Package: adductData Version: 1.21.0 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: 6f2999e0fca2651356c9ffa871606039 NeedsCompilation: no Title: Data from untargeted MS of modifications to Cys34 of serum albumin Description: mzXML files from Grigoryan et al 2016 (Anal Chem). biocViews: ExperimentData,MassSpectrometryData,ExperimentHub Author: Josie Hayes Maintainer: Josie Hayes VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/adductData git_branch: devel git_last_commit: 0f6c7cb git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/adductData_1.21.0.tar.gz vignettes: vignettes/adductData/inst/doc/adductData.html vignetteTitles: Raw mzXML data using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/adductData/inst/doc/adductData.R dependsOnMe: adductomicsR dependencyCount: 68 Package: affycompData Version: 1.43.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp License: GPL (>= 2) MD5sum: 4a2a7aace94377cbed3b239bfd0320f4 NeedsCompilation: no Title: affycomp data Description: Data needed by the affycomp package. biocViews: MicroarrayData Author: Rafael A. Irizarry and Zhijin Wu with contributions from Simon Cawley Maintainer: Robert D Shear URL: https://bioconductor.org/packages/affycompData BugReports: https://github.com/rafalab/affyCompData/issues git_url: https://git.bioconductor.org/packages/affycompData git_branch: devel git_last_commit: ac63752 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/affycompData_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: affycomp dependencyCount: 7 Package: affydata Version: 1.53.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Imports: methods Suggests: hgu95av2cdf, hgu133acdf License: GPL (>= 2) MD5sum: fcde1af5ce059bd58e0420582d461b65 NeedsCompilation: no Title: Affymetrix Data for Demonstration Purpose Description: Example datasets of a slightly large size. They represent 'real world examples', unlike the artificial examples included in the package affy. biocViews: ExperimentData, Tissue, MicroarrayData, TissueMicroarrayData Author: Laurent Gautier Maintainer: Robert D Shear URL: https://bioconductor.org/packages/affydata BugReports: https://github.com/rafalab/affydata/issues git_url: https://git.bioconductor.org/packages/affydata git_branch: devel git_last_commit: 48ca847 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/affydata_1.53.0.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: Biostrings, Harman, TurboNorm, affyPLM, affy, affycoretools, arrayMvout, bgx, gcrma, mimager, puma, pvac, vsn, RobLoxBioC dependencyCount: 12 Package: Affyhgu133A2Expr Version: 1.41.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 6702ecfec763ed90285e6f20ba497ad2 NeedsCompilation: no Title: Affymetrix Human Genome U133A 2.0 Array (GPL571) Expression Data Package Description: Contains pre-built human (GPL571) databases of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133A2Expr git_branch: devel git_last_commit: 6a6203e git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/Affyhgu133A2Expr_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: Affyhgu133aExpr Version: 1.43.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 50e596a3491ddd9f1377aa4546a926c1 NeedsCompilation: no Title: Affymetrix Human hgu133a Array (GPL96) Expression Data Package Description: Contains pre-built human (GPL96) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133aExpr git_branch: devel git_last_commit: 96b9884 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/Affyhgu133aExpr_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: Affyhgu133Plus2Expr Version: 1.39.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 18cbc82ef16a3eefae93d994cb63a671 NeedsCompilation: no Title: Affyhgu133Plus2Expr (GPL570) Expression Data Package Description: Contains pre-built human (GPL570) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133Plus2Expr git_branch: devel git_last_commit: 0f7a588 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/Affyhgu133Plus2Expr_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: AffymetrixDataTestFiles Version: 0.43.0 Depends: R (>= 2.5.0) License: LGPL-2.1 MD5sum: cf2c0618922d869499d4fb45ac4c5ed0 NeedsCompilation: no Title: Affymetrix Data Files (CEL, CDF, CHP, EXP, PGF, PSI) for Testing Description: This package contains annotation data files and sample data files of Affymetrix file formats. The files originate from the Affymetrix' Fusion SDK distribution and other official sources. biocViews: ExperimentData, MicroarrayData Author: Henrik Bengtsson [aut, cre], James Bullard [aut], Kasper Daniel Hansen [aut] Maintainer: Henrik Bengtsson git_url: https://git.bioconductor.org/packages/AffymetrixDataTestFiles git_branch: devel git_last_commit: 4f9fe69 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/AffymetrixDataTestFiles_0.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: affxparser, affyILM, aroma.affymetrix dependencyCount: 0 Package: Affymoe4302Expr Version: 1.43.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: ab1c8f9ab073d9a293cdd9a2089f65ec NeedsCompilation: no Title: Affymetrix Mouse Genome 430 2.0 Array (GPL1261) Expression Data Package Description: Contains pre-built mouse (GPL1261) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Mus_musculus_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affymoe4302Expr git_branch: devel git_last_commit: 35741bc git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/Affymoe4302Expr_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: airway Version: 1.25.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: knitr, GEOquery, markdown License: LGPL MD5sum: 8821d2fe3ad502c00c157d6599ea50b8 NeedsCompilation: no Title: RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014 Description: This package provides a RangedSummarizedExperiment object of read counts in genes for an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. Details on the gene model and read counting procedure are provided in the package vignette. The citation for the experiment is: Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri R Jr, Tantisira KG, Weiss ST, Lu Q. 'RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells.' PLoS One. 2014 Jun 13;9(6):e99625. PMID: 24926665. GEO: GSE52778. biocViews: ExperimentData, SequencingData, RNASeqData, GEO Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/airway git_branch: devel git_last_commit: ac6837b git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/airway_1.25.0.tar.gz vignettes: vignettes/airway/inst/doc/airway.html vignetteTitles: Airway smooth muscle cells hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/airway/inst/doc/airway.R dependsOnMe: rnaseqGene importsMe: NetActivity, consensusDE suggestsMe: BioCor, BiocSet, CeTF, DESeq2, DelayedArray, EnhancedVolcano, EnrichmentBrowser, ExperimentSubset, IHW, InteractiveComplexHeatmap, OPWeight, PCAtools, Rvisdiff, SummarizedExperiment, TTMap, apeglm, awst, biobroom, gg4way, iSEEde, iSEEpathways, iSEEu, ideal, pathwayPCA, pcaExplorer, progeny, runibic, weitrix, IHWpaper, RegParallel, seqgendiff dependencyCount: 36 Package: ALL Version: 1.47.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Suggests: rpart License: Artistic-2.0 MD5sum: e09ed8b2e4fe15cbb5308cfbab038b0f NeedsCompilation: no Title: A data package Description: Data of T- and B-cell Acute Lymphocytic Leukemia from the Ritz Laboratory at the DFCI (includes Apr 2004 versions) biocViews: ExperimentData, CancerData, LeukemiaCancerData Author: Xiaochun Li Maintainer: Robert Gentleman git_url: https://git.bioconductor.org/packages/ALL git_branch: devel git_last_commit: 2b00f16 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/ALL_1.47.0.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: BioNet, Biobase, Category, CellMapper, ChromHeatMap, EnrichmentBrowser, GOstats, GSAR, GSEAlm, GeneSelectMMD, MLInterfaces, ReportingTools, SNAGEE, a4Base, a4Classif, a4Preproc, a4, clipper, esetVis, genefilter, graphite, npGSEA, pathRender, rScudo, topGO, SNAGEEdata, MMDvariance, nlcv dependencyCount: 6 Package: ALLMLL Version: 1.45.0 Depends: R (>= 2.10), affy (>= 1.23.4) License: GPL-2 MD5sum: cacbfd1827547ef23048299c7690c5a2 NeedsCompilation: no Title: A subset of arrays from a large acute lymphoblastic leukemia (ALL) study Description: This package provides probe-level data for 20 HGU133A and 20 HGU133B arrays which are a subset of arrays from a large ALL study. The data is for the MLL arrays. This data was published in Mary E. Ross, Xiaodong Zhou, Guangchun Song, Sheila A. Shurtleff, Kevin Girtman, W. Kent Williams, Hsi-Che Liu, Rami Mahfouz, Susana C. Raimondi, Noel Lenny, Anami Patel, and James R. Downing (2003) Classification of pediatric acute lymphoblastic leukemia by gene expression profiling Blood 102: 2951-2959 biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData Author: B. M. Bolstad git_url: https://git.bioconductor.org/packages/ALLMLL git_branch: devel git_last_commit: be4af05 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/ALLMLL_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQualityMetrics, pvac dependencyCount: 12 Package: AmpAffyExample Version: 1.45.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Suggests: hgu133acdf License: LGPL (>= 2) MD5sum: cbcaad94efc86b7f771861598a418139 NeedsCompilation: no Title: Example of Amplified Data Description: Six arrays. Three from amplified RNA, three from the typical procedure. biocViews: ExperimentData, MicroarrayData Author: Rafael A. Irizarry Maintainer: Robert D Shear URL: https://bioconductor.org/packages/AmpAffyExample BugReports: https://github.com/rafalab/AmpAffyExample/issues git_url: https://git.bioconductor.org/packages/AmpAffyExample git_branch: devel git_last_commit: 03e3dc0 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/AmpAffyExample_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: AffyRNADegradation dependencyCount: 12 Package: AneuFinderData Version: 1.33.0 Depends: R (>= 3.3) License: file LICENSE MD5sum: d68455035ffec8a98f153aae21b9cd29 NeedsCompilation: no Title: WGSCS Data for Demonstration Purposes Description: Whole-genome single cell sequencing data for demonstration purposes in the AneuFinder package. biocViews: CopyNumberVariationData, LungCancerData, Homo_sapiens_Data, SequencingData Author: Aaron Taudt Maintainer: Aaron Taudt git_url: https://git.bioconductor.org/packages/AneuFinderData git_branch: devel git_last_commit: 64adf44 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/AneuFinderData_1.33.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: AneuFinder dependencyCount: 0 Package: antiProfilesData Version: 1.41.0 Depends: Biobase, Suggests: frma, GEOquery, GEOmetadb License: Artistic-2.0 MD5sum: 78cdf58c935b2e6d2bbd053938d45092 NeedsCompilation: no Title: Normal colon and cancer preprocessed affy data for antiProfile building. Description: Colon normal tissue and cancer samples used in Corrada Bravo, et al. gene expression anti-profiles paper: BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272. Measurements are z-scores obtained from the GeneExpression Barcode in the 'frma' package biocViews: ExperimentData, MicroarrayData, Tissue, CancerData, ColonCancerData Author: Hector Corrada Bravo, Matthew McCall and Rafael A. Irizarry Maintainer: Hector Corrada Bravo git_url: https://git.bioconductor.org/packages/antiProfilesData git_branch: devel git_last_commit: 53e10f1 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/antiProfilesData_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: antiProfiles, epivizrChart, epivizr, messina dependencyCount: 6 Package: aracne.networks Version: 1.31.0 Depends: R (>= 3.3), viper License: file LICENSE MD5sum: dc0c2e1b1bd046f5b7acc2179a037287 NeedsCompilation: no Title: ARACNe-inferred gene networks from TCGA tumor datasets Description: This package contains ARACNe-inferred networks from TCGA tumor datasets. It also contains a function to export them into plain-text format. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData Author: Federico M. Giorgi Maintainer: Federico M. Giorgi , Mariano Alvarez git_url: https://git.bioconductor.org/packages/aracne.networks git_branch: devel git_last_commit: d086378 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/aracne.networks_1.31.0.tar.gz vignettes: vignettes/aracne.networks/inst/doc/aracne.networks.pdf vignetteTitles: Using aracne.networks hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/aracne.networks/inst/doc/aracne.networks.R dependencyCount: 90 Package: ARRmData Version: 1.41.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: 3572bff3528a4b410e7cae12291341b8 NeedsCompilation: no Title: Example dataset for normalization of Illumina 450k Methylation data Description: Raw Beta values from 36 samples across 3 groups from Illumina 450k methylation arrays biocViews: ExperimentData, MethylationArrayData Author: Jean-Philippe Fortin, Celia M.T. Greenwood, Aurelie Labbe Maintainer: Jean-Philippe Fortin git_url: https://git.bioconductor.org/packages/ARRmData git_branch: devel git_last_commit: 1831c7c git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/ARRmData_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ARRmNormalization dependencyCount: 0 Package: AshkenazimSonChr21 Version: 1.35.0 Suggests: knitr, VariantAnnotation License: Artistic-2.0 MD5sum: 26fde4a9ac891713b080e59bdf14a12c NeedsCompilation: no Title: Annotated variants on the chromosome 21, human genome 19, Ashkenazim Trio son sample Description: SonVariantsChr21 is a dataset of annotated genomic variants coming from Complete Genomics whole genome sequencing. Data comes from GIAB project, Ashkenazim Trio, sample HG002 run 1. Both vcf and annotated data frame are provided. biocViews: GenomicVariation, Sequencing, WholeGenome Author: Tomasz Stokowy Maintainer: Who to complain to VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/AshkenazimSonChr21 git_branch: devel git_last_commit: 716ae65 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/AshkenazimSonChr21_1.35.0.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: 1.25.0 Depends: R (>= 3.5) Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 05e454066adedf1e16b62b2941a3d9f6 NeedsCompilation: no Title: Example of 1D NMR spectra data for ASICS package Description: 1D NMR example spectra and additional data for use with the ASICS package. Raw 1D Bruker spectral data files were found in the MetaboLights database (https://www.ebi.ac.uk/metabolights/, study MTBLS1). biocViews: ExperimentData, Homo_sapiens_Data Author: Gaëlle Lefort [aut, cre], Rémi Servien [aut], Nathalie Villa-Vialaneix [aut] Maintainer: Gaëlle Lefort VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ASICSdata git_branch: devel git_last_commit: 6664ec5 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/ASICSdata_1.25.0.tar.gz vignettes: vignettes/ASICSdata/inst/doc/ASICSdata.html vignetteTitles: ASICSdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ASICS dependencyCount: 0 Package: bcellViper Version: 1.41.0 Depends: R(>= 2.14.0), Biobase, methods License: GPL (>=2) MD5sum: dbeead015dd8ba22070e34265b91c165 NeedsCompilation: no Title: Human B-cell transcriptional interactome and normal human B-cell expression data Description: This package provides a human B-cell context-specific transcriptional regulatory network and a human normal B-cells dataset for the examples in package viper. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData Author: Mariano Javier Alvarez Maintainer: Mariano Javier Alvarez git_url: https://git.bioconductor.org/packages/bcellViper git_branch: devel git_last_commit: 58ec361 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/bcellViper_1.41.0.tar.gz vignettes: vignettes/bcellViper/inst/doc/bcellViper.pdf vignetteTitles: Using bcellViper hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bcellViper/inst/doc/bcellViper.R importsMe: dorothea suggestsMe: GenomicSuperSignature, pageRank, viper dependencyCount: 6 Package: beadarrayExampleData Version: 1.43.0 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>= 2.0.0) License: GPL-2 MD5sum: f226a8a390c6bd4b7b29d9fe1daba195 NeedsCompilation: no Title: Example data for the beadarray package Description: An small dataset that can be used to run examples from the beadarray vignette and examples biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/beadarrayExampleData git_branch: devel git_last_commit: 3ca3b75 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/beadarrayExampleData_1.43.0.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: MiRaGE, beadarray, RobLoxBioC dependencyCount: 81 Package: BeadArrayUseCases Version: 1.43.0 Imports: beadarray (>= 2.3.18), limma, GEOquery Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db License: GPL-2 MD5sum: 6540429ac7c52046a6bf1aa3c7eb2100 NeedsCompilation: no Title: Analysing Illumina BeadArray expression data using Bioconductor Description: Example data files and use cases for processing Illumina BeadArray expression data using Bioconductor biocViews: MicroarrayData Author: Mark Dunning, Wei Shi, Andy Lynch, Mike Smith, Matt Ritchie Maintainer: Mike Smith git_url: https://git.bioconductor.org/packages/BeadArrayUseCases git_branch: devel git_last_commit: ae870e6 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-07 source.ver: src/contrib/BeadArrayUseCases_1.43.0.tar.gz vignettes: vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.pdf vignetteTitles: BeadArrayUseCases.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.R dependencyCount: 99 Package: BeadSorted.Saliva.EPIC Version: 1.13.0 Depends: R (>= 4.1), minfi(>= 1.36.0), ExperimentHub Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 84ab7231683751143fd99932d5d90c1b NeedsCompilation: no Title: Illumina EPIC data on BeadSorted child saliva cells Description: Raw data objects used to estimate saliva cell proportion estimates in ewastools. The FlowSorted.Saliva.EPIC object is constructed from samples assayed by Lauren Middleton et. al. (2021). biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData, Genome, MethylationArrayData, ExperimentHub Author: Jonah Fisher [aut, cre], Kelly Bakulski [aut], Lauren Middleton [aut] Maintainer: Jonah Fisher VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/BeadSorted.Saliva.EPIC git_branch: devel git_last_commit: fcd6eac git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/BeadSorted.Saliva.EPIC_1.13.0.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: 148 Package: benchmarkfdrData2019 Version: 1.19.0 Depends: R (>= 3.6.0), SummarizedExperiment, ExperimentHub Imports: utils Suggests: rmarkdown, knitr, BiocStyle, testthat, SummarizedBenchmark, dplyr, ggplot2, rlang License: MIT + file LICENSE MD5sum: 27e8a3bf6fa9047314f0a56b26d021a4 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: devel git_last_commit: 23fee96 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/benchmarkfdrData2019_1.19.0.tar.gz vignettes: vignettes/benchmarkfdrData2019/inst/doc/benchmarkfdrData2019.html vignetteTitles: Exploring and updating FDR benchmarking results hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/benchmarkfdrData2019/inst/doc/benchmarkfdrData2019.R dependencyCount: 78 Package: beta7 Version: 1.43.0 Depends: R (>= 2.4.0), marray License: LGPL MD5sum: ee6765e83b5416cd567bf5f7e684143e NeedsCompilation: no Title: Rodriguez et al. (2004) Differential Gene Expression by Memory/Effector T Helper Cells Bearing the Gut-Homing Receptor Integrin alpha4 beta7. Description: Data from 6 gpr files aims to identify differential expressed genes between the beta 7+ and beta 7- memory T helper cells. biocViews: ExperimentData, Homo_sapiens_Data, CGHData, MicroarrayData Author: Jean Yang Maintainer: Jean Yang git_url: https://git.bioconductor.org/packages/beta7 git_branch: devel git_last_commit: eeecaf4 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/beta7_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 8 Package: BioImageDbs Version: 1.13.0 Depends: R (>= 4.1.0) Imports: ExperimentHub, AnnotationHub, markdown, rmarkdown, EBImage, magick, magrittr, filesstrings, animation, einsum Suggests: knitr, BiocStyle, purrr License: Artistic-2.0 MD5sum: 901f10b1928ff221f20a198f7dc521a6 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://kumes.github.io/BioImageDbs/ VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/BioImageDbs git_branch: devel git_last_commit: 9f180ad git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/BioImageDbs_1.13.0.tar.gz vignettes: vignettes/BioImageDbs/inst/doc/BioImageBbs_Datasets.html, vignettes/BioImageDbs/inst/doc/BioImageDbs.html vignetteTitles: The BioImageBbs Datasets, Providing Bioimage Dataset for ExperimentHub hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BioImageDbs/inst/doc/BioImageBbs_Datasets.R, vignettes/BioImageDbs/inst/doc/BioImageDbs.R dependencyCount: 103 Package: BioPlex Version: 1.11.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: BiocFileCache, GenomicRanges, GenomeInfoDb, GEOquery, graph, methods, utils Suggests: AnnotationDbi, AnnotationHub, BiocStyle, DEXSeq, ExperimentHub, GenomicFeatures, S4Vectors, depmap, knitr, rmarkdown License: Artistic-2.0 MD5sum: 6dd2ce0d528bcdd51a5ec02a016ffa3a NeedsCompilation: no Title: R-side access to BioPlex protein-protein interaction data Description: The BioPlex package implements access to the BioPlex protein-protein interaction networks and related resources from within R. Besides protein-protein interaction networks for HEK293 and HCT116 cells, this includes access to CORUM protein complex data, and transcriptome and proteome data for the two cell lines. Functionality focuses on importing the various data resources and storing them in dedicated Bioconductor data structures, as a foundation for integrative downstream analysis of the data. biocViews: CellCulture, ColonCancerData, ExperimentHub, ExpressionData, GEO, Genome, Homo_sapiens_Data, MassSpectrometryData, Proteome, ReproducibleResearch, RNASeqData Author: Ludwig Geistlinger [aut, cre], Robert Gentleman [aut] Maintainer: Ludwig Geistlinger URL: https://github.com/ccb-hms/BioPlex VignetteBuilder: knitr BugReports: https://github.com/ccb-hms/BioPlex/issues git_url: https://git.bioconductor.org/packages/BioPlex git_branch: devel git_last_commit: 5aac40a git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/BioPlex_1.11.0.tar.gz vignettes: vignettes/BioPlex/inst/doc/BasicChecks.html, vignettes/BioPlex/inst/doc/BioPlex.html vignetteTitles: 2. Data checks, 1. Data retrieval hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BioPlex/inst/doc/BasicChecks.R, vignettes/BioPlex/inst/doc/BioPlex.R dependencyCount: 84 Package: biotmleData Version: 1.29.0 Depends: R (>= 3.5.0) Suggests: Biobase, SummarizedExperiment License: file LICENSE MD5sum: 16eb671f0335fe7b727897ca590b710e NeedsCompilation: no Title: Example experimental microarray data set for the "biotmle" R package Description: Microarray data (from the Illumina Ref-8 BeadChips platform) and phenotype-level data from an epidemiological investigation of benzene exposure, packaged using "SummarizedExperiemnt", for use as an example with the "biotmle" R package. biocViews: GeneExpression, DifferentialExpression, Sequencing, Microarray, RNASeq Author: Nima Hejazi [aut, cre] Maintainer: Nima Hejazi git_url: https://git.bioconductor.org/packages/biotmleData git_branch: devel git_last_commit: df40c6a git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/biotmleData_1.29.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: biotmle dependencyCount: 0 Package: biscuiteerData Version: 1.19.0 Depends: R (>= 4.1.0), ExperimentHub Imports: AnnotationHub, utils, curl, GenomicRanges Suggests: knitr, rmarkdown, markdown License: GPL-3 MD5sum: 509215a3c55634aef762216d6469d9be NeedsCompilation: no Title: Data Package for Biscuiteer Description: Contains default datasets used by the Bioconductor package biscuiteer. biocViews: ExperimentHub, ExperimentData, Genome, Homo_sapiens_Data Author: Tim Triche, Jr. [aut, cre], Wanding Zhou [aut], Ben Johnson [aut], Jacob Morrison [aut], Lyong Heo [aut] Maintainer: "Jacob Morrison" VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/biscuiteerData git_branch: devel git_last_commit: 7667fb8 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/biscuiteerData_1.19.0.tar.gz vignettes: vignettes/biscuiteerData/inst/doc/biscuiteerData.html vignetteTitles: Biscuiteer User Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/biscuiteerData/inst/doc/biscuiteerData.R dependsOnMe: biscuiteer dependencyCount: 68 Package: bladderbatch Version: 1.43.0 Depends: Biobase License: Artistic-2.0 MD5sum: 01f7ca582633c3146149eb86652299b5 NeedsCompilation: no Title: Bladder gene expression data illustrating batch effects Description: This package contains microarray gene expression data on 57 bladder samples from 5 batches. The data are used as an illustrative example for the sva package. biocViews: ExperimentData, CancerData, MicroarrayData Author: Jeffrey T. Leek Maintainer: Jeffrey T. Leek git_url: https://git.bioconductor.org/packages/bladderbatch git_branch: devel git_last_commit: d411841 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/bladderbatch_1.43.0.tar.gz vignettes: vignettes/bladderbatch/inst/doc/bladderbatch.pdf vignetteTitles: bladderbatchTutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bladderbatch/inst/doc/bladderbatch.R importsMe: RUVcorr suggestsMe: BatchQC, Harman, sva dependencyCount: 6 Package: blimaTestingData Version: 1.25.0 Depends: R(>= 3.0.0) Suggests: blima, beadarray, illuminaHumanv4.db, BiocStyle License: GPL-3 MD5sum: 0dc4e43fe209afd75a5e05d3ca5f5d70 NeedsCompilation: no Title: Data for testing of the package blima. Description: Experiment data package. The set were prepared using microarray images of human mesenchymal cells treated with various supplements. This package is intended to provide example data to test functionality provided by blima. biocViews: MicroarrayData, ExperimentData, GEO Author: Vojtech Kulvait Maintainer: Vojtech Kulvait URL: https://bitbucket.org/kulvait/blima git_url: https://git.bioconductor.org/packages/blimaTestingData git_branch: devel git_last_commit: 46298ef git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/blimaTestingData_1.25.0.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: 1.25.0 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: 2361638a5dd165ff87148601698a9788 NeedsCompilation: no Title: "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al. - experimental data and complete analysis Description: The package contains data of the Primary Blood Cancer Encyclopedia (PACE) project together with a complete executable transcript of the statistical analysis and reproduces figures presented in the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) 128(1):427-445. doi:10.1172/JCI93801. biocViews: ExperimentData, ReproducibleResearch, CancerData, LeukemiaCancerData Author: Malgorzata Oles, Sascha Dietrich, Junyan Lu, Britta Velten, Andreas Mock, Vladislav Kim, Wolfgang Huber Maintainer: Malgorzata Oles VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/BloodCancerMultiOmics2017 git_branch: devel git_last_commit: c58b0c8 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/BloodCancerMultiOmics2017_1.25.0.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: 163 Package: bodymapRat Version: 1.21.0 Depends: R (>= 3.6.0), SummarizedExperiment, ExperimentHub Imports: utils Suggests: rmarkdown, knitr, BiocStyle, testthat License: CC BY 4.0 MD5sum: 88ececa33bbf781d0fc00b5328b3ac1e 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: devel git_last_commit: 23003c0 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/bodymapRat_1.21.0.tar.gz vignettes: vignettes/bodymapRat/inst/doc/bodymapRat.html vignetteTitles: The bodymapRat data user's guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bodymapRat/inst/doc/bodymapRat.R suggestsMe: qsmooth dependencyCount: 78 Package: breakpointRdata Version: 1.23.0 Depends: R (>= 3.5) Suggests: knitr, BiocStyle, License: file LICENSE MD5sum: 6b1d1ba7f400250b7664f97ab419305a NeedsCompilation: no Title: Strand-seq data for demonstration purposes Description: Strand-seq data to demonstrate functionalities of breakpointR package. biocViews: ExperimentData, Homo_sapiens_Data, SequencingData, DNASeqData, Genome, SingleCellData Author: David Porubsky, Aaron Taudt, Ashley Sanders Maintainer: David Porubsky URL: https://github.com/daewoooo/breakpointRdata VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/breakpointRdata git_branch: devel git_last_commit: ef97152 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/breakpointRdata_1.23.0.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: 1.43.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: b411c100d39cadd12d2978b3a328f6d5 NeedsCompilation: no Title: Gene expression dataset published by Schmidt et al. [2008] (MAINZ). Description: Gene expression data from the breast cancer study published by Schmidt et al. in 2008, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerMAINZ git_branch: devel git_last_commit: e58c496 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/breastCancerMAINZ_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: DART, MineICA, genefu dependencyCount: 0 Package: breastCancerNKI Version: 1.43.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: a0ed23c922939754c6656b6524729c29 NeedsCompilation: no Title: Genexpression dataset published by van't Veer et al. [2002] and van de Vijver et al. [2002] (NKI). Description: Genexpression data from a breast cancer study published by van't Veer et al. in 2002 and van de Vijver et al. in 2002, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, CGHData, MicroarrayData, OneChannelData, ChipOnChipData Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerNKI git_branch: devel git_last_commit: ddc56e3 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/breastCancerNKI_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: SigCheck, genefu, seventyGeneData dependencyCount: 0 Package: breastCancerTRANSBIG Version: 1.43.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 6d1d3fc939f8f63570d5b1ca27196ee4 NeedsCompilation: no Title: Gene expression dataset published by Desmedt et al. [2007] (TRANSBIG). Description: Gene expression data from a breast cancer study published by Desmedt et al. in 2007, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerTRANSBIG git_branch: devel git_last_commit: a6f5deb git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/breastCancerTRANSBIG_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSgalgoR, MineICA, genefu dependencyCount: 0 Package: breastCancerUNT Version: 1.43.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 5500008bfe381b42bcf215debe2505fa NeedsCompilation: no Title: Gene expression dataset published by Sotiriou et al. [2007] (UNT). Description: Gene expression data from a breast cancer study published by Sotiriou et al. in 2007, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, TwoChannelData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerUNT git_branch: devel git_last_commit: 60a6d27 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/breastCancerUNT_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu dependencyCount: 0 Package: breastCancerUPP Version: 1.43.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 1c4fce9f2edd8ce3b25f521448600697 NeedsCompilation: no Title: Gene expression dataset published by Miller et al. [2005] (UPP). Description: Gene expression data from a breast cancer study published by Miller et al. in 2005, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerUPP git_branch: devel git_last_commit: 41de6e4 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/breastCancerUPP_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSgalgoR, MineICA, genefu, safe dependencyCount: 0 Package: breastCancerVDX Version: 1.43.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 72957883220c4e56ec7def05bb74fe20 NeedsCompilation: no Title: Gene expression datasets published by Wang et al. [2005] and Minn et al. [2007] (VDX). Description: Gene expression data from a breast cancer study published by Wang et al. in 2005 and Minn et al. in 2007, provided as an eSet. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData, BreastCancerData, LungCancerData, MicroarrayData, OneChannelData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerVDX git_branch: devel git_last_commit: dd7c00b git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/breastCancerVDX_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: BAGS suggestsMe: AIMS, DART, MineICA, genefu dependencyCount: 0 Package: brgedata Version: 1.27.0 Depends: R (>= 3.5.0), Biobase Imports: SummarizedExperiment Suggests: minfi, MultiAssayExperiment, knitr, rmarkdown, rexposome, BiocStyle License: MIT + file LICENSE MD5sum: 6017698e81e7105249ef24675800bfeb NeedsCompilation: no Title: Exposures, Gene Expression and Methylation data for ilustration purpouses Description: This package contains several sets of omics data including Gene Expression (ExpressionSet), Methylation (GenomicRatioSet), Proteome and Exposome (ExposomeSet). This data is used in vignettes and exaples at MEAL, MultiDataSet and omicRexposome. biocViews: ExperimentData,Homo_sapiens_Data,MicroarrayData,MethylationArrayData Author: Dolors Pelegri-Siso [aut, cre], Carlos Ruiz-Arenas [aut], Carles Hernandez-Ferrer [aut], Juan R. Gonzalez [aut] Maintainer: Dolors Pelegri-Siso VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/brgedata git_branch: devel git_last_commit: 61a6b12 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/brgedata_1.27.0.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: 36 Package: bronchialIL13 Version: 1.43.0 Depends: R(>= 2.10.0), affy (>= 1.23.4) License: GPL-2 MD5sum: 71174e5ddc9a342cf6f0f47d163a02a4 NeedsCompilation: no Title: time course experiment involving il13 Description: derived from CNMC (pepr.cnmcresearch.org) http://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=95 Human Bronchial Cell line A549 biocViews: ExperimentData, MicroarrayData Author: Vince Carey Maintainer: Vince Carey URL: http://www.biostat.harvard.edu/~carey git_url: https://git.bioconductor.org/packages/bronchialIL13 git_branch: devel git_last_commit: d940a5f git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/bronchialIL13_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 12 Package: bsseqData Version: 0.43.0 Depends: R (>= 3.5.0), bsseq (>= 1.16.0) License: Artistic-2.0 MD5sum: 4c87e8363d0f909cac95d1022b0b4d8b NeedsCompilation: no Title: Example whole genome bisulfite data for the bsseq package Description: Example whole genome bisulfite data for the bsseq package biocViews: Genome, CancerData, ColonCancerData, SequencingData Author: Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/bsseqData git_branch: devel git_last_commit: c29c464 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/bsseqData_0.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: bsseq, methylSig dependencyCount: 88 Package: cancerdata Version: 1.43.0 Depends: R (>= 2.10.1), Biobase License: GPL (>= 2) MD5sum: 5911d08acd940818491fe6b4efaec239 NeedsCompilation: no Title: Development and validation of diagnostic tests from high-dimensional molecular data: Datasets Description: Dataset for the R package cancerclass biocViews: CancerData, MicroarrayData Author: Jan Budczies, Daniel Kosztyla Maintainer: Daniel Kosztyla git_url: https://git.bioconductor.org/packages/cancerdata git_branch: devel git_last_commit: 63ca809 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/cancerdata_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: cancerclass dependencyCount: 6 Package: CardinalWorkflows Version: 1.37.0 Depends: R (>= 2.10), Cardinal, methods Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: f9fcdc6662042a8230851d76ccff5084 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: devel git_last_commit: 0985fe4 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/CardinalWorkflows_1.37.0.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: 68 Package: ccdata Version: 1.31.0 Depends: R (>= 3.3) License: MIT + file LICENSE MD5sum: 5307a7ad3c259c74795d9e45cc006d16 NeedsCompilation: no Title: Data for Combination Connectivity Mapping (ccmap) Package Description: This package contains microarray gene expression data generated from the Connectivity Map build 02 and LINCS l1000. The data are used by the ccmap package to find drugs and drug combinations to mimic or reverse a gene expression signature. biocViews: ExperimentData, MicroarrayData, ExpressionData Author: Alex Pickering Maintainer: Alex Pickering git_url: https://git.bioconductor.org/packages/ccdata git_branch: devel git_last_commit: 64abe0b git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/ccdata_1.31.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE importsMe: ccmap suggestsMe: retriever dependencyCount: 0 Package: CCl4 Version: 1.43.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), limma License: Artistic-2.0 MD5sum: 39237d3b01c496bb6371c86084b58cd9 NeedsCompilation: no Title: Carbon Tetrachloride (CCl4) treated hepatocytes Description: NChannelSet for rat hepatocytes treated with Carbon Tetrachloride (CCl4) data from LGC company. biocViews: ExperimentData, Genome, Rattus_norvegicus_Data, MicroarrayData Author: Audrey Kauffmann, Wolfgang Huber Maintainer: Audrey Kauffmann git_url: https://git.bioconductor.org/packages/CCl4 git_branch: devel git_last_commit: 3ef4451 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/CCl4_1.43.0.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: celarefData Version: 1.23.0 Depends: R (>= 3.5.0) Suggests: ExperimentHub, knitr, rmarkdown License: GPL-3 MD5sum: a053f496960550edcde3d4368115c0f9 NeedsCompilation: no Title: Processed scRNA data for celaref Vignette - cell labelling by reference Description: This experiment data contains some processed data used in the celaref package vignette. These are publically available datasets, that have been processed by celaref package, and can be manipulated further with it. biocViews: ExperimentData, SingleCellData, ExperimentHub Author: Sarah Williams [aut, cre] Maintainer: Sarah Williams VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/celarefData git_branch: devel git_last_commit: 4bdeffa git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/celarefData_1.23.0.