.10.0 Depends: R (>= 3.5.0), MultiAssayExperiment Suggests: knitr, kableExtra, rmarkdown License: GPL-3 MD5sum: 2f37a7d97a6618bc1ffe640114508f68 NeedsCompilation: no Title: Supporting data for package OMICsPCA Description: Supporting data for package OMICsPCA biocViews: RepositoryData, TechnologyData, ChIPSeqData, SequencingData, ExpressionData, ENCODE Author: Subhadeep Das Maintainer: Subhadeep Das VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/OMICsPCAdata git_branch: RELEASE_3_13 git_last_commit: e5f0199 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/OMICsPCAdata_1.10.0.tar.gz vignettes: vignettes/OMICsPCAdata/inst/doc/vignettes.html vignetteTitles: OMICsPCAdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/OMICsPCAdata/inst/doc/vignettes.R dependsOnMe: OMICsPCA dependencyCount: 47 Package: OnassisJavaLibs Version: 1.14.0 Depends: R (>= 3.4) Imports: rJava Suggests: BiocStyle, rmarkdown, knitr License: GPL-2 MD5sum: 6d9f047237911f8d1b76ae4a10db14aa NeedsCompilation: no Title: OnassisJavaLibs, java libraries to run conceptmapper and semantic similarity Description: A package that contains java libraries to call conceptmapper and compute semnatic similarity from R biocViews: ExperimentData Author: Eugenia Galeota Maintainer: Eugenia Galeota SystemRequirements: Java (>= 1.8) VignetteBuilder: rmarkdown, knitr git_url: https://git.bioconductor.org/packages/OnassisJavaLibs git_branch: RELEASE_3_13 git_last_commit: 0ea7a6f git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/OnassisJavaLibs_1.14.0.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: 1.4.0 Depends: R (>= 4.0) Suggests: knitr, BiocStyle, rmarkdown, magick License: Artistic-2.0 MD5sum: a8cc4f07e340a558f5990c33353df230 NeedsCompilation: no Title: optimalFlowData Description: Data files used as examples and for testing of the software provided in the optimalFlow package. biocViews: ExperimentData, PackageTypeData, ImmunoOncologyData, FlowCytometryData Author: Hristo Inouzhe Maintainer: Hristo Inouzhe VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/optimalFlowData git_branch: RELEASE_3_13 git_last_commit: 82c6207 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/optimalFlowData_1.4.0.tar.gz vignettes: vignettes/optimalFlowData/inst/doc/optimalFlowData_vignette.html vignetteTitles: optimalFlow: optimal-transport approach to Flow Cytometry analysis hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/optimalFlowData/inst/doc/optimalFlowData_vignette.R dependsOnMe: optimalFlow dependencyCount: 0 Package: parathyroidSE Version: 1.30.0 Depends: SummarizedExperiment, R (>= 2.10) Suggests: Rsamtools, GenomicAlignments, GEOquery, SRAdb, GenomicFeatures, BiocStyle License: LGPL MD5sum: 43a65e8c4bd83e469a201c4a1564074a NeedsCompilation: no Title: RangedSummarizedExperiment for RNA-Seq of primary cultures of parathyroid tumors by Haglund et al., J Clin Endocrinol Metab 2012. Description: This package provides RangedSummarizedExperiment objects of read counts in genes and exonic parts for paired-end RNA-Seq data from experiments on primary cultures of parathyroid tumors. The data were presented in the article "Evidence of a Functional Estrogen Receptor in Parathyroid Adenomas" by Haglund F, Ma R, Huss M, Sulaiman L, Lu M, Nilsson IL, Hoog A, Juhlin CC, Hartman J, Larsson C, J Clin Endocrinol Metab. jc.2012-2484, Epub 2012 Sep 28, PMID: 23024189. The sequencing was performed on tumor cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control). One control sample was omitted by the paper authors due to low quality. The package vignette describes the creation of the object from raw sequencing data provided by NCBI Gene Expression Omnibus under accession number GSE37211. The gene and exon features are the GRCh37 Ensembl annotations. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love git_url: https://git.bioconductor.org/packages/parathyroidSE git_branch: RELEASE_3_13 git_last_commit: 778fd9d git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/parathyroidSE_1.30.0.tar.gz vignettes: vignettes/parathyroidSE/inst/doc/parathyroidSE.pdf vignetteTitles: parathyroidGenesSE hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/parathyroidSE/inst/doc/parathyroidSE.R suggestsMe: ClassifyR, DEXSeq dependencyCount: 26 Package: pasilla Version: 1.20.0 Depends: R (>= 3.3.0) Suggests: DEXSeq, rmarkdown, BiocStyle, knitr License: LGPL MD5sum: 1dd4c7c4c3120ed33e2ab0a4a498a32f NeedsCompilation: no Title: Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011. Description: This package provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in the article "Conservation of an RNA regulatory map between Drosophila and mammals" by Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR, Genome Res. 2011 Feb;21(2):193-202, Epub 2010 Oct 4, PMID: 20921232. The experiment studied the effect of RNAi knockdown of Pasilla, the Drosophila melanogaster ortholog of mammalian NOVA1 and NOVA2, on the transcriptome. The package vignette describes how the data provided here were derived from the RNA-Seq read sequence data that are provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. biocViews: ExperimentData, Genome, Drosophila_melanogaster_Data, RNASeqData Author: Wolfgang Huber, Alejandro Reyes Maintainer: Alejandro Reyes VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/pasilla git_branch: RELEASE_3_13 git_last_commit: db2121e git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/pasilla_1.20.0.tar.gz vignettes: vignettes/pasilla/inst/doc/create_objects.html vignetteTitles: "Data preprocessing and creation of the data objects pasillaGenes and pasillaExons" hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pasilla/inst/doc/create_objects.R importsMe: blacksheepr suggestsMe: BADER, DESeq2, DEXSeq, EnhancedVolcano, regionReport, ReportingTools, tidybulk, pasillaBamSubset dependencyCount: 0 Package: pasillaBamSubset Version: 0.30.0 Suggests: pasilla License: LGPL MD5sum: 63ee14564613fbb3f6562d46581b4ee6 NeedsCompilation: no Title: Subset of BAM files from "Pasilla" experiment Description: Subset of BAM files untreated1.bam (single-end reads) and untreated3.bam (paired-end reads) from "Pasilla" experiment (Pasilla knock-down by Brooks et al., Genome Research 2011). See the vignette in the pasilla data package for how BAM files untreated1.bam and untreated3.bam were obtained from the RNA-Seq read sequence data that is provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. Also contains the DNA sequence for fly chromosome 4 to which the reads can be mapped. biocViews: ExperimentData, Genome, DNASeqData, RNASeqData Author: Hervé Pagès Maintainer: Hervé Pagès git_url: https://git.bioconductor.org/packages/pasillaBamSubset git_branch: RELEASE_3_13 git_last_commit: f636417 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/pasillaBamSubset_0.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: APAlyzer, GenomicAlignments, GenomicFeatures, GenomicRanges, gmoviz, IRanges, karyoploteR, plyranges, TransView dependencyCount: 0 Package: PasillaTranscriptExpr Version: 1.20.0 Depends: R (>= 3.3.0) Suggests: rtracklayer, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: f8aa49aa589adcf28c73e443d399aaed NeedsCompilation: no Title: Data package with transcript expression obtained with kallisto from pasilla knock-down RNA-Seq data from Brooks et al. Description: Provides kallisto workflow and transcript expression of RNA-Seq data from Brooks et al. biocViews: Drosophila_melanogaster_Data, Genome, RNASeqData, ExperimentData, SequencingData, ExpressionData, GEO Author: Malgorzata Nowicka [aut, cre] Maintainer: Malgorzata Nowicka VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/PasillaTranscriptExpr git_branch: RELEASE_3_13 git_last_commit: 9c046fe git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/PasillaTranscriptExpr_1.20.0.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: 1.28.0 Depends: R (>= 1.14.0) License: GPL-3 MD5sum: 539da46f1b33c24aaffcd73bea1ee8c2 NeedsCompilation: no Title: Experimental data for the PathNet package Description: This package contains the data employed in the vignette of the PathNet package. These data belong to the following publication: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J., Source Code for Biology and Medicine 2012 Sep 24;7(1):10. biocViews: ExperimentData, PathwayInteractionDatabase Author: Bhaskar Dutta , Anders Wallqvist , and Jaques Reifman Maintainer: Ludwig Geistlinger git_url: https://git.bioconductor.org/packages/PathNetData git_branch: RELEASE_3_13 git_last_commit: 3eb61b2 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/PathNetData_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PathNet dependencyCount: 0 Package: PCHiCdata Version: 1.20.0 Depends: R (>= 3.2), Chicago Suggests: testthat, BiocStyle, knitr License: Artistic-2.0 MD5sum: 334fe6c44943e265f179a4cbbb8ee271 NeedsCompilation: no Title: Promoter Capture Hi-C data Description: Subsets of Promoter Capture Hi-C data conveniently packaged for Chicago users. Data includes interactions detected for chromosomes 20 and 21 in GM12878 cells and for chromosomes 18 and 19 in mESC. biocViews: ExperimentData, SequencingData, Homo_sapiens_Data, Mus_musculus_Data, StemCell Author: Paula Freire-Pritchett, Jonathan Cairns, Steven Wingett, Mikhail Spivakov Maintainer: Paula Freire-Pritchett VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/PCHiCdata git_branch: RELEASE_3_13 git_last_commit: 4eccdc9 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/PCHiCdata_1.20.0.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: 71 Package: pcxnData Version: 2.14.0 Depends: R (>= 3.4) Suggests: pcxn License: MIT + file LICENSE MD5sum: 295e1d6d525813829a865061934ee45d NeedsCompilation: no Title: Correlation coefficients and p values between pre-defined pathway/gene sets Description: PCxN database contains correlation coefficients and p values between pre-defined gene sets within MSigDB H hallmark gene sets, MSigDB C2 CP (Canonical pathways), MSigDB C5 GO BP gene sets and Pathprint respectively, as well as adjusted pathway correlations to account for the shared genes between pathway pairs. biocViews: ExperimentData, ExpressionData, MicroarrayData, GEO, Homo_sapiens_Data, OneChannelData, PathwayInteractionDatabase Author: Sokratis Kariotis, Yered Pita-Juarez, Wenbin Wei, Winston Hide Maintainer: Sokratis Kariotis git_url: https://git.bioconductor.org/packages/pcxnData git_branch: RELEASE_3_13 git_last_commit: 9a6ca1b git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/pcxnData_2.14.0.tar.gz vignettes: vignettes/pcxnData/inst/doc/usingpcxnData.pdf vignetteTitles: pcxnData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/pcxnData/inst/doc/usingpcxnData.R dependsOnMe: pcxn dependencyCount: 0 Package: pd.atdschip.tiling Version: 0.30.0 Depends: R (>= 2.14.0), methods, RSQLite (>= 0.10.0), oligoClasses (>= 1.15.58), oligo (>= 1.17.3), DBI Imports: Biostrings (>= 2.21.11), IRanges (>= 1.11.31), S4Vectors License: Artistic-2.0 MD5sum: 097e91ac8b4eb5ce360c67d3e429b5bc NeedsCompilation: no Title: Platform Design Info for Affymetrix Atdschip_tiling Description: Platform Design Info for Affymetrix Atdschip_tiling biocViews: Arabidopsis_thaliana_Data, MicroarrayData, SNPData Author: Kristof De Beuf Maintainer: Kristof De Beuf git_url: https://git.bioconductor.org/packages/pd.atdschip.tiling git_branch: RELEASE_3_13 git_last_commit: 99e327d git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/pd.atdschip.tiling_0.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 54 Package: pepDat Version: 1.12.0 Depends: R(>= 3.0.0) Imports: GenomicRanges Suggests: knitr License: Artistic-2.0 MD5sum: 9b9daf371467cbfeecd21beda27c88d5 NeedsCompilation: no Title: Peptide microarray data package Description: Provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV. biocViews: MicroarrayData Author: Renan Sauteraud, Raphael Gottardo Maintainer: Renan Sauteraud VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/pepDat git_branch: RELEASE_3_13 git_last_commit: 02f73f0 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/pepDat_1.12.0.tar.gz vignettes: vignettes/pepDat/inst/doc/pepDat.pdf vignetteTitles: The pepDat users guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pepDat/inst/doc/pepDat.R suggestsMe: pepStat, Pviz dependencyCount: 17 Package: PepsNMRData Version: 1.10.0 Depends: R (>= 3.5) Suggests: knitr, markdown, rmarkdown, BiocStyle License: GPL-2 | file LICENSE MD5sum: d83160d0ca9a97deda2b68f4abe0c9d7 NeedsCompilation: no Title: Datasets for the PepsNMR package Description: This package contains all the datasets used in the PepsNMR package. biocViews: ExperimentData, OrganismData, Homo_sapiens_Data Author: Manon Martin [aut, cre], Bernadette Govaerts [aut, ths], Pascal de Tullio [dtc] Maintainer: Manon Martin BugReports: https://github.com/ManonMartin/PepsNMRData/issues git_url: https://git.bioconductor.org/packages/PepsNMRData git_branch: RELEASE_3_13 git_last_commit: 5af38f0 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/PepsNMRData_1.10.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: PepsNMR dependencyCount: 0 Package: PhyloProfileData Version: 1.6.1 Depends: R (>= 4.1.0) Imports: ExperimentHub, Biostrings, BiocStyle Suggests: knitr, rmarkdown, markdown License: MIT + file LICENSE MD5sum: e41b7f872ac91b570675c7f9d7b5b45c 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: RELEASE_3_13 git_last_commit: 78e6f1f git_last_commit_date: 2021-06-29 Date/Publication: 2021-07-01 source.ver: src/contrib/PhyloProfileData_1.6.1.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: 98 Package: plasFIA Version: 1.20.0 Depends: proFIA License: LGPL MD5sum: fdfdb217041525938b240e1a87bef200 NeedsCompilation: no Title: FIA-HRMS plasma dataset Description: Positive Ionization FIA-HRMS data of human plasma spiked with a pool of 40 compounds acquired in FIA-HRMS mode on an orbitrap fusion. plasFIA also include the result of the processing by the proFIA package with adapted parameters for an Orbitrap Fusion. biocViews: ExperimentData, MassSpectrometryData Author: Alexis Delabriere, Etienne Thevenot, Ulli Hohenester and Christophe Junot. Maintainer: Alexis Delabriere git_url: https://git.bioconductor.org/packages/plasFIA git_branch: RELEASE_3_13 git_last_commit: 1012776 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/plasFIA_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: proFIA dependencyCount: 105 Package: ppiData Version: 0.30.0 Depends: graph Imports: AnnotationDbi Suggests: org.Sc.sgd.db, ppiStats License: Artistic-2.0 MD5sum: f75077fc98b27962137a970e0e09a021 NeedsCompilation: no Title: A package that contains the bait to prey directed graphs for protein-protein interactions. Description: This package contains the directed graphs for protein interaction data as derived from Y2H and APMS as well as the code used to obtain the y2h data from IntAct Repository. biocViews: ExperimentData Author: Tony Chiang Maintainer: Bioconductor Package Maintainer git_url: https://git.bioconductor.org/packages/ppiData git_branch: RELEASE_3_13 git_last_commit: 3ae652d git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ppiData_0.30.0.tar.gz vignettes: vignettes/ppiData/inst/doc/ppiData.pdf vignetteTitles: Using the package ppiStats hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ppiData/inst/doc/ppiData.R dependsOnMe: ppiStats suggestsMe: ScISI dependencyCount: 47 Package: prebsdata Version: 1.28.0 Depends: R (>= 2.14.0) License: Artistic-2.0 MD5sum: 725ae22138fb53ed6f13b0e4278ecd21 NeedsCompilation: no Title: Data for 'prebs' package Description: This package contains data required to run examples in 'prebs' package. The data files include: 1) Small sample bam files for demonstration purposes 2) Probe sequence mappings for Custom CDF (taken from http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp) 3) Probe sequence mappings for manufacturer's CDF (manually created using bowtie) biocViews: ExperimentData, SequencingData, RNASeqData Author: Karolis Uziela and Antti Honkela Maintainer: Karolis Uziela git_url: https://git.bioconductor.org/packages/prebsdata git_branch: RELEASE_3_13 git_last_commit: 5c30e81 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/prebsdata_1.28.0.tar.gz vignettes: vignettes/prebsdata/inst/doc/prebsdata.pdf vignetteTitles: prebsdata User Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: prebs, SigFuge dependencyCount: 0 Package: preciseTADhub Version: 1.0.0 Depends: R (>= 4.1) Imports: ExperimentHub Suggests: knitr, rmarkdown, BiocStyle, preciseTAD License: MIT + file LICENSE MD5sum: a9c95b1be4fc7fe9bf94417954c6dc7c 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, cre], Mikhail Dozmorov [aut] Maintainer: Spiro Stilianoudakis URL: https://github.com/dozmorovlab/preciseTADhub VignetteBuilder: knitr BugReports: https://github.com/dozmorovlab/preciseTADhub/issues git_url: https://git.bioconductor.org/packages/preciseTADhub git_branch: RELEASE_3_13 git_last_commit: 467a789 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/preciseTADhub_1.0.0.