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: 1.15.0 Depends: SummarizedExperiment Imports: utils, methods, Matrix, ExperimentHub, AnnotationHub, AnnotationDbi, S4Vectors, DelayedArray, DelayedMatrixStats, gypsum, alabaster.base, alabaster.matrix, alabaster.se, DBI, RSQLite, jsonlite Suggests: testthat, knitr, rmarkdown, BiocStyle, DT, jsonvalidate, BiocManager, ensembldb License: GPL-3 MD5sum: 793407542907dfdf2ab56ce0d8532b5d NeedsCompilation: no Title: Index of Reference Cell Type Datasets Description: Provides a collection of reference expression datasets with curated cell type labels, for use in procedures like automated annotation of single-cell data or deconvolution of bulk RNA-seq. biocViews: ExperimentHub, ExperimentData, ExpressionData, SequencingData, RNASeqData Author: Dvir Aran [aut], Aaron Lun [aut, cre, cph], Daniel Bunis [aut], Jared Andrews [aut], Friederike Dündar [aut] Maintainer: Aaron Lun URL: https://github.com/LTLA/celldex VignetteBuilder: knitr BugReports: https://support.bioconductor.org/ git_url: https://git.bioconductor.org/packages/celldex git_branch: devel git_last_commit: 41cd4a6 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/celldex_1.15.0.tar.gz vignettes: vignettes/celldex/inst/doc/userguide.html vignetteTitles: Cell type references hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/celldex/inst/doc/userguide.R dependsOnMe: OSCA.basic, OSCA.workflows, SingleRBook importsMe: singleCellTK suggestsMe: SingleR, ontoProc, sketchR, tidySingleCellExperiment, tidySpatialExperiment dependencyCount: 95 Package: CellMapperData Version: 1.31.0 Depends: ExperimentHub, CellMapper Suggests: BiocStyle License: Artistic-2.0 MD5sum: cc10d8bc6d52248f1042e30ba92d08bb NeedsCompilation: no Title: Pre-processed data for use with the CellMapper package Description: Experiment data package. Contains microarray data from several large expression compendia that have been pre-processed for use with the CellMapper package. This pre-processed data is recommended for routine searches using the CellMapper package. biocViews: ExperimentData, MicroarrayData, ExpressionData Author: Brad Nelms Maintainer: Brad Nelms git_url: https://git.bioconductor.org/packages/CellMapperData git_branch: devel git_last_commit: af6e286 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/CellMapperData_1.31.0.tar.gz vignettes: vignettes/CellMapperData/inst/doc/CellMapperData.pdf vignetteTitles: CellMapperData Introduction hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CellMapperData/inst/doc/CellMapperData.R suggestsMe: CellMapper dependencyCount: 68 Package: cfToolsData Version: 1.3.0 Depends: R (>= 4.3.0) Imports: utils, ExperimentHub Suggests: BiocStyle, knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0) License: file LICENSE MD5sum: 84ff716ea9e7f2ef023092f7e7bf5ec9 NeedsCompilation: no Title: ExperimentHub data for the cfTools package Description: The cfToolsData package supplies the data for the cfTools package. It contains two pre-trained deep neural network (DNN) models for the cfSort function. Additionally, it includes the shape parameters of beta distribution characterizing methylation markers associated with four tumor types for the CancerDetector function, as well as the parameters characterizing methylation markers specific to 29 primary human tissue types for the cfDeconvolve function. biocViews: ExperimentHub, ExperimentData, ReproducibleResearch, DiseaseModel, CancerData, Tissue Author: Ran Hu [aut, cre] (), Shuo Li [aut] (), Xianghong Jasmine Zhou [aut] (), Wenyuan Li [aut] () Maintainer: Ran Hu URL: https://github.com/jasminezhoulab/cfToolsData VignetteBuilder: knitr BugReports: https://github.com/jasminezhoulab/cfToolsData/issues git_url: https://git.bioconductor.org/packages/cfToolsData git_branch: devel git_last_commit: e5b0c4c git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/cfToolsData_1.3.0.tar.gz vignettes: vignettes/cfToolsData/inst/doc/cfToolsData.html vignetteTitles: cfToolsData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/cfToolsData/inst/doc/cfToolsData.R importsMe: cfTools dependencyCount: 67 Package: ChAMPdata Version: 2.37.0 Depends: R (>= 3.5.0), GenomicRanges (>= 1.22.4), BiocGenerics (>= 0.16.1) License: GPL-3 MD5sum: 3406af601673cc3d129ada61e2923d8d NeedsCompilation: no Title: Data Packages for ChAMP package Description: Provides datasets needed for ChAMP including a test dataset and blood controls for CNA analysis. biocViews: ExperimentData Author: Yuan Tian [ctb,aut], Tiffany Morris [cre,aut], Lee Stirling [ctb] and Andrew Teschendorff [ctb] Maintainer: Yuan Tian git_url: https://git.bioconductor.org/packages/ChAMPdata git_branch: devel git_last_commit: 38aa067 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/ChAMPdata_2.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ChAMP, methyLImp2 dependencyCount: 23 Package: ChimpHumanBrainData Version: 1.43.0 Depends: affy,qvalue,limma,hexbin,statmod Suggests: hgu95av2cdf License: MIT MD5sum: df82023041795f154e63fb3140467035 NeedsCompilation: no Title: Chimp and human brain data package Description: This data package contains chimp and human brain data extracted from the ArrayExpress accession E-AFMX-2. Both human and chimp RNAs were run on human hgu95av2 Affymetrix arrays. It is a useful dataset for tutorials. biocViews: Tissue, Homo_sapiens_Data, Pan_troglodytes_Data, MicroarrayData, TissueMicroarrayData, GEO Author: Roman Jaksik, Naomi Altman, and Sean Davis Maintainer: Sean Davis git_url: https://git.bioconductor.org/packages/ChimpHumanBrainData git_branch: devel git_last_commit: 7d26247 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/ChimpHumanBrainData_1.43.0.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: 52 Package: chipenrich.data Version: 2.29.0 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: e5645090f3fb9c7850fc6a9561bef775 NeedsCompilation: no Title: Companion package to chipenrich Description: Supporting data for the chipenrich package. Includes pre-defined gene sets, gene locus definitions, and mappability estimates. biocViews: ChIPSeq, Epigenetics, FunctionalGenomics, GeneSetEnrichment, HistoneModification, Regression Author: Ryan P. Welch [aut, cph], Chee Lee [aut], Raymond G. Cavalcante [aut], Kai Wang [cre], Laura J. Scott [ths], Maureen A. Sartor [ths] Maintainer: Kai Wang VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/chipenrich.data git_branch: devel git_last_commit: f4f56e6 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/chipenrich.data_2.29.0.tar.gz vignettes: vignettes/chipenrich.data/inst/doc/chipenrich.data-vignette.html vignetteTitles: chipenrich.data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/chipenrich.data/inst/doc/chipenrich.data-vignette.R importsMe: chipenrich dependencyCount: 90 Package: ChIPexoQualExample Version: 1.29.0 Depends: R (>= 3.3) Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 5d59506bf8467795cf84774b4ee9159e NeedsCompilation: no Title: Example data for the ChIPexoQual package, which implements a quality control pipeline for ChIP-exo data Description: Data for the ChIPexoQual package, consisting of (3) chromosome 1 aligned reads from a ChIP-exo experiment for FoxA1 in mouse liver cell lines aligned to the mm9 genome. biocViews: ExperimentData, Genome Author: Rene Welch, Dongjun Chung, Sunduz Keles Maintainer: Rene Welch URL: http://www.github.com/keleslab/ChIPexoQualExample VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ChIPexoQualExample git_branch: devel git_last_commit: 9db61b1 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/ChIPexoQualExample_1.29.0.tar.gz vignettes: vignettes/ChIPexoQualExample/inst/doc/vignette.html vignetteTitles: ChIPexoQualExample hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ChIPexoQualExample/inst/doc/vignette.R suggestsMe: ChIPexoQual dependencyCount: 0 Package: chipseqDBData Version: 1.21.0 Imports: AnnotationHub, ExperimentHub, Rsamtools, S4Vectors Suggests: knitr, BiocStyle, rmarkdown License: CC BY 4.0 MD5sum: c9c459867c0c4cac3388c477cbc4d2cb NeedsCompilation: no Title: Data for the chipseqDB Workflow Description: Sorted and indexed BAM files for ChIP-seq libraries, for use in the chipseqDB workflow. BAM indices are also included. biocViews: SequencingData, ChIPSeqData, ExperimentHub Author: Aaron Lun [aut, cre] Maintainer: Aaron Lun VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/chipseqDBData git_branch: devel git_last_commit: a6e5a87 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/chipseqDBData_1.21.0.tar.gz vignettes: vignettes/chipseqDBData/inst/doc/chipseqDBData.html vignetteTitles: File manifest and statistics hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/chipseqDBData/inst/doc/chipseqDBData.R dependsOnMe: csawBook suggestsMe: chipseqDB dependencyCount: 80 Package: ChIPXpressData Version: 1.43.0 Depends: bigmemory License: GPL (>=2) MD5sum: 44a1ce90e230f0f8e860d8229008d969 NeedsCompilation: no Title: ChIPXpress Pre-built Databases Description: Contains pre-built mouse (GPL1261) and human (GPL570) database of gene expression profiles to be used for ChIPXpress ranking. biocViews: Homo_sapiens_Data, Mus_musculus_Data, GEO Author: George Wu Maintainer: George Wu git_url: https://git.bioconductor.org/packages/ChIPXpressData git_branch: devel git_last_commit: 7bba6e1 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/ChIPXpressData_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ChIPXpress dependencyCount: 7 Package: chromstaRData Version: 1.31.0 Depends: R (>= 3.3) License: GPL-3 MD5sum: 7fc79e419afa2c08fa63cfb84b64f3c8 NeedsCompilation: no Title: ChIP-seq data for Demonstration Purposes Description: ChIP-seq data for demonstration purposes in the chromstaR package. biocViews: Mus_musculus_Data, StemCell, ChIPSeqData Author: Aaron Taudt Maintainer: Aaron Taudt git_url: https://git.bioconductor.org/packages/chromstaRData git_branch: devel git_last_commit: 7b0a058 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/chromstaRData_1.31.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: chromstaR suggestsMe: epigraHMM dependencyCount: 0 Package: CLL Version: 1.45.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: LGPL MD5sum: 550ec2d9e273fa08a3610420bed3b66c NeedsCompilation: no Title: A Package for CLL Gene Expression Data Description: The CLL package contains the chronic lymphocytic leukemia (CLL) gene expression data. The CLL data had 24 samples that were either classified as progressive or stable in regards to disease progression. The data came from Dr. Sabina Chiaretti at Division of Hematology, Department of Cellular Biotechnologies and Hematology, University La Sapienza, Rome, Italy and Dr. Jerome Ritz at Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts. biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData Author: Elizabeth Whalen Maintainer: Robert Gentleman git_url: https://git.bioconductor.org/packages/CLL git_branch: devel git_last_commit: 1517992 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/CLL_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: phenomis dependencyCount: 12 Package: CLLmethylation Version: 1.25.0 Depends: R (>= 3.5.0) Imports: SummarizedExperiment, ExperimentHub Suggests: BiocStyle, ggplot2, knitr, rmarkdown License: LGPL MD5sum: 9bfb91636f3573ffa42823c665abe329 NeedsCompilation: no Title: Methylation data of primary CLL samples in PACE project Description: The package includes DNA methylation data for the primary Chronic Lymphocytic Leukemia samples included in the Primary Blood Cancer Encyclopedia (PACE) project. Raw data from the 450k DNA methylation arrays is stored in the European Genome-Phenome Archive (EGA) under accession number EGAS0000100174. For more information concerning the project please refer to the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) and R/Bioconductor package BloodCancerMultiOmics2017. biocViews: ExperimentData, DiseaseModel, CancerData, LeukemiaCancerData Author: Malgorzata Oles, Andreas Mock Maintainer: Malgorzata Oles , Andreas Mock VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/CLLmethylation git_branch: devel git_last_commit: dfde90b git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/CLLmethylation_1.25.0.tar.gz vignettes: vignettes/CLLmethylation/inst/doc/CLLmethylation.html vignetteTitles: CLLmethylation hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CLLmethylation/inst/doc/CLLmethylation.R dependencyCount: 78 Package: CluMSIDdata Version: 1.21.0 Depends: R (>= 3.6) License: MIT + file LICENSE MD5sum: 331e335044b493752e58c869b0da0724 NeedsCompilation: no Title: Data for the CluMSID package Description: This package contains various LC-MS/MS and GC-MS data that is used in vignettes and examples in the CluMSID package. biocViews: ExperimentData, MassSpectrometryData Author: Tobias Depke [aut, cre] Maintainer: Tobias Depke git_url: https://git.bioconductor.org/packages/CluMSIDdata git_branch: devel git_last_commit: 6bd486a git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/CluMSIDdata_1.21.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: CluMSID dependencyCount: 0 Package: clustifyrdatahub Version: 1.15.0 Depends: R (>= 4.0), ExperimentHub Imports: utils Suggests: clustifyr, Seurat, usethis, rmarkdown, knitr, tidyr, BiocStyle License: MIT + file LICENSE MD5sum: 0938c235a5a25ef43acf2e96f52b845d 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] (), Kent Riemondy [aut, cre] (), RNA Bioscience Initiative [fnd], Austin Gillen [ctb] (), Jay Hesselberth [ctb] (), Sidhant Puntambekar [ctb] Maintainer: Kent Riemondy URL: https://rnabioco.github.io/clustifyrdatahub/ VignetteBuilder: knitr BugReports: https://github.com/rnabioco/clustifyrdatahub/issues git_url: https://git.bioconductor.org/packages/clustifyrdatahub git_branch: devel git_last_commit: fba3944 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/clustifyrdatahub_1.15.0.tar.gz vignettes: vignettes/clustifyrdatahub/inst/doc/clustifyrdatahub.html vignetteTitles: clustifyrdatahub hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/clustifyrdatahub/inst/doc/clustifyrdatahub.R dependencyCount: 67 Package: cMap2data Version: 1.41.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 1a5d88a2a3cded9a4c082d875c26583b NeedsCompilation: no Title: Connectivity Map (version 2) Data Description: Data package which provides default drug profiles for the DrugVsDisease package as well as associated gene lists and data clusters used by the DrugVsDisease package. biocViews: Homo_sapiens_Data, MicroarrayData, GEO Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/cMap2data git_branch: devel git_last_commit: e5ed472 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/cMap2data_1.41.0.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: 1.41.0 Depends: R (>= 2.10), cnvGSA License: LGPL MD5sum: 97e7ada3540c4d7542d04a28bde24b5b NeedsCompilation: no Title: Data used in the vignette of the cnvGSA package Description: This package contains the data used in the vignette of the cnvGSA package. biocViews: ExperimentData, Genome, CopyNumberVariationData Author: Joseph Lugo Maintainer: Joseph Lugo git_url: https://git.bioconductor.org/packages/cnvGSAdata git_branch: devel git_last_commit: fc50834 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/cnvGSAdata_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: cnvGSA dependencyCount: 33 Package: COHCAPanno Version: 1.41.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 381ae9e2bfbe68bdd54602a277599ffe NeedsCompilation: no Title: Annotations for City of Hope CpG Island Analysis Pipeline Description: Provides genomic location, nearby CpG island and nearby gene information for common Illumina methylation array platforms biocViews: Homo_sapiens_Data, MicroarrayData, MethylationArrayData, CpGIslandData, GEO, ArrayExpress Author: Charles Warden Maintainer: Charles Warden git_url: https://git.bioconductor.org/packages/COHCAPanno git_branch: devel git_last_commit: 32e2c92 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/COHCAPanno_1.41.0.tar.gz vignettes: vignettes/COHCAPanno/inst/doc/COHCAPanno.pdf vignetteTitles: COHCAPanno Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/COHCAPanno/inst/doc/COHCAPanno.R dependencyCount: 0 Package: colonCA Version: 1.47.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: 60495706645d15e6be77f384e777dc76 NeedsCompilation: no Title: exprSet for Alon et al. (1999) colon cancer data Description: exprSet for Alon et al. (1999) colon cancer data biocViews: ExperimentData, Tissue, CancerData, ColonCancerData, MicroarrayData, TissueMicroarrayData Author: Sylvia Merk Maintainer: W Sylvia Merk git_url: https://git.bioconductor.org/packages/colonCA git_branch: devel git_last_commit: dc8a3f1 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/colonCA_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: clustComp, copa dependencyCount: 6 Package: CONFESSdata Version: 1.33.0 Depends: R (>= 3.3) License: GPL-2 MD5sum: c25cf78fcd3a28be82804f7b8bcf3a21 NeedsCompilation: no Title: Example dataset for CONFESS package Description: Example text-converted C01 image files for use in the CONFESS Bioconductor package. biocViews: HighThroughputImagingData,CellCulture,Homo_sapiens_Data,ExpressionData Author: Diana LOW and Efthimios MOTAKIS Maintainer: Diana LOW git_url: https://git.bioconductor.org/packages/CONFESSdata git_branch: devel git_last_commit: 42e7d75 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/CONFESSdata_1.33.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CONFESS dependencyCount: 0 Package: ConnectivityMap Version: 1.41.0 Depends: R (>= 2.15.1) Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 05783858509d8906bb4eddaa8dc9ab6a NeedsCompilation: no Title: Functional connections between drugs, genes and diseases as revealed by common gene-expression changes Description: The Broad Institute's Connectivity Map (cmap02) is a "large reference catalogue of gene-expression data from cultured human cells perturbed with many chemicals and genetic reagents", containing more than 7000 gene expression profiles and 1300 small molecules. biocViews: ExperimentData, CancerData, MicroarrayData Author: Paul Shannon Maintainer: Paul Shannon git_url: https://git.bioconductor.org/packages/ConnectivityMap git_branch: devel git_last_commit: 94489a2 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/ConnectivityMap_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: COPDSexualDimorphism.data Version: 1.41.0 License: LGPL-2.1 MD5sum: ea026c35750938baa26a207df691fcf5 NeedsCompilation: no Title: Data to support sexually dimorphic and COPD differential analysis for gene expression and methylation. Description: Datasets to support COPDSexaulDimorphism Package. biocViews: ExperimentData, Tissue, COPDData Author: J Fah Sathirapongsasuti Maintainer: J Fah Sathirapongsasuti git_url: https://git.bioconductor.org/packages/COPDSexualDimorphism.data git_branch: devel git_last_commit: b31dc87 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/COPDSexualDimorphism.data_1.41.0.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: 1.37.0 Depends: R (>= 3.5.0) Suggests: BiocStyle License: GPL-2 MD5sum: 2f9dc7b5e7762333fc374343c89fbdb5 NeedsCompilation: no Title: Helper files for CopywriteR Description: This package contains the helper files that are required to run the Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content and mappability files for the reference genomes hg18, hg19, hg38, mm9 and mm10. In addition, it contains a blacklist filter to remove regions that display CNV. Files are stored as GRanges objects from the GenomicRanges Bioconductor package. biocViews: Homo_sapiens, GenomicSequence Author: Thomas Kuilman Maintainer: Oscar Krijgsman git_url: https://git.bioconductor.org/packages/CopyhelpeR git_branch: devel git_last_commit: 3601d77 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/CopyhelpeR_1.37.0.tar.gz vignettes: vignettes/CopyhelpeR/inst/doc/CopyhelpeR.pdf vignetteTitles: CopyhelpeR hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CopyhelpeR/inst/doc/CopyhelpeR.R dependencyCount: 0 Package: CopyNeutralIMA Version: 1.23.0 Depends: R (>= 3.5.0) Imports: ExperimentHub,Rdpack (>= 0.8) Suggests: BiocStyle,knitr,rmarkdown,minfi,conumee,minfiData License: Artistic-2.0 MD5sum: 16f8e879a2ad3bc125b23fcdd2497c50 NeedsCompilation: no Title: Copy Neutral Illumina Methylation Arrays Description: Provides a set of genomic copy neutral samples hybridized using Illumina Methylation arrays (450k and EPIC). biocViews: ExperimentData,Homo_sapiens_Data,MicroarrayData,TwoChannelData,MethylationArrayData,GEO Author: Xavier Pastor Hostench [aut, cre], Moritz Przybilla [aut] Maintainer: Xavier Pastor Hostench VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/CopyNeutralIMA git_branch: devel git_last_commit: 119ea9d git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/CopyNeutralIMA_1.23.0.tar.gz vignettes: vignettes/CopyNeutralIMA/inst/doc/CopyNeutralIMA.html vignetteTitles: CopyNeutralIMA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CopyNeutralIMA/inst/doc/CopyNeutralIMA.R dependencyCount: 69 Package: COSMIC.67 Version: 1.41.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, SummarizedExperiment, VariantAnnotation Suggests: testthat, BiocStyle, knitr License: GPL-3 MD5sum: e03016564fed93ae3bba3e0c41fa37a4 NeedsCompilation: no Title: COSMIC.67 Description: COSMIC: Catalogue Of Somatic Mutations In Cancer, version 67 (2013-10-24) biocViews: ExperimentData, Genome, CancerData Author: Julian Gehring Maintainer: Julian Gehring VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/COSMIC.67 git_branch: devel git_last_commit: 1bf8a8a git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/COSMIC.67_1.41.0.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: 79 Package: CRCL18 Version: 1.25.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: dca6488bd381a5e8aa4f195058a2d374 NeedsCompilation: no Title: CRC cell line dataset Description: colorectal cancer mRNA and miRNA on 18 cell lines biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/CRCL18 git_branch: devel git_last_commit: 2ef06fb git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/CRCL18_1.25.0.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: 6 Package: crisprScoreData Version: 1.9.0 Depends: ExperimentHub Imports: AnnotationHub, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 2e58b1f12eb4a07657f321c6d9149863 NeedsCompilation: no Title: Pre-trained models for the crisprScore package Description: Provides an interface to access pre-trained models for on-target and off-target gRNA activity prediction algorithms implemented in the crisprScore package. Pre-trained model data are stored in the ExperimentHub database. Users should consider using the crisprScore package directly to use and load the pre-trained models. biocViews: ExperimentHub, Homo_sapiens_Data Author: Jean-Philippe Fortin [aut, cre, cph] Maintainer: Jean-Philippe Fortin URL: https://github.com/crisprVerse/crisprScoreData/issues VignetteBuilder: knitr BugReports: https://github.com/crisprVerse/crisprScoreData git_url: https://git.bioconductor.org/packages/crisprScoreData git_branch: devel git_last_commit: a078887 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/crisprScoreData_1.9.0.tar.gz vignettes: vignettes/crisprScoreData/inst/doc/crisprScoreData.html vignetteTitles: crisprScoreData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/crisprScoreData/inst/doc/crisprScoreData.R dependsOnMe: crisprScore importsMe: crisprVerse dependencyCount: 67 Package: curatedAdipoArray Version: 1.17.0 Depends: R (>= 4.0) Suggests: knitr, rmarkdown, ExperimentHub, SummarizedExperiment License: GPL-3 + file LICENSE MD5sum: 12ff0a74a4a6c2996da1d1a01f2aa755 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: devel git_last_commit: 8f20c33 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/curatedAdipoArray_1.17.0.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: 1.21.0 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: 8b818affbd5c1b668bf3dedc7eb07b4a 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: devel git_last_commit: 4ba3459 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/curatedAdipoChIP_1.21.0.tar.gz vignettes: vignettes/curatedAdipoChIP/inst/doc/curatedAdipoChIP.html vignetteTitles: Using curatedAdipoChIP hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedAdipoChIP/inst/doc/curatedAdipoChIP.R dependencyCount: 78 Package: curatedAdipoRNA Version: 1.21.0 Depends: R (>= 3.6), SummarizedExperiment Suggests: knitr, rmarkdown, DESeq2, fastqcr, devtools, testthat, readr, dplyr, tidyr, ggplot2, S4Vectors License: GPL-3 MD5sum: 3238f44f7c5ff996a5ff7e3c57dcf523 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: devel git_last_commit: c52ba62 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/curatedAdipoRNA_1.21.0.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: 36 Package: curatedBladderData Version: 1.41.0 Depends: R (>= 2.10.0), affy Suggests: BiocStyle, survival, xtable, sva, genefilter, logging License: Artistic-2.0 MD5sum: 3bede808d4a6bc0b2cee33853efe997e NeedsCompilation: no Title: Bladder Cancer Gene Expression Analysis Description: The curatedBladderData package provides relevant functions and data for gene expression analysis in patients with bladder cancer. biocViews: ExperimentData, CancerData, OvarianCancerData, MicroarrayData, ExpressionData Author: Markus Riester Maintainer: Markus Riester URL: https://github.com/lima1/curatedBladderData git_url: https://git.bioconductor.org/packages/curatedBladderData git_branch: devel git_last_commit: 1a7442d git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/curatedBladderData_1.41.0.tar.gz vignettes: vignettes/curatedBladderData/inst/doc/curatedBladderData_vignette.pdf vignetteTitles: curatedBladderData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedBladderData/inst/doc/curatedBladderData_vignette.R suggestsMe: covEB dependencyCount: 12 Package: curatedBreastData Version: 2.33.0 Depends: R (>= 3.0.0), XML, ggplot2, impute, Biobase, BiocStyle Imports: methods, stats License: GPL (>= 2) MD5sum: 432a59f2fd68b131cf46f463c044440d NeedsCompilation: no Title: Curated breast cancer gene expression data with survival and treatment information Description: Curated human breast cancer tissue S4 ExpresionSet datasets from over 16 clinical trials comprising over 2,000 patients. All datasets contain at least one type of outcomes variable and treatment information (minimum level: whether they had chemotherapy and whether they had hormonal therapy). Includes code to post-process these datasets. biocViews: ExperimentData, ExpressionData, CancerData, Tissue, BreastCancerData, qPCRData, MicroarrayData, TissueMicroarrayData, GEO Author: Katie Planey Maintainer: Katie Planey git_url: https://git.bioconductor.org/packages/curatedBreastData git_branch: devel git_last_commit: 37a7629 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/curatedBreastData_2.33.0.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: 64 Package: curatedMetagenomicData Version: 3.13.0 Depends: R (>= 4.1.0), SummarizedExperiment, TreeSummarizedExperiment Imports: AnnotationHub, ExperimentHub, S4Vectors, dplyr, magrittr, mia, purrr, rlang, stringr, tibble, tidyr, tidyselect Suggests: BiocStyle, DT, knitr, readr, rmarkdown, scater, testthat, utils, uwot, vegan License: Artistic-2.0 MD5sum: dfe6ca7eaf5beb692669ac5352bc7f45 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: devel git_last_commit: 3e51dcd git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/curatedMetagenomicData_3.13.0.tar.gz vignettes: vignettes/curatedMetagenomicData/inst/doc/curatedMetagenomicData.html vignetteTitles: curatedMetagenomicData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedMetagenomicData/inst/doc/curatedMetagenomicData.R suggestsMe: MMUPHin, lefser dependencyCount: 157 Package: curatedOvarianData Version: 1.43.0 Depends: R (>= 3.0.0), Biobase Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle License: Artistic-2.0 MD5sum: 189a2cc6dcddeb454ea2ac57fdee97d3 NeedsCompilation: no Title: Clinically Annotated Data for the Ovarian Cancer Transcriptome Description: The curatedOvarianData package provides data for gene expression analysis in patients with ovarian cancer. biocViews: ExperimentData, RNASeqData, CancerData, OvarianCancerData, MicroarrayData Author: Benjamin F. Ganzfried, Markus Riester, Steve Skates, Victoria Wang, Thomas Risch, Benjamin Haibe-Kains, Svitlana Tyekucheva, Jie Ding, Ina Jazic, Michael Birrer, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron Maintainer: Levi Waldron URL: http://bcb.dfci.harvard.edu/ovariancancer git_url: https://git.bioconductor.org/packages/curatedOvarianData git_branch: devel git_last_commit: 1a104f1 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/curatedOvarianData_1.43.0.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: TOP, doppelgangR dependencyCount: 6 Package: curatedPCaData Version: 1.1.1 Depends: R (>= 4.4.0), S4Vectors (>= 0.23.18), MultiAssayExperiment, RaggedExperiment Imports: ExperimentHub, AnnotationHub, utils, methods, rlang, stats, reshape2 Suggests: BiocStyle, knitr, ggplot2, rmarkdown, survival, survminer, ComplexHeatmap, corrplot, formatR License: CC BY 4.0 MD5sum: 5a895243f59edda38b69b13ca0cde59e NeedsCompilation: no Title: Curated Prostate Cancer Data Description: The package curatedPCaData offers a selection of annotated prostate cancer datasets featuring multiple omics, manually curated metadata, and derived downstream variables. The studies are offered as MultiAssayExperiment (MAE) objects via ExperimentHub, and comprise of clinical characteristics tied to gene expression, copy number alteration and somatic mutation data. Further, downstream features computed from these multi-omics data are offered. Multiple vignettes help grasp characteristics of the various studies and provide example exploratory and meta-analysis of leveraging the multiple studies provided here-in. biocViews: ExperimentHub, ExperimentData, ProstateCancerData, CancerData, Homo_sapiens_Data, MicroarrayData, RNASeqData, ExpressionData, CopyNumberVariationData, Somatic, GEO, ReproducibleResearch Author: Teemu Daniel Laajala [aut, cre] (), Jordan Creed [ctb], Christelle Colin Leitzinger [ctb], Varsha Sreekanth [ctb], Federico Calboli [ctb], Kalaimathy Singaravelu [ctb], Michael Orman [ctb], Alex Soupir [ctb], Anni Halkola [ctb] Maintainer: Teemu Daniel Laajala URL: https://github.com/Syksy/curatedPCaData VignetteBuilder: knitr BugReports: https://github.com/Syksy/curatedPCaData/issues git_url: https://git.bioconductor.org/packages/curatedPCaData git_branch: devel git_last_commit: bd9b303 git_last_commit_date: 2024-05-28 Date/Publication: 2024-05-30 source.ver: src/contrib/curatedPCaData_1.1.1.tar.gz vignettes: vignettes/curatedPCaData/inst/doc/overview.html vignetteTitles: Overview to curatedPCaData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedPCaData/inst/doc/overview.R dependencyCount: 81 Package: curatedTBData Version: 2.1.0 Depends: R (>= 4.3.0) Imports: AnnotationHub, ExperimentHub, MultiAssayExperiment, rlang, stats Suggests: BiocStyle, DT, dplyr, HGNChelper, knitr, methods, rmarkdown, SummarizedExperiment, sva, testthat License: MIT + file LICENSE MD5sum: 272c002d5ade8d44d0756f134c73222f NeedsCompilation: no Title: Curation of existing tuberculosis transcriptomic studies Description: The curatedTBData is an R package that provides standardized, curated tuberculosis(TB) transcriptomic studies. The initial release of the package contains 49 studies. The curatedTBData package allows users to access tuberculosis trancriptomic efficiently and to make efficient comparison for different TB gene signatures across multiple datasets. biocViews: ExperimentHub, GEO, Homo_sapiens_Data Author: Xutao Wang [aut, cre], W. Evan Johnson [aut], Prasad Patil [aut] Maintainer: Xutao Wang URL: https://github.com/compbiomed/curatedTBData VignetteBuilder: knitr BugReports: https://github.com/compbiomed/curatedTBData/issues git_url: https://git.bioconductor.org/packages/curatedTBData git_branch: devel git_last_commit: 531a90e git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/curatedTBData_2.1.0.tar.gz vignettes: vignettes/curatedTBData/inst/doc/curatedTBData.html vignetteTitles: curatedTBData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/curatedTBData/inst/doc/curatedTBData.R dependencyCount: 80 Package: curatedTCGAData Version: 1.27.0 Depends: MultiAssayExperiment Imports: AnnotationHub, ExperimentHub, HDF5Array, methods, S4Vectors, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, RaggedExperiment, readr, rmarkdown, TCGAutils, testthat License: Artistic-2.0 MD5sum: e0b221a9833a23db2c96e08ca440b286 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: devel git_last_commit: 74c1385 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/curatedTCGAData_1.27.0.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, TCGAutils, dce, glmSparseNet, netDx dependencyCount: 84 Package: CytoMethIC Version: 1.1.0 Depends: R (>= 4.4.0), ExperimentHub Imports: tibble, utils, stats, tools, sesame, methods, sesameData, BiocParallel, BiocManager Suggests: BiocStyle, randomForest, testthat, knitr, rmarkdown, e1071, xgboost, keras, tensorflow License: Artistic-2.0 MD5sum: fd4c32d1a9b607572d8836fa4edf403d NeedsCompilation: no Title: DNA methylation-based classification and regression Description: This package provides DNA methylation-based prediction of cancer type, molecular signature and clinical outcomes. It provides convenience functions for missing value imputation, probe ID conversion, model interpretation and visualization. The package links to our models on ExperimentHub. The package currently supports HM450, EPIC and EPICv2. biocViews: ExperimentData, MicroarrayData, Genome, ExperimentHub, MethylationArrayData, CancerData, PackageTypeData Author: Wanding Zhou [aut] (), Jacob Fanale [aut, cre] () Maintainer: Jacob Fanale URL: https://github.com/zhou-lab/CytoMethIC VignetteBuilder: knitr BugReports: https://github.com/zhou-lab/CytoMethIC/issues git_url: https://git.bioconductor.org/packages/CytoMethIC git_branch: devel git_last_commit: 171f69b git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/CytoMethIC_1.1.0.tar.gz vignettes: vignettes/CytoMethIC/inst/doc/CytoMethIC.html vignetteTitles: CytoMethIC User Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CytoMethIC/inst/doc/CytoMethIC.R dependencyCount: 115 Package: DAPARdata Version: 1.35.0 Depends: R (>= 4.3.0), MSnbase Imports: utils Suggests: knitr, DAPAR, BiocStyle License: GPL-2 MD5sum: f8daf127019616bcad36751a772b15a3 NeedsCompilation: no Title: Data accompanying the DAPAR and Prostar packages Description: Mass-spectrometry based UPS proteomics data sets from Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssie D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianferani S, Ferro M, Dorssaeler AV, Burlet-Schiltz O, Schaeffer C, Coute Y, Gonzalez de Peredo A. Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods. Data Brief. 2015 Dec 17;6:286-94 and Giai Gianetto, Q., Combes, F., Ramus, C., Bruley, C., Coute, Y., Burger, T. (2016). Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments. Proteomics, 16(1), 29-32. biocViews: ExperimentData, MassSpectrometryData, Proteome Author: Samuel Wieczorek [cre,aut], Thomas Burger [aut], Enora Fremy [aut] Maintainer: Samuel Wieczorek URL: http://www.prostar-proteomics.org/ VignetteBuilder: knitr BugReports: https://github.com/prostarproteomics/DAPARdata/issues git_url: https://git.bioconductor.org/packages/DAPARdata git_branch: devel git_last_commit: e1e0d93 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/DAPARdata_1.35.0.tar.gz vignettes: vignettes/DAPARdata/inst/doc/dapardata.html vignetteTitles: DAPARdata User Manual hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DAPARdata/inst/doc/dapardata.R importsMe: DAPAR, Prostar dependencyCount: 137 Package: davidTiling Version: 1.45.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db License: LGPL MD5sum: fcf886b9478b9fadc1d7a93b34d18962 NeedsCompilation: no Title: Data and analysis scripts for David, Huber et al. yeast tiling array paper Description: This package contains the data for the paper by L. David et al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix genechips, an ExpressionSet object with the raw feature data, a probe annotation data structure for the chip and the yeast genome annotation (GFF file) that was used. In addition, some custom-written analysis functions are provided, as well as R scripts in the scripts directory. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, MicroarrayData, ReproducibleResearch Author: Wolfgang Huber , Joern Toedling Maintainer: Wolfgang Huber URL: http://www.ebi.ac.uk/huber git_url: https://git.bioconductor.org/packages/davidTiling git_branch: devel git_last_commit: db98743 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/davidTiling_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 88 Package: depmap Version: 1.19.0 Depends: R (>= 3.6), methods, dplyr Imports: utils, ExperimentHub, AnnotationHub, BiocFileCache, httr2, curl, tibble Suggests: knitr, rmarkdown, BiocStyle, viridis, gridExtra, ggplot2, readr, stringr, tidyverse, magick License: Artistic-2.0 MD5sum: ba3126da849ac93029cdd4848628c360 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: devel git_last_commit: 50d225d git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/depmap_1.19.0.tar.gz vignettes: vignettes/depmap/inst/doc/depmap.html, vignettes/depmap/inst/doc/using_depmap.html vignetteTitles: depmap, depmap use cases hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/depmap/inst/doc/depmap.R, vignettes/depmap/inst/doc/using_depmap.R importsMe: CBNplot, MAGeCKFlute suggestsMe: CRISPRball, mastR, BioPlex dependencyCount: 68 Package: derfinderData Version: 2.23.0 Depends: R (>= 3.5.0) Suggests: sessioninfo, knitr (>= 1.6), RefManageR, rmarkdown (>= 0.3.3), BiocStyle License: Artistic-2.0 MD5sum: 35e5cf92e61607f2561f4e012a072baa 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: devel git_last_commit: 587adcd git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/derfinderData_2.23.0.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: derfinderPlot, derfinder dependencyCount: 0 Package: DeSousa2013 Version: 1.41.0 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: 78196e038b4c60d0acb1b499b3dcbd4e NeedsCompilation: no Title: Poor prognosis colon cancer is defined by a molecularly distinct subtype and precursor lesion Description: This package reproduces the main pipeline to analyze the AMC-AJCCII-90 microarray data set in De Sousa et al. accepted by Nature Medicine in 2013. biocViews: CancerData, ColonCancerData, MicroarrayData Author: Xin Wang Maintainer: Xin Wang git_url: https://git.bioconductor.org/packages/DeSousa2013 git_branch: devel git_last_commit: b531d8e git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/DeSousa2013_1.41.0.tar.gz vignettes: vignettes/DeSousa2013/inst/doc/DeSousa2013-Vignette.pdf vignetteTitles: Main vignette:Poor prognosis colon cancer is defined by a molecular distinct subtype and develops from serrated precursor lesions hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DeSousa2013/inst/doc/DeSousa2013-Vignette.R dependencyCount: 127 Package: DExMAdata Version: 1.13.0 Depends: R (>= 4.1) Imports: Biobase Suggests: BiocStyle License: GPL-2 MD5sum: cba58dbea8d4efa2f454d9188b8b4d41 NeedsCompilation: no Title: Data package for DExMA package Description: Data objects needed to allSameID() function of DExMA package. There are also some objects that are necessary to be able to apply the examples of the DExMA package, which illustrate package functionality. biocViews: ExperimentData, OrganismData, MicroarrayData Author: Juan Antonio Villatoro-García [aut, cre], Pedro Carmona-Sáez [aut] Maintainer: Juan Antonio Villatoro-García git_url: https://git.bioconductor.org/packages/DExMAdata git_branch: devel git_last_commit: 5a0628e git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/DExMAdata_1.13.0.