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: 88 Package: PREDAsampledata Version: 0.32.0 Depends: R (>= 2.10.0), methods, PREDA, Biobase, affy, annotate Suggests: hgu133plus2.db, hgu133plus2cdf License: Artistic-2.0 MD5sum: f6156cdca052b6c263a249fc6307cefa NeedsCompilation: no Title: expression and copy number data on clear cell renal carcinoma samples Description: Sample data for PREDA package. (annotations objects synchronized with GeneAnnot custom CDFs version 2.2.0) biocViews: ExperimentData, Tissue, CancerData, KidneyCancerData, MicroarrayData, TissueMicroarrayData, ArrayExpress Author: I. Cifola et al. in Cristina Battaglia Lab, University of Milan Maintainer: Francesco Ferrari git_url: https://git.bioconductor.org/packages/PREDAsampledata git_branch: RELEASE_3_13 git_last_commit: 747f27f git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/PREDAsampledata_0.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PREDA dependencyCount: 63 Package: ProData Version: 1.30.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL MD5sum: fc962fa7d85a3b492ed8d68dc496a1b9 NeedsCompilation: no Title: SELDI-TOF data of Breast cancer samples Description: A data package of SELDI-TOF protein mass spectrometry data of 167 breast cancer and normal samples. biocViews: ExperimentData, CancerData, BreastCancerData, MassSpectrometryData, NCI Author: Xiaochun Li Maintainer: Xiaochun Li git_url: https://git.bioconductor.org/packages/ProData git_branch: RELEASE_3_13 git_last_commit: bf5b143 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ProData_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CorrectedFDR dependencyCount: 7 Package: pRolocdata Version: 1.30.0 Depends: R (>= 3.6.3), MSnbase Imports: Biobase, utils Suggests: pRoloc (>= 1.13.8), testthat License: GPL-2 MD5sum: 0d6a71aad496d2846057c1432b210797 NeedsCompilation: no Title: Data accompanying the pRoloc package Description: Mass-spectrometry based spatial proteomics data sets and protein complex separation data. Also contains the time course expression experiment from Mulvey et al. 2015. biocViews: ExperimentData, Homo_sapiens_Data, MassSpectrometryData, Arabidopsis_thaliana_Data, Drosophila_melanogaster_Data, Mus_musculus_Data, StemCell, Proteome Author: Laurent Gatto, Oliver M. Crook and Lisa M. Breckels Maintainer: Laurent Gatto URL: https://github.com/lgatto/pRolocdata BugReports: https://github.com/lgatto/pRolocdata/issues git_url: https://git.bioconductor.org/packages/pRolocdata git_branch: RELEASE_3_13 git_last_commit: 2db8c63 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/pRolocdata_1.30.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: proteomics suggestsMe: MSnbase, pRoloc, pRolocGUI, RforProteomics dependencyCount: 77 Package: prostateCancerCamcap Version: 1.20.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: d76a598e09b359a94cb7ac351ffe566b NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Ross-Adams (2015) Prostate Cancer dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerCamcap git_branch: RELEASE_3_13 git_last_commit: 7f4412b git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/prostateCancerCamcap_1.20.0.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: 1.20.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: c6b0297e0033928232e407861563b95b NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Grasso (2012) Prostate Cancer dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerGrasso git_branch: RELEASE_3_13 git_last_commit: caed370 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/prostateCancerGrasso_1.20.0.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: 1.20.0 Depends: Biobase , R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 7f4f8d5c66ad0e7bd09337b2bf547b05 NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Stockholm dataset biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerStockholm git_branch: RELEASE_3_13 git_last_commit: f9ba354 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/prostateCancerStockholm_1.20.0.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: 1.20.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery, org.Hs.eg.db License: Artistic-2.0 MD5sum: 92d78ac6ed9a72ddc6c68373b6301d90 NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Taylor et al (2010) dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerTaylor git_branch: RELEASE_3_13 git_last_commit: ddd1eac git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/prostateCancerTaylor_1.20.0.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: 1.20.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 5f1de9b92392c6f21e8ebaec9f5067c9 NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Varambally dataset biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerVarambally git_branch: RELEASE_3_13 git_last_commit: 48ef870 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/prostateCancerVarambally_1.20.0.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: ptairData Version: 1.0.1 Imports: rhdf5, signal, stats, graphics Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 8680e8d6b82d747910bb637f43966bd4 NeedsCompilation: no Title: PTR-TOF-MS volatolomics raw datasets from exhaled air and cell culture headspace Description: The package ptairData contains two raw datasets from Proton-Transfer-Reaction Time-of-Flight mass spectrometer acquisitions (PTR-TOF-MS), in the HDF5 format. One from the exhaled air of two volunteer healthy individuals with three replicates, and one from the cell culture headspace from two mycobacteria species and one control (culture medium only) with two replicates. Those datasets are used in the examples and in the vignette of the ptairMS package (PTR-TOF-MS data pre-processing). There are also used to gererate the ptrSet in the ptairMS data : exhaledPtrset and mycobacteriaSet biocViews: ExperimentData, MassSpectrometryData, CellCulture Author: camille Roquencourt [aut, cre] Maintainer: camille Roquencourt VignetteBuilder: knitr BugReports: https://github.com/camilleroquencourt/ptairData/issues git_url: https://git.bioconductor.org/packages/ptairData git_branch: RELEASE_3_13 git_last_commit: 166f440 git_last_commit_date: 2021-09-20 Date/Publication: 2021-09-21 source.ver: src/contrib/ptairData_1.0.1.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: 1.18.0 Depends: R (>= 3.3), xcms, CAMERA, LOBSTAHS, methods, utils Suggests: gplots, RColorBrewer, cluster, vegan, clustsig License: MIT + file LICENSE MD5sum: cc37c45f5bf2c2016283a9577872f53d NeedsCompilation: no Title: P. tricornutum HPLC-ESI-MS Lipid Data from van Creveld et al. (2015) Description: Annotated HPLC-ESI-MS lipid data in positive ionization mode from an experiment in which cultures of the marine diatom Phaeodactylum tricornutum were treated with various concentrations of hydrogen peroxide (H2O2) to induce oxidative stress. The experiment is described in Graff van Creveld, et al., 2015, "Early perturbation in mitochondria redox homeostasis in response to environmental stress predicts cell fate in diatoms," ISME Journal 9:385-395. PtH2O2lipids consists of two objects: A CAMERA xsAnnotate object (ptH2O2lipids$xsAnnotate) and LOBSTAHS LOBSet object (ptH2O2lipids$xsAnnotate$LOBSet). The LOBSet includes putative compound assignments from the default LOBSTAHS database. Isomer annotation is recorded in three other LOBSet slots. biocViews: ReproducibleResearch, CellCulture, MassSpectrometryData, Phaeodactylum_tricornutum_data Author: Shiri Graff van Creveld [aut], Shilo Rosenwasser [aut], Daniella Schatz [aut], Ilan Koren [aut], Assaf Vardi [aut], James Collins [cre] Maintainer: James Collins URL: http://dx.doi.org/10.1038/ismej.2014.136, https://github.com/vanmooylipidomics/PtH2O2lipids, http://www.whoi.edu/page.do?pid=133616&tid=282&cid=192529 BugReports: https://github.com/vanmooylipidomics/PtH2O2lipids/issues/new git_url: https://git.bioconductor.org/packages/PtH2O2lipids git_branch: RELEASE_3_13 git_last_commit: 663e113 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/PtH2O2lipids_1.18.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: LOBSTAHS dependencyCount: 127 Package: pumadata Version: 2.28.0 Depends: R (>= 3.2.0), Biobase (>= 2.5.5),puma, oligo(>= 1.32.0) License: LGPL MD5sum: 4c397d3f3274f16c929c515ad9b51a2e NeedsCompilation: no Title: Various data sets for use with the puma package Description: This is a simple data package including various data sets derived from the estrogen data for use with the puma (Propagating Uncertainty in Microarray Analysis) package. biocViews: ExperimentData, MicroarrayData, SNPData Author: Richard Pearson Maintainer: Xuejun liu URL: http://umber.sbs.man.ac.uk/resources/puma git_url: https://git.bioconductor.org/packages/pumadata git_branch: RELEASE_3_13 git_last_commit: a5f91b6 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/pumadata_2.28.0.tar.gz vignettes: vignettes/pumadata/inst/doc/pumadata.pdf vignetteTitles: pumadata User Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pumadata/inst/doc/pumadata.R suggestsMe: puma dependencyCount: 57 Package: PWMEnrich.Dmelanogaster.background Version: 4.26.1 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: b3788300eccf983ff93737f2e575f409 NeedsCompilation: no Title: D. melanogaster background for PWMEnrich Description: PWMEnrich pre-compiled background objects for Drosophila melanogaster and MotifDb D. melanogaster motifs. biocViews: Drosophila_melanogaster_Data Author: Robert Stojnic Maintainer: Diego Diez git_url: https://git.bioconductor.org/packages/PWMEnrich.Dmelanogaster.background git_branch: RELEASE_3_13 git_last_commit: a61fc38 git_last_commit_date: 2021-05-25 Date/Publication: 2021-05-27 source.ver: src/contrib/PWMEnrich.Dmelanogaster.background_4.26.1.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 25 Package: PWMEnrich.Hsapiens.background Version: 4.26.1 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: 79d6a76de9432619543db88811e51613 NeedsCompilation: no Title: H. sapiens background for PWMEnrich Description: PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs. biocViews: Homo_sapiens_Data, CGHData Author: Robert Stojnic Maintainer: Diego Diez git_url: https://git.bioconductor.org/packages/PWMEnrich.Hsapiens.background git_branch: RELEASE_3_13 git_last_commit: 87b8fa8 git_last_commit_date: 2021-05-25 Date/Publication: 2021-05-27 source.ver: src/contrib/PWMEnrich.Hsapiens.background_4.26.1.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 25 Package: PWMEnrich.Mmusculus.background Version: 4.26.1 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: fb6c2acbf757ccc8e8079d4d6782b694 NeedsCompilation: no Title: M. musculus background for PWMEnrich Description: PWMEnrich pre-compiled background objects for M.musculus (mouse) and MotifDb M. musculus motifs. biocViews: Mus_musculus_Data Author: Robert Stojnic Maintainer: Diego Diez git_url: https://git.bioconductor.org/packages/PWMEnrich.Mmusculus.background git_branch: RELEASE_3_13 git_last_commit: 01e8132 git_last_commit_date: 2021-05-25 Date/Publication: 2021-05-27 source.ver: src/contrib/PWMEnrich.Mmusculus.background_4.26.1.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 25 Package: pwrEWAS.data Version: 1.6.0 Imports: ExperimentHub Suggests: knitr, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 184d3e18c60bdc0369167465e92177c2 NeedsCompilation: no Title: pwrEWAS.data: Reference data accompanying pwrEWAS Description: This package provides reference data required for pwrEWAS. pwrEWAS is a user-friendly tool to estimate power in EWAS as a function of sample and effect size for two-group comparisons of DNAm (e.g., case vs control, exposed vs non-exposed, etc.). biocViews: ExperimentHub, MethylationArrayData, MicroarrayData, TissueMicroarrayData, Tissue Author: Stefan Graw Maintainer: Stefan Graw VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/pwrEWAS.data git_branch: RELEASE_3_13 git_last_commit: a36a8df git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/pwrEWAS.data_1.6.0.tar.gz vignettes: vignettes/pwrEWAS.data/inst/doc/pwrEWAS.data.pdf vignetteTitles: pwrEWAS.data: Reference data accompanying pwrEWAS hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: pwrEWAS dependencyCount: 88 Package: QDNAseq.hg19 Version: 1.22.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: 21c64a0e2256a1318342d1682b35e132 NeedsCompilation: no Title: QDNAseq bin annotation for hg19 Description: This package provides QDNAseq bin annotations for the human genome build hg19. biocViews: ExperimentData, OrganismData, Homo_sapiens_Data Author: Daoud Sie [aut, cre] Maintainer: Daoud Sie URL: https://github.com/tgac-vumc/QDNAseq.hg19 BugReports: https://github.com/tgac-vumc/QDNAseq.hg19/issues git_url: https://git.bioconductor.org/packages/QDNAseq.hg19 git_branch: RELEASE_3_13 git_last_commit: 62ef9a5 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/QDNAseq.hg19_1.22.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: biscuiteer, QDNAseq dependencyCount: 49 Package: QDNAseq.mm10 Version: 1.22.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: 65233c43c1471b136ffff6a001e1e17f NeedsCompilation: no Title: Bin annotation mm10 Description: This package provides QDNAseq bin annotations for the mouse genome build mm10. biocViews: ExperimentData, OrganismData, Mus_musculus_Data Author: Daoud Sie [aut, cre] Maintainer: Daoud Sie URL: https://github.com/tgac-vumc/QDNAseq.mm10 BugReports: https://github.com/tgac-vumc/QDNAseq.mm10/issues git_url: https://git.bioconductor.org/packages/QDNAseq.mm10 git_branch: RELEASE_3_13 git_last_commit: 4e12c81 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/QDNAseq.mm10_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: biscuiteer, QDNAseq dependencyCount: 49 Package: qPLEXdata Version: 1.10.0 Depends: R (>= 3.5), qPLEXanalyzer Imports: utils, knitr, MSnbase, dplyr License: GPL-2 MD5sum: 3dc9bfc99b29d666576fabf678432679 NeedsCompilation: no Title: Data accompanying qPLEXanalyzer package Description: qPLEX-RIME and Full proteome TMT mass spectrometry datasets. biocViews: ExperimentData, MassSpectrometryData, Proteome Author: Kamal Kishore Developer [aut, cre] Maintainer: Kamal Kishore Developer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/qPLEXdata git_branch: RELEASE_3_13 git_last_commit: 2be2f5e git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/qPLEXdata_1.10.0.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: 109 Package: QUBICdata Version: 1.20.0 Depends: R (>= 3.1) Suggests: knitr, rmarkdown License: Unlimited | file LICENSE MD5sum: 4bdf65fda03c034ab6631dca69e1e4b3 NeedsCompilation: no Title: Data employed in the vignette of the QUBIC package Description: The data employed in the vignette of the QUBIC package. These data belong to Many Microbe Microarrays Database and STRING v10. biocViews: Escherichia_coli_Data, OrganismData, ExperimentData Author: Yu Zhang [aut, cre], Qin Ma [aut] Maintainer: Yu Zhang URL: http://github.com/zy26/QUBICdata VignetteBuilder: knitr BugReports: http://github.com/zy26/QUBICdata/issues git_url: https://git.bioconductor.org/packages/QUBICdata git_branch: RELEASE_3_13 git_last_commit: 8d9a673 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/QUBICdata_1.20.0.tar.gz vignettes: vignettes/QUBICdata/inst/doc/qubic_data_vignette.pdf vignetteTitles: QUBIC Data Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/QUBICdata/inst/doc/qubic_data_vignette.R suggestsMe: QUBIC dependencyCount: 0 Package: rcellminerData Version: 2.14.0 Depends: R (>= 3.5.0), Biobase Suggests: knitr, testthat, BiocStyle, rcellminer License: LGPL-3 + file LICENSE MD5sum: 72e6cc16b7820384f4d00f52db8cdaf0 NeedsCompilation: no Title: rcellminerData: Molecular Profiles and Drug Response for the NCI-60 Cell Lines Description: The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data. biocViews: CancerData, CopyNumberVariationData, ExpressionData, SNPData, NCI, MicroarrayData, miRNAData Author: Augustin Luna, Vinodh Rajapakse, Fabricio Sousa Maintainer: Augustin Luna , Vinodh Rajapakse , Fathi Elloumi VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/rcellminerData git_branch: RELEASE_3_13 git_last_commit: 5d8f4bd git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/rcellminerData_2.14.0.