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: 6 Package: diffloopdata Version: 1.33.0 Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: c21959f36bb804613052d882733b3162 NeedsCompilation: no Title: Example ChIA-PET Datasets for the diffloop Package Description: ChIA-PET example datasets and additional data for use with the diffloop package. biocViews: ExperimentData, SequencingData Author: Caleb Lareau [aut], Martin Aryee [aut, cre] Maintainer: Caleb Lareau VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/diffloopdata git_branch: devel git_last_commit: 6daa4f5 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/diffloopdata_1.33.0.tar.gz vignettes: vignettes/diffloopdata/inst/doc/diffloopdata.html vignetteTitles: diffloopdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: diggitdata Version: 1.37.0 Depends: R(>= 2.14.0), Biobase, methods Imports: viper License: GPL (>=2) MD5sum: f96336d04b4279a1622745bea38b2800 NeedsCompilation: no Title: Example data for the diggit package Description: This package provides expression profile and CNV data for glioblastoma from TCGA, and transcriptional and post-translational regulatory networks assembled with the ARACNe and MINDy algorithms, respectively. biocViews: ExperimentData, Cancer Author: Mariano Javier Alvarez Maintainer: Mariano Javier Alvarez git_url: https://git.bioconductor.org/packages/diggitdata git_branch: devel git_last_commit: 6bb3a58 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/diggitdata_1.37.0.tar.gz vignettes: vignettes/diggitdata/inst/doc/diggitdata.pdf vignetteTitles: Using bcellViper hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/diggitdata/inst/doc/diggitdata.R suggestsMe: diggit dependencyCount: 90 Package: DLBCL Version: 1.45.0 Depends: R(>= 2.11.0), Biobase, graph License: GPL (>=2) MD5sum: 99377c81d6c5ac1c15070c06d2bc141d NeedsCompilation: no Title: Diffuse large B-cell lymphoma expression data Description: This package provides additional expression data on diffuse large B-cell lymphomas for the BioNet package. biocViews: ExperimentData, CancerData, MicroarrayData, ChipOnChipData Author: Marcus Dittrich and Daniela Beisser Maintainer: Marcus Dittrich URL: http://bionet.bioapps.biozentrum.uni-wuerzburg.de/ git_url: https://git.bioconductor.org/packages/DLBCL git_branch: devel git_last_commit: 77ce361 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/DLBCL_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: BioNet dependencyCount: 8 Package: DmelSGI Version: 1.37.0 Depends: R (>= 3.0) Imports: grid, TSP, limma, rhdf5, knitr, abind, gplots, igraph, grDevices, graphics, stats Suggests: BiocStyle, EBImage, RColorBrewer, RNAinteractMAPK, hwriter, xtable, beeswarm License: Artistic-2.0 MD5sum: a4f0d7af10a602b42c62e78a54785269 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: devel git_last_commit: a3f0b3c git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/DmelSGI_1.37.0.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 suggestsMe: FeatSeekR dependencyCount: 38 Package: DMRcatedata Version: 2.23.0 Depends: R (>= 4.0), ExperimentHub Imports: GenomicFeatures, Gviz, readxl, plyr, rtracklayer, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr License: GPL-3 MD5sum: 2cfd849bf3c63f53a0fbc8ab1e186da9 NeedsCompilation: no Title: Data Package for DMRcate Description: This package contains 9 data objects supporting functionality and examples of the Bioconductor package DMRcate. biocViews: ExperimentHub, ExperimentData, SNPData, Homo_sapiens_Data, Mus_musculus_Data, SequencingData, MicroarrayData, Genome Author: Tim Peters Maintainer: Tim Peters VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DMRcatedata git_branch: devel git_last_commit: 690bdde git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/DMRcatedata_2.23.0.tar.gz vignettes: vignettes/DMRcatedata/inst/doc/DMRcatedata.pdf vignetteTitles: The DMRcate package user's guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DMRcatedata/inst/doc/DMRcatedata.R suggestsMe: DMRcate dependencyCount: 205 Package: DNAZooData Version: 1.5.0 Depends: R (>= 4.2), HiCExperiment Imports: BiocFileCache, S4Vectors, rjson, utils, tools Suggests: dplyr, testthat, methods, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 442365821d3785c7e234a36f6a471a69 NeedsCompilation: no Title: DNA Zoo data package Description: DNAZooData is a data package giving programmatic access to genome assemblies and Hi-C contact matrices uniformly processed by the [DNA Zoo Consortium](https://www.dnazoo.org/). The matrices are available in the multi-resolution `.hic` format. A URL to corrected genome assemblies in `.fastq` format is also provided to the end-user. biocViews: ExperimentData, SequencingData Author: Jacques Serizay [aut, cre] Maintainer: Jacques Serizay URL: https://github.com/js2264/DNAZooData VignetteBuilder: knitr BugReports: https://github.com/js2264/DNAZooData/issues git_url: https://git.bioconductor.org/packages/DNAZooData git_branch: devel git_last_commit: 1d21892 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/DNAZooData_1.5.0.tar.gz vignettes: vignettes/DNAZooData/inst/doc/DNAZooData.html vignetteTitles: DNAZooData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/DNAZooData/inst/doc/DNAZooData.R importsMe: OHCA dependencyCount: 91 Package: DonaPLLP2013 Version: 1.43.0 Depends: EBImage, parallel License: Artistic-2.0 MD5sum: 458cd642de39e57020dd89ca1db9f580 NeedsCompilation: no Title: Supplementary data package for Dona et al. (2013) containing example images and tables Description: An experiment data package associated with the publication Dona et al. (2013). Package contains runnable vignettes showing an example image segmentation for one posterior lateral line primordium, and also the data table and code used to analyze tissue-scale lifetime-ratio statistics. biocViews: ExperimentData, Tissue Author: Erika Dona, Joseph D. Barry, Guillaume Valentin, Charlotte Quirin, Anton Khmelinskii, Andreas Kunze, Sevi Durdu, Lionel R. Newton, Ana Fernandez-Minan, Wolfgang Huber, Michael Knop, Darren Gilmour Maintainer: Joseph D. Barry git_url: https://git.bioconductor.org/packages/DonaPLLP2013 git_branch: devel git_last_commit: e9de434 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/DonaPLLP2013_1.43.0.tar.gz vignettes: vignettes/DonaPLLP2013/inst/doc/PLLPanalysis.pdf, vignettes/DonaPLLP2013/inst/doc/PLLPstatistics.pdf vignetteTitles: PLLP image analysis, PLLP tissue-scale ratio statistics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DonaPLLP2013/inst/doc/PLLPanalysis.R, vignettes/DonaPLLP2013/inst/doc/PLLPstatistics.R dependencyCount: 46 Package: dorothea Version: 1.17.0 Depends: R (>= 4.0) Imports: dplyr, magrittr, bcellViper, decoupleR, Suggests: Biobase, BiocStyle, OmnipathR, viper, knitr, pheatmap, pkgdown, rmarkdown, Seurat, SingleCellExperiment, SummarizedExperiment, testthat (>= 2.1.0), tibble, tidyr, utils License: GPL-3 + file LICENSE MD5sum: af8ff78af41457841645edc0b3e524c1 NeedsCompilation: no Title: Collection Of Human And Mouse TF Regulons Description: DoRothEA is a gene regulatory network containing signed transcription factor (TF) - target gene interactions. DoRothEA regulons, the collection of a TF and its transcriptional targets, were curated and collected from different types of evidence for both human and mouse. A confidence level was assigned to each TF-target interaction based on the number of supporting evidence. biocViews: ExperimentData, Homo_sapiens_Data, Mus_musculus_Data Author: Pau Badia-i-Mompel [cre] (), Daniel Dimitrov [aut] (), Christian H. Holland [aut] (), Luz Garcia-Alonso [aut], Alberto Valdeolivas [ctb], Minoo Ashtiani [ctb], Attila Gabor [ctb] Maintainer: Pau Badia-i-Mompel URL: https://saezlab.github.io/dorothea/, https://github.com/saezlab/dorothea VignetteBuilder: knitr BugReports: https://github.com/saezlab/dorothea/issues git_url: https://git.bioconductor.org/packages/dorothea git_branch: devel git_last_commit: 82df493 git_last_commit_date: 2024-04-30 Date/Publication: 2024-06-13 source.ver: src/contrib/dorothea_1.17.0.tar.gz vignettes: vignettes/dorothea/inst/doc/dorothea.html vignetteTitles: DoRothEA regulons. hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/dorothea/inst/doc/dorothea.R importsMe: cosmosR, easier suggestsMe: MethReg, epiregulon.extra dependencyCount: 46 Package: dressCheck Version: 0.43.0 Depends: R (>= 2.10.1), methods, Biobase (>= 2.5.5) Suggests: survival, chron License: Artistic-2.0 MD5sum: 98f3f91d07bbde9195c49b3e62161d3a NeedsCompilation: no Title: data and software for checking Dressman JCO 25(5) 2007 Description: data and software for checking Dressman JCO 25(5) 2007 biocViews: ExperimentData, Genome Author: Vincent Carey Maintainer: Vincent Carey git_url: https://git.bioconductor.org/packages/dressCheck git_branch: devel git_last_commit: e699529 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/dressCheck_0.43.0.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: 6 Package: DropletTestFiles Version: 1.15.0 Imports: utils, ExperimentHub, AnnotationHub, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, testthat, DropletUtils License: GPL-3 MD5sum: 09724d80cf41af9940b23268eae13a29 NeedsCompilation: no Title: Test Files for Single-Cell Droplet Utilities Description: Assorted files generated from droplet-based single-cell protocols, to be used for testing functions in DropletUtils. Primarily intended for storing files that directly come out of processing pipelines like 10X Genomics' CellRanger software, prior to the formation of a SingleCellExperiment object. Unlike other packages, this is not designed to provide objects that are immediately ready for analysis. biocViews: ExperimentHub, ExperimentData, ExpressionData, SequencingData, RNASeqData, SingleCellData Author: Aaron Lun [ctb, cre] Maintainer: Aaron Lun VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DropletTestFiles git_branch: devel git_last_commit: dec85df git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/DropletTestFiles_1.15.0.tar.gz vignettes: vignettes/DropletTestFiles/inst/doc/motivation.html vignetteTitles: Test files for droplet-based single-cell utilities hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DropletTestFiles/inst/doc/motivation.R dependsOnMe: OSCA.advanced, OSCA.intro, OSCA.workflows suggestsMe: DropletUtils, TENxIO dependencyCount: 67 Package: DrugVsDiseasedata Version: 1.41.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: a9c385803ec91e51aaa67286303e2d97 NeedsCompilation: no Title: Drug versus Disease Data Description: Data package which provides default disease expression profiles, clusters and annotation information for use with the DrugVsDisease package. biocViews: Homo_sapiens_Data, MicroarrayData Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/DrugVsDiseasedata git_branch: devel git_last_commit: bcfe6ea git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/DrugVsDiseasedata_1.41.0.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: 1.23.0 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: 974a75303f319e1be25b85bae8779045 NeedsCompilation: no Title: Data, Clustering Results and Visualization Functions From Duò et al (2018) Description: Preprocessed experimental and simulated scRNA-seq data sets used for evaluation of clustering methods for scRNA-seq data in Duò et al (2018). Also contains results from applying several clustering methods to each of the data sets, and functions for plotting method performance. biocViews: SingleCellData, ExperimentData Author: Angelo Duò, Charlotte Soneson Maintainer: Angelo Duò VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DuoClustering2018 git_branch: devel git_last_commit: dc13238 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/DuoClustering2018_1.23.0.tar.gz vignettes: vignettes/DuoClustering2018/inst/doc/combine_data_clustering.html, vignettes/DuoClustering2018/inst/doc/plot_performance.html, vignettes/DuoClustering2018/inst/doc/run_clustering.html vignetteTitles: Visualize data sets and clustering results with iSEE, Plot performance summaries, Apply clustering method hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DuoClustering2018/inst/doc/combine_data_clustering.R, vignettes/DuoClustering2018/inst/doc/plot_performance.R, vignettes/DuoClustering2018/inst/doc/run_clustering.R suggestsMe: corral, scry dependencyCount: 91 Package: DvDdata Version: 1.41.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 6d9f30cea644597d9fe9e20e73de35cf NeedsCompilation: no Title: Drug versus Disease Data Description: Data package which provides default drug and disease expression profiles for the DvD package. biocViews: GEO Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/DvDdata git_branch: devel git_last_commit: eb458e3 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/DvDdata_1.41.0.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: 1.45.0 Depends: R (>= 1.4.1), marray, GEOquery Suggests: dyebias, convert, Biobase License: GPL-3 MD5sum: 7ea64141a8bafa8c4965c23461763c3a NeedsCompilation: no Title: Example data for the dyebias package, which implements the GASSCO method. Description: Data for the dyebias package, consisting of 4 self-self hybrizations of self-spotted yeast slides, as well as data from Array Express accession E-MTAB-32 biocViews: ExperimentData, SAGEData, CGHData, MicroarrayData, TwoChannelData, ArrayExpress Author: Philip Lijnzaad and Thanasis Margaritis Maintainer: Philip Lijnzaad URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad git_url: https://git.bioconductor.org/packages/dyebiasexamples git_branch: devel git_last_commit: 46652d5 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/dyebiasexamples_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: dyebias dependencyCount: 49 Package: easierData Version: 1.11.0 Depends: R (>= 4.1.0) Imports: ExperimentHub, AnnotationHub, utils, SummarizedExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 63e253a59c977e4677dc0bf9a74e02a7 NeedsCompilation: no Title: easier internal data and exemplary dataset from IMvigor210CoreBiologies package Description: Access to internal data required for the functional performance of easier package and exemplary bladder cancer dataset with both processed RNA-seq data and information on response to ICB therapy generated by Mariathasan et al. "TGF-B attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells", published in Nature, 2018 [doi:10.1038/nature25501](https://doi.org/10.1038/nature25501). The data is made available via [`IMvigor210CoreBiologies`](http://research-pub.gene.com/IMvigor210CoreBiologies/) package under the CC-BY license. biocViews: RNASeqData, ExperimentHub, ReproducibleResearch, ImmunoOncologyData, CancerData, ExperimentData Author: Oscar Lapuente-Santana [aut, cre] (), Federico Marini [aut] (), Arsenij Ustjanzew [aut] (), Francesca Finotello [aut] (), Federica Eduati [aut] () Maintainer: Oscar Lapuente-Santana VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/easierData git_branch: devel git_last_commit: 768730d git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/easierData_1.11.0.tar.gz vignettes: vignettes/easierData/inst/doc/easierData.html vignetteTitles: easier data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/easierData/inst/doc/easierData.R importsMe: easier dependencyCount: 78 Package: EatonEtAlChIPseq Version: 0.43.0 Depends: GenomicRanges (>= 1.5.42), ShortRead, rtracklayer License: Artistic 2.0 MD5sum: 73c418734427b06f93e710f517da1c15 NeedsCompilation: no Title: ChIP-seq data of ORC-binding sites in Yeast excerpted from Eaton et al. 2010 Description: ChIP-seq analysis subset from "Conserved nucleosome positioning defines replication origins" (PMID 20351051) biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, ChIPSeqData, GEO Author: Patrick Aboyoun Maintainer: Patrick Aboyoun git_url: https://git.bioconductor.org/packages/EatonEtAlChIPseq git_branch: devel git_last_commit: d78be85 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/EatonEtAlChIPseq_0.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 70 Package: ecoliLeucine Version: 1.45.0 Depends: R (>= 1.9.0), affy (>= 1.23.4), ecolicdf License: GPL (>= 2) MD5sum: 9c63aad08aa734290eea5081d4536348 NeedsCompilation: no Title: Experimental data with Affymetrix E. coli chips Description: Experimental data with Affymetrix E. coli chips, as reported in She-pin Hung, Pierre Baldi, and G. Wesley Hatfield, J. Biol. Chem., Vol. 277, Issue 43, 40309-40323, October 25, 2002 biocViews: ExperimentData, MicroarrayData Author: Laurent Gautier Maintainer: Laurent Gautier git_url: https://git.bioconductor.org/packages/ecoliLeucine git_branch: devel git_last_commit: 1eaeea6 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/ecoliLeucine_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ecolitk dependencyCount: 50 Package: EGSEAdata Version: 1.33.0 Depends: R (>= 3.4) Suggests: EGSEA License: file LICENSE MD5sum: 2e4b04269714261fb29d9ab9ea563a2a NeedsCompilation: no Title: Gene set collections for the EGSEA package Description: This package includes gene set collections that are used for the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. It includes Human and Mouse versions of the MSidDB (Subramanian, et al. (2005) PNAS, 102(43):15545-15550) and GeneSetDB (Araki, et al. (2012) FEBS Open Bio, 2:76-82) collections. biocViews: ExperimentData, Homo_sapiens_Data, Mus_musculus_Data, Rattus_norvegicus_Data Author: Monther Alhamdoosh, Yifang Hu and Gordon K. Smyth Maintainer: Monther Alhamdoosh git_url: https://git.bioconductor.org/packages/EGSEAdata git_branch: devel git_last_commit: bffeb76 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/EGSEAdata_1.33.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE importsMe: EGSEA dependencyCount: 0 Package: ELMER.data Version: 2.29.0 Depends: R (>= 3.5.0) Imports: GenomicRanges Suggests: BiocStyle, knitr, dplyr, devtools, DT, rmarkdown License: GPL-3 MD5sum: 6c2b9283b6da6f3a7792d26b9f883523 NeedsCompilation: no Title: Data for the ELMER package Description: Supporting data for the ELMER package. It includes: - elmer.data.example.promoter: mae.promoter - elmer.data.example: data - EPIC.hg38.manifest - EPIC.hg19.manifest - hm450.hg38.manifest - hm450.hg19.manifest - hocomoco.table - human.TF - LUSC_meth_refined: Meth - LUSC_RNA_refined: GeneExp - Probes.motif.hg19.450K - Probes.motif.hg19.EPIC - Probes.motif.hg38.450K - Probes.motif.hg38.EPIC - TF.family - TF.subfamily - Human_genes__GRCh37_p13 - Human_genes__GRCh38_p12 - Human_genes__GRCh37_p13__tss - Human_genes__GRCh38_p12__tss biocViews: AssayDomainData, TechnologyData, OrganismData Author: Tiago Chedraoui Silva, Lijing Yao Simon Coetzee, Benjamin P. Berman Maintainer: Tiago Chedraoui Silva VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ELMER.data git_branch: devel git_last_commit: 8bbee34 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/ELMER.data_2.29.0.tar.gz vignettes: vignettes/ELMER.data/inst/doc/vignettes.html vignetteTitles: ELMER.data: Supporting data for the ELMER package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ELMER.data/inst/doc/vignettes.R dependsOnMe: ELMER importsMe: EpiMix dependencyCount: 23 Package: emtdata Version: 1.13.0 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: 7a43c53a342c9d3421fbf5cb27e6342d 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: devel git_last_commit: 0f34525 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/emtdata_1.13.0.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: 83 Package: EpiMix.data Version: 1.7.0 Depends: R (>= 4.2.0), ExperimentHub (>= 0.99.6) Suggests: rmarkdown, knitr License: GPL-3 MD5sum: 9ecd90c7f687d0fccc3344d628109f71 NeedsCompilation: no Title: Data for the EpiMix package Description: Supporting data for the EpiMix R package. It include: - HM450_lncRNA_probes.rda - HM450_miRNA_probes.rda - EPIC_lncRNA_probes.rda - EPIC_miRNA_probes.rda - EpigenomeMap.rda - LUAD.sample.annotation - TCGA_BatchData - MET.data - mRNA.data - microRNA.data - lncRNA.data - Sample_EpiMixResults_lncRNA - Sample_EpiMixResults_miRNA - Sample_EpiMixResults_Regular - Sample_EpiMixResults_Enhancer - lncRNA expression data of tumors from TCGA that are stored in the ExperimentHub. biocViews: ExperimentData, ExperimentHub, Genome, RNASeqData, ExpressionData Author: Yuanning Zheng [aut, cre] Maintainer: Yuanning Zheng VignetteBuilder: knitr BugReports: https://github.com/gevaertlab/EpiMix/issues git_url: https://git.bioconductor.org/packages/EpiMix.data git_branch: devel git_last_commit: c42e1da git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/EpiMix.data_1.7.0.tar.gz vignettes: vignettes/EpiMix.data/inst/doc/RetrieveData.html vignetteTitles: vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/EpiMix.data/inst/doc/RetrieveData.R dependsOnMe: EpiMix dependencyCount: 67 Package: epimutacionsData Version: 1.9.0 Depends: R (>= 4.2.0) Suggests: rmarkdown, BiocStyle, knitr, ExperimentHub, minfi License: MIT + file LICENSE MD5sum: 5ce557fd9cec9165be14b66ab12fc1bc NeedsCompilation: no Title: Data for epimutacions package Description: This package includes the data necessary to run functions and examples in epimutacions package. Collection of DNA methylation data. The package contains 2 datasets: (1) Control ( GEO: GSE104812), (GEO: GSE97362) case samples; and (2) reference panel (GEO: GSE127824). It also contains candidate regions to be epimutations in 450k methylation arrays. biocViews: ExperimentHub, Homo_sapiens_Data, MethylationArrayData, MicroarrayData Author: Leire Abarrategui [aut, cre], Juan R. Gonzalez [aut], Carlos Ruiz-Arenas [aut], Carles Hernandez-Ferrer [aut] Maintainer: Leire Abarrategui URL: https://github.com/LeireAbarrategui/epimutacionsData VignetteBuilder: knitr BugReports: https://github.com/LeireAbarrategui/epimutacionsData/issues git_url: https://git.bioconductor.org/packages/epimutacionsData git_branch: devel git_last_commit: d47f4ab git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/epimutacionsData_1.9.0.tar.gz vignettes: vignettes/epimutacionsData/inst/doc/epimutacionsData.html vignetteTitles: data repository for epimutacions package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/epimutacionsData/inst/doc/epimutacionsData.R dependsOnMe: epimutacions dependencyCount: 0 Package: estrogen Version: 1.51.0 Suggests: affy, hgu95av2.db, hgu95av2cdf, vsn, knitr, genefilter License: LGPL MD5sum: 49204fe1985b9499f79f427e8757a821 NeedsCompilation: no Title: Microarray dataset that can be used as example for 2x2 factorial designs Description: Data from 8 Affymetrix genechips, looking at a 2x2 factorial design (with 2 repeats per level). biocViews: ExperimentData, MicroarrayData Author: Wolfgang Huber, Robert Gentleman Maintainer: Wolfgang Huber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/estrogen git_branch: devel git_last_commit: 99804b5 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/estrogen_1.51.0.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: 1.33.0 Depends: R (>= 3.3), Biobase, metagenomeSeq(>= 1.12.0) License: Artistic-2.0 MD5sum: fcaa0b82c184de2e434fce35b0422c7e NeedsCompilation: no Title: Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment Description: 16S rRNA gene sequencing data to study changes in the faecal microbiota of 12 volunteers during a human challenge study with ETEC (H10407) and subsequent treatment with ciprofloxacin. biocViews: ExperimentData, SequencingData, MicrobiomeData Author: Joseph N. Paulson Maintainer: Joseph N. Paulson git_url: https://git.bioconductor.org/packages/etec16s git_branch: devel git_last_commit: 8e40bc6 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/etec16s_1.33.0.tar.gz vignettes: vignettes/etec16s/inst/doc/etec16s.pdf vignetteTitles: etec16s hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/etec16s/inst/doc/etec16s.R dependencyCount: 32 Package: ewceData Version: 1.13.0 Depends: R (>= 4.1), ExperimentHub Suggests: knitr, BiocStyle, ggplot2, cowplot, rmarkdown, markdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: dfac72d509432b38471e3a75de675843 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: devel git_last_commit: aec1c88 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/ewceData_1.13.0.tar.gz vignettes: vignettes/ewceData/inst/doc/ewceData.html vignetteTitles: Data package for Expression Weighted Celltype Enrichment EWCE hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ewceData/inst/doc/ewceData.R importsMe: EWCE dependencyCount: 67 Package: faahKO Version: 1.45.0 Depends: R (>= 2.10), xcms (>= 3.4.0) License: LGPL MD5sum: f6852d09225b122d53e09a8e27af7023 NeedsCompilation: no Title: Saghatelian et al. (2004) FAAH knockout LC/MS data Description: Positive ionization mode data in NetCDF file format. Centroided subset from 200-600 m/z and 2500-4500 seconds. Data originally reported in "Assignment of Endogenous Substrates to Enzymes by Global Metabolite Profiling" Biochemistry; 2004; 43(45). Also includes detected peaks in an xcmsSet. biocViews: ExperimentData, MassSpectrometryData Author: Colin A. Smith Maintainer: Steffen Neumann URL: http://dx.doi.org/10.1021/bi0480335 git_url: https://git.bioconductor.org/packages/faahKO git_branch: devel git_last_commit: f8c9d28 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/faahKO_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: cosmiq suggestsMe: CAMERA, IPO, MAIT, peakPantheR, xcms dependencyCount: 147 Package: fabiaData Version: 1.43.0 Depends: R (>= 2.10.0), Biobase Imports: utils Suggests: fabia License: LGPL (>= 2.1) MD5sum: 13c412687164eef5eff9f661c3a1df99 NeedsCompilation: no Title: Data sets for FABIA (Factor Analysis for Bicluster Acquisition) Description: Supplying gene expression data sets for the demos of the biclustering method "Factor Analysis for Bicluster Acquisition" (FABIA). The following three data sets are provided: A) breast cancer (van't Veer, Nature, 2002), B) multiple tissues (Su, PNAS, 2002), and C) diffuse large-B-cell lymphoma (Rosenwald, N Engl J Med, 2002). biocViews: CancerData, BreastCancerData, MicroarrayData Author: Sepp Hochreiter Maintainer: Sepp Hochreiter URL: http://www.bioinf.jku.at/software/fabia/fabia.html git_url: https://git.bioconductor.org/packages/fabiaData git_branch: devel git_last_commit: 7acc4cb git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/fabiaData_1.43.0.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: 6 Package: FANTOM3and4CAGE Version: 1.41.0 Depends: R (>= 2.15.0) License: GPL-3 MD5sum: d15541d057aa23c6ccb3bbeef188be59 NeedsCompilation: no Title: CAGE data from FANTOM3 and FANTOM4 projects Description: CAGE (Cap Analysis Gene Expression) data from FANTOM3 and FANTOM4 projects produced by RIKEN Omics Science Center. biocViews: ExperimentData, Tissue Author: Vanja Haberle, Department of Biology, University of Bergen, Norway Maintainer: Vanja Haberle git_url: https://git.bioconductor.org/packages/FANTOM3and4CAGE git_branch: devel git_last_commit: bbc0728 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/FANTOM3and4CAGE_1.41.0.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: 1.43.0 Depends: R (>= 2.10.0), lumi Suggests: genefilter, affy License: GPL (>2) MD5sum: b323f9b7030acb020077e7fe9609a9d2 NeedsCompilation: no Title: Illumina DASL example microarray data Description: A subset of GSE17565 (April et al. 2009) containing 32 FFPE samples of Burkitts Lymphoma and Breast Adenocarcinoma, with a dilution series in technical duplicate. biocViews: Tissue, Genome, MicroarrayData, TissueMicroarrayData, GEO Author: Levi Waldron Maintainer: Levi Waldron git_url: https://git.bioconductor.org/packages/ffpeExampleData git_branch: devel git_last_commit: 877da1e git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/ffpeExampleData_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ffpe dependencyCount: 161 Package: fibroEset Version: 1.47.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: a0f78f7da8ec80113e105f0eb54e1a45 NeedsCompilation: no Title: exprSet for Karaman et al. (2003) fibroblasts data Description: exprSet for Karaman et al. (2003) human, bonobo and gorilla fibroblasts data biocViews: ExperimentData, Genome, Homo_sapiens_Data, MicroarrayData, ChipOnChipData Author: Sylvia Merk Maintainer: Sylvia Merk git_url: https://git.bioconductor.org/packages/fibroEset git_branch: devel git_last_commit: 40ef8f4 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/fibroEset_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: biocGraph, clusterStab, geneplotter dependencyCount: 6 Package: FieldEffectCrc Version: 1.15.0 Depends: utils Imports: BiocStyle, RUnit, SummarizedExperiment, ExperimentHub (>= 0.99.6), AnnotationHub, DESeq2 Suggests: knitr, rmarkdown, BiocGenerics, sva, BiocManager License: Artistic-2.0 MD5sum: 736ba5fb37ef834f8e9d27dae3f3e22b 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: devel git_last_commit: f560142 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/FieldEffectCrc_1.15.0.tar.gz vignettes: vignettes/FieldEffectCrc/inst/doc/FieldEffectCrc.html vignetteTitles: SummarizedExperiments of colorectal transcriptomes hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FieldEffectCrc/inst/doc/FieldEffectCrc.R dependencyCount: 122 Package: FIs Version: 1.33.0 Depends: R (>= 3.3) License: GPL-3 MD5sum: fc14a32b6a6dd88073e957886c0fe596 NeedsCompilation: no Title: Human Functional Interactions (FIs) for splineTimeR package Description: Data set containing two complete lists of identified functional interaction partners in Human. Data are derived from Reactome and BioGRID databases. biocViews: PathwayInteractionDatabase, Homo_sapiens_Data Author: Agata Michna Maintainer: Herbert Braselmann , Martin Selmansberger git_url: https://git.bioconductor.org/packages/FIs git_branch: devel git_last_commit: 6835b03 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/FIs_1.33.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: splineTimeR dependencyCount: 0 Package: fission Version: 1.25.0 Depends: R (>= 2.10), SummarizedExperiment Suggests: knitr, markdown License: LGPL MD5sum: 7f2d89a255c483510496e717a6d69bfb NeedsCompilation: no Title: RangedSummarizedExperiment for time course RNA-Seq of fission yeast in response to stress, by Leong et al., Nat Commun 2014. Description: This package provides a RangedSummarizedExperiment object of read counts in genes for a time course RNA-Seq experiment of fission yeast (Schizosaccharomyces pombe) in response to oxidative stress (1M sorbitol treatment) at 0, 15, 30, 60, 120 and 180 mins. The samples are further divided between a wild-type group and a group with deletion of atf21. The read count matrix was prepared and provided by the author of the study: Leong HS, Dawson K, Wirth C, Li Y, Connolly Y, Smith DL, Wilkinson CR, Miller CJ. "A global non-coding RNA system modulates fission yeast protein levels in response to stress". Nat Commun 2014 May 23;5:3947. PMID: 24853205. GEO: GSE56761. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData, GEO Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/fission git_branch: devel git_last_commit: c808ac6 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/fission_1.25.0.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: 36 Package: Fletcher2013a Version: 1.41.0 Depends: R (>= 2.15), limma Imports: Biobase ,VennDiagram, gplots,grid License: GPL (>= 2) MD5sum: bc02d22583054b9aebaa373cde9b6429 NeedsCompilation: no Title: Gene expression data from breast cancer cells under FGFR2 signalling perturbation Description: The package Fletcher2013a contains time-course gene expression data from MCF-7 cells treated under different experimental systems in order to perturb FGFR2 signalling. The data comes from Fletcher et al. (Nature Comms 4:2464, 2013) where further details about the background and the experimental design of the study can be found. biocViews: ExperimentData, ExpressionData, CancerData, BreastCancerData, MicroarrayData Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin Meyer. Maintainer: Mauro Castro URL: http://dx.doi.org/10.1038/ncomms3464 git_url: https://git.bioconductor.org/packages/Fletcher2013a git_branch: devel git_last_commit: cab5f6d git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/Fletcher2013a_1.41.0.tar.gz vignettes: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.pdf vignetteTitles: Main vignette:Fletcher2013a hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.R dependsOnMe: Fletcher2013b suggestsMe: NetActivity dependencyCount: 20 Package: Fletcher2013b Version: 1.41.0 Depends: R (>= 2.15), Fletcher2013a, RTN (>= 1.1.2), RedeR (>= 1.8.1), igraph Imports: RColorBrewer License: GPL (>= 2) MD5sum: f398886230ce68004d5d73c34a8fbda9 NeedsCompilation: no Title: Master regulators of FGFR2 signalling and breast cancer risk Description: This package reproduces the systems biology analysis for the data in package Fletcher2013a using RTN. biocViews: ExperimentData, ChIPSeqData, CancerData, BreastCancerData, SNPData Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin Meyer. Maintainer: Mauro Castro URL: http://dx.doi.org/10.1038/ncomms3464 git_url: https://git.bioconductor.org/packages/Fletcher2013b git_branch: devel git_last_commit: 4303098 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/Fletcher2013b_1.41.0.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: RTNsurvival, geneplast dependencyCount: 142 Package: flowPloidyData Version: 1.31.0 Suggests: knitr, rmarkdown, flowCore License: GPL-3 MD5sum: b7d5aff0b828a72a48c2457791c9f96f NeedsCompilation: no Title: Example Flow Cytometry Data Description: A collection of raw flow cytometry data for use in vignettes for the flowPloidy package. biocViews: FlowCytometryData Author: Tyler Smith Maintainer: Tyler Smith VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/flowPloidyData git_branch: devel git_last_commit: df538a1 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/flowPloidyData_1.31.0.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: 1.43.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 74b5434f9b034e1d4f6f2660d6aa8453 NeedsCompilation: no Title: Illumina HumanMethylation data on sorted blood cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays, and an object depicting which CpGs on the array are associated with cell type. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Andrew E Jaffe Maintainer: Andrew E Jaffe git_url: https://git.bioconductor.org/packages/FlowSorted.Blood.450k git_branch: devel git_last_commit: 05e243c git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/FlowSorted.Blood.450k_1.43.0.tar.gz vignettes: vignettes/FlowSorted.Blood.450k/inst/doc/FlowSorted.Blood.450k.pdf vignetteTitles: FlowSorted Blood 450k Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.Blood.450k/inst/doc/FlowSorted.Blood.450k.R dependsOnMe: methylCC, methylationArrayAnalysis suggestsMe: mCSEA, minfi, wateRmelon, FlowSorted.Blood.EPIC dependencyCount: 140 Package: FlowSorted.Blood.EPIC Version: 2.9.0 Depends: R (>= 3.5), minfi(>= 1.21.2), ExperimentHub Imports: genefilter, nlme, quadprog, graphics, stats, utils, AnnotationHub, SummarizedExperiment, S4Vectors Suggests: knitr,rmarkdown, FlowSorted.CordBlood.450k, FlowSorted.Blood.450k(>= 1.0.1), EpiDISH,FlowSorted.CordBloodNorway.450k, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Enhances: FlowSorted.CordBloodCombined.450k(>= 1.11.5) License: GPL-3 MD5sum: b889cba814e834b10a6396851885bd1b NeedsCompilation: no Title: Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells Description: Raw data objects to be used for blood cell proportion estimation in minfi and similar packages. The FlowSorted.Blood.EPIC object is based in samples assayed by Brock Christensen and colleagues; for details see Salas et al. 2018. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, Genome, TissueMicroarrayData, MethylationArrayData Author: Lucas A. Salas [cre, aut], Devin C. Koestler [aut], Rondi A. Butler [ctb], Helen M. Hansen [ctb], John K. Wiencke [ctb], Karl T. Kelsey [ctb], Brock C. Christensen [ctb], Kasper Daniel Hansen [ctb] (author and maintainer of the original minfi estimateCellCounts and internal functions), Jean-Philippe Fortin [ctb] (contributor in the original minfi estimateCellCounts and internal functions), Shan V. Andrews [ctb] (contributor in the original minfi estimateCellCounts and internal functions), E. Andres Houseman [ctb] (author of the original quadratic programming function used for cell projection), Andrew E Jaffe [ctb] (author of the original estimateCellCounts and internal functions within minfi) Maintainer: Lucas A. Salas URL: https://github.com/immunomethylomics/FlowSorted.Blood.EPIC VignetteBuilder: knitr BugReports: https://github.com/immunomethylomics/FlowSorted.Blood.EPIC/issues. git_url: https://git.bioconductor.org/packages/FlowSorted.Blood.EPIC git_branch: devel git_last_commit: afe5df1 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/FlowSorted.Blood.EPIC_2.9.0.tar.gz vignettes: vignettes/FlowSorted.Blood.EPIC/inst/doc/FlowSorted.Blood.EPIC.html vignetteTitles: FlowSorted.Blood.EPIC hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.Blood.EPIC/inst/doc/FlowSorted.Blood.EPIC.R importsMe: HiBED suggestsMe: DMRcate, wateRmelon, FlowSorted.CordBloodCombined.450k dependencyCount: 148 Package: FlowSorted.CordBlood.450k Version: 1.33.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 36a2e9ca5c71555ccfe9bc804cb3d167 NeedsCompilation: no Title: Illumina 450k data on sorted cord blood cells Description: Raw data objects to be used for cord blood cell proportion estimation in minfi. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Shan V. Andrews [cre, aut], Kelly M. Bakulski [aut] Maintainer: Shan V. Andrews git_url: https://git.bioconductor.org/packages/FlowSorted.CordBlood.450k git_branch: devel git_last_commit: 2d503ea git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/FlowSorted.CordBlood.450k_1.33.0.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: 140 Package: FlowSorted.CordBloodCombined.450k Version: 1.21.0 Depends: R (>= 3.6), minfi (>= 1.21.2), ExperimentHub(>= 1.9.1) Imports: SummarizedExperiment, IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b4.hg19, utils, AnnotationHub Suggests: FlowSorted.Blood.EPIC, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: GPL-3 MD5sum: cbbfae6575938f63101c822e88216ad9 NeedsCompilation: no Title: Illumina 450k/EPIC data on FACS and MACS umbilical blood cells Description: Raw data objects to be used for umbilical cord blood cell proportion estimation in minfi and similar packages. The FlowSorted.CordBloodCombined.450k object is based in samples assayed by Bakulski et al, Gervin et al., de Goede et al., and Lin et al. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, Genome, TissueMicroarrayData, MethylationArrayData, ExperimentHub Author: Lucas A. Salas [cre, aut], Kristina Gervin [aut], Meaghan C. Jones [aut], Kelly M. Bakulski [ctb], Devin C. Koestler [ctb], John K. Wiencke [ctb], Karl T. Kelsey [ctb], Robert Lyle [ctb], Brock C. Christensen [ctb], Janine Felix [ctb] Maintainer: Lucas A. Salas URL: https://github.com/immunomethylomics/FlowSorted.CordBloodCombined.450k VignetteBuilder: knitr BugReports: https://github.com/immunomethylomics/FlowSorted.CordBloodCombined.450k/issues. git_url: https://git.bioconductor.org/packages/FlowSorted.CordBloodCombined.450k git_branch: devel git_last_commit: a4aa2e8 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/FlowSorted.CordBloodCombined.450k_1.21.0.tar.gz vignettes: vignettes/FlowSorted.CordBloodCombined.450k/inst/doc/FlowSorted.CordBloodCombined.450k.html vignetteTitles: FlowSorted.CordBloodCombined.450k hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.CordBloodCombined.450k/inst/doc/FlowSorted.CordBloodCombined.450k.R dependencyCount: 150 Package: FlowSorted.CordBloodNorway.450k Version: 1.31.