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: 1.12.0 Depends: R (>= 3.3) Imports: data.table License: GPL-3 MD5sum: 99d4f824cea97104e358a52982472290 NeedsCompilation: no Title: RcisTarget motif databases for human (hg19) - Subset of 4.6k motifs Description: RcisTarget databases: Gene-based motif rankings and annotation to transcription factors. This package contains a subset of 4.6k motifs (cisbp motifs), scored only within 500bp upstream and the TSS. See RcisTarget tutorial to download the full databases, containing 20k motifs and search space up to 10kbp around the TSS. biocViews: Homo_sapiens_Data Author: Sara Aibar, Gert Hulselmans, Stein Aerts. Laboratory of Computational Biology, KU Leuven Center for Human Genetics. Leuven, Belgium. Maintainer: Sara Aibar URL: http://scenic.aertslab.org git_url: https://git.bioconductor.org/packages/RcisTarget.hg19.motifDBs.cisbpOnly.500bp git_branch: RELEASE_3_13 git_last_commit: a74b953 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.12.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RcisTarget dependencyCount: 2 Package: ReactomeGSA.data Version: 1.6.0 Depends: R (>= 3.6), limma, edgeR, ReactomeGSA, Seurat License: Artistic-2.0 MD5sum: 251e1e74a2aece8f0957c3807326db0d NeedsCompilation: no Title: Companion data package for the ReactomeGSA package Description: Companion data sets to showcase the functionality of the ReactomeGSA package. This package contains proteomics and RNA-seq data of the melanoma B-cell induction study by Griss et al. and scRNA-seq data from Jerby-Arnon et al. biocViews: ExpressionData, RNASeqData, Proteome, Homo_sapiens_Data Author: Johannes Griss [aut, cre] () Maintainer: Johannes Griss URL: https://github.com/reactome/ReactomeGSA.data/issues BugReports: https://github.com/reactome/ReactomeGSA.data git_url: https://git.bioconductor.org/packages/ReactomeGSA.data git_branch: RELEASE_3_13 git_last_commit: 1f86180 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/ReactomeGSA.data_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ReactomeGSA dependencyCount: 148 Package: RegParallel Version: 1.10.0 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: e6036e244518090ca839f83537433f8a NeedsCompilation: no Title: Standard regression functions in R enabled for parallel processing over large data-frames Description: In many analyses, a large amount of variables have to be tested independently against the trait/endpoint of interest, and also adjusted for covariates and confounding factors at the same time. The major bottleneck in these is the amount of time that it takes to complete these analyses. With RegParallel, a large number of tests can be performed simultaneously. On a 12-core system, 144 variables can be tested simultaneously, with 1000s of variables processed in a matter of seconds via 'nested' parallel processing. Works for logistic regression, linear regression, conditional logistic regression, Cox proportional hazards and survival models, and Bayesian logistic regression. Also caters for generalised linear models that utilise survey weights created by the 'survey' CRAN package and that utilise 'survey::svyglm'. biocViews: DiseaseModel Author: Kevin Blighe [aut, cre], Sarega Gurudas [ctb], Jessica Lasky-Su [aut] Maintainer: Kevin Blighe URL: https://github.com/kevinblighe/RegParallel VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RegParallel git_branch: RELEASE_3_13 git_last_commit: 86b45ce git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RegParallel_1.10.0.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: 32 Package: restfulSEData Version: 1.14.0 Depends: R (>= 3.4), SummarizedExperiment, ExperimentHub Imports: utils, methods Suggests: knitr License: Artistic-2.0 MD5sum: 2b8299e5197f287ed063892224a0cdce NeedsCompilation: no Title: Example metadata for the "restfulSE" R package Description: Metadata RangedSummarizedExperiment shell for use with restfulSE. biocViews: ExperimentData, Mus_musculus_Data, Homo_sapiens_Data, ExpressionData, SequencingData Author: Vincent Carey [aut], Shweta Gopaulakrishnan [cre, aut] Maintainer: Bioconductor Package Maintainer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/restfulSEData git_branch: RELEASE_3_13 git_last_commit: 60068b1 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/restfulSEData_1.14.0.tar.gz vignettes: vignettes/restfulSEData/inst/doc/restfulSEData.pdf vignetteTitles: restfulSEData -- SummarizedExperiment shells for remote assay data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/restfulSEData/inst/doc/restfulSEData.R suggestsMe: restfulSE dependencyCount: 96 Package: RforProteomics Version: 1.30.1 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, isobar, 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: bbb1b8738acb405a47ebaf0573e0a3ec NeedsCompilation: no Title: Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication Description: This package contains code to illustrate the 'Using R and Bioconductor for proteomics data analysis' and 'Visualisation of proteomics data using R and Bioconductor' manuscripts. The vignettes describe the code and data needed to reproduce the examples and figures described in the paper and functionality for proteomics visualisation. It also contain various function to discover R software for mass spectrometry and proteomics. biocViews: ExperimentData, MassSpectrometryData, ReproducibleResearch Author: Laurent Gatto [aut, cre], Sebastian Gibb [ctb], Vlad Petyuk [ctb], Thomas Pedersen Lin [ctb] Maintainer: Laurent Gatto URL: http://lgatto.github.com/RforProteomics/ VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RforProteomics git_branch: RELEASE_3_13 git_last_commit: 748f078 git_last_commit_date: 2021-08-20 Date/Publication: 2021-08-21 source.ver: src/contrib/RforProteomics_1.30.1.tar.gz vignettes: vignettes/RforProteomics/inst/doc/RforProteomics.html, vignettes/RforProteomics/inst/doc/RProtVis.html vignetteTitles: Using R for proteomics data analysis, Visualisation of proteomics data using R and Bioconductor hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RforProteomics/inst/doc/RforProteomics.R, vignettes/RforProteomics/inst/doc/RProtVis.R suggestsMe: MSstatsQC dependencyCount: 87 Package: RGMQLlib Version: 1.12.0 Depends: R(>= 3.4.2) Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 87f79871c1267afd6fc24540199fc9f3 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: RELEASE_3_13 git_last_commit: 49814de git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RGMQLlib_1.12.0.tar.gz vignettes: vignettes/RGMQLlib/inst/doc/RGMQLlib.pdf vignetteTitles: RGMQLlib: scala Libraries to support GMQL hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: RGMQL dependencyCount: 0 Package: rheumaticConditionWOLLBOLD Version: 1.30.0 Depends: R (>= 2.10.0) Suggests: genefilter, Biobase, hgu133plus2.db License: Artistic-2.0 MD5sum: 72d736e758ffe09725bc32bfd39f3da1 NeedsCompilation: no Title: Normalized gene expression dataset published by Wollbold et al. [2009] (WOLLBOLD). Description: Normalized gene expression data from rheumatic diseases from study published by Wollbold et al. in 2009, provided as an eSet. biocViews: ExperimentData, Tissue, MicroarrayData, MultiChannelData, ChipOnChipData, TissueMicroarrayData, GEO, ArrayExpress Author: Alejandro Quiroz-Zarate, John Quackenbush Maintainer: Alejandro Quiroz-Zarate URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/rheumaticConditionWOLLBOLD git_branch: RELEASE_3_13 git_last_commit: b0a96b8 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/rheumaticConditionWOLLBOLD_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: RITANdata Version: 1.16.0 Depends: R (>= 3.4) License: file LICENSE MD5sum: 8be8bdff4741e4df48fe2b3cf229dfa3 NeedsCompilation: no Title: This package contains the annotation and network data sets Description: Data such as is contained in these two R data files in this package are required for the RITAN package. Users may use their own or additional resources in conjunction with RITANdata. See the RITAN vignettes for more information. biocViews: AnnotationData, Homo_sapiens Author: Michael Zimmermann Maintainer: Michael Zimmermann VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RITANdata git_branch: RELEASE_3_13 git_last_commit: 3622990 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RITANdata_1.16.0.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: 1.30.0 Suggests: RMassBank License: Artistic-2.0 MD5sum: 49560f7d436995f4879d8fa008467747 NeedsCompilation: no Title: Test dataset for RMassBank Description: Example spectra, example compound list(s) and an example annotation list for a narcotics dataset; required to test RMassBank. The package is described in the man page for RMassBankData. Includes new XCMS test data. biocViews: ExperimentData, MassSpectrometryData Author: Michael Stravs, Emma Schymanski, Steffen Neumann Maintainer: Michael Stravs, Emma Schymanski git_url: https://git.bioconductor.org/packages/RMassBankData git_branch: RELEASE_3_13 git_last_commit: 1fcd99b git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RMassBankData_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: RNAinteractMAPK Version: 1.30.0 Depends: R (>= 2.12.0), sparseLDA, RNAinteract Imports: grid, gdata, MASS, genefilter, methods, fields, utils, lattice, Biobase Suggests: qvalue License: Artistic-2.0 MD5sum: e9e9d278ffb92366d0c9ccf8050ec684 NeedsCompilation: no Title: Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi Description: This package includes all data used in the paper -Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi- by Horn, Sandmann, Fischer et al.., Nat. Methods, 2011. The package vignette shows the R code to reproduce all figures in the paper. biocViews: ExperimentData, MicrotitrePlateAssayData, Drosophila_melanogaster_Data, CellCulture Author: Bernd Fischer [aut], Wolfgang Huber [ctb], Mike Smith [cre] Maintainer: Mike Smith git_url: https://git.bioconductor.org/packages/RNAinteractMAPK git_branch: RELEASE_3_13 git_last_commit: 4ce0068 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RNAinteractMAPK_1.30.0.tar.gz vignettes: vignettes/RNAinteractMAPK/inst/doc/RNAinteractMAPK.pdf vignetteTitles: RNAinteractMAPK hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RNAinteractMAPK/inst/doc/RNAinteractMAPK.R suggestsMe: DmelSGI dependencyCount: 120 Package: RNAmodR.Data Version: 1.6.0 Depends: R (>= 3.6), ExperimentHub, ExperimentHubData (>= 1.9.2) Imports: utils Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, sessioninfo, testthat License: Artistic-2.0 MD5sum: 708e2ccfb0522da007256d1c6bece562 NeedsCompilation: no Title: Example data for the RNAmodR package Description: RNAmodR.Data contains example data, which is used for vignettes and example workflows in the RNAmodR and dependent packages. biocViews: ExperimentData, SequencingData, RNASeqData Author: Felix G.M. Ernst [aut, cre], Denis L.J. Lafontaine [ctb, fnd] Maintainer: Felix G.M. Ernst URL: https://github.com/FelixErnst/RNAmodR.Data VignetteBuilder: knitr BugReports: https://github.com/FelixErnst/RNAmodR.Data/issues git_url: https://git.bioconductor.org/packages/RNAmodR.Data git_branch: RELEASE_3_13 git_last_commit: 3823c8d git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RNAmodR.Data_1.6.0.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: 136 Package: RNAseqData.HNRNPC.bam.chr14 Version: 0.30.0 Suggests: GenomicAlignments, BiocManager License: LGPL MD5sum: 9a4deb75539ef73a5f42477226b85382 NeedsCompilation: no Title: Aligned reads from RNAseq experiment: Transcription profiling by high throughput sequencing of HNRNPC knockdown and control HeLa cells Description: The package contains 8 BAM files, 1 per sequencing run. Each BAM file was obtained by (1) aligning the reads (paired-end) to the full hg19 genome with TopHat2, and then (2) subsetting to keep only alignments on chr14. See accession number E-MTAB-1147 in the ArrayExpress database for details about the experiment, including links to the published study (by Zarnack et al., 2012) and to the FASTQ files. biocViews: ExperimentData, Genome, Homo_sapiens_Data, SequencingData, GEO, NCI, RNASeqData, ArrayExpress Author: Hervé Pagès Maintainer: Hervé Pagès URL: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1147/ git_url: https://git.bioconductor.org/packages/RNAseqData.HNRNPC.bam.chr14 git_branch: RELEASE_3_13 git_last_commit: d1daba1 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RNAseqData.HNRNPC.bam.chr14_0.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: sequencing suggestsMe: BiocParallel, GenomicAlignments, GenomicFiles, GenomicRanges, roar, Rsamtools, SplicingGraphs dependencyCount: 0 Package: RNASeqRData Version: 1.10.0 Depends: R (>= 3.5.0) Suggests: png, grid License: Artistic-2.0 MD5sum: 0d709b0dc5af7a2274cdeef2b46173f8 NeedsCompilation: no Title: RNASeqRData: sample data for RNASeqR software package demonstration Description: RNASeqRData is a helper experiment package for vignette demonstration purpose in RNASeqR software package. biocViews: ExperimentData, Saccharomyces_cerevisiae_Data Author: Kuan-Hao Chao Maintainer: Kuan-Hao Chao git_url: https://git.bioconductor.org/packages/RNASeqRData git_branch: RELEASE_3_13 git_last_commit: b6c0570 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RNASeqRData_1.10.0.tar.gz vignettes: vignettes/RNASeqRData/inst/doc/RNASeqRData.html vignetteTitles: RNASeqRData.html hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RNASeqR dependencyCount: 0 Package: RnaSeqSampleSizeData Version: 1.24.0 Depends: edgeR,R (>= 2.10) Suggests: BiocStyle, knitr License: GPL (>= 2) MD5sum: aa8a48d9a69e94a5e959ab84fc5fba19 NeedsCompilation: no Title: RnaSeqSampleSizeData Description: RnaSeqSampleSizeData package provides the read counts and dispersion distribution from real RNA-seq experiments. It can be used by RnaSeqSampleSize package to estimate sample size and power for RNA-seq experiment design. biocViews: ExperimentData, CancerData, RNASeqData Author: Shilin Zhao, Chung-I Li, Yan Guo, Quanhu Sheng, Yu Shyr Maintainer: Shilin Zhao VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RnaSeqSampleSizeData git_branch: RELEASE_3_13 git_last_commit: 06b3b1b git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RnaSeqSampleSizeData_1.24.0.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: 1.24.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 907d7d69519c5c8dfae7a7cfdc8f9c63 NeedsCompilation: no Title: RnBeads.hg19 Description: Automatically generated RnBeads annotation package for the assembly hg19. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.hg19 git_branch: RELEASE_3_13 git_last_commit: 01cc87d git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RnBeads.hg19_1.24.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: MAGAR suggestsMe: RnBeads dependencyCount: 17 Package: RnBeads.hg38 Version: 1.24.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: dfe49a68eeab2741bdc331a4fdd6cdc4 NeedsCompilation: no Title: RnBeads.hg38 Description: Automatically generated RnBeads annotation package for the assembly hg38. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.hg38 git_branch: RELEASE_3_13 git_last_commit: 7511310 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RnBeads.hg38_1.24.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 17 Package: RnBeads.mm10 Version: 2.0.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: d6bb7d10b6612067909845d97d669891 NeedsCompilation: no Title: RnBeads.mm10 Description: Automatically generated RnBeads annotation package for the assembly mm10. Author: RnBeads Team Maintainer: RnBeads Team git_url: https://git.bioconductor.org/packages/RnBeads.mm10 git_branch: RELEASE_3_13 git_last_commit: 8bbe8f8 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RnBeads.mm10_2.0.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 17 Package: RnBeads.mm9 Version: 1.24.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: a83f09f56c11d8531f9ffcef6c851c46 NeedsCompilation: no Title: RnBeads.mm9 Description: Automatically generated RnBeads annotation package for the assembly mm9. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.mm9 git_branch: RELEASE_3_13 git_last_commit: 4f03e57 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RnBeads.mm9_1.24.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RnBeads dependencyCount: 17 Package: RnBeads.rn5 Version: 1.24.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 5d616e5b6f6280774f52181280549d9c NeedsCompilation: no Title: RnBeads.rn5 Description: Automatically generated RnBeads annotation package for the assembly rn5. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.rn5 git_branch: RELEASE_3_13 git_last_commit: 6266f18 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RnBeads.rn5_1.24.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 17 Package: RRBSdata Version: 1.12.0 Depends: R (>= 3.1.0), BiSeq (>= 1.9.2) License: LGPL-3 MD5sum: 954402579d8472e200ec14707b7e1ffa NeedsCompilation: no Title: An RRBS data set with 12 samples and 10,000 simulated DMRs Description: RRBS data set comprising 12 samples with simulated differentially methylated regions (DMRs). biocViews: ExperimentData, CancerData, SequencingData, CpGIslandData Author: Katja Hebestreit, Hans-Ulrich Klein Maintainer: Katja Hebestreit git_url: https://git.bioconductor.org/packages/RRBSdata git_branch: RELEASE_3_13 git_last_commit: bb2749a git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RRBSdata_1.12.0.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: 86 Package: rRDPData Version: 1.12.0 Depends: rRDP License: GPL-2 MD5sum: 4e69e3ec88187f1a1766da4135558028 NeedsCompilation: no Title: Database for the Default RDP Classifier Description: Database used by the default RDP Classifier biocViews: SequencingData, MicrobiomeData Author: Michael Hahsler, Anurag Nagar Maintainer: Michael Hahsler SystemRequirements: Java git_url: https://git.bioconductor.org/packages/rRDPData git_branch: RELEASE_3_13 git_last_commit: 1d86673 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/rRDPData_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: rRDP dependencyCount: 20 Package: RTCGA.clinical Version: 20151101.22.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: cb61381568b50bc34f25a23c4cfeda2e NeedsCompilation: no Title: Clinical datasets from The Cancer Genome Atlas Project Description: Package provides clinical datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Clinical data format is explained here https://wiki.nci.nih.gov/display/TCGA/Clinical+Data+Overview. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.clinical git_branch: RELEASE_3_13 git_last_commit: 1131558 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RTCGA.clinical_20151101.22.0.tar.gz vignettes: vignettes/RTCGA.clinical/inst/doc/downloading_clinical_datasets.html vignetteTitles: Using RTCGA to download clinical data as included in RTCGA.clinical hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.clinical/inst/doc/downloading_clinical_datasets.R suggestsMe: RTCGA dependencyCount: 135 Package: RTCGA.CNV Version: 1.20.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 2c44e4942feb0c596d43f5cc5f81c79e NeedsCompilation: no Title: CNV (Copy-number variation) datasets from The Cancer Genome Atlas Project Description: Package provides CNV (based on Merge snp) datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Retrieving +Data+Using+the+Data+Matrix. Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Przemyslaw Biecek Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.CNV git_branch: RELEASE_3_13 git_last_commit: 8b83ef1 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RTCGA.CNV_1.20.0.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: 135 Package: RTCGA.methylation Version: 1.20.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: a75084e96313e7c6646f3672580b05e0 NeedsCompilation: no Title: Methylation datasets from The Cancer Genome Atlas Project Description: Package provides methylation (humanmethylation27) datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/DNA+methylation Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Marcin Kosinski [aut, cre], Witold Chodor [aut] Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.methylation git_branch: RELEASE_3_13 git_last_commit: 24058bd git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RTCGA.methylation_1.20.0.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: 135 Package: RTCGA.miRNASeq Version: 1.20.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: ad24ae391e1b6491b6828447b23f06e4 NeedsCompilation: no Title: miRNASeq datasets from The Cancer Genome Atlas Project Description: Package provides miRNASeq datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/miRNASeq#miRNASeq-DataOverview Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.miRNASeq git_branch: RELEASE_3_13 git_last_commit: 9219468 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RTCGA.miRNASeq_1.20.0.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: 135 Package: RTCGA.mRNA Version: 1.20.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 308d0fa365fff0017bf6d6adba57d1a1 NeedsCompilation: no Title: mRNA datasets from The Cancer Genome Atlas Project Description: Package provides mRNA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Gene+expression+data Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.mRNA git_branch: RELEASE_3_13 git_last_commit: 0e09681 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RTCGA.mRNA_1.20.0.tar.gz vignettes: vignettes/RTCGA.mRNA/inst/doc/downloading_mRNA_datasets.html vignetteTitles: Using RTCGA to download mRNA data as included in RTCGA.mRNA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.mRNA/inst/doc/downloading_mRNA_datasets.R suggestsMe: CancerSubtypes, RTCGA dependencyCount: 135 Package: RTCGA.mutations Version: 20151101.22.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: e2b07846b74456b0a3f4929cdb4abb1c NeedsCompilation: no Title: Mutations datasets from The Cancer Genome Atlas Project Description: Package provides mutations datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Mutations data format is explained here https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+(MAF)+Specification. There is extra one column with patients' barcodes. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.mutations git_branch: RELEASE_3_13 git_last_commit: ea2bfb7 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RTCGA.mutations_20151101.22.0.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: 135 Package: RTCGA.PANCAN12 Version: 1.20.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 5bf7cae75839f98dd275a6d723b49ace NeedsCompilation: no Title: PanCan 12 from Genome Cancer Browser Description: Package provides clinical, expression, cnv and mutation data from Genome Cancer Browser. biocViews: AnnotationData Author: Przemyslaw Biecek Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.PANCAN12 git_branch: RELEASE_3_13 git_last_commit: 5b77712 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RTCGA.PANCAN12_1.20.0.tar.gz vignettes: vignettes/RTCGA.PANCAN12/inst/doc/pancan12.html vignetteTitles: Using RTCGA.PANCAN12 to compare time to death hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.PANCAN12/inst/doc/pancan12.R suggestsMe: GOpro, RTCGA dependencyCount: 135 Package: RTCGA.rnaseq Version: 20151101.22.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: fd942fdb854a1d36149a0e83cf52f5a5 NeedsCompilation: no Title: Rna-seq datasets from The Cancer Genome Atlas Project Description: Package provides rna-seq datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Rna-seq data format is explained here https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2. Data source is illumina hiseq Level 3 RSEM normalized expression data. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.rnaseq git_branch: RELEASE_3_13 git_last_commit: 3f17759 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RTCGA.rnaseq_20151101.22.0.tar.gz vignettes: vignettes/RTCGA.rnaseq/inst/doc/downloading_rnaseq_datasets.html vignetteTitles: Using RTCGA to download RNAseq data as included in RTCGA.rnaseq hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.rnaseq/inst/doc/downloading_rnaseq_datasets.R suggestsMe: RTCGA, FSelectorRcpp dependencyCount: 135 Package: RTCGA.RPPA Version: 1.20.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 066d8ee2ccf1adbd2fe90e45e7d9a8e3 NeedsCompilation: no Title: RPPA datasets from The Cancer Genome Atlas Project Description: Package provides RPPA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Protein+Array +Data+Format+Specification?src=search biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.RPPA git_branch: RELEASE_3_13 git_last_commit: 5d281f8 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RTCGA.RPPA_1.20.0.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: 135 Package: RUVnormalizeData Version: 1.12.0 Depends: R (>= 2.10.0), Biobase License: GPL-3 MD5sum: 12f415ab25f7c2aba7e78ddbe635d306 NeedsCompilation: no Title: Gender data for the RUVnormalize package Description: Microarray gene expression data from the study of Vawter et al., 2004. biocViews: MicroarrayData Author: Laurent Jacob Maintainer: Laurent Jacob git_url: https://git.bioconductor.org/packages/RUVnormalizeData git_branch: RELEASE_3_13 git_last_commit: 9a7816f git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/RUVnormalizeData_1.12.0.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: 1.16.0 Depends: R (>= 3.4), SummarizedExperiment Suggests: BiocStyle License: Artistic-2.0 MD5sum: ba438daea4c44ebcc4040064af8fe098 NeedsCompilation: no Title: Pre-processed data for use with the sampleClassifier package Description: This package contains two microarray and two RNA-seq datasets that have been preprocessed for use with the sampleClassifier package. The RNA-seq data are derived from Fagerberg et al. (2014) and the Illumina Body Map 2.0 data. The microarray data are derived from Roth et al. (2006) and Ge et al. (2005). biocViews: ExperimentData, ExpressionData, MicroarrayData, SequencingData, RNASeqData, ArrayExpress Author: Khadija El Amrani Maintainer: Khadija El Amrani git_url: https://git.bioconductor.org/packages/sampleClassifierData git_branch: RELEASE_3_13 git_last_commit: 9a87b8d git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/sampleClassifierData_1.16.0.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: 26 Package: SBGNview.data Version: 1.6.0 Depends: R (>= 3.6) Imports: knitr, rmarkdown, bookdown Suggests: SummarizedExperiment License: AGPL-3 MD5sum: 363be9712c6bfc7e1f177aa1f00b92e3 NeedsCompilation: no Title: Supporting datasets for SBGNview package Description: This package contains: 1. A microarray gene expression dataset from a human breast cancer study. 2. A RNA-Seq gene expression dataset from a mouse study on IFNG knockout. 3. ID mapping tables between gene IDs and SBGN-ML file glyph IDs. 4. Percent of orthologs detected in other species of the genes in a pathway. Cutoffs of this percentage for defining if a pathway exists in another species. 5. XML text of SBGN-ML files for all pre-collected pathways. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO, RNASeqData Author: Xiaoxi Dong*, Kovidh Vegesna*, Weijun Luo Maintainer: Weijun Luo VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/SBGNview.data git_branch: RELEASE_3_13 git_last_commit: 24c7da4 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/SBGNview.data_1.6.0.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: 24 Package: SCATEData Version: 1.2.0 Depends: ExperimentHub, GenomicAlignments, GenomicRanges, base Imports: utils Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 080bd673f3e171e21692283a4ec0cd46 NeedsCompilation: no Title: Data for SCATE (Single-cell ATAC-seq Signal Extraction and Enhancement) Description: SCATEData is an ExperimentHub package for SCATE which is a software tool for extracting and enhancing the sparse and discrete Single-cell ATAC-seq Signal. biocViews: ExperimentHub, ExperimentData Author: Zhicheng Ji [aut], Weiqiang Zhou [aut], Wenpin Hou [cre, aut] (), Hongkai Ji [aut] Maintainer: Wenpin Hou VignetteBuilder: knitr BugReports: https://github.com/Winnie09/SCATEData/issues git_url: https://git.bioconductor.org/packages/SCATEData git_branch: RELEASE_3_13 git_last_commit: ae2aef5 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/SCATEData_1.2.0.tar.gz vignettes: vignettes/SCATEData/inst/doc/SCATEData_package.html vignetteTitles: 1. SCATEData package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/SCATEData/inst/doc/SCATEData_package.R dependsOnMe: SCATE dependencyCount: 107 Package: SCLCBam Version: 1.24.0 Depends: R(>= 2.10) Suggests: BiocStyle License: GPL-2 MD5sum: c67d9daab74f905eb606776c92d5ef8e NeedsCompilation: no Title: Sequence data from chromosome 4 of a small-cell lung tumor Description: Whole-exome sequencing data from a murine small-cell lung tumor; only contains data of chromosome 4. biocViews: SequencingData, LungCancerData Author: Thomas Kuilman Maintainer: Oscar Krijgsman git_url: https://git.bioconductor.org/packages/SCLCBam git_branch: RELEASE_3_13 git_last_commit: 45616e2 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/SCLCBam_1.24.0.tar.gz vignettes: vignettes/SCLCBam/inst/doc/SCLCBam.pdf vignetteTitles: SCLCBam hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SCLCBam/inst/doc/SCLCBam.R suggestsMe: CopywriteR dependencyCount: 0 Package: scpdata Version: 1.0.0 Depends: R (>= 4.1), QFeatures, ExperimentHub Imports: utils, AnnotationHub, SingleCellExperiment, S4Vectors Suggests: scp, magrittr, dplyr, knitr, BiocStyle, BiocCheck, rmarkdown, testthat License: GPL-2 MD5sum: b63a8a9e071af138a35a4da1351ddb8b 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 Author: Christophe Vanderaa [aut, cre] (), Laurent Gatto [aut] () Maintainer: Christophe Vanderaa VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/scpdata git_branch: RELEASE_3_13 git_last_commit: 7512de1 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/scpdata_1.0.0.tar.gz vignettes: vignettes/scpdata/inst/doc/scpdata.html vignetteTitles: Data Package for Single Cell Proteomics hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scpdata/inst/doc/scpdata.R dependencyCount: 107 Package: scRNAseq Version: 2.6.1 Depends: SingleCellExperiment Imports: utils, methods, BiocGenerics, S4Vectors, GenomicRanges, SummarizedExperiment, ExperimentHub, AnnotationHub, AnnotationDbi, ensembldb, GenomicFeatures Suggests: BiocStyle, knitr, rmarkdown, BiocFileCache, testthat, rappdirs, tools License: CC0 MD5sum: 88e7b134781f1df31d5b6a0501e61c8d 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] Maintainer: Aaron Lun VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/scRNAseq git_branch: RELEASE_3_13 git_last_commit: 23a11e3 git_last_commit_date: 2021-05-23 Date/Publication: 2021-05-25 source.ver: src/contrib/scRNAseq_2.6.1.tar.gz vignettes: vignettes/scRNAseq/inst/doc/scRNAseq.html vignetteTitles: User's Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scRNAseq/inst/doc/scRNAseq.R importsMe: singleCellTK suggestsMe: batchelor, bluster, dittoSeq, iSEE, iSEEu, miQC, mumosa, scater, scClassifR, scDblFinder, scFeatureFilter, scone, scran, scuttle, SingleCellExperiment, SingleR, snifter, SummarizedBenchmark, velociraptor, zellkonverter, zinbwave dependencyCount: 123 Package: scTHI.data Version: 1.4.0 Depends: R (>= 4.0) License: GPL-2 MD5sum: 934ddabeb602eadf3adc82acf2b51aa1 NeedsCompilation: no Title: The package contains examples of single cell data used in vignettes and examples of the scTHI package; data contain both tumor cells and immune cells from public dataset of glioma Description: Data for the vignette and tutorial of the package scTHI. biocViews: ExperimentData, SingleCellData Author: Francesca Pia Caruso [aut], Michele Ceccarelli [aut, cre] Maintainer: Michele Ceccarelli git_url: https://git.bioconductor.org/packages/scTHI.data git_branch: RELEASE_3_13 git_last_commit: 7cb364f git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/scTHI.data_1.4.