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 4f1df799af25861228b41afd1f0c6a73 NeedsCompilation: no Title: Illumina HumanMethylation data on sorted cord blood cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays, for cell type composition estimation. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: kristina gervin [cre, aut], Kasper Daniel Hansen [aut] Maintainer: kristina gervin URL: https://bitbucket.com/kasperdanielhansen/Illumina_CordBlood git_url: https://git.bioconductor.org/packages/FlowSorted.CordBloodNorway.450k git_branch: devel git_last_commit: 0f0bf4f git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/FlowSorted.CordBloodNorway.450k_1.31.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 140 Package: FlowSorted.DLPFC.450k Version: 1.41.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 943ee5c35820eb5dfd8c9934d73d981f NeedsCompilation: no Title: Illumina HumanMethylation data on sorted frontal cortex cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Andrew E Jaffe, Zachary A. Kaminsky Maintainer: Andrew E Jaffe git_url: https://git.bioconductor.org/packages/FlowSorted.DLPFC.450k git_branch: devel git_last_commit: 46c4bc2 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/FlowSorted.DLPFC.450k_1.41.0.tar.gz vignettes: vignettes/FlowSorted.DLPFC.450k/inst/doc/FlowSorted.DLPFC.450k.pdf vignetteTitles: FlowSorted DLPFC 450k Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.DLPFC.450k/inst/doc/FlowSorted.DLPFC.450k.R importsMe: HiBED dependencyCount: 140 Package: flowWorkspaceData Version: 3.17.0 License: GPL-2 MD5sum: 78eb3d31a70c075f8b5ab2ac38cd9605 NeedsCompilation: no Title: A data package containing two flowJo, one diva xml workspace and the associated fcs files as well as three GatingSets for testing the flowWorkspace, openCyto and CytoML packages. Description: The necessary external data to run the flowWorkspace and openCyto vignette is found in this package. biocViews: ExperimentData, FlowCytometryData Author: Greg Finak Maintainer: Mike Jiang git_url: https://git.bioconductor.org/packages/flowWorkspaceData git_branch: devel git_last_commit: ef8d303 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/flowWorkspaceData_3.17.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: COMPASS, CytoML, flowClust, flowCore, flowWorkspace, ggcyto, openCyto dependencyCount: 0 Package: fourDNData Version: 1.5.0 Depends: R (>= 4.2) Imports: BiocFileCache, HiCExperiment, GenomicRanges, IRanges, S4Vectors, utils, tools Suggests: rtracklayer, dplyr, testthat, methods, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 5a2a7cc1a622ef048bc392a4a4178976 NeedsCompilation: no Title: 4DN data package Description: fourDNData is a data package giving programmatic access to Hi-C contact matrices uniformly processed by the [4DN consortium](https://www.4dnucleome.org/). The matrices are available in the multi-resolution `.mcool` format. biocViews: ExperimentData, SequencingData Author: Jacques Serizay [aut, cre] Maintainer: Jacques Serizay URL: https://github.com/js2264/fourDNData VignetteBuilder: knitr BugReports: https://github.com/js2264/fourDNData/issues git_url: https://git.bioconductor.org/packages/fourDNData git_branch: devel git_last_commit: ee492ab git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/fourDNData_1.5.0.tar.gz vignettes: vignettes/fourDNData/inst/doc/fourDNData.html vignetteTitles: fourDNData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/fourDNData/inst/doc/fourDNData.R importsMe: OHCA dependencyCount: 90 Package: frmaExampleData Version: 1.41.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 97c81c472070d56652a7de2a91d5b099 NeedsCompilation: no Title: Frma Example Data Description: Data files used by the examples in frma and frmaTools packages biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/frmaExampleData git_branch: devel git_last_commit: 0548dc5 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/frmaExampleData_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: frmaTools, frma dependencyCount: 0 Package: furrowSeg Version: 1.33.0 Depends: R (>= 3.3), EBImage Imports: abind, dplyr, locfit, tiff Suggests: BiocStyle, ggplot2, knitr License: Artistic-2.0 MD5sum: 657fa13627261b01567f4ceb8b132836 NeedsCompilation: no Title: Furrow Segmentation Description: Image feature data and analysis codes for the Guglielmi, Barry et al. paper describing the application of an optogenetics tools to disrupt Drosophila embryo furrowing. biocViews: ExperimentData, Drosophila_melanogaster_Data, Tissue, ReproducibleResearch Author: Joseph Barry Maintainer: Joseph Barry VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/furrowSeg git_branch: devel git_last_commit: 54bed66 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/furrowSeg_1.33.0.tar.gz vignettes: vignettes/furrowSeg/inst/doc/exampleFurrowSegmentation.pdf, vignettes/furrowSeg/inst/doc/genPaperFigures.pdf vignetteTitles: Supplementary Methods - Example furrow segmentation, Supplementary Methods - Automatic generation of paper figures hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/furrowSeg/inst/doc/exampleFurrowSegmentation.R, vignettes/furrowSeg/inst/doc/genPaperFigures.R dependencyCount: 56 Package: gageData Version: 2.43.0 Depends: R (>= 2.10) Suggests: gage, pathview, genefilter License: GPL (>=2.0) MD5sum: 5a02da6be2185aef41c792d7d25540c1 NeedsCompilation: no Title: Auxillary data for gage package Description: This is a supportive data package for the software package, gage. However, the data supplied here are also useful for gene set or pathway analysis or microarray data analysis in general. In this package, we provide two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and BMP6 (originally published as an demo dataset for GAGE, also registered as GSE13604 in GEO). This package also includes commonly used gene set data based on KEGG pathways and GO terms for major research species, including human, mouse, rat and budding yeast. Mapping data between common gene IDs for budding yeast are also included. biocViews: ExperimentData, StemCell, CancerData, BreastCancerData, MicroarrayData, GEO Author: Weijun Luo Maintainer: Weijun Luo git_url: https://git.bioconductor.org/packages/gageData git_branch: devel git_last_commit: bb5b119 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/gageData_2.43.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: gage dependencyCount: 0 Package: gaschYHS Version: 1.43.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 0acc8100a01da2b338eca02f9a41b049 NeedsCompilation: no Title: ExpressionSet for response of yeast to heat shock and other environmental stresses Description: Data from PMID 11102521 biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data Author: Audrey Gasch and colleagues Maintainer: Vince Carey URL: http://genome-www.stanford.edu/yeast_stress/data/rawdata/complete_dataset.txt git_url: https://git.bioconductor.org/packages/gaschYHS git_branch: devel git_last_commit: e61a66f git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/gaschYHS_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 6 Package: gcspikelite Version: 1.43.0 Depends: R (>= 2.5.0) License: LGPL MD5sum: 79ba6f322a0de545876790bffbd691b0 NeedsCompilation: no Title: Spike-in data for GC/MS data and methods within flagme Description: Spike-in data for GC/MS data and methods within flagme biocViews: MassSpectrometryData Author: Mark Robinson Maintainer: Mark Robinson git_url: https://git.bioconductor.org/packages/gcspikelite git_branch: devel git_last_commit: c52976c git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/gcspikelite_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: flagme suggestsMe: erah dependencyCount: 0 Package: gDNAinRNAseqData Version: 1.5.0 Depends: R (>= 4.3) Imports: RCurl, XML, ExperimentHub, BiocGenerics, Rsamtools Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 6eb5c3023097b68c183066f1219c2b35 NeedsCompilation: no Title: RNA-seq data with different levels of gDNA contamination Description: Provides access to BAM files generated from RNA-seq data produced with different levels of gDNA contamination. It currently allows one to download a subset of the data published by Li et al., BMC Genomics, 23:554, 2022. This subset of data is formed by BAM files with about 100,000 alignments with three different levels of gDNA contamination. biocViews: ExperimentHub, ExperimentData, ExpressionData, SequencingData, RNASeqData, Homo_sapiens_Data Author: Robert Castelo [aut, cre] () Maintainer: Robert Castelo URL: https://github.com/functionalgenomics/gDNAinRNAseqData VignetteBuilder: knitr BugReports: https://github.com/functionalgenomics/gDNAinRNAseqData git_url: https://git.bioconductor.org/packages/gDNAinRNAseqData git_branch: devel git_last_commit: 50db323 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/gDNAinRNAseqData_1.5.0.tar.gz vignettes: vignettes/gDNAinRNAseqData/inst/doc/gDNAinRNAseqData.html vignetteTitles: RNA-seq data with different levels of gDNA contamination hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/gDNAinRNAseqData/inst/doc/gDNAinRNAseqData.R suggestsMe: gDNAx dependencyCount: 82 Package: gDRtestData Version: 1.3.1 Depends: R (>= 4.2) Imports: checkmate, data.table Suggests: BiocStyle, gDRstyle (>= 1.1.5), knitr, qs, reshape2, rmarkdown, SummarizedExperiment, testthat, yaml License: Artistic-2.0 MD5sum: e7062e7a4e1090573ba159e0d9953e0e NeedsCompilation: no Title: gDRtestData - R data package with testing dose response data Description: R package with internal dose-response test data. Package provides functions to generate input testing data that can be used as the input for gDR pipeline. It also contains qs files with MAE data processed by gDR. biocViews: ExperimentData, TechnologyData Author: Aleksander Chlebowski [aut], Bartosz Czech [aut] (), Arkadiusz Gladki [cre, aut] (), Marc Hafner [aut] (), Marcin Kamianowski [aut], Sergiu Mocanu [aut], Natalia Potocka [aut], Dariusz Scigocki [aut], Janina Smola [aut], Allison Voung [aut] Maintainer: Arkadiusz Gladki URL: https://github.com/gdrplatform/gDRtestData, https://gdrplatform.github.io/gDRtestData/ VignetteBuilder: knitr BugReports: https://github.com/gdrplatform/gDRtestData/issues git_url: https://git.bioconductor.org/packages/gDRtestData git_branch: devel git_last_commit: e7bfa27 git_last_commit_date: 2024-05-28 Date/Publication: 2024-05-28 source.ver: src/contrib/gDRtestData_1.3.1.tar.gz vignettes: vignettes/gDRtestData/inst/doc/gDRtestData.html vignetteTitles: gDRtestData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/gDRtestData/inst/doc/gDRtestData.R suggestsMe: gDR, gDRcore, gDRimport, gDRutils dependencyCount: 5 Package: geneLenDataBase Version: 1.41.2 Depends: R (>= 2.11.0) Imports: utils, rtracklayer, GenomicFeatures, txdbmaker License: LGPL (>= 2) MD5sum: fa7c7a0c9764fde60a7e8f02c65840ad NeedsCompilation: no Title: Lengths of mRNA transcripts for a number of genomes Description: Length of mRNA transcripts for a number of genomes and gene ID formats, largely based on UCSC table browser. Data objects are provided as individual pieces of information to be retrieved and loaded. A variety of different gene identifiers and genomes is supported to ensure wide applicability. biocViews: ExperimentData, Genome Author: Matthew Young [aut], Nadia Davidson [aut], Federico Marini [ctb, cre] () Maintainer: Federico Marini URL: https://github.com/federicomarini/geneLenDataBase BugReports: https://github.com/federicomarini/geneLenDataBase/issues git_url: https://git.bioconductor.org/packages/geneLenDataBase git_branch: devel git_last_commit: f060519 git_last_commit_date: 2024-06-12 Date/Publication: 2024-06-13 source.ver: src/contrib/geneLenDataBase_1.41.2.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: goseq importsMe: SMITE dependencyCount: 102 Package: genomationData Version: 1.37.0 Suggests: knitr License: GPL-3 MD5sum: 180bcd6f71408a1a4f1361b8dca34379 NeedsCompilation: no Title: Experimental data for showing functionalities of the genomation package Description: The package contains Chip Seq, Methylation and Cage data, downloaded from Encode biocViews: ExperimentData, Genome, StemCell, SequencingData, ChIPSeqData, ChipOnChipData, ENCODE Author: Altuna Akalin, Vedran Franke Maintainer: Vedran Franke VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/genomationData git_branch: devel git_last_commit: 08a7b50 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/genomationData_1.37.0.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: 1.13.0 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: 87635253c9f57aebf3f66920e58a635c NeedsCompilation: no Title: Reference data for GenomicDistributions package Description: This package provides ready to use reference data for GenomicDistributions package. Raw data was obtained from ensembldb and processed with helper functions. Data files are available for the following genome assemblies: hg19, hg38, mm9 and mm10. biocViews: ExperimentHub, ExperimentData, Genome Author: Michal Stolarczyk [aut], Kristyna Kupkova [aut, cre], Jose Verdezoto [aut], John Lawson [ctb], Jason Smith [ctb], Nathan C. Sheffield [ctb] Maintainer: Kristyna Kupkova VignetteBuilder: knitr BugReports: http://github.com/databio/GenomicDistributionsData git_url: https://git.bioconductor.org/packages/GenomicDistributionsData git_branch: devel git_last_commit: c4865e9 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/GenomicDistributionsData_1.13.0.tar.gz vignettes: vignettes/GenomicDistributionsData/inst/doc/intro.html vignetteTitles: 1. Getting started with GenomicDistributionsData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/GenomicDistributionsData/inst/doc/intro.R suggestsMe: GenomicDistributions dependencyCount: 104 Package: GeuvadisTranscriptExpr Version: 1.33.0 Depends: R (>= 3.5.0) Suggests: limma, rtracklayer, GenomicRanges, Rsamtools, VariantAnnotation, tools, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: b3c5142cf2b7f2f37c89d2646b525cf8 NeedsCompilation: no Title: Data package with transcript expression and bi-allelic genotypes from the GEUVADIS project Description: Provides transcript expression and bi-allelic genotypes corresponding to the chromosome 19 for CEU individuals from the GEUVADIS project, Lappalainen et al. biocViews: Homo_sapiens_Data, SNPData, Genome, RNASeqData, SequencingData, ExpressionData Author: Malgorzata Nowicka [aut, cre] Maintainer: Malgorzata Nowicka VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GeuvadisTranscriptExpr git_branch: devel git_last_commit: 2d40295 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/GeuvadisTranscriptExpr_1.33.0.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: 1.23.0 Depends: R (>= 3.5) Suggests: GIGSEA, knitr, rmarkdown License: LGPL-3 MD5sum: cdf70418cf9d6367e6dc2be98a499cf6 NeedsCompilation: no Title: Gene set collections for the GIGSEA package Description: The gene set collection used for the GIGSEA package. biocViews: ExperimentData, Homo_sapiens_Data Author: Shijia Zhu Maintainer: Shijia Zhu VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GIGSEAdata git_branch: devel git_last_commit: 0b163f4 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/GIGSEAdata_1.23.0.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: 1.47.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: LGPL MD5sum: 1b0b9aad7e62424b9b32593cca5ca639 NeedsCompilation: no Title: exprSets for golub leukemia data Description: representation of public golub data with some covariate data of provenance unknown to the maintainer at present; now employs ExpressionSet format biocViews: ExperimentData, Genome, CancerData, LeukemiaCancerData Author: Todd Golub Maintainer: Vince Carey git_url: https://git.bioconductor.org/packages/golubEsets git_branch: devel git_last_commit: 775a489 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/golubEsets_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: Biobase, GlobalAncova, MLInterfaces, RDRToolbox, adSplit, biosigner, globaltest, idiogram, pvca, twilight dependencyCount: 6 Package: gpaExample Version: 1.17.0 Depends: R (>= 4.0.0) License: GPL (>= 2) MD5sum: a2ed5e68e7457f3995d82d22e1c722c7 NeedsCompilation: no Title: Example data for the GPA package (Genetic analysis incorporating Pleiotropy and Annotation) Description: Example data for the GPA package, consisting of the p-values of 1,219,805 SNPs for five psychiatric disorder GWAS from the psychiatric GWAS consortium (PGC), with the annotation data using genes preferentially expressed in the central nervous system (CNS). biocViews: ExperimentData, Homo_sapiens_Data, SNPData Author: Dongjun Chung, Carter Allen Maintainer: Dongjun Chung URL: http://dongjunchung.github.io/GPA/ git_url: https://git.bioconductor.org/packages/gpaExample git_branch: devel git_last_commit: fe2d92f git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/gpaExample_1.17.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GPA dependencyCount: 0 Package: grndata Version: 1.37.0 Depends: R (>= 2.10) Suggests: RUnit, BiocGenerics, knitr License: GPL-3 MD5sum: 97d0205e489eb95eb81a0c06fc5eea9d NeedsCompilation: no Title: Synthetic Expression Data for Gene Regulatory Network Inference Description: Simulated expression data for five large Gene Regulatory Networks from different simulators biocViews: ExperimentData, NetworkInference, GeneExpression, Microarray, GeneRegulation, Network Author: Pau Bellot, Catharina Olsen, Patrick E Meyer Maintainer: Pau Bellot VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/grndata git_branch: devel git_last_commit: 62f3d39 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/grndata_1.37.0.tar.gz vignettes: vignettes/grndata/inst/doc/grndata.html vignetteTitles: GRNdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: GSBenchMark Version: 1.25.0 Depends: R (>= 2.13.1) License: GPL-2 MD5sum: cd618464e454a61349b4178878630ab8 NeedsCompilation: no Title: Gene Set Benchmark Description: Benchmarks for Machine Learning Analysis of the Gene Sets. The package contains a list of pathways and gene expression data sets used in "Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)" (2010) by Eddy et al. biocViews: MicroarrayData Author: Bahman Afsari , Elana J. Fertig Maintainer: Bahman Afsari git_url: https://git.bioconductor.org/packages/GSBenchMark git_branch: devel git_last_commit: f7eb0a3 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/GSBenchMark_1.25.0.tar.gz vignettes: vignettes/GSBenchMark/inst/doc/GSBenchMark.pdf vignetteTitles: Working with the GSBenchMark package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GSBenchMark/inst/doc/GSBenchMark.R suggestsMe: GSReg dependencyCount: 0 Package: GSE103322 Version: 1.11.0 Depends: Biobase, GEOquery Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown, SummarizedExperiment, SingleCellExperiment License: Artistic-2.0 MD5sum: fb4c15d8106a97f3f462666bfabf3e64 NeedsCompilation: no Title: GEO accession data GSE103322 as a SingleCellExperiment Description: Single cell RNA-Seq data for 5902 cells from 18 patients with oral cavity head and neck squamous cell carcinoma available as GEO accession [GSE103322] (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE103322). GSE103322 data have been parsed into a SincleCellExperiment object available in ExperimentHub. biocViews: ExperimentData, Genome, DNASeqData, RNASeqData, ExperimentData, ExpressionData, RNASeqData, Homo_sapiens_Data, CancerData, SingleCellData, GEO, ExperimentHub Author: Mariano Alvarez [aut, cre] Maintainer: Mariano Alvarez VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GSE103322 git_branch: devel git_last_commit: 1876764 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/GSE103322_1.11.0.tar.gz vignettes: vignettes/GSE103322/inst/doc/GSE103322.html vignetteTitles: scRNASeq HNSC data using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GSE103322/inst/doc/GSE103322.R dependencyCount: 48 Package: GSE13015 Version: 1.13.0 Depends: Biobase, GEOquery Imports: preprocessCore, SummarizedExperiment, GEOquery, Biobase Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown License: MIT License MD5sum: 1de1500a86c169875487c18b1168db9e 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: devel git_last_commit: d1c058a git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/GSE13015_1.13.0.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: 74 Package: GSE159526 Version: 1.11.0 Suggests: ExperimentHub, BiocStyle, RefManageR, knitr, rmarkdown, testthat, minfi, tibble, sessioninfo License: MIT + file LICENSE MD5sum: 89bede6d4dd75bcb0deb58db5830e25e NeedsCompilation: no Title: Placental cell DNA methylation data from GEO accession GSE159526 Description: 19 term and 9 first trimester placental chorionic villi and matched cell-sorted samples ran on Illumina HumanMethylationEPIC DNA methylation microarrays. This data was made available on GEO accession [GSE159526](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159526). Both the raw and processed data has been made available on \code{ExperimentHub}. Raw unprocessed data formatted as an RGChannelSet object for integration and normalization using minfi and other existing Bioconductor packages. Processed normalized data is also available as a DNA methylation \code{matrix}, with a corresponding phenotype information as a \code{data.frame} object. biocViews: ExperimentData, ExperimentHub, GEO, Genome, Tissue, MethylationArrayData, Homo_sapiens_Data Author: Victor Yuan [aut, cre] () Maintainer: Victor Yuan URL: https://github.com/wvictor14/GSE159526 VignetteBuilder: knitr BugReports: https://github.com/wvictor14/GSE159526/issues git_url: https://git.bioconductor.org/packages/GSE159526 git_branch: devel git_last_commit: 8fc7918 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/GSE159526_1.11.0.tar.gz vignettes: vignettes/GSE159526/inst/doc/GSE159526.html vignetteTitles: Introduction to GSE159526 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/GSE159526/inst/doc/GSE159526.R dependencyCount: 0 Package: GSE62944 Version: 1.33.0 Depends: Biobase, GEOquery Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown, DESeq2 License: Artistic-2.0 MD5sum: ef8fe2ed80a40d724e671814ad858b5c NeedsCompilation: no Title: GEO accession data GSE62944 as a SummarizedExperiment Description: TCGA processed RNA-Seq data for 9264 tumor and 741 normal samples across 24 cancer types and made them available as GEO accession [GSE62944](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944). GSE62944 data have been parsed into a SummarizedExperiment object available in ExperimentHub. biocViews: ExperimentData, Genome, DNASeqData, RNASeqData Author: Sonali Arora Maintainer: Bioconductor Package Maintainer URL: http://bioconductor.org/packages/release/bioc/html/GSE62944.html VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GSE62944 git_branch: devel git_last_commit: d7b052a git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/GSE62944_1.33.0.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: 48 Package: GSVAdata Version: 1.41.0 Depends: R (>= 3.5), Biobase, GSEABase, hgu95a.db License: Artistic-2.0 MD5sum: 459045d2131fafdc35f237f2f544978e 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: devel git_last_commit: 878c249 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/GSVAdata_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: singleCellTK, RVA suggestsMe: GSAR, GSVA dependencyCount: 52 Package: GWASdata Version: 1.43.0 Depends: GWASTools Suggests: ncdf4 License: Artistic-2.0 MD5sum: 79f2470ea204139c1dee97b92ed4d9e9 NeedsCompilation: no Title: Data used in the examples and vignettes of the GWASTools package Description: Selected Affymetrix and Illlumina SNP data for HapMap subjects. Data provided by the Center for Inherited Disease Research at Johns Hopkins University and the Broad Institute of MIT and Harvard University. biocViews: ExperimentData, MicroarrayData, SNPData, HapMap Author: Stephanie Gogarten Maintainer: Stephanie Gogarten git_url: https://git.bioconductor.org/packages/GWASdata git_branch: devel git_last_commit: f38d3bd git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/GWASdata_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GENESIS, GWASTools dependencyCount: 94 Package: h5vcData Version: 2.25.0 Suggests: h5vc License: GPL (>= 3) MD5sum: 71d0b0a6794366ef74b8ae5e82d25666 NeedsCompilation: no Title: Example data for the h5vc package Description: This package contains the data used in the vignettes and examples of the 'h5vc' package biocViews: CancerData Author: Paul Theodor Pyl Maintainer: Paul Theodor Pyl git_url: https://git.bioconductor.org/packages/h5vcData git_branch: devel git_last_commit: 587b79b git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/h5vcData_2.25.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: h5vc suggestsMe: HDF5Array dependencyCount: 0 Package: hapmap100khind Version: 1.47.0 Suggests: oligo License: GPL MD5sum: 4e7e2ae12eebbc4ae978d57409359e53 NeedsCompilation: no Title: Sample data - Hapmap 100K HIND Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap100khind git_branch: devel git_last_commit: a5fa844 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/hapmap100khind_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmap100kxba Version: 1.47.0 Suggests: oligo License: GPL MD5sum: 36ec89c8a41245e63e94e7bc1ba5b355 NeedsCompilation: no Title: Sample data - Hapmap 100K XBA Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap100kxba git_branch: devel git_last_commit: 58d0485 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/hapmap100kxba_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligo dependencyCount: 0 Package: hapmap500knsp Version: 1.47.0 Suggests: oligo License: GPL MD5sum: 48ff3f7db9443113dbda1e4e7f008cdf NeedsCompilation: no Title: Sample data - Hapmap 500K NSP Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap500knsp git_branch: devel git_last_commit: f28c8d5 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/hapmap500knsp_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmap500ksty Version: 1.47.0 Suggests: oligo License: GPL MD5sum: a8dfc18d1c61e6d014161dc1de569908 NeedsCompilation: no Title: Sample data - Hapmap 500K STY Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap500ksty git_branch: devel git_last_commit: db10d2f git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/hapmap500ksty_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmapsnp5 Version: 1.47.0 Suggests: oligo License: GPL MD5sum: e3328efd4d31d12f3c6e3d93853e0703 NeedsCompilation: no Title: Sample data - Hapmap SNP 5.0 Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData, SNPData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmapsnp5 git_branch: devel git_last_commit: 89a2890 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/hapmapsnp5_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligoClasses dependencyCount: 0 Package: hapmapsnp6 Version: 1.47.0 Depends: R (>= 2.15) Suggests: oligo, oligoClasses License: GPL MD5sum: 432a3cc658cff5ad01fc9e1f109860b0 NeedsCompilation: no Title: Sample data - Hapmap SNP 6.0 Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, SNPData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmapsnp6 git_branch: devel git_last_commit: f1e1563 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/hapmapsnp6_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: crlmm, oligoClasses dependencyCount: 0 Package: harbChIP Version: 1.43.0 Depends: R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5), Biostrings Imports: methods, stats License: Artistic-2.0 MD5sum: 2c6746ac1779692ed7e5f20008a25e7a NeedsCompilation: no Title: Experimental Data Package: harbChIP Description: data from a yeast ChIP-chip experiment biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/harbChIP git_branch: devel git_last_commit: 7731876 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/harbChIP_1.43.0.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: 26 Package: HarmanData Version: 1.33.0 Depends: R (>= 3.5.0) Suggests: BiocGenerics, BiocStyle, knitr, rmarkdown, Harman (>= 1.23.3) License: GPL-3 MD5sum: 91bdaa37d9e48d4d727445e56722eceb NeedsCompilation: no Title: Data for the Harman package Description: Datasets of accompany Harman, a PCA and constrained optimisation based technique. Contains three example datasets: IMR90, Human lung fibroblast cells exposed to nitric oxide; NPM, an experiment to test skin penetration of metal oxide nanoparticles following topical application of sunscreens in non-pregnant mice; OLF; an experiment to gauge the response of human olfactory neurosphere-derived (hONS) cells to ZnO nanoparticles. Since version 1.24, this package also contains the Infinium5 dataset, a set of batch correction adjustments across 5 Illumina Infinium Methylation BeadChip datasets. This file does not contain methylation data, but summary statistics of 5 datasets after correction. There is also an EpiSCOPE_sample file as exampling for the new methylation clustering functionality in Harman. biocViews: ExpressionData, MicroarrayData, ExperimentData, Homo_sapiens_Data, Mus_musculus_Data Author: Yalchin Oytam [aut], Josh Bowden [aut], Jason Ross [aut, cre] Maintainer: Jason Ross URL: http://www.bioinformatics.csiro.au/harman/ VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/HarmanData git_branch: devel git_last_commit: cd1093c git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/HarmanData_1.33.0.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: 1.27.0 Depends: R (>= 3.4.0) Imports: ExperimentHub Suggests: AnnotationHub, knitr, rmarkdown, igraph, survival, ANF, stats, testthat License: GPL-3 MD5sum: f439db85f645ee6f000d5a5169c98f42 NeedsCompilation: no Title: Processed Harmonized TCGA Data of Five Selected Cancer Types Description: This package contains the processed harmonized TCGA data of five cancer types used in "Tianle Ma and Aidong Zhang, Integrate Multi-omic Data Using Affinity Network Fusion (ANF) for Cancer Patient Clustering". biocViews: CancerData, ReproducibleResearch Author: Tianle Ma Maintainer: Tianle Ma VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/HarmonizedTCGAData git_branch: devel git_last_commit: f9ba285 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/HarmonizedTCGAData_1.27.0.tar.gz vignettes: vignettes/HarmonizedTCGAData/inst/doc/HarmonizedTCGAData.html vignetteTitles: Patient Affinity Matrices Derived from Harmonized TCGA Dataset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HarmonizedTCGAData/inst/doc/HarmonizedTCGAData.R dependencyCount: 67 Package: HCAData Version: 1.21.0 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: b1c3ca622e347169d39428a589add9b9 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: devel git_last_commit: 27673df git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/HCAData_1.21.0.tar.gz vignettes: vignettes/HCAData/inst/doc/hcadata.html vignetteTitles: Accessing the Human Cell Atlas datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HCAData/inst/doc/hcadata.R dependsOnMe: OSCA.workflows dependencyCount: 83 Package: HCATonsilData Version: 1.3.0 Depends: R (>= 4.3.0) Imports: ExperimentHub, SingleCellExperiment, SpatialExperiment, HDF5Array, SummarizedExperiment, S4Vectors, htmltools, rmarkdown, base64enc, utils Suggests: knitr, ggplot2, testthat (>= 3.0.0), scater, Seurat, Signac, zellkonverter, iSEE, ggspavis, kableExtra, BiocStyle License: MIT + file LICENSE MD5sum: 784b7cf0a87a1ef31954f8945589a591 NeedsCompilation: no Title: Provide programmatic access to the tonsil cell atlas datasets Description: This package provides access to the scRNA-seq, scATAC-seq, multiome, CITE-seq and spatial transcriptomics (Visium) data generated by the tonsil cell atlas in the context of the Human Cell Atlas (HCA). The data is provided via the Bioconductor project in the form of SingleCellExperiments. Additionally, information on the whole compendium of identified cell types is provided in form of a glossary. biocViews: SingleCellData, ExperimentData, RNASeqData, ExperimentHub, ExpressionData, SpatialData Author: Ramon Massoni-Badosa [aut, cre] (), Federico Marini [aut] (), Alan O'Callaghan [aut], Helena L. Crowell [aut] () Maintainer: Ramon Massoni-Badosa URL: https://github.com/massonix/HCATonsilData VignetteBuilder: knitr BugReports: https://github.com/massonix/HCATonsilData/issues git_url: https://git.bioconductor.org/packages/HCATonsilData git_branch: devel git_last_commit: 00086ba git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/HCATonsilData_1.3.0.tar.gz vignettes: vignettes/HCATonsilData/inst/doc/HCATonsilData.html vignetteTitles: HCATonsilData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HCATonsilData/inst/doc/HCATonsilData.R dependencyCount: 101 Package: HD2013SGI Version: 1.45.0 Depends: R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots, limma, vcd, LSD,EBImage Suggests: BiocStyle License: Artistic-2.0 MD5sum: a1253dd2dbfa4dd3fb07151798fad940 NeedsCompilation: no Title: Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping Description: This package contains the experimental data and a complete executable transcript (vignette) of the analysis of the HCT116 genetic interaction matrix presented in the paper "Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping" by C. Laufer, B. Fischer, M. Billmann, W. Huber, M. Boutros; Nature Methods (2013) 10:427-31. doi: 10.1038/nmeth.2436. biocViews: ExperimentData, CancerData, ColonCancerData, MicrotitrePlateAssayData, CellCulture, Homo_sapiens_Data, HighThroughputImagingData Author: Bernd Fischer Maintainer: Mike Smith SystemRequirements: GNU make git_url: https://git.bioconductor.org/packages/HD2013SGI git_branch: devel git_last_commit: f46ea75 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/HD2013SGI_1.45.0.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: 90 Package: HDCytoData Version: 1.25.0 Depends: ExperimentHub, SummarizedExperiment, flowCore Imports: utils, methods Suggests: BiocStyle, knitr, rmarkdown, Rtsne, umap, ggplot2, FlowSOM, mclust License: MIT + file LICENSE MD5sum: 875b9c429c8d6b7c3ba9ba71e5761b7a NeedsCompilation: no Title: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats Description: Data package containing a set of publicly available high-dimensional cytometry benchmark datasets, formatted into SummarizedExperiment and flowSet Bioconductor object formats, including all required metadata. Row metadata includes sample IDs, group IDs, patient IDs, reference cell population or cluster labels (where available), and labels identifying 'spiked in' cells (where available). Column metadata includes channel names, protein marker names, and protein marker classes (cell type or cell state). biocViews: ExperimentHub, ExperimentData, ExpressionData, FlowCytometryData, SingleCellData, Homo_sapiens_Data, ImmunoOncologyData Author: Lukas M. Weber [aut, cre], Charlotte Soneson [aut] Maintainer: Lukas M. Weber URL: https://github.com/lmweber/HDCytoData VignetteBuilder: knitr BugReports: https://github.com/lmweber/HDCytoData/issues git_url: https://git.bioconductor.org/packages/HDCytoData git_branch: devel git_last_commit: 40bf880 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/HDCytoData_1.25.0.tar.gz vignettes: vignettes/HDCytoData/inst/doc/Contribution_guidelines.html, vignettes/HDCytoData/inst/doc/Examples_and_use_cases.html, vignettes/HDCytoData/inst/doc/HDCytoData_package.html vignetteTitles: 3. Contribution guidelines, 2. Examples and use cases, 1. HDCytoData package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HDCytoData/inst/doc/Contribution_guidelines.R, vignettes/HDCytoData/inst/doc/Examples_and_use_cases.R, vignettes/HDCytoData/inst/doc/HDCytoData_package.R dependsOnMe: cytofWorkflow suggestsMe: CytoMDS, diffcyt dependencyCount: 84 Package: healthyControlsPresenceChecker Version: 1.9.0 Depends: R (>= 4.0.0) Imports: xml2, GEOquery, geneExpressionFromGEO, magrittr Suggests: RUnit, BiocGenerics, markdown, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 6184b854f3ebc82c236e78fed121a19f NeedsCompilation: no Title: Dowloads A Gene Expression Dataset From GEO And Checks If It Contains Data Of Healthy Controls Or Not Description: A function that reads in the GEO accession code of a gene expression dataset, retrieves its data from GEO, and checks if data of healthy controls are present in the dataset. It returns true if healthy controls data are found, and false otherwise. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL . biocViews: GEO, RepositoryData, ExpressionData Author: Davide Chicco [aut, cre] () Maintainer: Davide Chicco URL: https://github.com/davidechicco/healthyControlsPresenceChecker VignetteBuilder: knitr BugReports: https://github.com/davidechicco/healthyControlsPresenceChecker/issues git_url: https://git.bioconductor.org/packages/healthyControlsPresenceChecker git_branch: devel git_last_commit: da08da6 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/healthyControlsPresenceChecker_1.9.0.tar.gz vignettes: vignettes/healthyControlsPresenceChecker/inst/doc/healthyControlsPresenceChecker.html vignetteTitles: healthyControlsPresenceChecker vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/healthyControlsPresenceChecker/inst/doc/healthyControlsPresenceChecker.R dependencyCount: 81 Package: healthyFlowData Version: 1.43.0 Depends: R (>= 2.15.0), flowCore Imports: methods License: Artistic-2.0 MD5sum: 3e1ac004b154492426270139cec7cb19 NeedsCompilation: no Title: Healthy dataset used by the flowMatch package Description: A healthy dataset with 20 flow cytometry samples used by the flowMatch package. biocViews: FlowCytometryData Author: Ariful Azad Maintainer: Ariful Azad git_url: https://git.bioconductor.org/packages/healthyFlowData git_branch: devel git_last_commit: 54c1696 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/healthyFlowData_1.43.0.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: 17 Package: HEEBOdata Version: 1.43.0 License: LGPL MD5sum: b5afc1388abb5d073d0ca30685523069 NeedsCompilation: no Title: HEEBO set and HEEBO controls. Description: R objects describing the HEEBO oligo set. biocViews: ExperimentData Author: Agnes Paquet Maintainer: Agnes Paquet URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/ git_url: https://git.bioconductor.org/packages/HEEBOdata git_branch: devel git_last_commit: 6726cfa git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/HEEBOdata_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQuality dependencyCount: 0 Package: HelloRangesData Version: 1.31.0 Suggests: BiocStyle License: GPL (>= 2) MD5sum: a705f284fd9ca453fb1a813fc3d5e373 NeedsCompilation: no Title: Data for the HelloRanges tutorial vignette Description: Provides the data that were used in the bedtools tutorial by Aaron Quinlan (http://quinlanlab.org/tutorials/bedtools/bedtools.html). Includes a subset of the DnaseI hypersensitivity data from "Maurano et al. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA. Science. 2012. Vol. 337 no. 6099 pp. 1190-1195." The rest of the tracks were originally downloaded from the UCSC table browser. See the HelloRanges vignette for a port of the bedtools tutorial to R. biocViews: ExperimentData, SequencingData Author: Michael Lawrence Maintainer: Michael Lawrence git_url: https://git.bioconductor.org/packages/HelloRangesData git_branch: devel git_last_commit: 420c41f git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/HelloRangesData_1.31.0.