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: scTHI dependencyCount: 0 Package: seq2pathway.data Version: 1.24.0 Depends: R (>= 3.6.2) License: GPL (>= 2) MD5sum: 6a3a58a0b01ee8306c29f2a6f0314f0b NeedsCompilation: no Title: data set for R package seq2pathway Description: Supporting data for the seq2patheway package. Includes modified gene sets from MsigDB and org.Hs.eg.db; gene locus definitions from GENCODE project. biocViews: ExperimentData Author: Bin Wang Maintainer: Arjun Kinstlick git_url: https://git.bioconductor.org/packages/seq2pathway.data git_branch: RELEASE_3_13 git_last_commit: 14fc381 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/seq2pathway.data_1.24.0.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: 1.26.0 Depends: R (>= 2.10) Imports: utils, Biobase License: GPL-3 MD5sum: da005ee7ebf42ebf59e6c95a65a6d209 NeedsCompilation: no Title: RNA-seq data generated from SEQC (MAQC-III) study Description: The SEQC/MAQC-III Consortium has produced benchmark RNA-seq data for the assessment of RNA sequencing technologies and data analysis methods (Nat Biotechnol, 2014). Billions of sequence reads have been generated from ten different sequencing sites. This package contains the summarized read count data for ~2000 sequencing libraries. It also includes all the exon-exon junctions discovered from the study. TaqMan RT-PCR data for ~1000 genes and ERCC spike-in sequence data are included in this package as well. biocViews: ExperimentData, RNASeqData, qPCRData, SequencingData Author: Yang Liao and Wei Shi with contributions from Gordon K Smyth and Steve Lianoglou. Maintainer: Yang Liao and Wei Shi URL: http://bioconductor.org/packages/release/data/experiment/html/seqc.html git_url: https://git.bioconductor.org/packages/seqc git_branch: RELEASE_3_13 git_last_commit: b44b94d git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/seqc_1.26.0.tar.gz vignettes: vignettes/seqc/inst/doc/seqc.pdf vignetteTitles: SEQC Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/seqc/inst/doc/seqc.R dependencyCount: 7 Package: seqCNA.annot Version: 1.28.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: f4e72788e7e3c7ece80aec00066f010b NeedsCompilation: no Title: Annotation for the copy number analysis of deep sequencing cancer data with seqCNA Description: Provides annotation on GC content, mappability and genomic features for various genomes biocViews: Genome, CopyNumberVariationData Author: David Mosen-Ansorena Maintainer: David Mosen-Ansorena git_url: https://git.bioconductor.org/packages/seqCNA.annot git_branch: RELEASE_3_13 git_last_commit: fb9c158 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/seqCNA.annot_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: seqCNA dependencyCount: 0 Package: serumStimulation Version: 1.28.0 Depends: R (>= 2.10) License: GPL (>= 2) MD5sum: ce841efe10b5cc30cbef9828e1a0e6ad NeedsCompilation: no Title: serumStimulation is a data package which is used by examples in package pcaGoPromoter Description: Contains 13 micro array data results from a serum stimulation experiment biocViews: ExperimentData, MicroarrayData Author: Morten Hansen Maintainer: Morten Hansen, git_url: https://git.bioconductor.org/packages/serumStimulation git_branch: RELEASE_3_13 git_last_commit: bf46e8d git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/serumStimulation_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: sesameData Version: 1.10.1 Depends: R (>= 4.1), ExperimentHub, AnnotationHub, rmarkdown Imports: utils, curl Suggests: GenomicRanges, BiocGenerics, sesame, testthat, knitr License: Artistic-2.0 MD5sum: e820984f75fcdd4e2348951edf55db76 NeedsCompilation: no Title: Supporting Data for SeSAMe Package Description: Provides supporting annotation and test data for SeSAMe package. This includes chip tango addresses, mapping information, performance annotation, and trained predictor for Infinium array data. This package provides user access to essential annotation data for working with many generations of the Infinium DNA methylation array. Current we support human array (HM27, HM450, EPIC), mouse array (MM285) and the HorvathMethylChip40 (Mammal40) array. biocViews: ExperimentData, MicroarrayData, Genome, ExperimentHub, MethylationArrayData Author: Wanding Zhou [aut, cre], Hui Shen [aut], Timothy Triche [ctb] Maintainer: Wanding Zhou VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/sesameData git_branch: RELEASE_3_13 git_last_commit: a4facd8 git_last_commit_date: 2021-10-07 Date/Publication: 2021-10-09 source.ver: src/contrib/sesameData_1.10.1.tar.gz vignettes: vignettes/sesameData/inst/doc/sesameData.html vignetteTitles: sesameData User Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/sesameData/inst/doc/sesameData.R dependsOnMe: sesame importsMe: MethReg suggestsMe: ELMER dependencyCount: 96 Package: seventyGeneData Version: 1.28.0 Depends: R (>= 2.13.0) Suggests: Biobase, gdata, limma, breastCancerNKI License: Artistic-2.0 MD5sum: 62c364f2ec3d1efb02e881ce7d6d8520 NeedsCompilation: no Title: ExpressionSets from the van't Veer and Van de Vijver breast cancer studies Description: Gene expression data for the two breast cancer cohorts published by van't Veer and Van de Vijver in 2002 biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData Author: Luigi Marchionni Maintainer: Luigi Marchionni URL: http://luigimarchionni.org/breastTSP.html git_url: https://git.bioconductor.org/packages/seventyGeneData git_branch: RELEASE_3_13 git_last_commit: e71fde4 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/seventyGeneData_1.28.0.tar.gz vignettes: vignettes/seventyGeneData/inst/doc/seventyGeneData.pdf vignetteTitles: Working with the seventyGeneData package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/seventyGeneData/inst/doc/seventyGeneData.R dependencyCount: 0 Package: shinyMethylData Version: 1.12.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: 6c57e2d495c1415947b1325be6467f54 NeedsCompilation: no Title: Example dataset of input data for shinyMethyl Description: Extracted data from 369 TCGA Head and Neck Cancer DNA methylation samples. The extracted data serve as an example dataset for the package shinyMethyl. Original samples are from 450k methylation arrays, and were obtained from The Cancer Genome Atlas (TCGA). 310 samples are from tumor, 50 are matched normals and 9 are technical replicates of a control cell line. biocViews: Genome, CancerData Author: Jean-Philippe Fortin [cre, aut], Kasper Daniel Hansen [aut] Maintainer: Jean-Philippe Fortin git_url: https://git.bioconductor.org/packages/shinyMethylData git_branch: RELEASE_3_13 git_last_commit: d144dcb git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/shinyMethylData_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: shinyMethyl dependencyCount: 0 Package: signatureSearchData Version: 1.6.0 Depends: R (>= 3.6) Imports: ExperimentHub, utils, affy, limma, Biobase, magrittr, dplyr, R.utils, stats, signatureSearch, rhdf5 Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 9fd4567b666beff53f010872d26de3f4 NeedsCompilation: no Title: Datasets for signatureSearch package Description: CMAP/LINCS hdf5 databases and other annotations used for signatureSearch software package. biocViews: ExperimentHub, ExperimentData, ExpressionData Author: Yuzhu Duan , Thomas Girke Maintainer: Yuzhu Duan VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/signatureSearchData git_branch: RELEASE_3_13 git_last_commit: 4912e80 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/signatureSearchData_1.6.0.tar.gz vignettes: vignettes/signatureSearchData/inst/doc/signatureSearchData.html vignetteTitles: signatureSearchData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/signatureSearchData/inst/doc/signatureSearchData.R suggestsMe: signatureSearch dependencyCount: 184 Package: SimBenchData Version: 1.0.0 Depends: ExperimentHub Imports: S4Vectors, utils Suggests: BiocStyle, knitr, rmarkdown, Seurat License: GPL-3 MD5sum: 00416c09020fcc8df04e467db235cd55 NeedsCompilation: no Title: SimBenchData: a collection of 35 single-cell RNA-seq data covering a wide range of data characteristics Description: The SimBenchData package contains a total of 35 single-cell RNA-seq datasets covering a wide range of data characteristics, including major sequencing protocols, multiple tissue types, and both human and mouse sources. biocViews: ExperimentHub, ExperimentData, SingleCellData, RNASeqData, Tissue, SequencingData Author: Yue Cao [aut, cre], Pengyi Yang [aut], Jean Yee Hwa Yang [aut] Maintainer: Yue Cao VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/SimBenchData git_branch: RELEASE_3_13 git_last_commit: d3bc3cf git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/SimBenchData_1.0.0.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: 88 Package: simpIntLists Version: 1.28.0 License: GPL (>= 2) MD5sum: 2f715681ea7582d2e22440b717b21485 NeedsCompilation: no Title: The package contains BioGRID interactions for various organisms in a simple format Description: The package contains BioGRID interactions for arabidopsis(thale cress), c.elegans, fruit fly, human, mouse, yeast( budding yeast ) and S.pombe (fission yeast) . Entrez ids, official names and unique ids can be used to find proteins. The format of interactions are lists. For each gene/protein, there is an entry in the list with "name" containing name of the gene/protein and "interactors" containing the list of genes/proteins interacting with it. biocViews: ExperimentData, Arabidopsis_thaliana_Data Author: Kircicegi Korkmaz, Volkan Atalay, Rengul Cetin-Atalay Maintainer: Kircicegi Korkmaz git_url: https://git.bioconductor.org/packages/simpIntLists git_branch: RELEASE_3_13 git_last_commit: 9d144d9 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/simpIntLists_1.28.0.tar.gz vignettes: vignettes/simpIntLists/inst/doc/simpIntLists.pdf vignetteTitles: simpIntLists hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/simpIntLists/inst/doc/simpIntLists.R dependsOnMe: ibh suggestsMe: GeneNetworkBuilder dependencyCount: 0 Package: Single.mTEC.Transcriptomes Version: 1.20.0 Depends: R (>= 3.5.0) Suggests: DESeq2, GenomicRanges, GenomicFeatures, genefilter, statmod, gdata, RColorBrewer, ggplot2, gplots, cluster, clue, grid, gridExtra, ggbio, Gviz, geneplotter, matrixStats, pheatmap, BiocStyle, knitr License: LGPL MD5sum: c456767d0151e042f30d5fd21f47424a NeedsCompilation: no Title: Single Cell Transcriptome Data and Analysis of Mouse mTEC cells Description: This data package contains the code used to analyse the single-cell RNA-seq and the bulk ATAC-seq data from the manuscript titled: Single-cell transcriptome analysis reveals coordinated ectopic-gene expression patterns in medullary thymic epithelial cells. This paper was published in Nature Immunology 16,933-941(2015). The data objects provided in this package has been pre-processed: the raw data files can be downloaded from ArrayExpress under the accession identifiers E-MTAB-3346 and E-MTAB-3624. The vignette of this data package provides a documented and reproducible workflow that includes the code that was used to generate each statistic and figure from the manuscript. biocViews: ExperimentData Author: Alejandro Reyes Maintainer: Alejandro Reyes VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/Single.mTEC.Transcriptomes git_branch: RELEASE_3_13 git_last_commit: d134c1b git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/Single.mTEC.Transcriptomes_1.20.0.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: 1.4.1 Depends: R (>= 4.1.0), MultiAssayExperiment Imports: AnnotationHub, BiocFileCache, BiocGenerics, ExperimentHub, HDF5Array, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, Matrix, methods, utils Suggests: BiocStyle, ggplot2, knitr, RaggedExperiment, rmarkdown, scater, scran, UpSetR, uwot License: Artistic-2.0 MD5sum: 5afcdaf3461f63d694c2250bbda82e92 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. biocViews: ExperimentData, SingleCellData, ReproducibleResearch, ExperimentHub, GEO Author: Marcel Ramos [aut, cre] (), Ricard Argelaguet [aut], Dario Righelli [aut], Kelly Eckenrode [aut], Levi Waldron [aut] Maintainer: Marcel Ramos VignetteBuilder: knitr BugReports: https://github.com/waldronlab/SingleCellMultiModal/issues git_url: https://git.bioconductor.org/packages/SingleCellMultiModal git_branch: RELEASE_3_13 git_last_commit: 5879cb8 git_last_commit_date: 2021-06-03 Date/Publication: 2021-06-05 source.ver: src/contrib/SingleCellMultiModal_1.4.1.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 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 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 dependencyCount: 127 Package: SingleMoleculeFootprintingData Version: 1.0.0 Imports: ExperimentHub, utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 2b6fd182d50720dc811d6230055fdaf5 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] (), Arnaud Krebs [aut] (), Mike Smith [ctb] () Maintainer: Guido Barzaghi VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/SingleMoleculeFootprintingData git_branch: RELEASE_3_13 git_last_commit: 5214e85 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/SingleMoleculeFootprintingData_1.0.0.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: 88 Package: SNAData Version: 1.38.0 Depends: R (>= 2.4.0), graph Suggests: Rgraphviz License: LGPL MD5sum: bb5de6b64075410cbd92333d8f1b2e55 NeedsCompilation: no Title: Social Networks Analysis Data Examples Description: Data from Wasserman & Faust (1999) "Social Network Analysis" biocViews: ExperimentData Author: Denise Scholtens Maintainer: Denise Scholtens git_url: https://git.bioconductor.org/packages/SNAData git_branch: RELEASE_3_13 git_last_commit: 626c979 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/SNAData_1.38.0.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: 1.28.0 Depends: R (>= 2.6.0) Suggests: ALL, hgu95av2.db, SNAGEE License: Artistic-2.0 MD5sum: 63a074d015d38ef772c3c44c21da9ef2 NeedsCompilation: no Title: SNAGEE data Description: SNAGEE data - gene list and correlation matrix biocViews: MicroarrayData Author: David Venet Maintainer: David Venet URL: http://fleming.ulb.ac.be/SNAGEE git_url: https://git.bioconductor.org/packages/SNAGEEdata git_branch: RELEASE_3_13 git_last_commit: 8c74b5b git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/SNAGEEdata_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: SNAGEE dependencyCount: 0 Package: SNPhoodData Version: 1.22.0 Depends: R (>= 3.2) Suggests: BiocStyle,knitr,rmarkdown License: LGPL (>= 3) MD5sum: b6082d53d4c8587a8c0487ccef083d09 NeedsCompilation: no Title: Additional and more complex example data for the SNPhood package Description: This companion package for SNPhood provides some example datasets of a larger size than allowed for the SNPhood package. They include full and real-world examples for performing analyses with the SNPhood package. biocViews: ExperimentData Author: Christian Arnold, Judith Zaugg Maintainer: Christian Arnold VignetteBuilder: knitr BugReports: christian.arnold@embl.de git_url: https://git.bioconductor.org/packages/SNPhoodData git_branch: RELEASE_3_13 git_last_commit: 6d4ed21 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/SNPhoodData_1.22.0.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: 1.30.0 Depends: R (>= 2.14) License: Artistic-2.0 MD5sum: acad574165d52c6f28554c84796ca043 NeedsCompilation: no Title: An example cancer whole genome sequencing data for the SomatiCA package Description: An example cancer whole genome sequencing data for the SomatiCA package biocViews: ExperimentData, Genome, CancerData, SequencingData Author: Mengjie Chen Maintainer: Mengjie Chen git_url: https://git.bioconductor.org/packages/SomatiCAData git_branch: RELEASE_3_13 git_last_commit: ddac1e8 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/SomatiCAData_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: SomaticCancerAlterations Version: 1.28.0 Depends: R (>= 3.0.0) Imports: GenomicRanges, IRanges, S4Vectors Suggests: testthat, ggbio, ggplot2, knitr License: GPL-3 MD5sum: 2a56b23b0fc73d92cb85c733ea98dc43 NeedsCompilation: no Title: Somatic Cancer Alterations Description: Collection of somatic cancer alteration datasets biocViews: ExperimentData, Genome, CancerData, Project1000genomes, NCI Author: Julian Gehring Maintainer: Julian Gehring VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/SomaticCancerAlterations git_branch: RELEASE_3_13 git_last_commit: 3cbc19d git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/SomaticCancerAlterations_1.28.0.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: 17 Package: spatialLIBD Version: 1.4.0 Depends: SpatialExperiment (>= 1.1.700), R (>= 3.6) Imports: shiny, golem, ggplot2, cowplot, plotly, viridisLite, shinyWidgets, Polychrome, sessioninfo, grid, grDevices, methods, AnnotationHub, utils, png, scater, DT, ExperimentHub, RColorBrewer, SummarizedExperiment, stats, graphics, S4Vectors, IRanges, fields, benchmarkme, SingleCellExperiment, BiocFileCache, jsonlite, tibble Suggests: knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager, rtracklayer, pryr License: Artistic-2.0 MD5sum: b59b6eeee824f93c3afb2bf3bbf6f1f6 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 Author: Leonardo Collado-Torres [aut, cre] (), Kristen R. Maynard [ctb] (), Andrew E. Jaffe [ctb] (), Brenda Pardo [ctb] (), Abby Spangler [ctb] (), Jesús Vélez Santiago [ctb] () Maintainer: Leonardo Collado-Torres URL: https://github.com/LieberInstitute/spatialLIBD VignetteBuilder: knitr BugReports: https://support.bioconductor.org/t/spatialLIBD git_url: https://git.bioconductor.org/packages/spatialLIBD git_branch: RELEASE_3_13 git_last_commit: 74ba278 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/spatialLIBD_1.4.0.tar.gz vignettes: vignettes/spatialLIBD/inst/doc/spatialLIBD.html, vignettes/spatialLIBD/inst/doc/TenX_data_download.html vignetteTitles: Introduction to spatialLIBD, Using spatialLIBD with 10x Genomics public datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/spatialLIBD/inst/doc/spatialLIBD.R, vignettes/spatialLIBD/inst/doc/TenX_data_download.R suggestsMe: BayesSpace dependencyCount: 210 Package: SpikeIn Version: 1.34.0 Depends: R (>= 1.6), affy (>= 1.23.4) License: Artistic-2.0 MD5sum: 766ed27077f13d149503d6123ccd79e2 NeedsCompilation: no Title: Affymetrix Spike-In Experiment Data Description: Contains the HGU133 and HGU95 spikein experiment data. biocViews: ExperimentData, MicroarrayData Author: Rafael Irizarry Maintainer: Rafael A. Irizarry git_url: https://git.bioconductor.org/packages/SpikeIn git_branch: RELEASE_3_13 git_last_commit: 830186e git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/SpikeIn_1.34.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PECA dependencyCount: 13 Package: SpikeInSubset Version: 1.32.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5), affy (>= 1.23.4) License: LGPL MD5sum: 9949bb752d59f98f07ea1dc21d5f6f77 NeedsCompilation: no Title: Part of Affymetrix's Spike-In Experiment Data Description: Includes probe-level and expression data for the HGU133 and HGU95 spike-in experiments biocViews: ExperimentData, MicroarrayData Author: Rafael Irizarry and Zhijin Wu Maintainer: Rafael A. Irizarry git_url: https://git.bioconductor.org/packages/SpikeInSubset git_branch: RELEASE_3_13 git_last_commit: 662a211 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/SpikeInSubset_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: logitT dependencyCount: 13 Package: spqnData Version: 1.4.0 Depends: R (>= 4.0), SummarizedExperiment License: Artistic-2.0 MD5sum: 05bab0a3b7a9fe854eb5c32ddf4559d9 NeedsCompilation: no Title: Data for the spqn package Description: Bulk RNA-seq from GTEx on 4,000 randomly selected, expressed genes. Data has been processed for co-expression analysis. biocViews: Homo_sapiens_Data, ExpressionData, Tissue, RNASeqData Author: Yi Wang [cre, aut], Kasper Daniel Hansen [aut] Maintainer: Yi Wang git_url: https://git.bioconductor.org/packages/spqnData git_branch: RELEASE_3_13 git_last_commit: 65830c1 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/spqnData_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: spqn dependencyCount: 26 Package: stemHypoxia Version: 1.28.0 Depends: R (>= 2.14.1) License: GPL (>=2) MD5sum: cd2293021ccca980d68c361c71b0d698 NeedsCompilation: no Title: Differentiation of Human Embryonic Stem Cells under Hypoxia gene expression dataset by Prado-Lopez et al. (2010) Description: Expression profiling using microarray technology to prove if 'Hypoxia Promotes Efficient Differentiation of Human Embryonic Stem Cells to Functional Endothelium' by Prado-Lopez et al. (2010) Stem Cells 28:407-418. Full data available at Gene Expression Omnibus series GSE37761. biocViews: ExperimentData, Tissue, StemCell, Homo_sapiens_Data, CancerData, MicroarrayData, TissueMicroarrayData, GEO Author: Cristobal Fresno and Elmer A. Fernandez Maintainer: Cristobal Fresno URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37761, http://onlinelibrary.wiley.com/doi/10.1002/stem.295/abstract git_url: https://git.bioconductor.org/packages/stemHypoxia git_branch: RELEASE_3_13 git_last_commit: 287f0b9 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/stemHypoxia_1.28.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: lmdme dependencyCount: 0 Package: STexampleData Version: 1.0.8 Depends: ExperimentHub, SpatialExperiment Imports: utils Suggests: BiocStyle, knitr License: MIT + file LICENSE MD5sum: 2973f4a2e3c30e4de6af08886b6325d7 NeedsCompilation: no Title: Collection of spatially resolved transcriptomics datasets in SpatialExperiment Bioconductor format Description: Collection of spatially resolved transcriptomics datasets in SpatialExperiment Bioconductor format, for use in examples, demonstrations, tutorials, and other purposes. The datasets have been sourced from various publicly available sources, and cover several technological platforms. biocViews: ExperimentHub, ExperimentData, ReproducibleResearch, ExpressionData, SingleCellData, Homo_sapiens_Data, Mus_musculus_Data Author: Lukas M. Weber [aut, cre] () Maintainer: Lukas M. Weber URL: https://github.com/lmweber/STexampleData VignetteBuilder: knitr BugReports: https://github.com/lmweber/STexampleData/issues git_url: https://git.bioconductor.org/packages/STexampleData git_branch: RELEASE_3_13 git_last_commit: 4209d42 git_last_commit_date: 2021-08-08 Date/Publication: 2021-08-10 source.ver: src/contrib/STexampleData_1.0.8.tar.gz vignettes: vignettes/STexampleData/inst/doc/STexampleData_overview.html vignetteTitles: STexampleData package overview hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/STexampleData/inst/doc/STexampleData_overview.R dependencyCount: 124 Package: stjudem Version: 1.32.0 Depends: R (>= 2.10), utils License: LGPL (>= 2) MD5sum: 2cd1a8b960b2c1d0ff4e4fc40e13faa7 NeedsCompilation: no Title: Microarray Data from Yeoh et al. in MACAT format Description: This is a microarray data set on acute lymphoblastic leukemia, published in 2002 (Yeoh et al.Cancer Cell 2002). The experiments were conducted in the St.Jude Children's Research Hospital, Memphis, Tenessee, USA. The raw data was preprocessed by variance stabilizing normalization (Huber et al.) on probe and subsequent summarization of probe expression values into probe set expression values using median polish. biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData, ChipOnChipData Author: Benjamin Georgi, Matthias Heinig, Sebastian Schmeier, Joern Toedling Maintainer: Joern Toedling git_url: https://git.bioconductor.org/packages/stjudem git_branch: RELEASE_3_13 git_last_commit: dbd8081 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/stjudem_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: macat dependencyCount: 1 Package: SVM2CRMdata Version: 1.24.0 Depends: R(>= 3.2.0) License: LGPL (>= 2) MD5sum: 96a5484793622f0c1eb06a77da350097 NeedsCompilation: no Title: An example dataset for use with the SVM2CRM package Description: An example dataset for use with the SVM2CRM package. biocViews: ExperimentData, ChIPSeq, HistoneModification, Preprocessing, DataImport Author: Guidantonio Malagoli Tagliazucchi Maintainer: Guidantonio Malagoli Tagliazucchi git_url: https://git.bioconductor.org/packages/SVM2CRMdata git_branch: RELEASE_3_13 git_last_commit: 81cb8e2 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/SVM2CRMdata_1.24.0.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: 1.30.0 Depends: R (>= 2.10), synapter (>= 1.99.2) Imports: utils License: GPL-2 MD5sum: c3de5f50a0fe17c665fc8625a7ae6fe8 NeedsCompilation: no Title: Data accompanying the synapter package Description: Data independant acquisition of UPS1 protein mix in an E. coli background obtained on a Waters Synapt G2 instrument. biocViews: ExperimentData, MassSpectrometryData Author: Laurent Gatto, Sebastian Gibb and Pavel V. Shliaha Maintainer: Laurent Gatto git_url: https://git.bioconductor.org/packages/synapterdata git_branch: RELEASE_3_13 git_last_commit: 6d83b4a git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/synapterdata_1.30.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 2 Package: systemPipeRdata Version: 1.20.0 Depends: methods Imports: BiocGenerics, jsonlite, remotes, GenomicFeatures, GenomicRanges, IRanges, Rsamtools, ShortRead, rtracklayer Suggests: RUnit, BiocStyle, knitr, rmarkdown, systemPipeR License: Artistic-2.0 MD5sum: c3d5fc43b19e9ce7effa9f812c21143b NeedsCompilation: no Title: systemPipeRdata: Workflow templates and sample data Description: systemPipeRdata is a helper package to generate with a single command NGS workflow templates that are intended to be used by its parent package systemPipeR. The latter is an environment for building end-to-end analysis pipelines with automated report generation for next generation sequence (NGS) applications such as RNA-Seq, RIBO-Seq, ChIP-Seq, VAR-Seq and many others. Detailed examples for using systemPipeRdata are given in systemPipeR's overview vignette. biocViews: Genetics, Infrastructure, DataImport, Sequencing, RNASeq, ChIPSeq, MethylSeq, SNP, GeneExpression, Coverage, GeneSetEnrichment, Alignment, QualityControl, ImmunoOncology, RiboSeq, WorkflowStep Author: Thomas Girke Maintainer: Thomas Girke URL: https://github.com/tgirke/systemPipeRdata VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/systemPipeRdata git_branch: RELEASE_3_13 git_last_commit: 64a893d git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/systemPipeRdata_1.20.0.tar.gz vignettes: vignettes/systemPipeRdata/inst/doc/systemPipeChIPseq.html, vignettes/systemPipeRdata/inst/doc/systemPipeRdata.html, vignettes/systemPipeRdata/inst/doc/systemPipeRIBOseq.html, vignettes/systemPipeRdata/inst/doc/systemPipeRNAseq.html, vignettes/systemPipeRdata/inst/doc/systemPipeVARseq.html vignetteTitles: WF: ChIP-Seq Workflow Template, systemPipeRdata: Workflow templates and sample data, WF: RIBO-Seq Workflow Template, WF: RNA-Seq Workflow Template, WF: VAR-Seq Template hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/systemPipeRdata/inst/doc/systemPipeChIPseq.R, vignettes/systemPipeRdata/inst/doc/systemPipeRdata.R, vignettes/systemPipeRdata/inst/doc/systemPipeRIBOseq.R, vignettes/systemPipeRdata/inst/doc/systemPipeRNAseq.R, vignettes/systemPipeRdata/inst/doc/systemPipeVARseq.R importsMe: RNASeqR suggestsMe: systemPipeR, systemPipeShiny dependencyCount: 102 Package: TabulaMurisData Version: 1.10.0 Depends: R (>= 3.5) Imports: ExperimentHub, utils Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran, scater, iSEE, testthat License: MIT + file LICENSE MD5sum: 8f646e6a02eb4dc783b19d0913fc8c38 NeedsCompilation: no Title: 10x And SmartSeq2 Data From The Tabula Muris Consortium Description: Access to processed 10x (droplet) and SmartSeq2 (on FACS-sorted cells) single-cell RNA-seq data from the Tabula Muris consortium (http://tabula-muris.ds.czbiohub.org/). biocViews: SingleCellData, ExperimentData, RNASeqData Author: Charlotte Soneson [aut, cre] () Maintainer: Charlotte Soneson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TabulaMurisData git_branch: RELEASE_3_13 git_last_commit: dba2931 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/TabulaMurisData_1.10.0.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: 88 Package: TargetScoreData Version: 1.28.0 Suggests: TargetScore, gplots License: GPL-2 MD5sum: 8173c049d1a0ead4897efb0a00c30d59 NeedsCompilation: no Title: TargetScoreData Description: Precompiled and processed miRNA-overexpression fold-changes from 84 Gene Expression Omnibus (GEO) series corresponding to 6 platforms, 77 human cells or tissues, and 113 distinct miRNAs. Accompanied with the data, we also included in this package the sequence feature scores from TargetScanHuman 6.1 including the context+ score and the probabilities of conserved targeting for each miRNA-mRNA interaction. Thus, the user can use these static sequence-based scores together with user-supplied tissue/cell-specific fold-change due to miRNA overexpression to predict miRNA targets using the package TargetScore (download separately) biocViews: ExperimentData, RNASeqData, miRNAData Author: Yue Li Maintainer: Yue Li git_url: https://git.bioconductor.org/packages/TargetScoreData git_branch: RELEASE_3_13 git_last_commit: f7f830d git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/TargetScoreData_1.28.0.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: 1.30.0 License: GPL (>= 2) MD5sum: 13954c82da6b10cdf2994980c511944d NeedsCompilation: no Title: Example GC-MS data for TargetSearch Package Description: This package provides example GC-MS data for TargetSearch Package. biocViews: ExperimentData, Escherichia_coli_Data Author: Alvaro Cuadros-Inostroza, Henning Redestig, Matt Hannah Maintainer: Alvaro Cuadros-Inostroza git_url: https://git.bioconductor.org/packages/TargetSearchData git_branch: RELEASE_3_13 git_last_commit: 6c286fc git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/TargetSearchData_1.30.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: TargetSearch dependencyCount: 0 Package: tartare Version: 1.6.0 Depends: R (>= 3.6), AnnotationHub (>= 2.16), ExperimentHub (>= 1.0) Imports: utils Suggests: BiocStyle, knitr, testthat, tools License: GPL-3 MD5sum: ecfaf9429a8eaa407532900e92bd29cf 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 rawDiag package (Trachsel, 2018 ) and the Spectra MsBackends. biocViews: ExperimentData, MassSpectrometryData, ExperimentHub Author: Christian Panse [aut, cre] (), Tobias Kockmann [aut] () Maintainer: Christian Panse URL: https://github.com/cpanse/tartare VignetteBuilder: knitr BugReports: https://github.com/cpanse/tartare/issues git_url: https://git.bioconductor.org/packages/tartare git_branch: RELEASE_3_13 git_last_commit: 882806f git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/tartare_1.6.0.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: rawrr dependencyCount: 88 Package: TBX20BamSubset Version: 1.28.0 Depends: Rsamtools (>= 1.9.8) Imports: xtable License: LGPL MD5sum: 5d29a3f0b8a3a07f1f12d6aa845f8812 NeedsCompilation: no Title: Subset of BAM files from the "TBX20" experiment Description: Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. A subset of the RNA-Seq data. biocViews: ExperimentData, SequencingData, RNASeqData Author: D. Bindreither Maintainer: D. Bindreither git_url: https://git.bioconductor.org/packages/TBX20BamSubset git_branch: RELEASE_3_13 git_last_commit: 8dcef47 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/TBX20BamSubset_1.28.0.tar.gz vignettes: vignettes/TBX20BamSubset/inst/doc/TBX20BamSubset.pdf vignetteTitles: TBX20 RNA-Seq data subset hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TBX20BamSubset/inst/doc/TBX20BamSubset.R importsMe: Rmmquant suggestsMe: APAlyzer dependencyCount: 30 Package: TCGAbiolinksGUI.data Version: 1.12.0 Depends: R (>= 3.5.0) Suggests: BiocStyle, knitr, readr, DT License: GPL-3 MD5sum: ecdc0b5edcfbb9def3f3d4cc9532ef8b NeedsCompilation: no Title: Data for the TCGAbiolinksGUI package Description: Supporting data for the TCGAbiolinksGUI package. biocViews: AssayDomainData, TechnologyData, OrganismData Author: Tiago Chedraoui Silva Maintainer: Tiago Chedraoui Silva URL: https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data VignetteBuilder: knitr BugReports: https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data/issues git_url: https://git.bioconductor.org/packages/TCGAbiolinksGUI.data git_branch: RELEASE_3_13 git_last_commit: f77c3a7 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/TCGAbiolinksGUI.data_1.12.0.tar.gz vignettes: vignettes/TCGAbiolinksGUI.data/inst/doc/vignettes.html vignetteTitles: Supporting data for the TCGAbiolinksGUI package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TCGAbiolinksGUI.data/inst/doc/vignettes.R dependsOnMe: TCGAbiolinksGUI importsMe: TCGAbiolinks dependencyCount: 0 Package: TCGAcrcmiRNA Version: 1.12.