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: 1.43.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: a3fc0e3594edfa6a67767cc80c0d5814 NeedsCompilation: no Title: hgu133a data for barcode Description: Data used by the barcode package for microarrays of type hgu133a. biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/hgu133abarcodevecs git_branch: devel git_last_commit: 9787d91 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/hgu133abarcodevecs_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hgu133plus2barcodevecs Version: 1.43.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 8735502feb085f63d02d8ad7613d040d NeedsCompilation: no Title: hgu133plus2 data for barcode Description: Data used by the barcode package for microarrays of type hgu133plus2. biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/hgu133plus2barcodevecs git_branch: devel git_last_commit: 1b0598e git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/hgu133plus2barcodevecs_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hgu133plus2CellScore Version: 1.25.0 Depends: R (>= 3.5.0) Imports: Biobase (>= 2.39.1) Suggests: knitr License: GPL-3 MD5sum: 4f2847665b4c65618ba00adf9bdab810 NeedsCompilation: no Title: CellScore Standard Cell Types Expression Dataset [hgu133plus2] Description: The CellScore Standard Dataset contains expression data from a wide variety of human cells and tissues, which should be used as standard cell types in the calculation of the CellScore. All data was curated from public databases such as Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) or ArrayExpress (https://www.ebi.ac.uk/arrayexpress/). This standard dataset only contains data from the Affymetrix GeneChip Human Genome U133 Plus 2.0 microarrays. Samples were manually annotated using the database information or consulting the publications in which the datasets originated. The sample annotations are stored in the phenoData slot of the expressionSet object. Raw data (CEL files) were processed with the affy package to generate present/absent calls (mas5calls) and background-subtracted values, which were then normalized by the R-package yugene to yield the final expression values for the standard expression matrix. The annotation table for the microarray was retrieved from the BioC annotation package hgu133plus2. All data are stored in an expressionSet object. biocViews: ExpressionData, MicroarrayData, GEO, ExperimentData, Homo_sapiens_Data, Genome, ArrayExpress Author: Nancy Mah, Katerina Taskova Maintainer: Nancy Mah VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/hgu133plus2CellScore git_branch: devel git_last_commit: b075277 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/hgu133plus2CellScore_1.25.0.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: 6 Package: hgu2beta7 Version: 1.45.0 Depends: R (>= 2.0.0) License: Artistic-2.0 MD5sum: bb5f36086082f68b6efa6c7eb80525f5 NeedsCompilation: no Title: A data package containing annotation data for hgu2beta7 Description: Annotation data file for hgu2beta7 assembled using data from public data repositories biocViews: Genome Author: Chenwei Lin Maintainer: Bioconductor Package Maintainer git_url: https://git.bioconductor.org/packages/hgu2beta7 git_branch: devel git_last_commit: 12fd133 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/hgu2beta7_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: HiBED Version: 1.3.0 Depends: R (>= 3.5.0) Imports: dplyr, FlowSorted.Blood.EPIC, tibble, FlowSorted.DLPFC.450k, minfi, utils, AnnotationHub, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, IlluminaHumanMethylation450kmanifest License: GPL-3 MD5sum: bd2a1173aa85495d181a93efd1020857 NeedsCompilation: no Title: HiBED Description: Hierarchical deconvolution for extensive cell type resolution in the human brain using DNA methylation. The HiBED deconvolution estimates proportions up to 7 cell types (GABAergic neurons, glutamatergic neurons, astrocytes, microglial cells, oligodendrocytes, endothelial cells, and stromal cells) in bulk brain tissues. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, Genome, MethylationArrayData, PackageTypeData Author: Ze Zhang [cre, aut] (), Lucas A. Salas [aut] Maintainer: Ze Zhang URL: https://github.com/SalasLab/HiBED VignetteBuilder: knitr BugReports: https://github.com/SalasLab/HiBED/issues. git_url: https://git.bioconductor.org/packages/HiBED git_branch: devel git_last_commit: c7d0642 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/HiBED_1.3.0.tar.gz vignettes: vignettes/HiBED/inst/doc/HiBED.html vignetteTitles: HiBED hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HiBED/inst/doc/HiBED.R dependencyCount: 150 Package: HiCDataHumanIMR90 Version: 1.25.0 Depends: R (>= 3.5.0) Suggests: HiTC, BiocStyle License: GPL-3 MD5sum: a7dedc5bcc7ea167d131a35c4a88f05b NeedsCompilation: no Title: Human IMR90 Fibroblast HiC data from Dixon et al. 2012 Description: The HiC data from Human Fibroblast IMR90 cell line (HindIII restriction) was retrieved from the GEO website, accession number GSE35156 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35156). The raw reads were processed as explained in Dixon et al. (Nature 2012). biocViews: ExperimentData, Genome, Homo_sapiens_Data, GEO Author: Nicolas Servant Maintainer: Nicolas Servant git_url: https://git.bioconductor.org/packages/HiCDataHumanIMR90 git_branch: devel git_last_commit: f1d0b93 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/HiCDataHumanIMR90_1.25.0.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: 1.41.0 Suggests: ShortRead License: GPL-3 MD5sum: e4946a438e199516d8b093164481ad82 NeedsCompilation: no Title: Human lymphoblastoid HiC data from Lieberman-Aiden et al. 2009 Description: The HiC data from human lymphoblastoid cell line (HindIII restriction) was retrieved from the sequence read archive and two ends of the paired reads were aligned separately with bowtie. biocViews: ExperimentData, Homo_sapiens_Data Author: Borbala Mifsud Maintainer: Borbala Mifsud git_url: https://git.bioconductor.org/packages/HiCDataLymphoblast git_branch: devel git_last_commit: d179b1e git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/HiCDataLymphoblast_1.41.0.tar.gz vignettes: vignettes/HiCDataLymphoblast/inst/doc/package_vignettes.pdf vignetteTitles: package_vignettes.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HiCDataLymphoblast/inst/doc/package_vignettes.R suggestsMe: GOTHiC dependencyCount: 0 Package: HiContactsData Version: 1.7.0 Depends: ExperimentHub Imports: BiocFileCache, AnnotationHub Suggests: testthat, methods, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 92c0dd68a4cfb1d8359e84fe09d3b8b3 NeedsCompilation: no Title: HiContacts companion data package Description: Provides a collection of Hi-C files (pairs, (m)cool and fastq). These datasets can be read into R and further investigated and visualized with the HiContacts package. Data includes yeast Hi-C data generated by the Koszul lab from the Pasteur Institute. biocViews: ExperimentHub, ExperimentData, SequencingData Author: Jacques Serizay [aut, cre] Maintainer: Jacques Serizay URL: https://github.com/js2264/HiContactsData VignetteBuilder: knitr BugReports: https://github.com/js2264/HiContactsData/issues git_url: https://git.bioconductor.org/packages/HiContactsData git_branch: devel git_last_commit: 6c3f8dd git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/HiContactsData_1.7.0.tar.gz vignettes: vignettes/HiContactsData/inst/doc/HiContactsData.html vignetteTitles: HiContactsData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HiContactsData/inst/doc/HiContactsData.R importsMe: OHCA suggestsMe: HiCExperiment, HiContacts, HiCool, plyinteractions dependencyCount: 67 Package: HighlyReplicatedRNASeq Version: 1.17.0 Depends: SummarizedExperiment, ExperimentHub Imports: S4Vectors Suggests: BiocStyle, BiocFileCache, knitr, rmarkdown License: MIT + file LICENSE MD5sum: fcf59c66a362aa8be1106047a42aa085 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: devel git_last_commit: 67977c7 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/HighlyReplicatedRNASeq_1.17.0.tar.gz vignettes: vignettes/HighlyReplicatedRNASeq/inst/doc/HighlyReplicatedRNASeq.html vignetteTitles: Exploring the 86 bulk RNA-seq samples from the Schurch et al. (2016) study hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HighlyReplicatedRNASeq/inst/doc/HighlyReplicatedRNASeq.R dependencyCount: 78 Package: Hiiragi2013 Version: 1.41.0 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: 71c665b10052ac72002701dd45990dc7 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: devel git_last_commit: 3911b68 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/Hiiragi2013_1.41.0.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: 79 Package: HIVcDNAvantWout03 Version: 1.45.0 License: GPL (>= 2) MD5sum: 2a6e3a0baf21bbbb0b9fce6a0e7f3133 NeedsCompilation: no Title: T cell line infections with HIV-1 LAI (BRU) Description: The expression levels of approximately 4600 cellular RNA transcripts were assessed in CD4+ T cell lines at different times after infection with HIV-1BRU using DNA microarrays. This data corresponds to the first block of a 12 block array image (001030_08_1.GEL) in the first data set (2000095918 A) in the first experiment (CEM LAI vs HI-LAI 24hr). There are two data sets, which are part of a dye-swap experiment with replicates, representing the Cy3 (green) absorption intensities for channel 1 (hiv1raw) and the Cy5 (red) absorption intensities for channel 2 (hiv2raw). biocViews: ExperimentData, MicroarrayData, TwoChannelData, HIVData Author: Dr. Angelique van't Wout, Department of Microbiology, University of Washington Maintainer: Chris Fraley URL: http://expression.microslu.washington.edu/expression/vantwoutjvi2002.html git_url: https://git.bioconductor.org/packages/HIVcDNAvantWout03 git_branch: devel git_last_commit: 33a1de8 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/HIVcDNAvantWout03_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: HMP16SData Version: 1.25.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: AnnotationHub, ExperimentHub, S4Vectors, assertthat, dplyr, kableExtra, knitr, magrittr, methods, readr, stringr, tibble, utils Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, circlize, cowplot, dendextend, devtools, ggplot2, gridExtra, haven, phyloseq, rmarkdown, roxygen2, stats, testthat, tidyr License: Artistic-2.0 MD5sum: 281748b66bb7c6348e64e11bf17aa50a 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: devel git_last_commit: 80677c1 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/HMP16SData_1.25.0.tar.gz vignettes: vignettes/HMP16SData/inst/doc/HMP16SData.html vignetteTitles: HMP16SData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HMP16SData/inst/doc/HMP16SData.R dependencyCount: 112 Package: HMP2Data Version: 1.19.0 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: c826ebc38ce303a314834ab864d85084 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: devel git_last_commit: 9537d9c git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/HMP2Data_1.19.0.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: 145 Package: homosapienDEE2CellScore Version: 1.1.0 Imports: Rtsne (>= 0.15), utils(>= 3.5.0), ExperimentHub, BiocGenerics, DESeq2, S4Vectors, SummarizedExperiment, getDEE2, MatrixGenerics Suggests: knitr, rmarkdown, devtools, Biobase (>= 2.39.1), BiocManager, AnnotationHubData, ExperimentHubData, AnnotationHub, CellScore (>= 1.21.4) License: GPL (>= 3) MD5sum: d9fbe08cb7225ad2199c4fb58166d0ea NeedsCompilation: no Title: Example Data Package for CellScore Description: This is a data package for normalised homosapien data downloaded from DEE2. The package both downloads, normalises, and filters the data, and provides a way to access the data from a canonical store without needing local processing. This package was built as a way to generate and store canonical test data for CellScore. biocViews: RNASeqData, Genome, ExperimentHub, ExpressionData Author: Justin Marsh [aut, cre] Maintainer: Justin Marsh VignetteBuilder: knitr BugReports: https://github.com/flaviusb/homosapienDEE2CellScore/issues git_url: https://git.bioconductor.org/packages/homosapienDEE2CellScore git_branch: devel git_last_commit: ec8c307 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/homosapienDEE2CellScore_1.1.0.tar.gz vignettes: vignettes/homosapienDEE2CellScore/inst/doc/use-data-package.html vignetteTitles: Use the Data in this Data Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/homosapienDEE2CellScore/inst/doc/use-data-package.R dependencyCount: 108 Package: HSMMSingleCell Version: 1.25.0 Depends: R (>= 2.10) License: Artistic-2.0 MD5sum: 3a4cebe44f14d8feeb54f58637e1855e NeedsCompilation: no Title: Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM) Description: Skeletal myoblasts undergo a well-characterized sequence of morphological and transcriptional changes during differentiation. In this experiment, primary human skeletal muscle myoblasts (HSMM) were expanded under high mitogen conditions (GM) and then differentiated by switching to low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several hundred cells taken over a time-course of serum-induced differentiation. Between 49 and 77 cells were captured at each of four time points (0, 24, 48, 72 hours) following serum switch using the Fluidigm C1 microfluidic system. RNA from each cell was isolated and used to construct mRNA-Seq libraries, which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell. biocViews: ExperimentData, RNASeqData Author: Cole Trapnell Maintainer: Cole Trapnell git_url: https://git.bioconductor.org/packages/HSMMSingleCell git_branch: devel git_last_commit: 3cce31c git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/HSMMSingleCell_1.25.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: monocle dependencyCount: 0 Package: HumanAffyData Version: 1.31.0 Depends: ExperimentHub, Biobase, R (>= 3.3) Suggests: BiocStyle License: Artistic-2.0 MD5sum: 9e7139c512e4edae41f45309ab8d6b46 NeedsCompilation: no Title: GEO accession GSE64985 and ArrayExpress accession E-MTAB-62 as ExpressionSet objects Description: Re-analysis of human gene expression data generated on the Affymetrix HG_U133PlusV2 (EH176) and Affymetrix HG_U133A (EH177) platforms. The original data were normalized using robust multiarray averaging (RMA) to obtain an integrated gene expression atlas across diverse biological sample types and conditions. The entire compendia comprisee 9395 arrays for EH176 and 5372 arrays for EH177. biocViews: ExperimentData, GEO, ArrayExpress, Homo_sapiens_Data, MicroarrayData, ExpressionData Author: Brad Nelms Maintainer: Brad Nelms git_url: https://git.bioconductor.org/packages/HumanAffyData git_branch: devel git_last_commit: 8e8f4b9 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/HumanAffyData_1.31.0.tar.gz vignettes: vignettes/HumanAffyData/inst/doc/HumanAffyData.pdf vignetteTitles: Intro to the HumanAffyData package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HumanAffyData/inst/doc/HumanAffyData.R suggestsMe: CellMapper dependencyCount: 67 Package: humanStemCell Version: 0.45.0 Depends: Biobase (>= 2.5.5), hgu133plus2.db License: Artistic-2.0 MD5sum: b30b6caad72252d5bbe16e41730999c7 NeedsCompilation: no Title: Human Stem Cells time course experiment Description: Affymetrix time course experiment on human stem cells (two time points: undifferentiated and differentiated). biocViews: ExperimentData, Homo_sapiens_Data Author: R. Gentleman, N. Le Meur, M. Tewari Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/humanStemCell git_branch: devel git_last_commit: b4ba76a git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/humanStemCell_0.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MiRaGE, rtracklayer dependencyCount: 47 Package: IHWpaper Version: 1.33.0 Depends: R (>= 3.3), IHW Imports: Rcpp, stats, splines, methods, utils, DESeq2, SummarizedExperiment, fdrtool, genefilter, qvalue, Biobase, BiocGenerics, BiocParallel, dplyr, grid, ggplot2, cowplot LinkingTo: Rcpp Suggests: testthat, RColorBrewer, wesanderson, scales, gridExtra, BiocStyle, knitr, rmarkdown, airway, locfdr, tidyr, latex2exp License: Artistic-2.0 MD5sum: 96e84741996e4d86a09248839c7a33e6 NeedsCompilation: yes Title: Reproduce figures in IHW paper Description: This package conveniently wraps all functions needed to reproduce the figures in the IHW paper (https://www.nature.com/articles/nmeth.3885) and the data analysis in https://rss.onlinelibrary.wiley.com/doi/10.1111/rssb.12411, cf. the arXiv preprint (http://arxiv.org/abs/1701.05179). Thus it is a companion package to the Bioconductor IHW package. biocViews: ReproducibleResearch, ExperimentData, RNASeqData, ExpressionData Author: Nikos Ignatiadis [aut, cre] Maintainer: Nikos Ignatiadis VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/IHWpaper git_branch: devel git_last_commit: d49c083 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/IHWpaper_1.33.0.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: 1.41.0 Depends: R (>= 3.0.1) License: GPL-3 MD5sum: 108cd7a51616205409a7b57a7b24eea8 NeedsCompilation: no Title: Annotation Package combining variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes Description: Includes details on variants for each probe on the 450k bead chip for each of the four populations (Asian, American, African and European) biocViews: Homo_sapiens_Data, CancerData, ChipOnChipData, SNPData Author: Lee Butcher Maintainer: Tiffany Morris git_url: https://git.bioconductor.org/packages/Illumina450ProbeVariants.db git_branch: devel git_last_commit: 36e3c3e git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/Illumina450ProbeVariants.db_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: IlluminaDataTestFiles Version: 1.43.0 License: Artistic-2.0 MD5sum: 47208959a9c1c2097ced566061fefd24 NeedsCompilation: no Title: Illumina microarray files (IDAT) for testing Description: Example data for Illumina microarray output files, for testing purposes biocViews: MicroarrayData Author: Kasper Daniel Hansen, Mike L. Smith Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/IlluminaDataTestFiles git_branch: devel git_last_commit: 1131004 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/IlluminaDataTestFiles_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: illuminaio dependencyCount: 0 Package: imcdatasets Version: 1.13.0 Depends: R (>= 4.4.0), SingleCellExperiment, SpatialExperiment, cytomapper, Imports: methods, utils, ExperimentHub, S4Vectors, DelayedArray, HDF5Array Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat License: GPL-3 + file LICENSE MD5sum: 96d0b1783414398b374b2c9c7c05d2d0 NeedsCompilation: no Title: Collection of publicly available imaging mass cytometry (IMC) datasets Description: The imcdatasets package provides access to publicly available IMC datasets. IMC is a technology that enables measurement of > 40 proteins from tissue sections. The generated images can be segmented to extract single cell data. Datasets typically consist of three elements: a SingleCellExperiment object containing single cell data, a CytoImageList object containing multichannel images and a CytoImageList object containing the cell masks that were used to extract the single cell data from the images. biocViews: ExperimentData, ExperimentHub, SingleCellData, SpatialData, Homo_sapiens_Data, ImmunoOncologyData, TechnologyData, PackageTypeData, ReproducibleResearch, Tissue Author: Nicolas Damond [aut, cre] (), 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: devel git_last_commit: 0ab0f4a git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/imcdatasets_1.13.0.tar.gz vignettes: vignettes/imcdatasets/inst/doc/Guidelines_Contribution_Dataset-formatting.html, vignettes/imcdatasets/inst/doc/imcdatasets.html vignetteTitles: "Contributing guidelines and datasets format", "Accessing IMC datasets" hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/imcdatasets/inst/doc/Guidelines_Contribution_Dataset-formatting.R, vignettes/imcdatasets/inst/doc/imcdatasets.R dependencyCount: 153 Package: ITALICSData Version: 2.43.0 Depends: R (>= 2.0.0) License: GPL MD5sum: e55a8aba719a01a7c2f75722f19573c3 NeedsCompilation: no Title: ITALICSData Description: Data needed to use the ITALICS package biocViews: ExperimentData, HapMap Author: Guillem Rigaill Maintainer: Guillem Rigaill URL: http://bioinfo.curie.fr git_url: https://git.bioconductor.org/packages/ITALICSData git_branch: devel git_last_commit: 405382e git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/ITALICSData_2.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ITALICS dependencyCount: 0 Package: Iyer517 Version: 1.47.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 1a00d925a7054c9a60b248c7bfbf7739 NeedsCompilation: no Title: exprSets for Iyer, Eisen et all 1999 Science paper Description: representation of public Iyer data from http://genome-www.stanford.edu/serum/clusters.html biocViews: ExperimentData Author: Vishy Iyer Maintainer: Vince Carey git_url: https://git.bioconductor.org/packages/Iyer517 git_branch: devel git_last_commit: 2282af8 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/Iyer517_1.47.0.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: 6 Package: JASPAR2014 Version: 1.41.0 Depends: R (>= 3.0.1), methods, Biostrings (>= 2.29.19) License: GPL-2 MD5sum: 9a3abd090a9f71e863dfa15d8c10824c NeedsCompilation: no Title: Data package for JASPAR Description: Data package for JASPAR 2014. To search this databases, please use the package TFBSTools. biocViews: ExperimentData, SequencingData Author: Ge Tan Maintainer: Ge Tan URL: http://jaspar.genereg.net/ git_url: https://git.bioconductor.org/packages/JASPAR2014 git_branch: devel git_last_commit: 68f14ec git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/JASPAR2014_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MatrixRider, TFBSTools dependencyCount: 25 Package: JASPAR2016 Version: 1.33.0 Depends: R (>= 3.2.2), methods License: GPL-2 MD5sum: e4ccad62b31962e2a61b904c1e208640 NeedsCompilation: no Title: Data package for JASPAR 2016 Description: Data package for JASPAR 2016. To search this databases, please use the package TFBSTools (>= 1.8.1). biocViews: ExperimentData, MotifAnnotation, GeneRegulation Author: Ge Tan Maintainer: Ge Tan URL: http://jaspar.genereg.net/ git_url: https://git.bioconductor.org/packages/JASPAR2016 git_branch: devel git_last_commit: 8284586 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/JASPAR2016_1.33.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: ATACCoGAPS suggestsMe: TFBSTools, chromVAR, CAGEWorkflow dependencyCount: 1 Package: JohnsonKinaseData Version: 1.1.0 Imports: ExperimentHub, BiocParallel, checkmate, dplyr, stats, stringr, tidyr, purrr, utils Suggests: knitr, BiocStyle, ExperimentHubData, testthat (>= 3.0.0), rmarkdown License: MIT + file LICENSE MD5sum: 0ca5e639e0fb0f2ef6a1bfab0e9d4ec1 NeedsCompilation: no Title: Kinase PWMs based on data published by Johnson et al. 2023 (doi:10.1038/s41586-022-05575-3) Description: The packages provides position specific weight matrices (PWMs) for 303 human serine/threonine kinases originally published in Johnson et al. 2023. It includes gene annotation for each kinase PWM and PWM matching scores for a set of 85603 curated human phosphosites which can be used to map a PWM score to its percentile rank. The package also includes basic functionality to score user provided phosphosites. biocViews: ExperimentHub, Homo_sapiens_Data, Proteome Author: Florian Geier [aut, cre] () Maintainer: Florian Geier URL: https://github.com/fgeier/JohnsonKinaseData/ VignetteBuilder: knitr BugReports: https://support.bioconductor.org/t/JohnsonKinaseData git_url: https://git.bioconductor.org/packages/JohnsonKinaseData git_branch: devel git_last_commit: 9a5c1a3 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/JohnsonKinaseData_1.1.0.tar.gz vignettes: vignettes/JohnsonKinaseData/inst/doc/JohnsonKinaseData.html vignetteTitles: JohnsonKinaseData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/JohnsonKinaseData/inst/doc/JohnsonKinaseData.R dependencyCount: 78 Package: KEGGandMetacoreDzPathwaysGEO Version: 1.25.0 Depends: R (>= 2.15.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: 56bfe971778169173fef97e816b5f2e6 NeedsCompilation: no Title: Disease Datasets from GEO Description: This is a collection of 18 data sets for which the phenotype is a disease with a corresponding pathway in either KEGG or metacore database.This collection of datasets were used as gold standard in comparing gene set analysis methods. biocViews: ExperimentData, GEO Author: Gaurav Bhatti Maintainer: Gaurav Bhatti git_url: https://git.bioconductor.org/packages/KEGGandMetacoreDzPathwaysGEO git_branch: devel git_last_commit: 5f008e2 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/KEGGandMetacoreDzPathwaysGEO_1.25.0.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: 6 Package: KEGGdzPathwaysGEO Version: 1.43.0 Depends: R (>= 2.13.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: c7afdfb011ee785e93a11c36e8b37dc9 NeedsCompilation: no Title: KEGG Disease Datasets from GEO Description: This is a collection of 24 data sets for which the phenotype is a disease with a corresponding pathway in the KEGG database.This collection of datasets were used as gold standard in comparing gene set analysis methods by the PADOG package. biocViews: MicroarrayData, GEO, ExperimentData Author: Gaurav Bhatti, Adi L. Tarca Maintainer: Gaurav Bhatti git_url: https://git.bioconductor.org/packages/KEGGdzPathwaysGEO git_branch: devel git_last_commit: 726bca5 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/KEGGdzPathwaysGEO_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: PADOG importsMe: GSEABenchmarkeR dependencyCount: 6 Package: kidpack Version: 1.47.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5) License: GPL-2 MD5sum: c4ab0d1b6b3d34510ea23665688cfd95 NeedsCompilation: no Title: DKFZ kidney package Description: kidney microarray data biocViews: ExperimentData, CancerData, KidneyCancerData, MicroarrayData, ArrayExpress Author: Wolfgang Huber Maintainer: Wolfgang Huber URL: http://www.dkfz.de/mga git_url: https://git.bioconductor.org/packages/kidpack git_branch: devel git_last_commit: b530aca git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/kidpack_1.47.0.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: 6 Package: KOdata Version: 1.31.0 Depends: R (>= 3.3.0) License: MIT + file LICENSE MD5sum: 2bc78a3d7c20b016849d1aecbaafe0da NeedsCompilation: no Title: LINCS Knock-Out Data Package Description: Contains consensus genomic signatures (CGS) for experimental cell-line specific gene knock-outs as well as baseline gene expression data for a subset of experimental cell-lines. Intended for use with package KEGGlincs. biocViews: ExpressionData, CancerData, Homo_sapiens_Data Author: Shana White Maintainer: Shana White git_url: https://git.bioconductor.org/packages/KOdata git_branch: devel git_last_commit: 36425c7 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/KOdata_1.31.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: KEGGlincs dependencyCount: 0 Package: leeBamViews Version: 1.41.0 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: 855e52b57b78ba465820086d02baef48 NeedsCompilation: no Title: leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009 Description: data from PMID 19096707; prototype for managing multiple NGS samples biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData, SNPData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/leeBamViews git_branch: devel git_last_commit: 7026ec5 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/leeBamViews_1.41.0.tar.gz vignettes: vignettes/leeBamViews/inst/doc/leeViews.pdf vignetteTitles: managing multiple NGS samples with bamViews hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/leeBamViews/inst/doc/leeViews.R suggestsMe: EDASeq dependencyCount: 59 Package: leukemiasEset Version: 1.41.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 242f05b8e98aeae585be2cfabc17ff2e NeedsCompilation: no Title: Leukemia's microarray gene expression data (expressionSet). Description: Expressionset containing gene expresion data from 60 bone marrow samples of patients with one of the four main types of leukemia (ALL, AML, CLL, CML) or non-leukemia. biocViews: Tissue, Genome, Homo_sapiens_Data, CancerData, LeukemiaCancerData, MicroarrayData, ChipOnChipData, TissueMicroarrayData, GEO Author: Sara Aibar, Celia Fontanillo and Javier De Las Rivas. Bioinformatics and Functional Genomics Group. Cancer Research Center (CiC-IBMCC, CSIC/USAL). Salamanca. Spain. Maintainer: Sara Aibar git_url: https://git.bioconductor.org/packages/leukemiasEset git_branch: devel git_last_commit: ce42ae0 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/leukemiasEset_1.41.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: geNetClassifier, mCSEA, multiclassPairs dependencyCount: 6 Package: LiebermanAidenHiC2009 Version: 0.43.0 Depends: KernSmooth, IRanges License: LGPL MD5sum: c0e701cb1669b1f5f580c6a5f4f486c4 NeedsCompilation: no Title: Selected data from the HiC paper of E. Lieberman-Aiden et al. in Science (2009) Description: This package provides data that were presented in the article "Comprehensive mapping of long-range interactions reveals folding principles of the human genome", Science 2009 Oct 9;326(5950):289-93. PMID: 19815776 biocViews: ExperimentData, Genome, SequencingData, DNASeqData, ChIPSeqData, miRNAData, SmallRNAData, ChipOnChipData, GEO, NCI, ENCODE Author: Wolfgang Huber, Felix Klein Maintainer: Felix Klein git_url: https://git.bioconductor.org/packages/LiebermanAidenHiC2009 git_branch: devel git_last_commit: b86fffd git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/LiebermanAidenHiC2009_0.43.0.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: 9 Package: ListerEtAlBSseq Version: 1.37.0 Depends: R (>= 3.1.1), methylPipe Suggests: BSgenome.Hsapiens.UCSC.hg18 License: Artistic 2.0 MD5sum: d7a5ae80f18ba4ba8fb437f81a6b35f5 NeedsCompilation: no Title: BS-seq data of H1 and IMR90 cell line excerpted from Lister et al. 2009 Description: Base resolution bisulfite sequencing data of Human DNA methylomes biocViews: ExperimentData, Homo_sapiens_Data, SequencingData Author: Mattia Pelizzola [aut], Kamal Kishore [aut], Mattia Furlan [ctb, cre] Maintainer: Mattia Furlan git_url: https://git.bioconductor.org/packages/ListerEtAlBSseq git_branch: devel git_last_commit: fc5e68e git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/ListerEtAlBSseq_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 165 Package: LRcellTypeMarkers Version: 1.13.0 Depends: R (>= 4.1) Imports: ExperimentHub Suggests: LRcell, BiocStyle, knitr, rmarkdown, roxygen2, testthat License: MIT + file LICENSE MD5sum: 6e6995c045fe85826d27cbfba857c727 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: devel git_last_commit: b651f2f git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/LRcellTypeMarkers_1.13.0.tar.gz vignettes: vignettes/LRcellTypeMarkers/inst/doc/LRcellTypeMarkers-vignette.html vignetteTitles: LRcellTypeMarkers: Marker gene information for LRcell R Bioconductor package using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/LRcellTypeMarkers/inst/doc/LRcellTypeMarkers-vignette.R suggestsMe: LRcell dependencyCount: 67 Package: lumiBarnes Version: 1.45.0 Depends: R (>= 2.0), Biobase (>= 2.5.5), lumi (>= 1.1.0) License: LGPL MD5sum: 4e7b9c06d5ebd3302429df28cda8b351 NeedsCompilation: no Title: Barnes Benchmark Illumina Tissues Titration Data Description: The Barnes benchmark dataset can be used to evaluate the algorithms for Illumina microarrays. It measured a titration series of two human tissues, blood and placenta, and includes six samples with the titration ratio of blood and placenta as 100:0, 95:5, 75:25, 50:50, 25:75 and 0:100. The samples were hybridized on HumanRef-8 BeadChip (Illumina, Inc) in duplicate. The data is loaded as an LumiBatch Object (see documents in the lumi package). biocViews: ExperimentData, Tissue, MicroarrayData, ChipOnChipData Author: Pan Du Maintainer: Pan Du git_url: https://git.bioconductor.org/packages/lumiBarnes git_branch: devel git_last_commit: e4b7984 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/lumiBarnes_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayMvout, lumi dependencyCount: 161 Package: LungCancerACvsSCCGEO Version: 1.41.0 Depends: R (>= 2.15.0) License: GPL-2 MD5sum: 98b460ee8f68b5947b3a3761b3826dc3 NeedsCompilation: no Title: A lung cancer dataset that can be used with maPredictDSC package for developing outcome prediction models from Affymetrix CEL files. Description: This package contains 30 Affymetrix CEL files for 7 Adenocarcinoma (AC) and 8 Squamous cell carcinoma (SCC) lung cancer samples taken at random from 3 GEO datasets (GSE10245, GSE18842 and GSE2109) and other 15 samples from a dataset produced by the organizers of the IMPROVER Diagnostic Signature Challenge available from GEO (GSE43580). biocViews: CancerData, LungCancerData, MicroarrayData, GEO Author: Adi Laurentiu Tarca Maintainer: Adi Laurentiu Tarca URL: http://bioinformaticsprb.med.wayne.edu/ git_url: https://git.bioconductor.org/packages/LungCancerACvsSCCGEO git_branch: devel git_last_commit: df25b70 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/LungCancerACvsSCCGEO_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: LungCancerLines Version: 0.43.0 Imports: Rsamtools License: Artistic-2.0 MD5sum: 9ba0e03bb4bbdca6e218a59e4706d058 NeedsCompilation: no Title: Reads from Two Lung Cancer Cell Lines Description: Reads from an RNA-seq experiment between two lung cancer cell lines: H1993 (met) and H2073 (primary). The reads are stored as Fastq files and are meant for use with the TP53Genome object in the gmapR package. biocViews: ExperimentData, Genome, CancerData, LungCancerData, RNASeqData Author: Cory Barr, Michael Lawrence Maintainer: Michael Lawrence git_url: https://git.bioconductor.org/packages/LungCancerLines git_branch: devel git_last_commit: 1002c51 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/LungCancerLines_0.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: HTSeqGenie, VariantTools, gmapR dependencyCount: 39 Package: lungExpression Version: 0.43.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: a2ca24bc3385ea142493a92848f0fa0a NeedsCompilation: no Title: ExpressionSets for Parmigiani et al., 2004 Clinical Cancer Research paper Description: Data from three large lung cancer studies provided as ExpressionSets biocViews: ExperimentData, CancerData, LungCancerData Author: Robert Scharpf , Simens Zhong , Giovanni Parmigiani Maintainer: Robert Scharpf git_url: https://git.bioconductor.org/packages/lungExpression git_branch: devel git_last_commit: 1a872a6 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/lungExpression_0.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: globaltest dependencyCount: 6 Package: lydata Version: 1.31.0 License: MIT + file LICENSE MD5sum: 369fa83c935cd4ddecb6c3694d4bf309 NeedsCompilation: no Title: Example Dataset for crossmeta Package Description: Raw data downloaded from GEO for the compound LY294002. Raw data is from multiple platforms from Affymetrix and Illumina. This data is used to illustrate the cross-platform meta-analysis of microarray data using the crossmeta package. biocViews: ExperimentData, MicroarrayData Author: Alex Pickering Maintainer: Alex Pickering git_url: https://git.bioconductor.org/packages/lydata git_branch: devel git_last_commit: e13f090 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/lydata_1.31.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: ccmap, crossmeta dependencyCount: 0 Package: M3DExampleData Version: 1.31.0 Depends: R (>= 3.3) License: GPL (>=2) MD5sum: 5f67b00672607f9ae150244a0c9af74a NeedsCompilation: no Title: M3Drop Example Data Description: Example data for M3Drop package. biocViews: Mus_musculus_Data, RNASeqData, ExpressionData, GEO, Tissue, ExperimentData Author: Tallulah Andrews Maintainer: Tallulah Andrews git_url: https://git.bioconductor.org/packages/M3DExampleData git_branch: devel git_last_commit: a7199f2 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/M3DExampleData_1.31.0.tar.gz hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: M3Drop, celda dependencyCount: 0 Package: macrophage Version: 1.21.0 Depends: R (>= 3.5.0) Suggests: knitr, markdown License: GPL (>= 2) MD5sum: 27691130b0198849e18a3632a7713a36 NeedsCompilation: no Title: Human macrophage immune response Description: This package provides the output of running Salmon on a set of 24 RNA-seq samples from Alasoo, et al. "Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response", published in Nature Genetics, January 2018. For details on version numbers and how the samples were processed see the package vignette. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/macrophage git_branch: devel git_last_commit: 56841a4 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/macrophage_1.21.0.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: GeDi, GeneTonic, fishpond, mosdef, quantiseqr, fluentGenomics dependencyCount: 0 Package: MACSdata Version: 1.13.0 License: file LICENSE MD5sum: ce4494041ec4ffd5b09c7d3ff25a40c5 NeedsCompilation: no Title: Test datasets for the MACSr package Description: Test datasets from the MACS3 test examples are use in the examples of the `MACSr` package. All 9 datasets are uploaded to the `ExperimentHub`. The original data can be found at: https://github.com/macs3-project/MACS/. biocViews: ExperimentHub, ExperimentData, ChIPSeqData Author: Qiang Hu [aut, cre] Maintainer: Qiang Hu git_url: https://git.bioconductor.org/packages/MACSdata git_branch: devel git_last_commit: 3120739 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/MACSdata_1.13.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: MACSr dependencyCount: 0 Package: mammaPrintData Version: 1.41.0 Depends: R (>= 2.13.0) Suggests: Biobase, readxl, limma License: Artistic-2.0 MD5sum: 42fcd8c5fa83266455e96a76667fe769 NeedsCompilation: no Title: RGLists from the Glas and Buyse breast cancer studies Description: Gene expression data for the two breast cancer cohorts published by Glas and Buyse in 2006. This cohorts were used to implement and validate the mammaPrint breast cancer test. biocViews: ExperimentData, ExpressionData, CancerData, BreastCancerData, MicroarrayData, TwoChannelData Author: Luigi Marchionni Maintainer: Luigi Marchionni URL: http://luigimarchionni.org/breastTSP.html git_url: https://git.bioconductor.org/packages/mammaPrintData git_branch: devel git_last_commit: b43adf1 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/mammaPrintData_1.41.0.tar.gz vignettes: vignettes/mammaPrintData/inst/doc/mammaPrintData.pdf vignetteTitles: Working with the mammaPrintData package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mammaPrintData/inst/doc/mammaPrintData.R dependencyCount: 0 Package: maqcExpression4plex Version: 1.49.0 Suggests: oligo, pdInfoBuilder License: GPL MD5sum: 25c87dd760ea5bd0154a7ad45ebbcde5 NeedsCompilation: no Title: Sample Expression Data - MAQC / HG18 - NimbleGen Description: Data from human (HG18) 4plex NimbleGen array. It has 24k genes with 3 60mer probes per gene. biocViews: ExperimentData, CancerData Author: NimbleGen Systems Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/maqcExpression4plex git_branch: devel git_last_commit: 1545c6f git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/maqcExpression4plex_1.49.