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 989d5ab3ad2b4d8070824182fcba2dea NeedsCompilation: no Title: TCGA CRC 450 miRNA dataset Description: colorectal cancer miRNA profile provided by TCGA biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/TCGAcrcmiRNA git_branch: RELEASE_3_13 git_last_commit: adc9511 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/TCGAcrcmiRNA_1.12.0.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: 1.12.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: a1d330b19a2c72caad32e08c96cb338b NeedsCompilation: no Title: TCGA CRC 450 mRNA dataset Description: colorectal cancer mRNA profile provided by TCGA biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/TCGAcrcmRNA git_branch: RELEASE_3_13 git_last_commit: 0607425 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/TCGAcrcmRNA_1.12.0.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: 1.28.0 License: GPL-2 MD5sum: 6021f590abab04702f5d0d936573eea3 NeedsCompilation: no Title: The Cancer Genome Atlas Illumina 450k methylation example data Description: The Cancer Genome Atlas (TCGA) is applying genomics technologies to over 20 different types of cancer. This package contains a small set of 450k array data in idat format. biocViews: Genome, CancerData, MethylationArrayData Author: Sean Davis Maintainer: Sean Davis git_url: https://git.bioconductor.org/packages/TCGAMethylation450k git_branch: RELEASE_3_13 git_last_commit: 6e29401 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/TCGAMethylation450k_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: methylumi dependencyCount: 0 Package: tcgaWGBSData.hg19 Version: 1.10.0 Depends: R (>= 3.5.0), ExperimentHub Imports: bsseq, knitr License: GPL-2 MD5sum: 4fc6c365bf5281bb345b54ceb64cb17e NeedsCompilation: no Title: Data Description: Data package for WGBS Data in TCGA. Data is stored as SummarizedExperiment Format. See vignette on how to extract the data and perform differential methylation analysis. biocViews: Genome, SequencingData, ExperimentData, Homo_sapiens_Data, CancerData Author: Divy Kangeyan Maintainer: Divy Kangeyan VignetteBuilder: knitr BugReports: https://github.com/aryeelab/tcgaWGBSData.hg19/issues git_url: https://git.bioconductor.org/packages/tcgaWGBSData.hg19 git_branch: RELEASE_3_13 git_last_commit: d16de6f git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/tcgaWGBSData.hg19_1.10.0.tar.gz vignettes: vignettes/tcgaWGBSData.hg19/inst/doc/tcgaWGBSData.hg19.html vignetteTitles: Vignette Title hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tcgaWGBSData.hg19/inst/doc/tcgaWGBSData.hg19.R dependencyCount: 141 Package: TCGAWorkflowData Version: 1.16.0 Depends: R (>= 3.5.0) Imports: SummarizedExperiment Suggests: knitr, rmarkdown, pander, testthat License: GPL-3 MD5sum: 5d3d1ac24a6cd403ec5fbfc46f8ef301 NeedsCompilation: no Title: Data for TCGA Workflow Description: This experimental data package contains 11 data sets necessary to follow the "TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages". biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData, CancerData Author: Tiago Chedraoui Silva Maintainer: Tiago Chedraoui Silva URL: https://f1000research.com/articles/5-1542/v2 VignetteBuilder: knitr BugReports: https://github.com/BioinformaticsFMRP/TCGAWorkflow/issues git_url: https://git.bioconductor.org/packages/TCGAWorkflowData git_branch: RELEASE_3_13 git_last_commit: 8b21eaf git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/TCGAWorkflowData_1.16.0.tar.gz vignettes: vignettes/TCGAWorkflowData/inst/doc/TCGAWorkflowData.html vignetteTitles: 'Example data for TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages' hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TCGAWorkflowData/inst/doc/TCGAWorkflowData.R importsMe: TCGAWorkflow dependencyCount: 26 Package: TENxBrainData Version: 1.12.0 Depends: SingleCellExperiment, HDF5Array Imports: AnnotationHub (>= 2.9.22), ExperimentHub Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel, data.table License: CC BY 4.0 MD5sum: e650e3566e648efbfd566ac30f7e2de3 NeedsCompilation: no Title: Data from the 10X 1.3 Million Brain Cell Study Description: Single-cell RNA-seq data for 1.3 million brain cells from E18 mice, generated by 10X Genomics. biocViews: SequencingData, RNASeqData, ExpressionData, SingleCellData Author: Aaron Lun [aut], Martin Morgan [aut], Bioconductor Package Maintainer [cre] Maintainer: Bioconductor Package Maintainer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TENxBrainData git_branch: RELEASE_3_13 git_last_commit: ed94852 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/TENxBrainData_1.12.0.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: 101 Package: TENxBUSData Version: 1.6.0 Imports: ExperimentHub, AnnotationHub, utils, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle License: BSD_2_clause + file LICENSE MD5sum: bf5774815f46fd3258bdff49eb22134d NeedsCompilation: no Title: Single cell dataset from 10x in BUS format Description: Download Barcode, UMI, and Set (BUS) format of 10x datasets from within R. This package accompanies the package BUSpaRse, which can load BUS format into R as a sparse matrix, and which has utility functions related to using the C++ command line package bustools. biocViews: SingleCellData, SequencingData, ExperimentHub, ExperimentData, ExpressionData Author: Lambda Moses [aut, cre] () Maintainer: Lambda Moses URL: https://github.com/BUStools/TENxBUSData VignetteBuilder: knitr BugReports: https://github.com/BUStools/TENxBUSData/issues git_url: https://git.bioconductor.org/packages/TENxBUSData git_branch: RELEASE_3_13 git_last_commit: 7cfdde0 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/TENxBUSData_1.6.0.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: 88 Package: TENxPBMCData Version: 1.10.0 Depends: SingleCellExperiment, HDF5Array Imports: AnnotationHub, ExperimentHub Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel License: CC BY 4.0 MD5sum: 1232005794a12c65326fffb418c0fdc4 NeedsCompilation: no Title: PBMC data from 10X Genomics Description: Single-cell RNA-seq data for on PBMC cells, generated by 10X Genomics. biocViews: SequencingData, RNASeqData, ExpressionData, ExperimentHub, ExperimentData, SingleCellData Author: Kasper D. Hansen [aut], Davide Risso [aut], Milan Malfait [ctb], Jeroen Gilis [ctb], Theodore Killian [ctb], Murat Cem Kose [ctb], Chong Tang [ctb], Teun van den Brand [ctb], Dania Machlab [ctb], Stephanie Hicks [aut, cre] Maintainer: Stephanie Hicks VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TENxPBMCData git_branch: RELEASE_3_13 git_last_commit: b7b97cf git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/TENxPBMCData_1.10.0.tar.gz vignettes: vignettes/TENxPBMCData/inst/doc/TENxPBMCData.html vignetteTitles: Obtaining scRNA-seq data on PBMCs from 10X Genomics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TENxPBMCData/inst/doc/TENxPBMCData.R importsMe: singleCellTK suggestsMe: celda, ExperimentSubset, fcoex, glmGamPoi, iSEE, mbkmeans, schex, scone, scry dependencyCount: 101 Package: TENxVisiumData Version: 1.0.2 Depends: ExperimentHub, SpatialExperiment Imports: utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 27d3f3e35ac5cd88a6ce002b49f7edfe 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] () Maintainer: Helena L. Crowell URL: https://github.com/helenalc/TENxVisiumData VignetteBuilder: knitr BugReports: https://github.com/helenalc/TENxVisiumData/issues git_url: https://git.bioconductor.org/packages/TENxVisiumData git_branch: RELEASE_3_13 git_last_commit: b221c93 git_last_commit_date: 2021-08-20 Date/Publication: 2021-08-21 source.ver: src/contrib/TENxVisiumData_1.0.2.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 dependencyCount: 124 Package: timecoursedata Version: 1.2.0 Depends: R (>= 4.0), SummarizedExperiment Suggests: testthat (>= 1.0.0), knitr, rmarkdown, covr, BiocStyle License: BSD 3-clause License + file LICENSE MD5sum: b3e3975ae4d672f6bba646120d06c66e NeedsCompilation: no Title: A data package for timecourse RNA-seq and microarray gene expression data sets Description: This data package contains timecourse gene expression data sets. The first dataset, from Shoemaker et al, consists of microarray samples from lung tissue of mice exposed to different influenzy strains from 14 timepoints. The two other datasets are leaf and root samples from sorghum crops exposed to pre- and post-flowering drought stress and a control condition, sampled across the plants lifetime. biocViews: ExpressionData, MicroarrayData, RNASeqData Author: Elizabeth Purdom [aut] (), Nelle Varoquaux [aut, cre] () Maintainer: Nelle Varoquaux VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/timecoursedata git_branch: RELEASE_3_13 git_last_commit: 35a7150 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/timecoursedata_1.2.0.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: 26 Package: TimerQuant Version: 1.22.0 Depends: shiny Imports: ggplot2, grid, gridExtra, deSolve, dplyr, locfit Suggests: BiocStyle, reshape2, knitr, shinyBS License: Artistic-2.0 MD5sum: c1a73bf59a651606dcbfaba6cea1cd40 NeedsCompilation: no Title: Timer Quantification Description: Supplementary Data package for tandem timer methods paper by Barry et al. (2015) including TimerQuant shiny applications. biocViews: ExperimentData, Danio_rerio_Data, HighThroughputImagingData, Tissue Author: Joseph Barry Maintainer: Joseph Barry VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TimerQuant git_branch: RELEASE_3_13 git_last_commit: 5cb266e git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/TimerQuant_1.22.0.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: 66 Package: tinesath1cdf Version: 1.30.0 License: Artistic-2.0 MD5sum: ba2f604556b939a161447a57dc5a82f7 NeedsCompilation: no Title: tinesath1cdf Description: A package containing an environment represeting the newcdf/tinesATH1.cdf.cdf file. biocViews: Arabidopsis_thaliana_Data, ChipOnChipData Author: Tine Casneuf Maintainer: Tine Casneuf git_url: https://git.bioconductor.org/packages/tinesath1cdf git_branch: RELEASE_3_13 git_last_commit: 6694a9b git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/tinesath1cdf_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: XhybCasneuf dependencyCount: 0 Package: tinesath1probe Version: 1.30.0 Depends: R (>= 1.6), AnnotationDbi (>= 1.11.9) License: LGPL MD5sum: e0c90118936724b34319f6ad5af43d91 NeedsCompilation: no Title: Probe sequence data for microarrays of type tinesath1 Description: This package was automatically created by package matchprobes version 1.4.0. The probe sequence data was obtained from http://www.affymetrix.com. biocViews: Arabidopsis_thaliana_Data, SequencingData, MicroarrayData Author: The Bioconductor Project www.bioconductor.org Maintainer: Tine Casneuf git_url: https://git.bioconductor.org/packages/tinesath1probe git_branch: RELEASE_3_13 git_last_commit: 4818dbe git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/tinesath1probe_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 46 Package: tissueTreg Version: 1.12.0 Depends: R (>= 3.5) Suggests: BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq, SummarizedExperiment License: GPL (>= 2) MD5sum: dc684fb688afa14b90ac612636efd8b0 NeedsCompilation: no Title: TWGBS and RNA-seq data from tissue T regulatory cells from mice Description: The package provides ready to use epigenomes (obtained from TWGBS) and transcriptomes (RNA-seq) from various tissues as obtained in the study (Delacher and Imbusch 2017, PMID: 28783152). Regulatory T cells (Treg cells) perform two distinct functions: they maintain self-tolerance, and they support organ homeostasis by differentiating into specialized tissue Treg cells. The underlying dataset characterises the epigenetic and transcriptomic modifications for specialized tissue Treg cells. biocViews: ExperimentData, Tissue, Mus_musculus_Data, SequencingData, RNASeqData Author: Charles Imbusch [aut, cre], Michael Delacher [aut], Markus Feuerer [aut], Benedikt Brors [aut] Maintainer: Charles Imbusch URL: https://github.com/cimbusch/tissueTreg VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tissueTreg git_branch: RELEASE_3_13 git_last_commit: f079a48 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/tissueTreg_1.12.0.tar.gz vignettes: vignettes/tissueTreg/inst/doc/tissueTreg.html vignetteTitles: tissueTreg hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tissueTreg/inst/doc/tissueTreg.R dependencyCount: 0 Package: TMExplorer Version: 1.2.1 Depends: R (>= 4.1), SingleCellExperiment, BiocFileCache Imports: methods, Matrix Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: b42852421615a0e7eb8379073b86d862 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], Parisa Shooshtari [aut] Maintainer: Erik Christensen VignetteBuilder: knitr BugReports: https://github.com/shooshtarilab/TMExplorer/issues git_url: https://git.bioconductor.org/packages/TMExplorer git_branch: RELEASE_3_13 git_last_commit: 80da7f6 git_last_commit_date: 2021-05-20 Date/Publication: 2021-05-22 source.ver: src/contrib/TMExplorer_1.2.1.tar.gz vignettes: vignettes/TMExplorer/inst/doc/TMExplorer.html vignetteTitles: TMExplorer hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TMExplorer/inst/doc/TMExplorer.R dependencyCount: 68 Package: tofsimsData Version: 1.20.0 Depends: R (>= 3.2.0) Suggests: knitr, rmarkdown, tools License: GPL-3 MD5sum: faa14048378ff09cab38277707999401 NeedsCompilation: no Title: Import, process and analysis of ToF-SIMS imaging data Description: This packages contains data to be used with the 'tofsims' package. biocViews: ExperimentData, MassSpectrometry, ImagingMassSpectrometry, DataImport Author: Lorenz Gerber, Viet Mai Hoang Maintainer: Lorenz Gerber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tofsimsData git_branch: RELEASE_3_13 git_last_commit: 4575656 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/tofsimsData_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: tofsims dependencyCount: 0 Package: topdownrdata Version: 1.14.0 Depends: topdownr License: GPL (>= 3) MD5sum: c317cf1ef1c14b5ad0675a4fefafa7ab NeedsCompilation: no Title: Example Files for the topdownr R Package Description: Example data for the topdownr package generated on a Thermo Orbitrap Fusion Lumos MS device. biocViews: ExperimentData, MassSpectrometryData Author: Sebastian Gibb [aut, cre], Pavel Shliaha [aut], Ole Nørregaard Jensen [aut] Maintainer: Sebastian Gibb URL: https://github.com/sgibb/topdownrdata/ BugReports: https://github.com/sgibb/topdownrdata/issues/ git_url: https://git.bioconductor.org/packages/topdownrdata git_branch: RELEASE_3_13 git_last_commit: 599265f git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/topdownrdata_1.14.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: topdownr dependencyCount: 85 Package: tweeDEseqCountData Version: 1.30.0 Depends: Biobase, R (>= 2.10) License: GPL (>=2) MD5sum: bca5308c4ccc5a06bdca06eca68e0bf8 NeedsCompilation: no Title: RNA-seq count data employed in the vignette of the tweeDEseq package Description: RNA-seq count data from Pickrell et al. (2010) employed to illustrate the use of the Poisson-Tweedie family of distributions with the tweeDEseq package. biocViews: Genome, Homo_sapiens_Data, RNASeqData Author: Juan R Gonzalez and Mikel Esnaola (with contributions from Robert Castelo ) Maintainer: Juan R Gonzalez URL: http://www.creal.cat/jrgonzalez/software.htm git_url: https://git.bioconductor.org/packages/tweeDEseqCountData git_branch: RELEASE_3_13 git_last_commit: 34e153b git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/tweeDEseqCountData_1.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSAR, missMethyl, tweeDEseq dependencyCount: 7 Package: tximportData Version: 1.20.0 Suggests: knitr, markdown License: GPL (>= 2) MD5sum: 7175bf7099b0f2b32aea15f2444016ca NeedsCompilation: no Title: tximportData Description: This package provides the output of running various transcript abundance quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project. The quantifiers were Cufflinks, RSEM, kallisto, Salmon and Sailfish. For details on version numbers, sample information, and details on calls, see the package vignette. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tximportData git_branch: RELEASE_3_13 git_last_commit: 28a9fb8 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/tximportData_1.20.0.tar.gz vignettes: vignettes/tximportData/inst/doc/tximportData.html vignetteTitles: Sample output files for tximport hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tximportData/inst/doc/tximportData.R suggestsMe: crossmeta, DESeq2, fishpond, HumanTranscriptomeCompendium, tximeta, tximport, variancePartition dependencyCount: 0 Package: VariantToolsData Version: 1.16.0 Depends: R (>= 2.10), VariantAnnotation (>= 1.7.35) Imports: BiocGenerics, GenomicRanges Suggests: VariantTools (>= 1.3.4), gmapR (>= 1.3.3), BiocStyle License: Artistic-2.0 MD5sum: 9b20477595a3dbc80cc4cbc538d1f280 NeedsCompilation: no Title: Data for the VariantTools tutorial Description: Data from the sequencing of a 50/50 mixture of HapMap trio samples NA12878 (CEU) and NA19240 (YRI), subset to the TP53 region. biocViews: ExperimentData, SequencingData, HapMap, SNPData Author: Michael Lawrence Maintainer: Michael Lawrence git_url: https://git.bioconductor.org/packages/VariantToolsData git_branch: RELEASE_3_13 git_last_commit: 77f6b94 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/VariantToolsData_1.16.0.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: 98 Package: vulcandata Version: 1.14.0 Imports: utils License: LGPL-3 MD5sum: 99b8f3d74364c38f43d20927e4f9230c NeedsCompilation: no Title: VirtUaL ChIP-Seq data Analysis using Networks, dummy dataset Description: This package provides a dummy regulatory network and ChIP-Seq dataset for running examples in the vulcan package biocViews: ExperimentData, Homo_sapiens_Data, CancerData, ChIPSeqData Author: Federico M. Giorgi, Andrew N. Holding, Florian Markowetz Maintainer: Federico M. Giorgi git_url: https://git.bioconductor.org/packages/vulcandata git_branch: RELEASE_3_13 git_last_commit: a4c773d git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/vulcandata_1.14.0.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: WES.1KG.WUGSC Version: 1.24.0 License: GPL-2 MD5sum: 8fd91edcd1e8eec76c25c77058a4beaa NeedsCompilation: no Title: Whole Exome Sequencing (WES) of chromosome 22 401st to 500th exon from the 1000 Genomes (1KG) Project by the Washington University Genome Sequencing Center (WUGSC). Description: The assembled .bam files of whole exome sequencing data from the 1000 Genomes Project. 46 samples sequenced by the Washington University Genome Sequencing Center are included. biocViews: ExperimentData, Project1000genomes, SequencingData, DNASeqData, Homo_sapiens_Data Author: Yuchao Jiang, Nancy R. Zhang Maintainer: Yuchao Jiang git_url: https://git.bioconductor.org/packages/WES.1KG.WUGSC git_branch: RELEASE_3_13 git_last_commit: c65166f git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/WES.1KG.WUGSC_1.24.0.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: 1.4.0 Depends: R (>= 3.6.0), GenomicRanges License: GPL-2 MD5sum: e79a906c56d93dfdd14f85e88c7436a3 NeedsCompilation: no Title: Mappability tracks of Whole-genome Sequencing from the ENCODE Project Description: This package provides whole-genome mappability tracks on human hg19/hg38 assembly. We employed the 100-mers mappability track from the ENCODE Project and computed weighted average of the mappability scores if multiple ENCODE regions overlap with the same bin. “Blacklist” bins, including segmental duplication regions and gaps in reference assembly from telomere, centromere, and/or heterochromatin regions are included. The dataset consists of three assembled .bam files of single-cell whole genome sequencing from 10X for illustration purposes. biocViews: ExperimentData, SequencingData, DNASeqData, SingleCellData, Homo_sapiens_Data, Genome, ENCODE Author: Rujin Wang Maintainer: Rujin Wang git_url: https://git.bioconductor.org/packages/WGSmapp git_branch: RELEASE_3_13 git_last_commit: adbeb81 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/WGSmapp_1.4.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: SCOPE dependencyCount: 17 Package: XhybCasneuf Version: 1.30.0 Depends: R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf , RColorBrewer , methods, grid License: Artistic-2.0 MD5sum: ed70932ad60da477a9883cb0e54bea86 NeedsCompilation: no Title: EBI/PSB cross-hybridisation study package Description: Cross-hybridisation study on the ATH1 Affymetrix GeneChip biocViews: ExperimentData, Tissue, MicroarrayData, TissueMicroarrayData Author: Tineke Casneuf Maintainer: Tineke Casneuf git_url: https://git.bioconductor.org/packages/XhybCasneuf git_branch: RELEASE_3_13 git_last_commit: 64387a9 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/XhybCasneuf_1.30.0.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: 1.32.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 5a167c3195790834046e3f99748d5d63 NeedsCompilation: no Title: Spellman et al. (1998) and Pramila/Breeden (2006) yeast cell cycle microarray data Description: ExpressionSet for Spellman et al. (1998) yeast cell cycle microarray experiment biocViews: ExperimentData, CellCulture, Saccharomyces_cerevisiae_Data, CancerData, MicroarrayData, OneChannelData, GEO Author: Sandrine Dudoit Maintainer: Sandrine Dudoit git_url: https://git.bioconductor.org/packages/yeastCC git_branch: RELEASE_3_13 git_last_commit: e15a70a git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/yeastCC_1.32.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: LiquidAssociation suggestsMe: fastLiquidAssociation, ibh dependencyCount: 7 Package: yeastExpData Version: 0.38.0 Depends: R (>= 2.4), graph (>= 1.9.26) Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db License: GPL MD5sum: ec5013a5289f2bd53a5e2a6208aaf28b NeedsCompilation: no Title: Yeast Experimental Data Description: A collection of different sets of experimental data from yeast. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data Author: R. Gentleman Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/yeastExpData git_branch: RELEASE_3_13 git_last_commit: 4f4384f git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/yeastExpData_0.38.0.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, ppiStats dependencyCount: 8 Package: yeastGSData Version: 0.30.0 License: Artistic-2.0 MD5sum: 4916cc5d72397431533411c4758bddf0 NeedsCompilation: no Title: Yeast Gold Standard Data Description: A collection of so-called gold (and other) standard data sets biocViews: ExperimentData, Saccharomyces_cerevisiae_Data Author: R. Gentleman Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/yeastGSData git_branch: RELEASE_3_13 git_last_commit: c83e841 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/yeastGSData_0.30.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: yeastNagalakshmi Version: 1.28.0 License: Artistic-2.0 MD5sum: 2a2c93a53d86b9e09b17caaaaf401216 NeedsCompilation: no Title: Yeast genome RNA sequencing data based on Nagalakshmi et. al. Description: The yeast genome data was retrieved from the sequence read archive, aligned with bwa, and converted to BAM format with samtools. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, SequencingData, BiocViews, ChIPSeqData Author: Martin Morgan Maintainer: Bioconductor Package Maintainer git_url: https://git.bioconductor.org/packages/yeastNagalakshmi git_branch: RELEASE_3_13 git_last_commit: 3334a77 git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/yeastNagalakshmi_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ShortRead dependencyCount: 0 Package: yeastRNASeq Version: 0.30.0 Depends: R (>= 2.4) Suggests: Biobase, ShortRead, IRanges License: GPL MD5sum: 4ad87f08a56cc3a03e100a1cdb507e7f NeedsCompilation: no Title: Yeast RNA-Seq Experimental Data from Lee et al. 2008 Description: A selection of RNA-Seq data from a yeast transcriptome experiment. biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData Author: James H. Bullard and Kasper D. Hansen Maintainer: J. Bullard git_url: https://git.bioconductor.org/packages/yeastRNASeq git_branch: RELEASE_3_13 git_last_commit: 739956c git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/yeastRNASeq_0.30.0.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: 1.12.0 Depends: R (>= 2.10) Suggests: BiocStyle, knitr License: GPL MD5sum: b8d149b3c2ddb73299113559f0b83d9d NeedsCompilation: no Title: Zebrafish RNA-Seq Experimental Data from Ferreira et al. (2014) Description: Gene-level read counts from RNA-Seq for gallein-treated and control zebrafish. biocViews: ExperimentData, Danio_rerio_Data, RNASeqData Author: Davide Risso Maintainer: Davide Risso VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/zebrafishRNASeq git_branch: RELEASE_3_13 git_last_commit: 935cbbc git_last_commit_date: 2021-05-19 Date/Publication: 2021-05-20 source.ver: src/contrib/zebrafishRNASeq_1.12.0.tar.gz vignettes: vignettes/zebrafishRNASeq/inst/doc/preprocessing.pdf vignetteTitles: Pre-Processing for the Zebrafish RNA-Seq Gene-Level Counts hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/zebrafishRNASeq/inst/doc/preprocessing.R suggestsMe: RUVSeq, sva dependencyCount: 0 Package: facsDorit Version: 1.34.0 Depends: R (>= 1.9.1), prada (>= 1.0.5) License: GPL-2 Title: DKFZ FACS example data Description: FACS example data for cell-based assays. This data is used in the examples and vignettes of the package prada. biocViews: ExperimentData, MicrotitrePlateAssayData Author: Florian Hahne Maintainer: Florian Hahne URL: http://www.dkfz.de/mga PackageStatus: Deprecated Package: hmyriB36 Version: 1.28.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.5.5), GGBase Suggests: GGtools, illuminaHumanv1.db License: Artistic-2.0 Title: YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes Description: YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes biocViews: ExperimentData, Genome, SNPData, HapMap Author: Vincent Carey Maintainer: Vincent Carey PackageStatus: Deprecated Package: ceuhm3 Version: 0.30.0 Depends: R (>= 2.12.0), GGBase, Biobase Imports: GGtools License: Artistic-2.0 Title: ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort Description: ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort biocViews: SNPData, HapMap Author: VJ Carey Maintainer: VJ Carey PackageStatus: Deprecated Package: ceu1kg Version: 0.30.0 Depends: R (>= 2.12.0), GGBase (>= 3.9.0), GGtools, Biobase Suggests: SNPlocs.Hsapiens.dbSNP.20101109 License: Artistic-2.0 Title: CEU (N=60) genotypes from 1000 genomes pilot phase I Description: CEU genotypes from 1000 genomes "low coverage" pilot phase I (approx 8 million SNP calls released July 2010); includes Wellcome trust GENEVAR expression for 43 indiv biocViews: SNPData, HapMap, Project1000genomes Author: VJ Carey Maintainer: VJ Carey PackageStatus: Deprecated Package: cgdv17 Version: 0.30.0 Depends: R (>= 2.15), methods, VariantAnnotation (>= 1.15.15) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biobase Suggests: parallel, GGtools, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, illuminaHumanv1.db License: Artistic-2.0 Title: Complete Genomics Diversity Panel, chr17 on 46 individuals Description: Complete Genomics Diversity Panel, chr17 on 46 individuals biocViews: SequencingData, SNPData, BiocViews Author: VJ Carey Maintainer: VJ Carey PackageStatus: Deprecated Package: dsQTL Version: 0.30.0 Depends: R (>= 2.15.0), utils, Biobase, SummarizedExperiment, GGBase (>= 3.31.1) Suggests: GGtools, rtracklayer License: Artistic-2.0 Title: dsQTL, data excerpt from Degner et al. 2012 Nature letter Description: dsQTL, excerpt from Degner et al. 2012 Nature letter on DNA variants associated with DnaseI hypersensitivity biocViews: ExperimentData, Genome, SequencingData, DNASeqData, NCI, Project1000genomes, BiocViews Author: VJ Carey Maintainer: VJ Carey PackageStatus: Deprecated Package: ceu1kgv Version: 0.34.0 Depends: R (>= 3.0), GGBase Imports: Biobase License: Artistic-2.0 Title: expression + genotype on 79 unrelated CEU individuals Description: expression + genotype on 79 unrelated CEU individuals biocViews: ArrayExpress Author: VJ Carey Maintainer: VJ Carey PackageStatus: Deprecated Package: yri1kgv Version: 0.34.0 Depends: GGBase Imports: Biobase License: Artistic-2.0 Title: expression + genotype on 79 unrelated YRI individuals Description: expression + genotype on 79 unrelated YRI individuals biocViews: ArrayExpress Author: VJ Carey Maintainer: VJ Carey PackageStatus: Deprecated Package: gskb Version: 1.24.0 Depends: R (>= 3.2.0) Suggests: PGSEA License: Artistic-2.0 Title: Gene Set data for pathway analysis in mouse Description: Gene Set Knowledgebase (GSKB) is a comprehensive knowledgebase for pathway analysis in mouse. Interpretation of high-throughput genomics data based on biological pathways constitutes a constant challenge, partly because of the lack of supporting pathway database. We created a functional genomics knowledgebase in mouse, which includes 33,261 pathways and gene sets compiled from 40 sources such as Gene Ontology, KEGG, GeneSetDB, PANTHER, microRNA and transcription factor target genes, etc. In addition, we also manually collected and curated 8,747 lists of differentially expressed genes from 2,526 published gene expression studies to enable the detection of similarity to previously reported gene expression signatures. These two types of data constitute a comprehensive Gene Set Knowledgebase (GSKB), which can be readily used by various pathway analysis software such as gene set enrichment analysis (GSEA). As a first step, we gathered annotation information from 40 existing databases for mouse-related gene sets. These gene sets are divided into 7 categories, namely, Gene Ontology, Curated pathways, Metabolic Pathways, Transcription Factor (TF) and microRNA target genes, location (cytogenetics band), and others. We used information in GeneSetDB for some of the databases. Detailed information on these 40 sources and the citations is available http://ge-lab.org/gskb/Table%201-sources.pdf . The gene lists from literature were retrieved manually from individual gene expression studies through a process similar to the one used to create AraPath, a similar resource for Arabidopsis[12]. As most expression studies upload raw data to repositories like GEO and ArrayExpress, we used the meta-data in these databases to search for publications. We scanned all datasets we can found and retrieved 4,313 potentially useful papers reporting gene expression studies in mouse. These papers were individually read by curators to identify lists of differentially expressed genes in various conditions. We compiled a total of 8,747 lists of differently expressed genes from 2,518 of papers. Each gene list was annotated with a unique name, brief description, and publication information, similar to the protocol used in MSigDB and Arapath. These gene lists constitute a large collection of published gene expression signatures that form a foundation for interpret new gene lists and expression profiles. More information about this data is available here http://ge-lab.org/gskb/. There is also a paper describing these data are currently in revision by Database: The Journal of Biological Databases and Curation. biocViews: ExperimentData, Mus_musculus Author: Valerie Bares, Xijin Ge Maintainer: Valerie Bares PackageStatus: Deprecated Package: JctSeqData Version: 1.22.0 Depends: R (>= 3.3) Suggests: knitr, BiocStyle, DESeq2, DEXSeq, edgeR, JunctionSeq License: file LICENSE NeedsCompilation: no Title: Example Junction Count data for use with JunctionSeq Description: Junction count data from an example dataset taken from a subset of the RNA-seq reads from six samples. Data was subsampled and modified to provide edge cases for testing and to reduce file sizes. biocViews: Rattus_norvegicus_Data, ExperimentData, Genome, RNASeqData, RepositoryData, GEO Author: Stephen Hartley [aut, cre] (PhD) Maintainer: Stephen Hartley URL: http://hartleys.github.io/JunctionSeq/ VignetteBuilder: knitr BugReports: http://github.com/hartleys/JunctionSeq/issues PackageStatus: Deprecated