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligo dependencyCount: 0 Package: MAQCsubset Version: 1.43.0 Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), lumi, methods Suggests: genefilter, codelink License: Artistic-2.0 MD5sum: 7c61a390d17bd2aadceaca866eb18ced NeedsCompilation: no Title: Experimental Data Package: MAQCsubset Description: Data Package automatically created on Sun Nov 19 15:59:29 2006. biocViews: ExperimentData, MicroarrayData, GEO Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/MAQCsubset git_branch: devel git_last_commit: 99b6664 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/MAQCsubset_1.43.0.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: 161 Package: marinerData Version: 1.5.0 Imports: utils, ExperimentHub Suggests: knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0) License: GPL-3 MD5sum: 97bb454be35ba8db76b2b23ca07bdb1e NeedsCompilation: no Title: ExperimentHub data for the mariner package Description: Subsampled Hi-C in HEK cells expressing the NHA9 fusion with an F to S mutated IDR ("FS") or without any mutations to the IDR ("Wildtype" or "WT"). These files are used for testing mariner functions and some examples. biocViews: ExperimentHub, ExperimentData, SequencingData Author: Eric Davis [aut, cre] () Maintainer: Eric Davis VignetteBuilder: knitr BugReports: https://support.bioconductor.org/t/marinerData git_url: https://git.bioconductor.org/packages/marinerData git_branch: devel git_last_commit: 3dbe780 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/marinerData_1.5.0.tar.gz vignettes: vignettes/marinerData/inst/doc/marinerData.html vignetteTitles: marinerData package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/marinerData/inst/doc/marinerData.R suggestsMe: mariner dependencyCount: 67 Package: mCSEAdata Version: 1.25.0 Depends: R (>= 3.5) Imports: GenomicRanges Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 37a7bf97b4585adb7830b4564831f7fc NeedsCompilation: no Title: Data package for mCSEA package Description: Data objects necessary to some mCSEA package functions. There are also example data objects to illustrate mCSEA package functionality. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData, ExperimentData Author: Jordi Martorell Marugán Maintainer: Jordi Martorell Marugán VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mCSEAdata git_branch: devel git_last_commit: 1feb06a git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/mCSEAdata_1.25.0.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: 23 Package: mcsurvdata Version: 1.23.0 Depends: R (>= 3.5), ExperimentHub Imports: AnnotationHub, Biobase Suggests: BiocStyle, knitr License: GPL (>=2) MD5sum: f9146f6164b59fb75fb83241ce7c3780 NeedsCompilation: no Title: Meta cohort survival data Description: This package stores two merged expressionSet objects that contain the gene expression profile and clinical information of -a- six breast cancer cohorts and -b- four colorectal cancer cohorts. Breast cancer data are employed in the vignette of the hrunbiased package for survival analysis of gene signatures. biocViews: ExperimentData, Homo_sapiens_Data, GEO, MicroarrayData Author: Adria Caballe Mestres [aut, cre], Antoni Berenguer Llergo [aut], Camille Stephan-Otto Attolini [aut] Maintainer: Adria Caballe Mestres URL: https://github.com/adricaba/mcsurvdata VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mcsurvdata git_branch: devel git_last_commit: 82e8512 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/mcsurvdata_1.23.0.tar.gz vignettes: vignettes/mcsurvdata/inst/doc/mcsurvdata.html vignetteTitles: analysis vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mcsurvdata/inst/doc/mcsurvdata.R dependencyCount: 67 Package: MEDIPSData Version: 1.41.0 Depends: R (>= 3.5.0) License: GPL (>= 2) MD5sum: 50c4f279e23203df7a6169cc593afdfc NeedsCompilation: no Title: Example data for MEDIPS and QSEA packages Description: Example data for MEDIPS and QSEA packages, consisting of chromosome 22 MeDIP and control/Input sample data. Additionally, the package contains MeDIP seq data from 3 NSCLC samples and adjacent normal tissue (chr 20-22). All data has been aligned to human genome hg19. biocViews: ExperimentData, Genome, SequencingData Author: Lukas Chavez Maintainer: Lukas Chavez git_url: https://git.bioconductor.org/packages/MEDIPSData git_branch: devel git_last_commit: 9d5541f git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/MEDIPSData_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MEDIPS, qsea dependencyCount: 0 Package: MEEBOdata Version: 1.43.0 License: LGPL MD5sum: a75ed927f49760c0c1367fedd936d5f1 NeedsCompilation: no Title: MEEBO set and MEEBO controls. Description: R objects describing the MEEBO set. biocViews: ExperimentData Author: Agnes Paquet Maintainer: Agnes Paquet URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/ git_url: https://git.bioconductor.org/packages/MEEBOdata git_branch: devel git_last_commit: 1ee4f16 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/MEEBOdata_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQuality dependencyCount: 0 Package: MerfishData Version: 1.7.0 Depends: R (>= 4.2.0), EBImage, SpatialExperiment Imports: grDevices, AnnotationHub, BumpyMatrix, ExperimentHub, S4Vectors, SingleCellExperiment, SummarizedExperiment Suggests: grid, ggplot2, ggpubr, knitr, rmarkdown, testthat, BiocStyle, DropletUtils License: Artistic-2.0 MD5sum: 3669b8bbbbc5359679f2ed05546e38fc NeedsCompilation: no Title: Collection of public MERFISH datasets Description: MerfishData is an ExperimentHub package that serves publicly available datasets obtained with Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH). MERFISH is a massively multiplexed single-molecule imaging technology capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells. The scope of the package is to provide MERFISH data for benchmarking and analysis. biocViews: ExperimentHub, ExpressionData, HighThroughputImagingData, Mus_musculus_Data, SingleCellData, SpatialData Author: Ludwig Geistlinger [aut, cre] (), Tyrone Lee [ctb], Helena Crowell [ctb] (), Jeffrey Moffitt [aut], Robert Gentleman [aut] Maintainer: Ludwig Geistlinger URL: https://github.com/ccb-hms/MerfishData VignetteBuilder: knitr BugReports: https://github.com/ccb-hms/MerfishData/issues git_url: https://git.bioconductor.org/packages/MerfishData git_branch: devel git_last_commit: 9133265 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/MerfishData_1.7.0.tar.gz vignettes: vignettes/MerfishData/inst/doc/Merfish_mouse_hypothalamus.html, vignettes/MerfishData/inst/doc/Merfish_mouse_ileum.html vignetteTitles: Mouse hypothalamus, Mouse ileum hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MerfishData/inst/doc/Merfish_mouse_hypothalamus.R, vignettes/MerfishData/inst/doc/Merfish_mouse_ileum.R dependencyCount: 106 Package: MetaGxBreast Version: 1.25.0 Depends: R (>= 3.6.0), Biobase, AnnotationHub, ExperimentHub Imports: stats, lattice, impute, SummarizedExperiment Suggests: testthat, xtable, tinytex License: Apache License (>= 2) MD5sum: 27c441733430fdb6af697fa9cf55f3df NeedsCompilation: no Title: Transcriptomic Breast Cancer Datasets Description: A collection of Breast Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium. biocViews: ExpressionData, ExperimentHub, CancerData, Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData, ExperimentData Author: Michael Zon [aut], Deena M.A. Gendoo [aut], Christopher Eeles [ctb], Benjamin Haibe-Kains [aut, cre] Maintainer: Benjamin Haibe-Kains git_url: https://git.bioconductor.org/packages/MetaGxBreast git_branch: devel git_last_commit: ce24c26 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/MetaGxBreast_1.25.0.tar.gz vignettes: vignettes/MetaGxBreast/inst/doc/MetaGxBreast.pdf vignetteTitles: MetaGxBreast: a package for breast cancer gene expression analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MetaGxBreast/inst/doc/MetaGxBreast.R dependencyCount: 79 Package: MetaGxOvarian Version: 1.25.0 Depends: Biobase, AnnotationHub, ExperimentHub, SummarizedExperiment, R (>= 3.6.0) Imports: stats, lattice, impute Suggests: testthat, xtable, rmarkdown, knitr, BiocStyle, markdown License: Artistic-2.0 MD5sum: be2b63168285734b4674d41ac544fd41 NeedsCompilation: no Title: Transcriptomic Ovarian Cancer Datasets Description: A collection of Ovarian Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium. biocViews: ExpressionData, ExperimentHub, CancerData, Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData, ExperimentData Author: Michael Zon [aut], Vandana Sandhu [aut], Christopher Eeles [ctb], Benjamin Haibe-Kains [aut, cre] Maintainer: Benjamin Haibe-Kains VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MetaGxOvarian git_branch: devel git_last_commit: 2043cd1 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/MetaGxOvarian_1.25.0.tar.gz vignettes: vignettes/MetaGxOvarian/inst/doc/MetaGxOvarian.html vignetteTitles: MetaGxOvarian: A Package for Ovarian Cancer Gene Expression Analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MetaGxOvarian/inst/doc/MetaGxOvarian.R dependencyCount: 79 Package: MetaGxPancreas Version: 1.25.0 Depends: SummarizedExperiment, ExperimentHub, R (>= 3.6.0) Imports: stats, impute, S4Vectors, AnnotationHub Suggests: testthat, knitr, BiocStyle, rmarkdown, markdown License: Artistic-2.0 MD5sum: 500834432faf84e270540283a76cba6b NeedsCompilation: no Title: Transcriptomic Pancreatic Cancer Datasets Description: A collection of pancreatic Cancer transcriptomic datasets that are part of the MetaGxData package compendium. This package contains multiple pancreas cancer datasets that have been downloaded from various resources and turned into SummarizedExperiment objects. The details of how the authors normalized the data can be found in the experiment data section of the objects. Additionally, the location the data was obtained from can be found in the url variables of the experiment data portion of each SE. biocViews: ExpressionData, ExperimentHub, CancerData, Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData, ExperimentData, SequencingData Author: Michael Zon [aut], Vandana Sandhu [aut], Christopher Eeles [ctb], Benjamin Haibe-Kains [aut, cre] Maintainer: Benjamin Haibe-Kains VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MetaGxPancreas git_branch: devel git_last_commit: 701474e git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/MetaGxPancreas_1.25.0.tar.gz vignettes: vignettes/MetaGxPancreas/inst/doc/MetaGxPancreas.html vignetteTitles: MetaGxPancreas: A Package for Pancreatic Cancer Gene Expression Analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MetaGxPancreas/inst/doc/MetaGxPancreas.R dependencyCount: 79 Package: metaMSdata Version: 1.41.0 License: GPL (>= 2) MD5sum: d19c8684f7d2fe4c1c3c43acdc32a950 NeedsCompilation: no Title: Example CDF data for the metaMS package Description: Example CDF data for the metaMS package biocViews: ExperimentData, MassSpectrometryData Author: Ron Wehrens [aut, cre], Pietro Franceschi [aut], Georg Weingart [ctb] Maintainer: Yann Guitton git_url: https://git.bioconductor.org/packages/metaMSdata git_branch: devel git_last_commit: 13a6d0b git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/metaMSdata_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CluMSID, metaMS dependencyCount: 0 Package: MetaScope Version: 1.5.1 Depends: R (>= 4.3.0) Imports: BiocFileCache, Biostrings, data.table, dplyr, ggplot2, magrittr, Matrix, MultiAssayExperiment, Rbowtie2, readr, rlang, Rsamtools, S4Vectors, stringr, SummarizedExperiment, taxize, tibble, tidyr, tools Suggests: animalcules, BiocStyle, biomformat, GenomicRanges, IRanges, knitr, lintr, plyr, rmarkdown, R.utils, Rsubread, spelling, sys, testthat, taxonomizr, usethis Enhances: BiocParallel License: GPL (>= 3) MD5sum: fab4d7b8ec78df3a79ad26815cff9bf5 NeedsCompilation: no Title: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data Description: This package contains tools and methods for preprocessing microbiome data. Functionality includes library generation, demultiplexing, alignment, and microbe identification. It is in part an R translation of the PathoScope 2.0 pipeline. biocViews: MicrobiomeData, ReproducibleResearch, SequencingData Author: Aubrey Odom [aut, cre] (), Rahul Varki [aut], W. Evan Johnson [aut] (), Howard Fan [ctb] Maintainer: Aubrey Odom URL: https://github.com/wejlab/metascope https://wejlab.github.io/metascope-docs/ VignetteBuilder: knitr BugReports: https://github.com/wejlab/MetaScope/issues git_url: https://git.bioconductor.org/packages/MetaScope git_branch: devel git_last_commit: 39ea371 git_last_commit_date: 2024-05-01 Date/Publication: 2024-05-02 source.ver: src/contrib/MetaScope_1.5.1.tar.gz vignettes: vignettes/MetaScope/inst/doc/MetaScope_vignette.html vignetteTitles: Introdution to MetaScope hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MetaScope/inst/doc/MetaScope_vignette.R dependencyCount: 172 Package: MethylAidData Version: 1.37.0 Depends: MethylAid, R (>= 3.2) Suggests: BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC License: GPL (>= 2) MD5sum: 1dd93349f93454b8d9d92519a38318a9 NeedsCompilation: no Title: MethylAid-summarized data for 2800 Illumina 450k array samples and 2620 EPIC array samples Description: A data package containing summarized Illumina 450k array data on 2800 samples and summarized EPIC data for 2620 samples. The data can be use as a background data set in the interactive application. biocViews: ExperimentData, TechnologyData, MicroarrayData, MethylationArrayData Author: Davy Cats, Tyler J. Gorrie-Stone, Bastiaan T. Heijmans, John W. Holloway, BIOS Consortium, Maarten van Iterson, Faisal I. Rezwam, Leonard Schalkwyk Maintainer: M. van Iterson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MethylAidData git_branch: devel git_last_commit: 6ec87a9 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/MethylAidData_1.37.0.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: 167 Package: methylclockData Version: 1.13.0 Imports: ExperimentHubData, ExperimentHub, utils Suggests: knitr, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: 2ba1791935ae758ac4d5e93f3d4bd934 NeedsCompilation: no Title: Data for methylclock package Description: Collection of 9 datasets, andrews and bakulski cord blood, blood gse35069, blood gse35069 chen, blood gse35069 complete, combined cord blood, cord bloo d gse68456, gervin and lyle cord blood, guintivano dlpfc and saliva gse48472". Data downloaded from [meffil](https://github.com/perishky/meffil/). Data used to estimate cell counts using Extrinsic epigenetic age acceleration (EEAA) method Collection of 12 datasets to use with MethylClock package to estimate chronological and gestational DNA methylationwith estimators to use wit different methylation clocks biocViews: SpecimenSource, ExperimentHub, Tissue, OrganismData, Homo_sapiens_Data Author: Juan R. Gonzalez [aut], Dolors Pelegri-Siso [aut, cre] Maintainer: Dolors Pelegri-Siso URL: https://github.com/isglobal-brge/methylclockData VignetteBuilder: knitr BugReports: https://github.com/isglobal-brge/methylclockData/issues git_url: https://git.bioconductor.org/packages/methylclockData git_branch: devel git_last_commit: e1481d9 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/methylclockData_1.13.0.tar.gz vignettes: vignettes/methylclockData/inst/doc/methylcockData.html vignetteTitles: References for metilclock using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/methylclockData/inst/doc/methylcockData.R dependsOnMe: methylclock dependencyCount: 126 Package: MethylSeqData Version: 1.15.0 Depends: SummarizedExperiment Imports: ExperimentHub, HDF5Array, rhdf5, GenomeInfoDb, S4Vectors, GenomicRanges, stats, IRanges, utils Suggests: BiocFileCache, BiocStyle, data.table, knitr, rmarkdown License: CC0 MD5sum: 15c799e236b58d88f765c4a58f8fc61b NeedsCompilation: no Title: Collection of Public DNA Methylation Sequencing Datasets Description: Base-level (i.e. cytosine-level) counts for a collection of public bisulfite-seq datasets (e.g., WGBS and RRBS), provided as SummarizedExperiment objects with sample- and base-level metadata. biocViews: ExperimentHub, ExperimentData, SequencingData, Homo_sapiens_Data, Mus_musculus_Data, MethylSeqData Author: Peter Hickey [aut, cre] Maintainer: Peter Hickey VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MethylSeqData git_branch: devel git_last_commit: fab5964 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/MethylSeqData_1.15.0.tar.gz vignettes: vignettes/MethylSeqData/inst/doc/MethylSeqData.html vignetteTitles: User's Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MethylSeqData/inst/doc/MethylSeqData.R dependencyCount: 82 Package: MicrobiomeBenchmarkData Version: 1.7.0 Depends: R (>= 4.2), SummarizedExperiment, TreeSummarizedExperiment Imports: BiocFileCache, tools, S4Vectors, ape, utils Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0), mia, ggplot2, tidyr, dplyr, magrittr, tibble, purrr License: Artistic-2.0 MD5sum: 76038857828a37f072c40135a142f895 NeedsCompilation: no Title: Datasets for benchmarking in microbiome research Description: The MicrobiomeBenchmarkData package provides functionality to access microbiome datasets suitable for benchmarking. These datasets have some biological truth, which allows to have expected results for comparison. The datasets come from various published sources and are provided as TreeSummarizedExperiment objects. Currently, only datasets suitable for benchmarking differential abundance methods are available. biocViews: ExperimentData, MicrobiomeData, ReproducibleResearch, SequencingData Author: Samuel Gamboa [aut, cre] (), Levi Waldron [aut] (), Marcel Ramos [ctb] Maintainer: Samuel Gamboa URL: https://github.com/waldronlab/MicrobiomeBenchmarkData, http://waldronlab.io/MicrobiomeBenchmarkData/ VignetteBuilder: knitr BugReports: https://github.com/waldronlab/MicrobiomeBenchmarkData/issues git_url: https://git.bioconductor.org/packages/MicrobiomeBenchmarkData git_branch: devel git_last_commit: 879f0eb git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/MicrobiomeBenchmarkData_1.7.0.tar.gz vignettes: vignettes/MicrobiomeBenchmarkData/inst/doc/datasets.html, vignettes/MicrobiomeBenchmarkData/inst/doc/MicrobiomeBenchmarkData.html, vignettes/MicrobiomeBenchmarkData/inst/doc/recalibrare_spikein_data.html vignetteTitles: Datasets in MicrobiomeBenchmarkData, MicrobiomeBenchmarkData, Recalibration of the Stammler_2016_16S_spikein dataset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MicrobiomeBenchmarkData/inst/doc/datasets.R, vignettes/MicrobiomeBenchmarkData/inst/doc/MicrobiomeBenchmarkData.R, vignettes/MicrobiomeBenchmarkData/inst/doc/recalibrare_spikein_data.R dependencyCount: 89 Package: microbiomeDataSets Version: 1.13.0 Depends: R (>= 4.1), SummarizedExperiment, TreeSummarizedExperiment, MultiAssayExperiment Imports: methods, utils, BiocGenerics, ExperimentHub, Biostrings, ape Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, testthat License: CC0 MD5sum: af86b49ca71819e7125a4098ab6670f1 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] (), Chouaib Benchraka [ctb] (), Yagmur Simsek [ctb] Maintainer: Leo Lahti VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/microbiomeDataSets git_branch: devel git_last_commit: 410c4d7 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/microbiomeDataSets_1.13.0.tar.gz vignettes: vignettes/microbiomeDataSets/inst/doc/microbiomeDataSets.html vignetteTitles: microbiomeDataSets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/microbiomeDataSets/inst/doc/microbiomeDataSets.R suggestsMe: miaViz, mia dependencyCount: 100 Package: microRNAome Version: 1.27.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: BiocGenerics, RUnit License: GPL (>= 2) MD5sum: 07bdd6257983745ef8de12a28c87928d NeedsCompilation: no Title: SummarizedExperiment for the microRNAome project Description: This package provides a SummarizedExperiment object of read counts for microRNAs across tissues, cell-types, and cancer cell-lines. The read count matrix was prepared and provided by the author of the study: Towards the human cellular microRNAome. biocViews: ExperimentData, CellCulture, CancerData, SequencingData, RNASeqData, miRNAData Author: Matthew N. McCall , Marc K. Halushka , Arun H. Patil Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/microRNAome git_branch: devel git_last_commit: 04d35ce git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/microRNAome_1.27.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 36 Package: minfiData Version: 0.51.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2), IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 License: Artistic-2.0 MD5sum: e95c7da103040c0e8a30e60c53347419 NeedsCompilation: no Title: Example data for the Illumina Methylation 450k array Description: Data from 6 samples across 2 groups from 450k methylation arrays. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData Author: Kasper Daniel Hansen, Martin Aryee, Winston Timp Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/minfiData git_branch: devel git_last_commit: bd0ab8b git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/minfiData_0.51.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: methylationArrayAnalysis suggestsMe: ENmix, Harman, MEAL, MethylAid, MultiDataSet, bigmelon, conumee, funtooNorm, mCSEA, minfi, missMethyl, recountmethylation, regionalpcs, shinyMethyl, shinyepico, skewr, MethylAidData dependencyCount: 142 Package: minfiDataEPIC Version: 1.31.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2), IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: Artistic-2.0 MD5sum: 342623354d0814aa669ee3984601b1a2 NeedsCompilation: no Title: Example data for the Illumina Methylation EPIC array Description: Data from 3 technical replicates of the cell line GM12878 from the EPIC methylation array. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData Author: Jean-Philippe Fortin, Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/minfiDataEPIC git_branch: devel git_last_commit: e1a8dab git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/minfiDataEPIC_1.31.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MethylAid, REMP, minfi, recountmethylation, MethylAidData dependencyCount: 142 Package: minionSummaryData Version: 1.35.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 4c36de995d3d3f0d7ff4f9a1e2f6b668 NeedsCompilation: no Title: Summarised MinION sequencing data published by Ashton et al. 2015 Description: Summarised MinION sequencing data for Salmonella Typhi published by Ashton et al. in 2015. Three replicate runs are each provided as Fast5Summary objects. biocViews: ExperimentData, SequencingData Author: Mike Smith [aut, cre] Maintainer: Mike Smith VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/minionSummaryData git_branch: devel git_last_commit: 83cff9d git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/minionSummaryData_1.35.0.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: 1.35.0 Depends: R (>= 3.2), Imports: utils License: GPL-3 | file LICENSE MD5sum: 408b0969623e337fc135e144e15da18f NeedsCompilation: no Title: Data used in the miRcomp package Description: Raw amplification data from a large microRNA mixture / dilution study. These data are used by the miRcomp package to assess the performance of methods that estimate expression from the amplification curves. biocViews: ExperimentData, ExpressionData, qPCRData, Homo_sapiens_Data Author: Matthew N. McCall Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/miRcompData git_branch: devel git_last_commit: dcd2bdd git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/miRcompData_1.35.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: miRcomp dependencyCount: 1 Package: miRNATarget Version: 1.43.0 Depends: R (>= 2.10), Biobase License: GPL MD5sum: 5aabb64c951eb025e214b87fdbda4873 NeedsCompilation: no Title: gene target tabale of miRNA for human/mouse used for MiRaGE package Description: gene target tabale of miRNA for human/mouse used for MiRaGE package biocViews: ExperimentData, Homo_sapiens_Data Author: Y-h. Taguchi Maintainer: Y-h. Taguchi git_url: https://git.bioconductor.org/packages/miRNATarget git_branch: devel git_last_commit: ca65e97 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/miRNATarget_1.43.0.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: 6 Package: MMDiffBamSubset Version: 1.41.0 Suggests: MMDiff2 License: LGPL MD5sum: aa616f8491ae659a353ffbe55e6f758b NeedsCompilation: no Title: Example ChIP-Seq data for the MMDiff package Description: Subset of BAM files, including WT_2.bam, Null_2.bam, Resc_2.bam, Input.bam from the "Cfp1" experiment (see Clouaire et al., Genes Dev. 2012). Data is available under ArrayExpress accession numbers E-ERAD-79. Additionally, corresponding subset of peaks called by MACS biocViews: ExperimentData, Genome, StemCell, Mus_musculus_Data, DNASeqData, ChIPSeqData, ArrayExpress Author: Gabriele Schweikert Maintainer: Gabriele Schweikert git_url: https://git.bioconductor.org/packages/MMDiffBamSubset git_branch: devel git_last_commit: 3ed106d git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/MMDiffBamSubset_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MMDiff2 dependencyCount: 0 Package: MOFAdata Version: 1.21.0 Depends: R (>= 3.5) Suggests: knitr, MultiAssayExperiment, rmarkdown, BiocStyle License: LGPL-3 MD5sum: 7cb6bb9883b655ef6d32a29f77b8ff8a NeedsCompilation: yes Title: Data package for Multi-Omics Factor Analysis (MOFA) Description: A collection of datasets to accompany the R package MOFA and illustrate running and analysing MOFA models. biocViews: ReproducibleResearch Author: Ricard Argelaguet, Britta Velten, Damien Arnol, Florian Buettner, Wolfgang Huber, Oliver Stegle Maintainer: Britta Velten VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MOFAdata git_branch: devel git_last_commit: b2dfe0c git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/MOFAdata_1.21.0.tar.gz vignettes: vignettes/MOFAdata/inst/doc/MOFAdata.html vignetteTitles: MOFAdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MOFAdata/inst/doc/MOFAdata.R importsMe: TDbasedUFE suggestsMe: TDbasedUFEadv dependencyCount: 0 Package: mosaicsExample Version: 1.43.0 Depends: R (>= 2.11.1) License: GPL (>= 2) MD5sum: 28e09d47792bcf3be53c5a307d7b082d NeedsCompilation: no Title: Example data for the mosaics package, which implements MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data for transcription factor binding and histone modification Description: Data for the mosaics package, consisting of (1) chromosome 22 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding and H3K4me3 modification in MCF7 cell line from ENCODE database (HG19) and (2) chromosome 21 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding, with mappability, GC content, and sequence ambiguity scores of human genome HG18. biocViews: ExperimentData, ChIPseqData, Homo_sapiens Author: Dongjun Chung, Pei Fen Kuan, Rene Welch, Sunduz Keles Maintainer: Dongjun Chung URL: http://groups.google.com/group/mosaics_user_group git_url: https://git.bioconductor.org/packages/mosaicsExample git_branch: devel git_last_commit: 8627375 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/mosaicsExample_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: mosaics dependencyCount: 0 Package: mouse4302barcodevecs Version: 1.43.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: d2090e62f04f7e1d42576d73f3a9b885 NeedsCompilation: no Title: mouse4302 data for barcode Description: Data used by the barcode package for microarrays of type mouse4302. biocViews: Mus_musculus_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/mouse4302barcodevecs git_branch: devel git_last_commit: 5287500 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/mouse4302barcodevecs_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: MouseAgingData Version: 1.1.0 Depends: R (>= 4.4.0), SingleCellExperiment Imports: AnnotationHub, ExperimentHub Suggests: BiocStyle, knitr, rmarkdown, scater License: Artistic-2.0 MD5sum: acd4c0fd89a012f414d50c8266a0ad43 NeedsCompilation: no Title: Multi-omics data access for studies investigating the effects of aging Description: The MouseAgingData package provides analysis-ready data resources from different studies focused on aging and rejuvenation in mice. The package currently provides two 10x Genomics single-cell RNA-seq datasets. The first study profiled the aging mouse brain measured across 37,089 cells (Ximerakis et al., 2019). The second study investigated parabiosis by profiling a total of 105,329 cells (Ximerakis & Holton et al., 2023). The datasets are provided as SingleCellExperiment objects and provide raw UMI counts and cell metadata. biocViews: ExperimentData, ExpressionData, SequencingData, RNASeqData, SingleCellData, ExperimentHub, PackageTypeData, Mus_musculus_Data Author: Tram Nguyen [aut, cre] (), Kris Holton [aut], Tyrone Lee [aut], Nitesh Turaga [ctb], Ludwig Geistlinger [aut], Robert Gentleman [aut] Maintainer: Tram Nguyen URL: https://github.com/ccb-hms/MouseAgingData VignetteBuilder: knitr BugReports: https://github.com/ccb-hms/MouseAgingData/issues git_url: https://git.bioconductor.org/packages/MouseAgingData git_branch: devel git_last_commit: a13e364 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/MouseAgingData_1.1.0.tar.gz vignettes: vignettes/MouseAgingData/inst/doc/MouseAgingData_parabiosis_droplet.html vignetteTitles: Accessing and Visualizing Parabiosis Droplet Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MouseAgingData/inst/doc/MouseAgingData_parabiosis_droplet.R dependencyCount: 79 Package: MouseGastrulationData Version: 1.19.0 Depends: R (>= 4.1), SingleCellExperiment, SummarizedExperiment, SpatialExperiment Imports: methods, ExperimentHub, BiocGenerics, S4Vectors, BumpyMatrix Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 16126f4e927357245915ba465dcd34e3 NeedsCompilation: no Title: Single-Cell -omics Data across Mouse Gastrulation and Early Organogenesis Description: Provides processed and raw count data for single-cell RNA sequencing, single-cell ATAC-seq, and seqFISH (spatial transcriptomic) experiments performed along a timecourse of mouse gastrulation and early organogenesis. biocViews: ExperimentData, ExpressionData, SequencingData, RNASeqData, SingleCellData, ExperimentHub, Mus_musculus_Data Author: Jonathan Griffiths [aut, cre], Aaron Lun [aut] Maintainer: Jonathan Griffiths URL: https://github.com/MarioniLab/MouseGastrulationData VignetteBuilder: knitr BugReports: https://github.com/MarioniLab/MouseGastrulationData/issues git_url: https://git.bioconductor.org/packages/MouseGastrulationData git_branch: devel git_last_commit: 46b6c07 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/MouseGastrulationData_1.19.0.tar.gz vignettes: vignettes/MouseGastrulationData/inst/doc/MouseGastrulationData.html vignetteTitles: Available datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MouseGastrulationData/inst/doc/MouseGastrulationData.R dependsOnMe: OSCA.multisample suggestsMe: miloR dependencyCount: 84 Package: MouseThymusAgeing Version: 1.13.0 Depends: SingleCellExperiment, SummarizedExperiment Imports: ExperimentHub, methods, BiocGenerics, S4Vectors Suggests: knitr, scuttle, rmarkdown, BiocStyle License: GPL-3 MD5sum: 99ea8978220d8b887a917005eb990533 NeedsCompilation: no Title: Single-cell Transcriptomics Data of the Ageing Mouse Thymus Description: This package provides data access to counts matrices and meta-data for single-cell RNA sequencing data of thymic epithlial cells across mouse ageing using SMARTseq2 and 10X Genommics chemistries. Access is provided as a data package via ExperimentHub. It is designed to facilitate the re-use of data from Baran-Gale _et al._ in a consistent format that includes relevant and informative meta-data. biocViews: ExperimentHub, SingleCellData, ExpressionData, ExperimentData Author: Mike Morgan [aut, cre], Jeanette Baran-Gale [aut] Maintainer: Mike Morgan VignetteBuilder: knitr BugReports: https://github.com/MarioniLab/MouseThymusAgeing/issues git_url: https://git.bioconductor.org/packages/MouseThymusAgeing git_branch: devel git_last_commit: b36aeeb git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/MouseThymusAgeing_1.13.0.tar.gz vignettes: vignettes/MouseThymusAgeing/inst/doc/MouseThymusAgeing.html vignetteTitles: Available datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MouseThymusAgeing/inst/doc/MouseThymusAgeing.R suggestsMe: miloR dependencyCount: 79 Package: msd16s Version: 1.25.0 Depends: R (>= 2.10), Biobase, metagenomeSeq, License: Artistic-2.0 MD5sum: 2f1e1f51527fd43615f898bc898357d1 NeedsCompilation: no Title: Healthy and moderate to severe diarrhea 16S expression data Description: Gut 16S sequencing expression data from 992 healthy and moderate-to-severe diarrhetic samples used in 'Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition'. biocViews: ExperimentData, SequencingData, MicrobiomeData Author: Joseph N. Paulson, Hector Corrada Bravo, Mihai Pop Maintainer: Joseph N. Paulson URL: http://www.cbcb.umd.edu/research/projects/GEMS-pathogen-discovery git_url: https://git.bioconductor.org/packages/msd16s git_branch: devel git_last_commit: 715dfe5 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/msd16s_1.25.0.tar.gz vignettes: vignettes/msd16s/inst/doc/msd16s.pdf vignetteTitles: msd16s hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/msd16s/inst/doc/msd16s.R suggestsMe: scTreeViz dependencyCount: 32 Package: msdata Version: 0.45.0 Depends: R (>= 3.5.0) Suggests: xcms, mzR, MSnbase License: GPL (>= 2) MD5sum: 857589a062cc24324f16c86b099639e4 NeedsCompilation: no Title: Various Mass Spectrometry raw data example files Description: Ion Trap positive ionization mode data in mzML file format. Subset from 500-850 m/z and 1190-1310 seconds, incl. MS2 and MS3, intensity threshold 100.000. Extracts from FTICR Apex III, m/z 400-450. Subset of UPLC - Bruker micrOTOFq data, both mzML and mz5. LC-MSMS and MRM files from proteomics experiments. PSI mzIdentML example files for various search engines. biocViews: ExperimentData, MassSpectrometryData Author: Steffen Neumann , Laurent Gatto with contriutions from Johannes Rainer Maintainer: Steffen Neumann , Laurent Gatto git_url: https://git.bioconductor.org/packages/msdata git_branch: devel git_last_commit: ab132bb git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/msdata_0.45.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: MsQuality suggestsMe: IPO, MSnbase, MetaboAnnotation, MsBackendSql, MsExperiment, PSMatch, QFeatures, Spectra, TargetDecoy, msqrob2, mzR, peakPantheR, xcms, RforProteomics dependencyCount: 0 Package: msigdb Version: 1.13.0 Depends: R (>= 4.1) Imports: ExperimentHub, utils, GSEABase, org.Mm.eg.db, org.Hs.eg.db, AnnotationDbi, methods, stats, AnnotationHub Suggests: singscore, vissE, knitr, prettydoc, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocFileCache, GO.db, stringr, limma License: CC BY 4.0 MD5sum: 54dadb02b9e61dad223aaa4f3e97d779 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: devel git_last_commit: e1dfd92 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/msigdb_1.13.0.tar.gz vignettes: vignettes/msigdb/inst/doc/msigdb.html vignetteTitles: msigdb hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/msigdb/inst/doc/msigdb.R importsMe: mastR, vissE dependencyCount: 74 Package: MSMB Version: 1.23.0 Depends: R (>= 3.5), tibble Suggests: knitr, BiocStyle License: LGPL MD5sum: f14c083bb2469248cfad57032d62e057 NeedsCompilation: no Title: Data sets for the book 'Modern Statistics for Biology' Description: Data sets for the book 'Modern Statistics for Modern Biology', S.P. Holmes and W. Huber. biocViews: ExperimentData Author: Wolfgang Huber, Andrzej Oles, Mike Smith Maintainer: Wolfgang Huber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MSMB git_branch: devel git_last_commit: ca81336 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/MSMB_1.23.0.tar.gz vignettes: vignettes/MSMB/inst/doc/MSMB.html vignetteTitles: Data sets for the book 'Modern Statistics for Biology' hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MSMB/inst/doc/MSMB.R dependencyCount: 14 Package: msPurityData Version: 1.33.0 Suggests: knitr License: GPL (>= 2) MD5sum: 44d560068bec9e7bb303913df72529fc NeedsCompilation: no Title: Fragmentation spectral libraries and data to test the msPurity package Description: Fragmentation spectral libraries and data to test the msPurity package biocViews: ExperimentData, MassSpectrometryData Author: Thomas N. Lawson Maintainer: Thomas N. Lawson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/msPurityData git_branch: devel git_last_commit: c46353d git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/msPurityData_1.33.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: msPurity dependencyCount: 0 Package: msqc1 Version: 1.33.0 Depends: R (>= 3.6), lattice, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, specL (>= 1.2) License: GPL MD5sum: 49e3e7dda2284ae4a4532c42eb06d264 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: devel git_last_commit: fef8c0a git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/msqc1_1.33.0.tar.gz vignettes: vignettes/msqc1/inst/doc/poster.pdf, vignettes/msqc1/inst/doc/chromatography.html, vignettes/msqc1/inst/doc/msqc1.html vignetteTitles: ASMS 2016 poster (in portrait) abstract ID number: 282492, LC Observations - Retention Time Stability, Introducing msqc1 - A Mass Spec Data set for Targeted Proteomics Performance Evaluation hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/msqc1/inst/doc/chromatography.R, vignettes/msqc1/inst/doc/msqc1.R, vignettes/msqc1/inst/doc/poster.R dependencyCount: 6 Package: mtbls2 Version: 1.35.0 Depends: R (>= 2.10) Suggests: xcms (>= 3.13.8), CAMERA, Risa (>= 1.0.0), knitr, Heatplus, pcaMethods, sp, rmarkdown License: CC0 MD5sum: 8ba9f41063a47c2e7fdcd49af11514f4 NeedsCompilation: no Title: MetaboLights MTBLS2: Comparative LC/MS-based profiling of silver nitrate-treated Arabidopsis thaliana leaves of wild-type and cyp79B2 cyp79B3 double knockout plants. Böttcher et al. (2004) Description: Indole-3-acetaldoxime (IAOx) represents an early intermediate of the biosynthesis of a variety of indolic secondary metabolites including the phytoanticipin indol-3-ylmethyl glucosinolate and the phytoalexin camalexin (3-thiazol-2'-yl-indole). Arabidopsis thaliana cyp79B2 cyp79B3 double knockout plants are completely impaired in the conversion of tryptophan to indole-3-acetaldoxime and do not accumulate IAOx-derived metabolites any longer. Consequently, comparative analysis of wild-type and cyp79B2 cyp79B3 plant lines has the potential to explore the complete range of IAOx-derived indolic secondary metabolites. biocViews: MassSpectrometryData, RepositoryData Author: Steffen Neumann Maintainer: Steffen Neumann URL: http://www.ebi.ac.uk/metabolights/MTBLS2, https://github.com/sneumann/mtbls2 VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mtbls2 git_branch: devel git_last_commit: 8dcbdff git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/mtbls2_1.35.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: IPO, yamss dependencyCount: 0 Package: MUGAExampleData Version: 1.25.0 Depends: R (>= 2.10.0) License: GPL-3 MD5sum: 9bc00cce20b1fe93f5a3243ba6eb843f NeedsCompilation: no Title: Example {M}ouse {U}niversal {G}enotyping {A}rray data for genome reconstruction and quantitative trait locus mapping. Description: This package contains example data for the MUGA array that is used by the R package DOQTL. biocViews: ExperimentData, Mus_musculus_Data Author: Daniel Gatti Maintainer: Daniel Gatti git_url: https://git.bioconductor.org/packages/MUGAExampleData git_branch: devel git_last_commit: 50c0e5b git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/MUGAExampleData_1.25.0.tar.gz vignettes: vignettes/MUGAExampleData/inst/doc/MUGAExampleData.pdf vignetteTitles: User Manual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MUGAExampleData/inst/doc/MUGAExampleData.R dependencyCount: 0 Package: muleaData Version: 1.1.0 Suggests: knitr, rmarkdown, ExperimentHub, dplyr License: MIT + file LICENSE MD5sum: 49e3a05d1cbf9531269ba6bd3f80c95c NeedsCompilation: no Title: Genes Sets for Functional Enrichment Analysis with the 'mulea' R Package Description: ExperimentHubData package for the 'mulea' comprehensive overrepresentation and functional enrichment analyser R package. Here we provide ontologies (gene sets) in a data.frame for 27 different organisms, ranging from Escherichia coli to human, all acquired from publicly available data sources. Each ontology is provided with multiple gene and protein identifiers. Please see the NEWS file for a list of changes in each version. biocViews: ExperimentData, ExperimentHub, Arabidopsis_thaliana_Data, Bacillus_subtilis_Data, Caenorhabditis_elegans_Data, Danio_rerio_Data, Drosophila_melanogaster_Data, Escherichia_coli_Data, Homo_sapiens_Data, Pan_troglodytes_Data, Pseudomonas_aeruginosa_Data, Rattus_norvegicus_Data, Saccharomyces_cerevisiae_Data, Staphylococcus_aureus_Data, ChIPSeqData, DNASeqData, ExpressionData, miRNAData Author: Eszter Ari [aut, cre] (), Márton Ölbei [aut] (), Lejla Gul [aut], Balázs Bohár [aut] (), Tamás Stirling [aut] () Maintainer: Eszter Ari URL: https://github.com/ELTEbioinformatics/muleaData VignetteBuilder: knitr BugReports: https://support.bioconductor.org/tag/muleaData/issues git_url: https://git.bioconductor.org/packages/muleaData git_branch: devel git_last_commit: 029dd87 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/muleaData_1.1.0.tar.gz vignettes: vignettes/muleaData/inst/doc/muleaData.html vignetteTitles: muleaData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/muleaData/inst/doc/muleaData.R dependencyCount: 0 Package: multiWGCNAdata Version: 1.3.0 Depends: ExperimentHub Imports: utils Suggests: BiocStyle, knitr, multiWGCNA, rmarkdown, SummarizedExperiment License: Artistic-2.0 MD5sum: ca203d46da5d8a9297856339c6453178 NeedsCompilation: no Title: Data Package for multiWGCNA Description: Stores expression profiling data from experiments compatible with the multiWGCNA R package. This includes human postmortem microarray data from patients and controls (GSE28521), astrocyte Ribotag RNA-seq data from EAE and wildtype mice (GSE100329), and mouse RNA-seq data from tau pathology (rTg4510) and wildtype control mice (GSE125957). These data can be accessed using the ExperimentHub workflow (see multiWGCNA vignettes). biocViews: ExperimentHub, ExpressionData, Homo_sapiens_Data, Mus_musculus_Data, RNASeqData, MicroarrayData Author: Dario Tommasini [aut, cre] () Maintainer: Dario Tommasini VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/multiWGCNAdata git_branch: devel git_last_commit: 0d0db56 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/multiWGCNAdata_1.3.0.tar.gz vignettes: vignettes/multiWGCNAdata/inst/doc/multiWGCNAdata.html vignetteTitles: Loading data through ExperimentHub hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/multiWGCNAdata/inst/doc/multiWGCNAdata.R dependencyCount: 67 Package: muscData Version: 1.19.0 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: b755e80dc18c3213b147a32c54fa0755 NeedsCompilation: no Title: Multi-sample multi-group scRNA-seq data Description: Data package containing a collection of multi-sample multi-group scRNA-seq datasets in SingleCellExperiment Bioconductor object format. biocViews: ExperimentHub, ExperimentData, ExpressionData, GEO, Homo_sapiens_Data, ImmunoOncologyData, SingleCellData Author: Helena L. Crowell [aut, cre] Maintainer: Helena L. Crowell URL: https://github.com/HelenaLC/muscData VignetteBuilder: knitr BugReports: https://github.com/HelenaLC/muscData/issues git_url: https://git.bioconductor.org/packages/muscData git_branch: devel git_last_commit: 0662add git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/muscData_1.19.0.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: 79 Package: mvoutData Version: 1.41.0 Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4), lumi License: Artistic-2.0 MD5sum: f90c34ca89a251588ea39dfe27febe15 NeedsCompilation: no Title: affy and illumina raw data for assessing outlier detector performance Description: affy and illumina raw data for assessing outlier detector performance biocViews: ExperimentData, MicroarrayData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/mvoutData git_branch: devel git_last_commit: 676fbe1 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/mvoutData_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayMvout dependencyCount: 161 Package: NanoporeRNASeq Version: 1.15.0 Depends: R(>= 4.0.0), ExperimentHub (>= 1.15.3) Suggests: knitr, bambu, ggbio, BSgenome.Hsapiens.NCBI.GRCh38, circlize, ComplexHeatmap, apeglm, rlang, rmarkdown, GenomicAlignments, Rsamtools Enhances: parallel License: GPL-3 + file LICENSE MD5sum: 62af5121b9015934e82a2cafeae598a2 NeedsCompilation: no Title: Nanopore RNA-Seq Example data Description: The NanoporeRNASeq package contains long read RNA-Seq data generated using Oxford Nanopore Sequencing. The data consists of 6 samples from two human cell lines (K562 and MCF7) that were generated by the SG-NEx project. Each of these cell lines has three replicates, with 1 direct RNA sequencing data and 2 cDNA sequencing data. Reads are aligned to chromosome 22 (Grch38) and stored as bam files. The original data is from the SG-NEx project. biocViews: ExperimentHub, ExperimentData, RNASeqData, Genome, SequencingData Author: Jonathan Goeke [aut], Ying Chen [cre], Yuk Kei Wan [aut] Maintainer: Ying Chen URL: https://github.com/GoekeLab/NanoporeRNASeq VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/NanoporeRNASeq git_branch: devel git_last_commit: 7b4ae3b git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/NanoporeRNASeq_1.15.0.tar.gz vignettes: vignettes/NanoporeRNASeq/inst/doc/NanoporeRNASeq.html vignetteTitles: NanoporeRNASeq hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/NanoporeRNASeq/inst/doc/NanoporeRNASeq.R suggestsMe: bambu dependencyCount: 67 Package: nanotubes Version: 1.21.0 Depends: R (>= 3.6) Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, rtracklayer, CAGEfightR License: GPL-3 MD5sum: 916117639adf98a080e0e2934cdfd2c8 NeedsCompilation: no Title: Mouse nanotube CAGE data Description: Cap Analysis of Gene Expression (CAGE) data from "Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo" by Bornholdt et al. supplied as CAGE Transcription Start Sites (CTSSs). biocViews: ExperimentData, SequencingData, ExpressionData Author: Malte Thodberg Maintainer: Malte Thodberg URL: https://github.com/MalteThodberg/nanotubes VignetteBuilder: knitr BugReports: https://github.com/MalteThodberg/nanotubes/issues git_url: https://git.bioconductor.org/packages/nanotubes git_branch: devel git_last_commit: 8bda8ad git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/nanotubes_1.21.0.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: 1.41.0 Depends: R (>= 2.10.0) Suggests: Rgraphviz License: GPL-3 MD5sum: 7250c63fdee02eb820a6d939d5bc7c80 NeedsCompilation: no Title: Data for the NCIgraph software package Description: Provides pathways from the NCI Pathways Database as R graph objects biocViews: NCI Author: Laurent Jacob Maintainer: Laurent Jacob git_url: https://git.bioconductor.org/packages/NCIgraphData git_branch: devel git_last_commit: 00f4ca3 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/NCIgraphData_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: NestLink Version: 1.21.0 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: 6f32e7d9eaf0f8cdee734d13421a9523 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: devel git_last_commit: bc4bcb8 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/NestLink_1.21.0.tar.gz vignettes: vignettes/NestLink/inst/doc/analyze-flycode-detectibilty.html, vignettes/NestLink/inst/doc/compare-predicted-observed-flycodes.html, vignettes/NestLink/inst/doc/link-nanobodies-flycodes.html, vignettes/NestLink/inst/doc/make-data.html, vignettes/NestLink/inst/doc/simulate-flycodes.html, vignettes/NestLink/inst/doc/supplement-note1.html vignetteTitles: 2. Analyze flycode detectability using ESP and SSRC prediction, 3. Compare Predicted and Observed flycodes hydrophobicity values using F255744., 1. Link high quality flycode and nanobody sequences by NGS filtering., 5. make-data, 0. Simulate flycode properties., 4. Control experiment to assess the robustness of protein detection via flycodes (NMETH-A35040 Suppl. notes 1). hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/NestLink/inst/doc/analyze-flycode-detectibilty.R, vignettes/NestLink/inst/doc/compare-predicted-observed-flycodes.R, vignettes/NestLink/inst/doc/link-nanobodies-flycodes.R, vignettes/NestLink/inst/doc/make-data.R, vignettes/NestLink/inst/doc/simulate-flycodes.R, vignettes/NestLink/inst/doc/supplement-note1.R dependencyCount: 107 Package: NetActivityData Version: 1.7.0 Depends: R (>= 4.2.0) Suggests: BiocStyle, knitr License: MIT + file LICENSE MD5sum: 4eee45eac1e19dbc77c0407a96cdd5cc NeedsCompilation: no Title: Data required for getting the gene set scores with NetActivity package Description: This package contains the weights from pre-trained shallow sparsely-connected autoencoders. This data is required for getting the gene set scores with NetActivity package. biocViews: ExperimentData, RepositoryData Author: Carlos Ruiz-Arenas [aut, cre] Maintainer: Carlos Ruiz-Arenas VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/NetActivityData git_branch: devel git_last_commit: 30b8cbb git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/NetActivityData_1.7.0.tar.gz vignettes: vignettes/NetActivityData/inst/doc/NetActivityData.html vignetteTitles: "NetActivityData" hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/NetActivityData/inst/doc/NetActivityData.R importsMe: NetActivity dependencyCount: 0 Package: Neve2006 Version: 0.43.0 Depends: R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0), hgu133a.db, annotate License: Artistic-2.0 MD5sum: 441616ee86fbc629b79261281ef6f691 NeedsCompilation: no Title: expression and CGH data on breast cancer cell lines Description: Experimental organization of combined expression and CGH data biocViews: ExperimentData, CancerData, BreastCancerData Author: M. Neve et al. in Gray Lab at LBL Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/Neve2006 git_branch: devel git_last_commit: c06e336 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/Neve2006_0.43.0.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: 50 Package: NGScopyData Version: 1.25.0 License: GPL (>=2) MD5sum: d3dec3e9edb2c8661025e8f444274991 NeedsCompilation: no Title: Subset of BAM files of human tumor and pooled normal sequencing data (Zhao et al. 2014) for the NGScopy package Description: Subset of BAM files of human lung tumor and pooled normal samples by targeted panel sequencing. [Zhao et al 2014. Targeted Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using the University of North Carolina (UNC) Sequencing Assay Captures Most Previously Described Genetic Aberrations in NSCLC. In preparation.] Each sample is a 10 percent random subsample drawn from the original sequencing data. The pooled normal sample has been rescaled accroding to the total number of normal samples in the "pool". Here provided is the subsampled data on chr6 (hg19). biocViews: ExperimentData, CancerData, LungCancerData, SequencingData Author: Xiaobei Zhao [aut, cre, cph] Maintainer: Xiaobei Zhao URL: http://www.bioconductor.org/packages/release/data/experiment/html/NGScopyData.html git_url: https://git.bioconductor.org/packages/NGScopyData git_branch: devel git_last_commit: 4894e0f git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/NGScopyData_1.25.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: nullrangesData Version: 1.11.0 Depends: R (>= 4.1.0), ExperimentHub, GenomicRanges, InteractionSet Imports: utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 32032fa587b87705d0404e1ee00c729d NeedsCompilation: no Title: ExperimentHub datasets for the nullranges package Description: Provides datasets for the nullranges package vignette, in particular example datasets for DNase hypersensitivity sites (DHS), CTCF binding sites, and CTCF genomic interactions. These are used to demonstrate generation of null hypothesis feature sets, either through block bootstrapping or matching, in the nullranges vignette. For more details, see the data object man pages, and the R scripts for object construction provided within the package. biocViews: ExperimentHub, Homo_sapiens_Data, SequencingData, ChIPSeqData, ENCODE Author: Michael Love [aut, cre] (), Wancen Mu [aut] (), Eric Davis [aut] (), Mikhail Dozmorov [aut] Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/nullrangesData git_branch: devel git_last_commit: 6be1a6f git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/nullrangesData_1.11.0.tar.gz vignettes: vignettes/nullrangesData/inst/doc/nullrangesData.html vignetteTitles: nullrangesData package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/nullrangesData/inst/doc/nullrangesData.R suggestsMe: iSEEhub, nullranges dependencyCount: 80 Package: NxtIRFdata Version: 1.11.0 Imports: ExperimentHub, BiocFileCache, rtracklayer, R.utils Suggests: testthat (>= 3.0.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: df62ddd523a009589eca094b798b8483 NeedsCompilation: no Title: Data for NxtIRF Description: NxtIRFdata is a companion package for SpliceWiz, an interactive analysis and visualization tool for alternative splicing quantitation (including intron retention) for RNA-seq BAM files. NxtIRFdata contains Mappability files required for the generation of human and mouse references. NxtIRFdata also contains a synthetic genome reference and example BAM files used to demonstrate SpliceWiz's functionality. BAM files are based on 6 samples from the Leucegene dataset provided by NCBI Gene Expression Omnibus under accession number GSE67039. biocViews: ExperimentData, PackageTypeData, Genome, RNASeqData, ExpressionData, ExperimentHub Author: Alex Chit Hei Wong [aut, cre, cph], Ulf Schmitz [ctb] Maintainer: Alex Chit Hei Wong URL: https://github.com/alexchwong/NxtIRFdata VignetteBuilder: knitr BugReports: https://support.bioconductor.org/ git_url: https://git.bioconductor.org/packages/NxtIRFdata git_branch: devel git_last_commit: bc5b4e2 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/NxtIRFdata_1.11.0.tar.gz vignettes: vignettes/NxtIRFdata/inst/doc/NxtIRFdata.html vignetteTitles: NxtIRFdata: a data package for NxtIRF hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/NxtIRFdata/inst/doc/NxtIRFdata.R dependsOnMe: SpliceWiz dependencyCount: 100 Package: ObMiTi Version: 1.13.0 Depends: R (>= 4.1), SummarizedExperiment, ExperimentHub Suggests: knitr, rmarkdown, BiocManager, GenomicFeatures, S4Vectors, devtools, testthat License: GPL-3 MD5sum: 5f56a6b7b11ccc6fc8c1c0ef6020f826 NeedsCompilation: no Title: Ob/ob Mice Data on Normal and High Fat Diet Description: The package provide RNA-seq count for 2 strains of mus musclus; Wild type and Ob/Ob. Each strain was divided into two groups, and each group received either chow diet or high fat diet. RNA expression was measured after 20 weeks in 7 tissues. biocViews: ExperimentHub, GEO, RNASeqData Author: Omar Elashkar [aut, cre] (), 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: devel git_last_commit: dd0e4e6 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/ObMiTi_1.13.0.tar.gz vignettes: vignettes/ObMiTi/inst/doc/ObMiTi.html vignetteTitles: Using ObMiTi hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ObMiTi/inst/doc/ObMiTi.R dependencyCount: 78 Package: oct4 Version: 1.21.0 Suggests: knitr, markdown License: GPL (>= 2) MD5sum: eb7e7967f5063efcae592e4a7e20f458 NeedsCompilation: no Title: Conditional knockdown of OCT4 in mouse ESCs Description: This package provides the output of running Salmon on a set of 12 RNA-seq samples from King & Klose, "The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells", published in eLIFE, March 2017. For details on version numbers and how the samples were processed see the package vignette. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/oct4 git_branch: devel git_last_commit: fdb4bb1 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/oct4_1.21.0.tar.gz vignettes: vignettes/oct4/inst/doc/oct4.html vignetteTitles: Salmon quantifications for condition OCT4 knockdown in mouse ESCs hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/oct4/inst/doc/oct4.R dependencyCount: 0 Package: octad.db Version: 1.7.0 Depends: R (>= 4.2.0), ExperimentHub Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 546f66c97dea3db3704fdf2fae0d8620 NeedsCompilation: no Title: Open Cancer TherApeutic Discovery (OCTAD) database Description: Open Cancer TherApeutic Discovery (OCTAD) package implies sRGES approach for the drug discovery. The essential idea is to identify drugs that reverse the gene expression signature of a disease by tamping down over-expressed genes and stimulating weakly expressed ones. The following package contains all required precomputed data for whole OCTAD pipeline computation. biocViews: ExperimentData, CancerData, ExperimentHub, SequencingData, ExpressionData Author: E. Chekalin [aut, cre], S. Paithankar [aut], B. Zeng [aut], B. Glicksberg [ctb], P. Newbury [ctb], J. Xing [ctb], K. Liu [ctb], A. Wen [ctb], D. Joseph [ctb], B. Chen [aut] Maintainer: E. Chekalin VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/octad.db git_branch: devel git_last_commit: d596337 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/octad.db_1.7.0.tar.gz vignettes: vignettes/octad.db/inst/doc/octad.db.html vignetteTitles: octad.db hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/octad.db/inst/doc/octad.db.R dependsOnMe: octad dependencyCount: 67 Package: OMICsPCAdata Version: 1.23.0 Depends: R (>= 3.5.0), MultiAssayExperiment Suggests: knitr, kableExtra, rmarkdown License: GPL-3 MD5sum: 5f2a07fae4e83c863f1060c7c7d5b632 NeedsCompilation: no Title: Supporting data for package OMICsPCA Description: Supporting data for package OMICsPCA biocViews: RepositoryData, TechnologyData, ChIPSeqData, SequencingData, ExpressionData, ENCODE Author: Subhadeep Das Maintainer: Subhadeep Das VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/OMICsPCAdata git_branch: devel git_last_commit: ef18c82 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/OMICsPCAdata_1.23.0.tar.gz vignettes: vignettes/OMICsPCAdata/inst/doc/vignettes.html vignetteTitles: OMICsPCAdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/OMICsPCAdata/inst/doc/vignettes.R dependsOnMe: OMICsPCA dependencyCount: 58 Package: OnassisJavaLibs Version: 1.27.0 Depends: R (>= 3.4) Imports: rJava Suggests: BiocStyle, rmarkdown, knitr License: GPL-2 MD5sum: 8ae799e8406dddd107fd8f762d95fa3f NeedsCompilation: no Title: OnassisJavaLibs, java libraries to run conceptmapper and semantic similarity Description: A package that contains java libraries to call conceptmapper and compute semnatic similarity from R biocViews: ExperimentData Author: Eugenia Galeota Maintainer: Eugenia Galeota SystemRequirements: Java (>= 1.8) VignetteBuilder: rmarkdown, knitr git_url: https://git.bioconductor.org/packages/OnassisJavaLibs git_branch: devel git_last_commit: 108f27f git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/OnassisJavaLibs_1.27.0.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: 1.17.0 Depends: R (>= 4.0) Suggests: knitr, BiocStyle, rmarkdown, magick License: Artistic-2.0 MD5sum: 57f4b75aa1f43fe64cf81eb51ee1952e NeedsCompilation: no Title: optimalFlowData Description: Data files used as examples and for testing of the software provided in the optimalFlow package. biocViews: ExperimentData, PackageTypeData, ImmunoOncologyData, FlowCytometryData Author: Hristo Inouzhe Maintainer: Hristo Inouzhe VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/optimalFlowData git_branch: devel git_last_commit: f42b84e git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/optimalFlowData_1.17.0.tar.gz vignettes: vignettes/optimalFlowData/inst/doc/optimalFlowData_vignette.html vignetteTitles: optimalFlow: optimal-transport approach to Flow Cytometry analysis hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/optimalFlowData/inst/doc/optimalFlowData_vignette.R dependsOnMe: optimalFlow dependencyCount: 0 Package: orthosData Version: 1.3.0 Imports: AnnotationHub, BiocFileCache, ExperimentHub, HDF5Array, stringr, SummarizedExperiment Suggests: BiocStyle, ggplot2, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 79a10927b6e728439eedc1ca64feb293 NeedsCompilation: no Title: Data for the orthos package Description: `orthosData` is the companion ExperimentData package to the `orthos` R package for mechanistic studies using differential gene expression experiments. It provides functions for retrieval from ExperimentHub and local caching of the models and datasets used internally in orthos. biocViews: ExperimentData, RNASeqData, ExperimentHub Author: Panagiotis Papasaikas [aut, cre] (), Charlotte Soneson [aut] (), Michael Stadler [aut] (), Friedrich Miescher Institute for Biomedical Research [cph] Maintainer: Panagiotis Papasaikas URL: https://github.com/fmicompbio/orthosData VignetteBuilder: knitr BugReports: https://github.com/fmicompbio/orthosData/issues git_url: https://git.bioconductor.org/packages/orthosData git_branch: devel git_last_commit: 7447a7b git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/orthosData_1.3.0.tar.gz vignettes: vignettes/orthosData/inst/doc/orthosData.html vignetteTitles: 1. Introduction to orthos hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/orthosData/inst/doc/orthosData.R importsMe: orthos dependencyCount: 82 Package: parathyroidSE Version: 1.43.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: Rsamtools, GenomicAlignments, GEOquery, SRAdb, GenomicFeatures, BiocStyle License: LGPL MD5sum: 1e65ae1c86ad412e58b32b4d4c697486 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: devel git_last_commit: 8433284 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/parathyroidSE_1.43.0.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: 36 Package: pasilla Version: 1.33.0 Depends: R (>= 3.5.0), DEXSeq Suggests: rmarkdown, BiocStyle, knitr, roxygen2 License: LGPL MD5sum: 9ef958e79b65ef073d95024663f64140 NeedsCompilation: no Title: Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011. Description: This package provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in the article "Conservation of an RNA regulatory map between Drosophila and mammals" by Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR, Genome Res. 2011 Feb;21(2):193-202, Epub 2010 Oct 4, PMID: 20921232. The experiment studied the effect of RNAi knockdown of Pasilla, the Drosophila melanogaster ortholog of mammalian NOVA1 and NOVA2, on the transcriptome. The package vignette describes how the data provided here were derived from the RNA-Seq read sequence data that are provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. biocViews: ExperimentData, Genome, Drosophila_melanogaster_Data, RNASeqData Author: Wolfgang Huber, Alejandro Reyes Maintainer: Alejandro Reyes VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/pasilla git_branch: devel git_last_commit: 1426242 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/pasilla_1.33.0.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, ReportingTools, gsean, regionReport, tidybulk, pasillaBamSubset dependencyCount: 119 Package: pasillaBamSubset Version: 0.43.0 Suggests: pasilla License: LGPL MD5sum: 9c3bfbd47adf2990174b32bf384297f7 NeedsCompilation: no Title: Subset of BAM files from "Pasilla" experiment Description: Subset of BAM files untreated1.bam (single-end reads) and untreated3.bam (paired-end reads) from "Pasilla" experiment (Pasilla knock-down by Brooks et al., Genome Research 2011). See the vignette in the pasilla data package for how BAM files untreated1.bam and untreated3.bam were obtained from the RNA-Seq read sequence data that is provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. Also contains the DNA sequence for fly chromosome 4 to which the reads can be mapped. biocViews: ExperimentData, Genome, DNASeqData, RNASeqData Author: Hervé Pagès Maintainer: Hervé Pagès git_url: https://git.bioconductor.org/packages/pasillaBamSubset git_branch: devel git_last_commit: 603e244 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/pasillaBamSubset_0.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: APAlyzer, DEXSeq, GenomicAlignments, GenomicFeatures, GenomicRanges, IRanges, TransView, gmoviz, karyoploteR, plyranges dependencyCount: 0 Package: PasillaTranscriptExpr Version: 1.33.0 Depends: R (>= 3.3.0) Suggests: rtracklayer, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: 90e4ec9cc4a2e56e8d096d3d45b6f5b0 NeedsCompilation: no Title: Data package with transcript expression obtained with kallisto from pasilla knock-down RNA-Seq data from Brooks et al. Description: Provides kallisto workflow and transcript expression of RNA-Seq data from Brooks et al. biocViews: Drosophila_melanogaster_Data, Genome, RNASeqData, ExperimentData, SequencingData, ExpressionData, GEO Author: Malgorzata Nowicka [aut, cre] Maintainer: Malgorzata Nowicka VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/PasillaTranscriptExpr git_branch: devel git_last_commit: 9df6247 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/PasillaTranscriptExpr_1.33.0.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: 1.41.0 Depends: R (>= 1.14.0) License: GPL-3 MD5sum: 48c714594ba17078ea02f6457a622d84 NeedsCompilation: no Title: Experimental data for the PathNet package Description: This package contains the data employed in the vignette of the PathNet package. These data belong to the following publication: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J., Source Code for Biology and Medicine 2012 Sep 24;7(1):10. biocViews: ExperimentData, PathwayInteractionDatabase Author: Bhaskar Dutta , Anders Wallqvist , and Jaques Reifman Maintainer: Ludwig Geistlinger git_url: https://git.bioconductor.org/packages/PathNetData git_branch: devel git_last_commit: 28bd489 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/PathNetData_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PathNet dependencyCount: 0 Package: PCHiCdata Version: 1.33.0 Depends: R (>= 3.2), Chicago Suggests: testthat, BiocStyle, knitr License: Artistic-2.0 MD5sum: e2750a1c78c2c7ca78e1c3c6fcd5e356 NeedsCompilation: no Title: Promoter Capture Hi-C data Description: Subsets of Promoter Capture Hi-C data conveniently packaged for Chicago users. Data includes interactions detected for chromosomes 20 and 21 in GM12878 cells and for chromosomes 18 and 19 in mESC. biocViews: ExperimentData, SequencingData, Homo_sapiens_Data, Mus_musculus_Data, StemCell Author: Paula Freire-Pritchett, Jonathan Cairns, Steven Wingett, Mikhail Spivakov Maintainer: Mikhail Spivakov VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/PCHiCdata git_branch: devel git_last_commit: 181798a git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/PCHiCdata_1.33.0.tar.gz vignettes: vignettes/PCHiCdata/inst/doc/PCHiCdata.html vignetteTitles: PCHiCdata Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/PCHiCdata/inst/doc/PCHiCdata.R suggestsMe: Chicago dependencyCount: 77 Package: pd.atdschip.tiling Version: 0.43.0 Depends: R (>= 3.5.0), methods, RSQLite (>= 0.10.0), oligoClasses (>= 1.15.58), oligo (>= 1.17.3), DBI Imports: Biostrings (>= 2.21.11), IRanges (>= 1.11.31), S4Vectors License: Artistic-2.0 MD5sum: ca955a186485bd367753ae85b668e663 NeedsCompilation: no Title: Platform Design Info for Affymetrix Atdschip_tiling Description: Platform Design Info for Affymetrix Atdschip_tiling biocViews: Arabidopsis_thaliana_Data, MicroarrayData, SNPData Author: Kristof De Beuf Maintainer: Kristof De Beuf git_url: https://git.bioconductor.org/packages/pd.atdschip.tiling git_branch: devel git_last_commit: 28dafd9 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/pd.atdschip.tiling_0.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 64 Package: pepDat Version: 1.25.0 Depends: R (>= 3.5.0) Imports: GenomicRanges Suggests: knitr License: Artistic-2.0 MD5sum: 9756c7867685651070ff0882ce2f3902 NeedsCompilation: no Title: Peptide microarray data package Description: Provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV. biocViews: MicroarrayData Author: Renan Sauteraud, Raphael Gottardo Maintainer: Renan Sauteraud VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/pepDat git_branch: devel git_last_commit: a63fadc git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/pepDat_1.25.0.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: Pviz, pepStat dependencyCount: 23 Package: PepsNMRData Version: 1.23.0 Depends: R (>= 3.5) Suggests: knitr, markdown, rmarkdown, BiocStyle License: GPL-2 | file LICENSE MD5sum: caf3057c3c92d7094dcae43aeff78612 NeedsCompilation: no Title: Datasets for the PepsNMR package Description: This package contains all the datasets used in the PepsNMR package. biocViews: ExperimentData, OrganismData, Homo_sapiens_Data Author: Manon Martin [aut, cre], Bernadette Govaerts [aut, ths], Pascal de Tullio [dtc] Maintainer: Manon Martin BugReports: https://github.com/ManonMartin/PepsNMRData/issues git_url: https://git.bioconductor.org/packages/PepsNMRData git_branch: devel git_last_commit: e4f3785 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/PepsNMRData_1.23.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: PepsNMR dependencyCount: 0 Package: PhyloProfileData Version: 1.19.0 Depends: R (>= 4.1.0) Imports: ExperimentHub, Biostrings, BiocStyle Suggests: knitr, rmarkdown, markdown License: MIT + file LICENSE MD5sum: 86e7f660678fadd0b0c75de98c491506 NeedsCompilation: yes Title: Data package for phylogenetic profile analysis using PhyloProfile tool Description: Two experimental datasets to illustrate running and analysing phylogenetic profiles with PhyloProfile package. biocViews: ExperimentData, ReproducibleResearch, ExperimentHub Author: Vinh Tran [aut, cre], Ingo Ebersberger [aut], Hannah Mülbaier [ctb], Arpit Jain [ctb] Maintainer: Vinh Tran URL: https://github.com/BIONF/PhyloProfileData VignetteBuilder: knitr BugReports: https://github.com/trvinh/PhyloProfileData/issues git_url: https://git.bioconductor.org/packages/PhyloProfileData git_branch: devel git_last_commit: 8cef79d git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/PhyloProfileData_1.19.0.tar.gz vignettes: vignettes/PhyloProfileData/inst/doc/PhyloProfileData.html vignetteTitles: PhyloProfileData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/PhyloProfileData/inst/doc/PhyloProfileData.R dependencyCount: 83 Package: plotgardenerData Version: 1.11.0 Depends: R (>= 4.1.0) Suggests: rmarkdown, knitr License: MIT + file LICENSE MD5sum: 1f9b396cbc3210f71ed3fc3348fc301d NeedsCompilation: no Title: Datasets and test data files for the plotgardener package Description: This is a supplemental data package for the plotgardener package. Includes example datasets used in plotgardener vignettes and example raw data files. For details on how to use these datasets, see the plotgardener package vignettes. biocViews: ExperimentData, Homo_sapiens_Data, ExpressionData, Genome, ChIPSeqData, ENCODE Author: Nicole Kramer [aut, cre] () Maintainer: Nicole Kramer URL: https://github.com/PhanstielLab/plotgardenerData, https://phanstiellab.github.io/plotgardener VignetteBuilder: knitr BugReports: https://github.com/PhanstielLab/plotgardenerData/issues git_url: https://git.bioconductor.org/packages/plotgardenerData git_branch: devel git_last_commit: 936fdbb git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/plotgardenerData_1.11.0.tar.gz vignettes: vignettes/plotgardenerData/inst/doc/plotgardenerData.html vignetteTitles: plotgardenerData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/plotgardenerData/inst/doc/plotgardenerData.R suggestsMe: plotgardener dependencyCount: 0 Package: prebsdata Version: 1.41.0 Depends: R (>= 2.14.0) License: Artistic-2.0 MD5sum: 173aee0769b7914d3aa690294f706b45 NeedsCompilation: no Title: Data for 'prebs' package Description: This package contains data required to run examples in 'prebs' package. The data files include: 1) Small sample bam files for demonstration purposes 2) Probe sequence mappings for Custom CDF (taken from http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp) 3) Probe sequence mappings for manufacturer's CDF (manually created using bowtie) biocViews: ExperimentData, SequencingData, RNASeqData Author: Karolis Uziela and Antti Honkela Maintainer: Karolis Uziela git_url: https://git.bioconductor.org/packages/prebsdata git_branch: devel git_last_commit: bde5919 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/prebsdata_1.41.0.tar.gz vignettes: vignettes/prebsdata/inst/doc/prebsdata.pdf vignetteTitles: prebsdata User Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: SigFuge, prebs dependencyCount: 0 Package: preciseTADhub Version: 1.13.0 Depends: R (>= 4.1) Imports: ExperimentHub Suggests: knitr, rmarkdown, markdown, BiocStyle, preciseTAD License: MIT + file LICENSE MD5sum: 7a2c5ddd1ecd417836657db140618726 NeedsCompilation: no Title: Pre-trained random forest models obtained using preciseTAD Description: An experimentdata package to supplement the preciseTAD package containing pre-trained models and the variable importances of each genomic annotation used to build the model parsed into list objects and available in ExperimentHub. In total, preciseTADhub provides access to n=84 random forest classification models optimized to predict TAD/chromatin loop boundary regions and stored as .RDS files. The value, n, comes from the fact that we considered l=2 cell lines {GM12878, K562}, g=2 ground truth boundaries {Arrowhead, Peakachu}, and c=21 autosomal chromosomes {CHR1, CHR2, ..., CHR22} (omitting CHR9). Furthermore, each object is itself a two-item list containing: (1) the model object, and (2) the variable importances for CTCF, RAD21, SMC3, and ZNF143 used to predict boundary regions. Each model is trained via a "holdout" strategy, in which data from chromosomes {CHR1, CHR2, ..., CHRi-1, CHRi+1, ..., CHR22} were used to build the model and the ith chromosome was reserved for testing. See https://doi.org/10.1101/2020.09.03.282186 for more detail on the model building strategy. biocViews: ExperimentData, PackageTypeData, ExperimentHub, Genome Author: Spiro Stilianoudakis [aut], Mikhail Dozmorov [aut, cre] Maintainer: Mikhail Dozmorov URL: https://github.com/dozmorovlab/preciseTADhub VignetteBuilder: knitr BugReports: https://github.com/dozmorovlab/preciseTADhub/issues git_url: https://git.bioconductor.org/packages/preciseTADhub git_branch: devel git_last_commit: 842246a git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/preciseTADhub_1.13.0.tar.gz vignettes: vignettes/preciseTADhub/inst/doc/preciseTADhub.html vignetteTitles: preciseTADhub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/preciseTADhub/inst/doc/preciseTADhub.R dependencyCount: 67 Package: PREDAsampledata Version: 0.45.0 Depends: R (>= 2.10.0), methods, PREDA, Biobase, affy, annotate Suggests: hgu133plus2.db, hgu133plus2cdf License: Artistic-2.0 MD5sum: 00244013ab7ed1faf4502322a0f4e95d NeedsCompilation: no Title: expression and copy number data on clear cell renal carcinoma samples Description: Sample data for PREDA package. (annotations objects synchronized with GeneAnnot custom CDFs version 2.2.0) biocViews: ExperimentData, Tissue, CancerData, KidneyCancerData, MicroarrayData, TissueMicroarrayData, ArrayExpress Author: I. Cifola et al. in Cristina Battaglia Lab, University of Milan Maintainer: Francesco Ferrari git_url: https://git.bioconductor.org/packages/PREDAsampledata git_branch: devel git_last_commit: e2c1e10 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/PREDAsampledata_0.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PREDA dependencyCount: 62 Package: ProData Version: 1.43.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL MD5sum: e5e2c38e168dda339f17bf71d3bb0037 NeedsCompilation: no Title: SELDI-TOF data of Breast cancer samples Description: A data package of SELDI-TOF protein mass spectrometry data of 167 breast cancer and normal samples. biocViews: ExperimentData, CancerData, BreastCancerData, MassSpectrometryData, NCI Author: Xiaochun Li Maintainer: Xiaochun Li git_url: https://git.bioconductor.org/packages/ProData git_branch: devel git_last_commit: 5b08395 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/ProData_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CorrectedFDR dependencyCount: 6 Package: pRolocdata Version: 1.43.0 Depends: R (>= 3.6.3), MSnbase Imports: Biobase, utils Suggests: pRoloc (>= 1.13.8), testthat, SummarizedExperiment License: GPL-2 MD5sum: 24efec277826cd6850614a10e00916f6 NeedsCompilation: no Title: Data accompanying the pRoloc package Description: Mass-spectrometry based spatial proteomics data sets and protein complex separation data. Also contains the time course expression experiment from Mulvey et al. 2015. biocViews: ExperimentData, Homo_sapiens_Data, MassSpectrometryData, Arabidopsis_thaliana_Data, Drosophila_melanogaster_Data, Mus_musculus_Data, StemCell, Proteome Author: Laurent Gatto [aut, cre] (), Oliver Crook [aut] (), Lisa Breckels [aut] () 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: devel git_last_commit: 6294f16 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/pRolocdata_1.43.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: bandle suggestsMe: MSnbase, pRolocGUI, pRoloc, RforProteomics dependencyCount: 137 Package: prostateCancerCamcap Version: 1.33.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 517266eeccc014d025c0c059d293b90a NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Ross-Adams (2015) Prostate Cancer dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerCamcap git_branch: devel git_last_commit: 9b23424 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/prostateCancerCamcap_1.33.0.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: 6 Package: prostateCancerGrasso Version: 1.33.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: dfa1357cd9306ddedccfcab062bf95ee NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Grasso (2012) Prostate Cancer dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerGrasso git_branch: devel git_last_commit: 9ea8f98 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/prostateCancerGrasso_1.33.0.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: 6 Package: prostateCancerStockholm Version: 1.33.0 Depends: Biobase , R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 6b7c9d148eae9f78c3ebfe3b66286805 NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Stockholm dataset biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerStockholm git_branch: devel git_last_commit: bcb7da2 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/prostateCancerStockholm_1.33.0.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: 6 Package: prostateCancerTaylor Version: 1.33.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery, org.Hs.eg.db License: Artistic-2.0 MD5sum: 37d37b4b6f4245c9052b4dd10405b9cb NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Taylor et al (2010) dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerTaylor git_branch: devel git_last_commit: a1e067f git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/prostateCancerTaylor_1.33.0.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: 6 Package: prostateCancerVarambally Version: 1.33.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: a960d7740fa8e9dc65a44e4462714a3f NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Varambally dataset biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerVarambally git_branch: devel git_last_commit: 3b55e6c git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/prostateCancerVarambally_1.33.0.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: 6 Package: ptairData Version: 1.13.0 Imports: rhdf5, signal, stats, graphics Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: e11e7dacf817089c78fc39c8eda59a6c NeedsCompilation: no Title: PTR-TOF-MS volatolomics raw datasets from exhaled air and cell culture headspace Description: The package ptairData contains two raw datasets from Proton-Transfer-Reaction Time-of-Flight mass spectrometer acquisitions (PTR-TOF-MS), in the HDF5 format. One from the exhaled air of two volunteer healthy individuals with three replicates, and one from the cell culture headspace from two mycobacteria species and one control (culture medium only) with two replicates. Those datasets are used in the examples and in the vignette of the ptairMS package (PTR-TOF-MS data pre-processing). There are also used to gererate the ptrSet in the ptairMS data : exhaledPtrset and mycobacteriaSet biocViews: ExperimentData, MassSpectrometryData, CellCulture Author: camille Roquencourt [aut, cre] Maintainer: camille Roquencourt VignetteBuilder: knitr BugReports: https://github.com/camilleroquencourt/ptairData/issues git_url: https://git.bioconductor.org/packages/ptairData git_branch: devel git_last_commit: 97ff01c git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/ptairData_1.13.0.tar.gz vignettes: vignettes/ptairData/inst/doc/ptairData_vignette.html vignetteTitles: PTR-TOF-MS dataset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ptairData/inst/doc/ptairData_vignette.R suggestsMe: ptairMS dependencyCount: 10 Package: PtH2O2lipids Version: 1.31.0 Depends: R (>= 3.3), xcms, CAMERA, LOBSTAHS, methods, utils Suggests: gplots, RColorBrewer, cluster, vegan License: MIT + file LICENSE MD5sum: 8cd4d825acd5b33bf89aa67769d61743 NeedsCompilation: no Title: P. tricornutum HPLC-ESI-MS Lipid Data from van Creveld et al. (2015) Description: Annotated HPLC-ESI-MS lipid data in positive ionization mode from an experiment in which cultures of the marine diatom Phaeodactylum tricornutum were treated with various concentrations of hydrogen peroxide (H2O2) to induce oxidative stress. The experiment is described in Graff van Creveld, et al., 2015, "Early perturbation in mitochondria redox homeostasis in response to environmental stress predicts cell fate in diatoms," ISME Journal 9:385-395. PtH2O2lipids consists of two objects: A CAMERA xsAnnotate object (ptH2O2lipids$xsAnnotate) and LOBSTAHS LOBSet object (ptH2O2lipids$xsAnnotate$LOBSet). The LOBSet includes putative compound assignments from the default LOBSTAHS database. Isomer annotation is recorded in three other LOBSet slots. biocViews: ReproducibleResearch, CellCulture, MassSpectrometryData, Phaeodactylum_tricornutum_data Author: Shiri Graff van Creveld [aut], Shilo Rosenwasser [aut], Daniella Schatz [aut], Ilan Koren [aut], Assaf Vardi [aut], James Collins [cre] Maintainer: James Collins URL: http://dx.doi.org/10.1038/ismej.2014.136, https://github.com/vanmooylipidomics/PtH2O2lipids, http://www.whoi.edu/page.do?pid=133616&tid=282&cid=192529 BugReports: https://github.com/vanmooylipidomics/PtH2O2lipids/issues/new git_url: https://git.bioconductor.org/packages/PtH2O2lipids git_branch: devel git_last_commit: 30faaa8 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/PtH2O2lipids_1.31.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: LOBSTAHS dependencyCount: 162 Package: pumadata Version: 2.41.0 Depends: R (>= 3.2.0), Biobase (>= 2.5.5),puma, oligo(>= 1.32.0) License: LGPL MD5sum: 6cd993b221ad88745df5d4e0998da4f6 NeedsCompilation: no Title: Various data sets for use with the puma package Description: This is a simple data package including various data sets derived from the estrogen data for use with the puma (Propagating Uncertainty in Microarray Analysis) package. biocViews: ExperimentData, MicroarrayData, SNPData Author: Richard Pearson Maintainer: Xuejun liu URL: http://umber.sbs.man.ac.uk/resources/puma git_url: https://git.bioconductor.org/packages/pumadata git_branch: devel git_last_commit: 94c4ba0 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/pumadata_2.41.0.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: 67 Package: PWMEnrich.Dmelanogaster.background Version: 4.39.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: f916ea60e0e939492cce8f86713fbc51 NeedsCompilation: no Title: D. melanogaster background for PWMEnrich Description: PWMEnrich pre-compiled background objects for Drosophila melanogaster and MotifDb D. melanogaster motifs. biocViews: Drosophila_melanogaster_Data Author: Robert Stojnic Maintainer: Diego Diez git_url: https://git.bioconductor.org/packages/PWMEnrich.Dmelanogaster.background git_branch: devel git_last_commit: 23f59db git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/PWMEnrich.Dmelanogaster.background_4.39.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 31 Package: PWMEnrich.Hsapiens.background Version: 4.39.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: 6d16fd15a764dd06be76adb99e0911ea NeedsCompilation: no Title: H. sapiens background for PWMEnrich Description: PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs. biocViews: Homo_sapiens_Data, CGHData Author: Robert Stojnic Maintainer: Diego Diez git_url: https://git.bioconductor.org/packages/PWMEnrich.Hsapiens.background git_branch: devel git_last_commit: 19419d3 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/PWMEnrich.Hsapiens.background_4.39.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 31 Package: PWMEnrich.Mmusculus.background Version: 4.39.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: c95db7f3057acfb531707e4910f6b747 NeedsCompilation: no Title: M. musculus background for PWMEnrich Description: PWMEnrich pre-compiled background objects for M.musculus (mouse) and MotifDb M. musculus motifs. biocViews: Mus_musculus_Data Author: Robert Stojnic Maintainer: Diego Diez git_url: https://git.bioconductor.org/packages/PWMEnrich.Mmusculus.background git_branch: devel git_last_commit: 0e22f61 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/PWMEnrich.Mmusculus.background_4.39.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 31 Package: QDNAseq.hg19 Version: 1.35.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: d8a9ea35e67f0f3ddcbab21da97ae0fd NeedsCompilation: no Title: QDNAseq bin annotation for hg19 Description: This package provides QDNAseq bin annotations for the human genome build hg19. biocViews: ExperimentData, OrganismData, Homo_sapiens_Data Author: Daoud Sie [aut, cre] Maintainer: Daoud Sie URL: https://github.com/tgac-vumc/QDNAseq.hg19 BugReports: https://github.com/tgac-vumc/QDNAseq.hg19/issues git_url: https://git.bioconductor.org/packages/QDNAseq.hg19 git_branch: devel git_last_commit: 1751992 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/QDNAseq.hg19_1.35.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: QDNAseq, biscuiteer dependencyCount: 59 Package: QDNAseq.mm10 Version: 1.35.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: 4323e94fd4a34f6c6d16ccfce5ab6888 NeedsCompilation: no Title: Bin annotation mm10 Description: This package provides QDNAseq bin annotations for the mouse genome build mm10. biocViews: ExperimentData, OrganismData, Mus_musculus_Data Author: Daoud Sie [aut, cre] Maintainer: Daoud Sie URL: https://github.com/tgac-vumc/QDNAseq.mm10 BugReports: https://github.com/tgac-vumc/QDNAseq.mm10/issues git_url: https://git.bioconductor.org/packages/QDNAseq.mm10 git_branch: devel git_last_commit: 8fcbb77 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/QDNAseq.mm10_1.35.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: QDNAseq, biscuiteer dependencyCount: 59 Package: qPLEXdata Version: 1.23.0 Depends: R (>= 3.5), qPLEXanalyzer Imports: utils, knitr, MSnbase, dplyr Suggests: statmod License: GPL-2 MD5sum: 0ba02d10ab417d8e7681a345bd4a9fe3 NeedsCompilation: no Title: Data accompanying qPLEXanalyzer package Description: qPLEX-RIME and Full proteome TMT mass spectrometry datasets. biocViews: ExperimentData, MassSpectrometryData, Proteome Author: Kamal Kishore Developer [aut, cre] Maintainer: Kamal Kishore Developer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/qPLEXdata git_branch: devel git_last_commit: d00eba5 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/qPLEXdata_1.23.0.tar.gz vignettes: vignettes/qPLEXdata/inst/doc/qPLEXdata.pdf vignetteTitles: qPLEXdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/qPLEXdata/inst/doc/qPLEXdata.R suggestsMe: qPLEXanalyzer dependencyCount: 150 Package: QUBICdata Version: 1.33.0 Depends: R (>= 3.1) Suggests: knitr, rmarkdown License: Unlimited | file LICENSE MD5sum: cf537f3cdf33a6caddd0e03441fe3d8b NeedsCompilation: no Title: Data employed in the vignette of the QUBIC package Description: The data employed in the vignette of the QUBIC package. These data belong to Many Microbe Microarrays Database and STRING v10. biocViews: Escherichia_coli_Data, OrganismData, ExperimentData Author: Yu Zhang [aut, cre], Qin Ma [aut] Maintainer: Yu Zhang URL: http://github.com/zy26/QUBICdata VignetteBuilder: knitr BugReports: http://github.com/zy26/QUBICdata/issues git_url: https://git.bioconductor.org/packages/QUBICdata git_branch: devel git_last_commit: 9d2e542 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/QUBICdata_1.33.0.tar.gz vignettes: vignettes/QUBICdata/inst/doc/qubic_data_vignette.pdf vignetteTitles: QUBIC Data Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/QUBICdata/inst/doc/qubic_data_vignette.R suggestsMe: QUBIC dependencyCount: 0 Package: raerdata Version: 1.3.0 Imports: ExperimentHub, Rsamtools, BiocGenerics, rtracklayer, SingleCellExperiment Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 94b2eff5dc4fa1d0f180280823468484 NeedsCompilation: no Title: A collection of datasets for use with raer package Description: raerdata is an ExperimentHub package that provides a collection of files useful for demostrating functionality in the raer package. Datasets include 10x genomics scRNA-seq, bulk RNA-seq, and paired whole-genome and RNA-seq data. Additionally databases of human and mouse RNA editing sites are provided. biocViews: SingleCellData, SequencingData, RNASeqData, ExperimentHub, PackageTypeData, ExpressionData Author: Kent Riemondy [aut, cre] () Maintainer: Kent Riemondy URL: https://github.com/rnabioco/raerdata VignetteBuilder: knitr BugReports: https://github.com/rnabioco/raerdata/issues git_url: https://git.bioconductor.org/packages/raerdata git_branch: devel git_last_commit: 97aa80d git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/raerdata_1.3.0.tar.gz vignettes: vignettes/raerdata/inst/doc/raerdata.html vignetteTitles: raerdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/raerdata/inst/doc/raerdata.R suggestsMe: raer dependencyCount: 98 Package: rcellminerData Version: 2.27.0 Depends: R (>= 3.5.0), Biobase Suggests: knitr, testthat, BiocStyle, rcellminer, rmarkdown License: LGPL-3 + file LICENSE MD5sum: 7a56c8a2b0e8a3a8df9d63bfabac9b8f NeedsCompilation: no Title: rcellminerData: Molecular Profiles and Drug Response for the NCI-60 Cell Lines Description: The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data. biocViews: CancerData, CopyNumberVariationData, ExpressionData, SNPData, NCI, MicroarrayData, miRNAData Author: Augustin Luna, Vinodh Rajapakse, Fabricio Sousa Maintainer: Augustin Luna , Vinodh Rajapakse , Fathi Elloumi VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/rcellminerData git_branch: devel git_last_commit: 9995bc2 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/rcellminerData_2.27.0.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: 6 Package: RcisTarget.hg19.motifDBs.cisbpOnly.500bp Version: 1.25.0 Depends: R (>= 3.3) Imports: data.table License: GPL-3 MD5sum: e2ea73d866752550e5e22167a08058f5 NeedsCompilation: no Title: RcisTarget motif databases for human (hg19) - Subset of 4.6k motifs Description: RcisTarget databases: Gene-based motif rankings and annotation to transcription factors. This package contains a subset of 4.6k motifs (cisbp motifs), scored only within 500bp upstream and the TSS. See RcisTarget tutorial to download the full databases, containing 20k motifs and search space up to 10kbp around the TSS. biocViews: Homo_sapiens_Data Author: Sara Aibar, Gert Hulselmans, Stein Aerts. Laboratory of Computational Biology, KU Leuven Center for Human Genetics. Leuven, Belgium. Maintainer: Sara Aibar URL: http://scenic.aertslab.org git_url: https://git.bioconductor.org/packages/RcisTarget.hg19.motifDBs.cisbpOnly.500bp git_branch: devel git_last_commit: d3eaa83 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.25.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RcisTarget dependencyCount: 2 Package: ReactomeGSA.data Version: 1.19.0 Depends: R (>= 3.6), limma, edgeR, ReactomeGSA, Seurat License: Artistic-2.0 MD5sum: 0afa1a305d6fe2323ba3734b2d87f385 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: devel git_last_commit: b01cd5f git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/ReactomeGSA.data_1.19.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ReactomeGSA dependencyCount: 164 Package: RegParallel Version: 1.23.0 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: a3667d941621ec3d016ee54db2d79ec5 NeedsCompilation: no Title: Standard regression functions in R enabled for parallel processing over large data-frames Description: In many analyses, a large amount of variables have to be tested independently against the trait/endpoint of interest, and also adjusted for covariates and confounding factors at the same time. The major bottleneck in these is the amount of time that it takes to complete these analyses. With RegParallel, a large number of tests can be performed simultaneously. On a 12-core system, 144 variables can be tested simultaneously, with 1000s of variables processed in a matter of seconds via 'nested' parallel processing. Works for logistic regression, linear regression, conditional logistic regression, Cox proportional hazards and survival models, and Bayesian logistic regression. Also caters for generalised linear models that utilise survey weights created by the 'survey' CRAN package and that utilise 'survey::svyglm'. biocViews: DiseaseModel Author: Kevin Blighe [aut, cre], Sarega Gurudas [ctb], Jessica Lasky-Su [aut] Maintainer: Kevin Blighe URL: https://github.com/kevinblighe/RegParallel VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RegParallel git_branch: devel git_last_commit: 7b30109 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-07 source.ver: src/contrib/RegParallel_1.23.0.tar.gz vignettes: vignettes/RegParallel/inst/doc/RegParallel.html vignetteTitles: Standard regression functions in R enabled for parallel processing over large data-frames hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RegParallel/inst/doc/RegParallel.R dependencyCount: 36 Package: RforProteomics Version: 1.43.0 Depends: R (>= 3.5), MSnbase (>= 2.5.3) Imports: R.utils, biocViews, BiocManager Suggests: AnnotationDbi, rpx (>= 2.0.3), DT, knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, MALDIquant (>= 1.12), MALDIquantForeign, readBrukerFlexData, Rdisop, OrgMassSpecR, SummarizedExperiment, BRAIN, rols, hpar, GO.db, org.Hs.eg.db, e1071, biomaRt, RColorBrewer, ggplot2, reshape2, xtable, lattice, mzID, pRoloc, pRolocdata, MSnID, msmsTests, msmsEDA, DEP, corrplot, beanplot, Heatplus, gplots, VennDiagram, protViz, genefilter, plotly, gridExtra, dplyr, lubridate, magick, cleaver License: Artistic-2.0 MD5sum: 5a48664428a0a39db2304f9bdeb29af1 NeedsCompilation: no Title: Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication Description: This package contains code to illustrate the 'Using R and Bioconductor for proteomics data analysis' and 'Visualisation of proteomics data using R and Bioconductor' manuscripts. The vignettes describe the code and data needed to reproduce the examples and figures described in the paper and functionality for proteomics visualisation. It also contain various function to discover R software for mass spectrometry and proteomics. biocViews: ExperimentData, MassSpectrometryData, ReproducibleResearch Author: Laurent Gatto [aut, cre], Sebastian Gibb [ctb], Vlad Petyuk [ctb], Thomas Pedersen Lin [ctb] Maintainer: Laurent Gatto URL: http://lgatto.github.com/RforProteomics/ VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RforProteomics git_branch: devel git_last_commit: e219147 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RforProteomics_1.43.0.tar.gz vignettes: vignettes/RforProteomics/inst/doc/RforProteomics.html, vignettes/RforProteomics/inst/doc/RProtVis.html vignetteTitles: Using R for proteomics data analysis, Visualisation of proteomics data using R and Bioconductor hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RforProteomics/inst/doc/RforProteomics.R, vignettes/RforProteomics/inst/doc/RProtVis.R suggestsMe: MSstatsQC dependencyCount: 146 Package: RGMQLlib Version: 1.25.0 Depends: R(>= 3.4.2) Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 80e368beff19d7b1b9f207b8c8cc6833 NeedsCompilation: no Title: RGMQLlib, java libraries to run GMQL scala API Description: A package that contains scala libraries to call GMQL from R used by RGMQL package. It contains a scalable data management engine written in Scala programming language. biocViews: ExperimentData,RepositoryData Author: Simone Pallotta [aut, cre], Marco Masseroli [aut] Maintainer: Simone Pallotta URL: http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/ VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RGMQLlib git_branch: devel git_last_commit: 5c479af git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RGMQLlib_1.25.0.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: 1.43.0 Depends: R (>= 2.10.0) Suggests: genefilter, Biobase, hgu133plus2.db License: Artistic-2.0 MD5sum: 35c23ff43fcce2b95496efc7becfdabd NeedsCompilation: no Title: Normalized gene expression dataset published by Wollbold et al. [2009] (WOLLBOLD). Description: Normalized gene expression data from rheumatic diseases from study published by Wollbold et al. in 2009, provided as an eSet. biocViews: ExperimentData, Tissue, MicroarrayData, MultiChannelData, ChipOnChipData, TissueMicroarrayData, GEO, ArrayExpress Author: Alejandro Quiroz-Zarate, John Quackenbush Maintainer: Alejandro Quiroz-Zarate URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/rheumaticConditionWOLLBOLD git_branch: devel git_last_commit: b990a60 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/rheumaticConditionWOLLBOLD_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: RITANdata Version: 1.29.0 Depends: R (>= 4.2) Suggests: knitr License: file LICENSE MD5sum: b5ede6746a02d3012899d705d28185b8 NeedsCompilation: no Title: This package contains reference annotation and network data sets Description: Data such as is contained in the two R data files in this package are required for the RITAN package examples. Users are highly encouraged to use their own or additional resources in conjunction with RITANdata. See the RITAN vignettes and RITAN.md for more information, such as gathering more up-to-date annotation data. biocViews: AnnotationData, Homo_sapiens Author: Michael Zimmermann [aut, cre] Maintainer: Michael Zimmermann VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RITANdata git_branch: devel git_last_commit: 1944515 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RITANdata_1.29.0.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: 1.43.0 Suggests: RMassBank License: Artistic-2.0 MD5sum: 5f9f6c2a701044b03e9e8691a52da2d0 NeedsCompilation: no Title: Test dataset for RMassBank Description: Example spectra, example compound list(s) and an example annotation list for a narcotics dataset; required to test RMassBank. The package is described in the man page for RMassBankData. Includes new XCMS test data. biocViews: ExperimentData, MassSpectrometryData Author: Michael Stravs, Emma Schymanski, Steffen Neumann Maintainer: Michael Stravs, Emma Schymanski git_url: https://git.bioconductor.org/packages/RMassBankData git_branch: devel git_last_commit: 7a8d9fd git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RMassBankData_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: RNAinteractMAPK Version: 1.41.0 Depends: R (>= 2.12.0), sparseLDA, RNAinteract Imports: grid, gdata, MASS, genefilter, methods, fields, utils, lattice, Biobase Suggests: qvalue License: Artistic-2.0 MD5sum: 41bafca51c673429835afbcf60b89454 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: devel git_last_commit: 6068e91 git_last_commit_date: 2023-10-24 Date/Publication: 2024-04-30 source.ver: src/contrib/RNAinteractMAPK_1.41.0.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: 123 Package: RNAmodR.Data Version: 1.19.0 Depends: R (>= 3.6), ExperimentHub, ExperimentHubData (>= 1.9.2) Imports: utils Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, sessioninfo, testthat License: Artistic-2.0 MD5sum: b8b56a5e310771c78f3076d338eaeb02 NeedsCompilation: no Title: Example data for the RNAmodR package Description: RNAmodR.Data contains example data, which is used for vignettes and example workflows in the RNAmodR and dependent packages. biocViews: ExperimentData, SequencingData, RNASeqData Author: Felix G.M. Ernst [aut, cre], Denis L.J. Lafontaine [ctb, fnd] Maintainer: Felix G.M. Ernst URL: https://github.com/FelixErnst/RNAmodR.Data VignetteBuilder: knitr BugReports: https://github.com/FelixErnst/RNAmodR.Data/issues git_url: https://git.bioconductor.org/packages/RNAmodR.Data git_branch: devel git_last_commit: 85abc2f git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RNAmodR.Data_1.19.0.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.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, RNAmodR dependencyCount: 126 Package: RNAseqData.HNRNPC.bam.chr14 Version: 0.43.0 Suggests: GenomicAlignments, BiocManager License: LGPL MD5sum: 30b9e27e4ffa8c8b500d6eb43eb54ced NeedsCompilation: no Title: Aligned reads from RNAseq experiment: Transcription profiling by high throughput sequencing of HNRNPC knockdown and control HeLa cells Description: The package contains 8 BAM files, 1 per sequencing run. Each BAM file was obtained by (1) aligning the reads (paired-end) to the full hg19 genome with TopHat2, and then (2) subsetting to keep only alignments on chr14. See accession number E-MTAB-1147 in the ArrayExpress database for details about the experiment, including links to the published study (by Zarnack et al., 2012) and to the FASTQ files. biocViews: ExperimentData, Genome, Homo_sapiens_Data, SequencingData, GEO, NCI, RNASeqData, ArrayExpress Author: Hervé Pagès Maintainer: Hervé Pagès URL: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1147/ git_url: https://git.bioconductor.org/packages/RNAseqData.HNRNPC.bam.chr14 git_branch: devel git_last_commit: 0c3ffaa git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RNAseqData.HNRNPC.bam.chr14_0.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: sequencing suggestsMe: BiocParallel, GenomicAlignments, GenomicFiles, GenomicRanges, Rsamtools, SplicingGraphs, roar dependencyCount: 0 Package: RnaSeqSampleSizeData Version: 1.37.0 Depends: edgeR,R (>= 2.10) Suggests: BiocStyle, knitr License: GPL (>= 2) MD5sum: de5230a8c044560a77804652cfd3f0ba NeedsCompilation: no Title: RnaSeqSampleSizeData Description: RnaSeqSampleSizeData package provides the read counts and dispersion distribution from real RNA-seq experiments. It can be used by RnaSeqSampleSize package to estimate sample size and power for RNA-seq experiment design. biocViews: ExperimentData, CancerData, RNASeqData Author: Shilin Zhao, Chung-I Li, Yan Guo, Quanhu Sheng, Yu Shyr Maintainer: Shilin Zhao VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RnaSeqSampleSizeData git_branch: devel git_last_commit: 03dd535 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RnaSeqSampleSizeData_1.37.0.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: 12 Package: RnBeads.hg19 Version: 1.37.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: f9b7b48ff0ae34a6c25b256927177ff6 NeedsCompilation: no Title: RnBeads.hg19 Description: Automatically generated RnBeads annotation package for the assembly hg19. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.hg19 git_branch: devel git_last_commit: 5b0fba7 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RnBeads.hg19_1.37.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: MAGAR suggestsMe: RnBeads dependencyCount: 23 Package: RnBeads.hg38 Version: 1.37.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: dbc8abc238802488228d42ee47c39845 NeedsCompilation: no Title: RnBeads.hg38 Description: RnBeads annotation package for genome assembly hg38. Author: RnBeads Team Maintainer: RnBeads Team git_url: https://git.bioconductor.org/packages/RnBeads.hg38 git_branch: devel git_last_commit: d13df70 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RnBeads.hg38_1.37.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: MAGAR suggestsMe: RnBeads dependencyCount: 23 Package: RnBeads.mm10 Version: 2.13.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 02ec8ed839f80424525cf5b901003d80 NeedsCompilation: no Title: RnBeads.mm10 Description: Automatically generated RnBeads annotation package for the assembly mm10. Author: RnBeads Team Maintainer: RnBeads Team git_url: https://git.bioconductor.org/packages/RnBeads.mm10 git_branch: devel git_last_commit: a6abf5e git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RnBeads.mm10_2.13.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 23 Package: RnBeads.mm9 Version: 1.37.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: b2792271e318d6e1266530d1bda1f8bb NeedsCompilation: no Title: RnBeads.mm9 Description: Automatically generated RnBeads annotation package for the assembly mm9. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.mm9 git_branch: devel git_last_commit: 049e067 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RnBeads.mm9_1.37.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RnBeads dependencyCount: 23 Package: RnBeads.rn5 Version: 1.37.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 1a0d2ef8fe210fa2e2c7826ddad8e8c2 NeedsCompilation: no Title: RnBeads.rn5 Description: Automatically generated RnBeads annotation package for the assembly rn5. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.rn5 git_branch: devel git_last_commit: 72768d3 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RnBeads.rn5_1.37.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 23 Package: RRBSdata Version: 1.25.0 Depends: R (>= 3.5.0), BiSeq (>= 1.9.2) License: LGPL-3 MD5sum: 101b70e19fab0129e6e4a44cea0034dc NeedsCompilation: no Title: An RRBS data set with 12 samples and 10,000 simulated DMRs Description: RRBS data set comprising 12 samples with simulated differentially methylated regions (DMRs). biocViews: ExperimentData, CancerData, SequencingData, CpGIslandData Author: Katja Hebestreit, Hans-Ulrich Klein Maintainer: Katja Hebestreit git_url: https://git.bioconductor.org/packages/RRBSdata git_branch: devel git_last_commit: cb02630 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RRBSdata_1.25.0.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: 92 Package: rRDPData Version: 1.25.0 Depends: rRDP License: GPL-2 MD5sum: ea81387f08f7c967897bd61f4752b53e NeedsCompilation: no Title: Databases for the Default RDP Classifier Description: The package provides the data for the RDP Classifier 2.14 released in August 2023. It contains the latest bacterial and archaeal taxonomy training set No. 19 as described in Wang Q, Cole JR. 2024. Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification. Microbiol Resour Announc 0:e01063-23. biocViews: SequencingData, MicrobiomeData, RNASeqData Author: Michael Hahsler [aut, cre] (), Nagar Anurag [aut] Maintainer: Michael Hahsler URL: https://github.com/mhahsler/rRDP git_url: https://git.bioconductor.org/packages/rRDPData git_branch: devel git_last_commit: 9f2042f git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/rRDPData_1.25.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: rRDP dependencyCount: 27 Package: RTCGA.clinical Version: 20151101.35.0 Depends: R (>= 3.2.0), RTCGA Suggests: rmarkdown, knitr License: GPL-2 MD5sum: 94264cd0c0d249b36e5532c29f1e7952 NeedsCompilation: no Title: Clinical datasets from The Cancer Genome Atlas Project Description: Package provides clinical datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Clinical data format is explained here https://wiki.nci.nih.gov/display/TCGA/Clinical+Data+Overview. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.clinical git_branch: devel git_last_commit: eda1a4a git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RTCGA.clinical_20151101.35.0.tar.gz vignettes: vignettes/RTCGA.clinical/inst/doc/downloading_clinical_datasets.html vignetteTitles: Using RTCGA to download clinical data as included in RTCGA.clinical hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.clinical/inst/doc/downloading_clinical_datasets.R suggestsMe: RTCGA, TDbasedUFEadv dependencyCount: 124 Package: RTCGA.CNV Version: 1.33.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: d6b94ebb08ba593868aea05a1de2026b NeedsCompilation: no Title: CNV (Copy-number variation) datasets from The Cancer Genome Atlas Project Description: Package provides CNV (based on Merge snp) datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Retrieving +Data+Using+the+Data+Matrix. Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Przemyslaw Biecek Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.CNV git_branch: devel git_last_commit: f115754 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RTCGA.CNV_1.33.0.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: 124 Package: RTCGA.methylation Version: 1.33.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: f24a26d60cf1af6453606f4f44f43e04 NeedsCompilation: no Title: Methylation datasets from The Cancer Genome Atlas Project Description: Package provides methylation (humanmethylation27) datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/DNA+methylation Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Marcin Kosinski [aut, cre], Witold Chodor [aut] Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.methylation git_branch: devel git_last_commit: d0bf5ae git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RTCGA.methylation_1.33.0.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: 124 Package: RTCGA.miRNASeq Version: 1.33.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 8e8b68a467c7057847396c93f0989e1a NeedsCompilation: no Title: miRNASeq datasets from The Cancer Genome Atlas Project Description: Package provides miRNASeq datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/miRNASeq#miRNASeq-DataOverview Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.miRNASeq git_branch: devel git_last_commit: b4b2e2a git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RTCGA.miRNASeq_1.33.0.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: 124 Package: RTCGA.mRNA Version: 1.33.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 6188038fe2a00122fed3bdfefa9b444b NeedsCompilation: no Title: mRNA datasets from The Cancer Genome Atlas Project Description: Package provides mRNA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Gene+expression+data Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.mRNA git_branch: devel git_last_commit: cecd9cc git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RTCGA.mRNA_1.33.0.tar.gz vignettes: vignettes/RTCGA.mRNA/inst/doc/downloading_mRNA_datasets.html vignetteTitles: Using RTCGA to download mRNA data as included in RTCGA.mRNA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.mRNA/inst/doc/downloading_mRNA_datasets.R suggestsMe: RTCGA dependencyCount: 124 Package: RTCGA.mutations Version: 20151101.35.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 9897a74aea252a93cbae709d8eee743a NeedsCompilation: no Title: Mutations datasets from The Cancer Genome Atlas Project Description: Package provides mutations datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Mutations data format is explained here https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+(MAF)+Specification. There is extra one column with patients' barcodes. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.mutations git_branch: devel git_last_commit: 0dcb53b git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RTCGA.mutations_20151101.35.0.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: 124 Package: RTCGA.PANCAN12 Version: 1.33.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: c90c6808f93920c2438583cdf5486cf8 NeedsCompilation: no Title: PanCan 12 from Genome Cancer Browser Description: Package provides clinical, expression, cnv and mutation data from Genome Cancer Browser. biocViews: AnnotationData Author: Przemyslaw Biecek Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.PANCAN12 git_branch: devel git_last_commit: 263359a git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RTCGA.PANCAN12_1.33.0.tar.gz vignettes: vignettes/RTCGA.PANCAN12/inst/doc/pancan12.html vignetteTitles: Using RTCGA.PANCAN12 to compare time to death hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.PANCAN12/inst/doc/pancan12.R suggestsMe: GOpro dependencyCount: 124 Package: RTCGA.rnaseq Version: 20151101.35.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 3e0701a16e8636ed962f933f471aa2e5 NeedsCompilation: no Title: Rna-seq datasets from The Cancer Genome Atlas Project Description: Package provides rna-seq datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Rna-seq data format is explained here https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2. Data source is illumina hiseq Level 3 RSEM normalized expression data. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.rnaseq git_branch: devel git_last_commit: 28611cc git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RTCGA.rnaseq_20151101.35.0.tar.gz vignettes: vignettes/RTCGA.rnaseq/inst/doc/downloading_rnaseq_datasets.html vignetteTitles: Using RTCGA to download RNAseq data as included in RTCGA.rnaseq hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.rnaseq/inst/doc/downloading_rnaseq_datasets.R suggestsMe: RTCGA, TDbasedUFEadv, FSelectorRcpp dependencyCount: 124 Package: RTCGA.RPPA Version: 1.33.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 792f3b0491b80379b8a053a673d84db3 NeedsCompilation: no Title: RPPA datasets from The Cancer Genome Atlas Project Description: Package provides RPPA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Protein+Array +Data+Format+Specification?src=search biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.RPPA git_branch: devel git_last_commit: caebd8e git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RTCGA.RPPA_1.33.0.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: 124 Package: RUVnormalizeData Version: 1.25.0 Depends: R (>= 2.10.0), Biobase License: GPL-3 MD5sum: fe09e6af327073ba7e19f58725413287 NeedsCompilation: no Title: Gender data for the RUVnormalize package Description: Microarray gene expression data from the study of Vawter et al., 2004. biocViews: MicroarrayData Author: Laurent Jacob Maintainer: Laurent Jacob git_url: https://git.bioconductor.org/packages/RUVnormalizeData git_branch: devel git_last_commit: acfe295 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/RUVnormalizeData_1.25.0.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: 6 Package: sampleClassifierData Version: 1.29.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: BiocStyle License: Artistic-2.0 MD5sum: ce42443b6d5dd579a4db3cf70e628eeb NeedsCompilation: no Title: Pre-processed data for use with the sampleClassifier package Description: This package contains two microarray and two RNA-seq datasets that have been preprocessed for use with the sampleClassifier package. The RNA-seq data are derived from Fagerberg et al. (2014) and the Illumina Body Map 2.0 data. The microarray data are derived from Roth et al. (2006) and Ge et al. (2005). biocViews: ExperimentData, ExpressionData, MicroarrayData, SequencingData, RNASeqData, ArrayExpress Author: Khadija El Amrani Maintainer: Khadija El Amrani git_url: https://git.bioconductor.org/packages/sampleClassifierData git_branch: devel git_last_commit: e9632f9 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/sampleClassifierData_1.29.0.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: 36 Package: SBGNview.data Version: 1.19.0 Depends: R (>= 3.6) Imports: knitr, rmarkdown, bookdown Suggests: SummarizedExperiment License: AGPL-3 MD5sum: f22a8457ce9c87391314485e68f78d2f NeedsCompilation: no Title: Supporting datasets for SBGNview package Description: This package contains: 1. A microarray gene expression dataset from a human breast cancer study. 2. A RNA-Seq gene expression dataset from a mouse study on IFNG knockout. 3. ID mapping tables between gene IDs and SBGN-ML file glyph IDs. 4. Percent of orthologs detected in other species of the genes in a pathway. Cutoffs of this percentage for defining if a pathway exists in another species. 5. XML text of SBGN-ML files for all pre-collected pathways. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO, RNASeqData Author: Xiaoxi Dong*, Kovidh Vegesna*, Weijun Luo Maintainer: Weijun Luo VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/SBGNview.data git_branch: devel git_last_commit: 641918b git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/SBGNview.data_1.19.0.tar.gz vignettes: vignettes/SBGNview.data/inst/doc/SBGNview.data.vignette.html vignetteTitles: Supporting Datasets for SBGNview Package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SBGNview.data/inst/doc/SBGNview.data.vignette.R dependsOnMe: SBGNview dependencyCount: 32 Package: scaeData Version: 1.1.1 Depends: R (>= 4.4.0) Imports: ExperimentHub Suggests: knitr, rmarkdown, markdown, SingleCellAlleleExperiment, Matrix, BiocStyle License: MIT + file LICENSE MD5sum: 59c8dad44acbb105246b06fecd30249e NeedsCompilation: no Title: Data Package for SingleCellAlleleExperiment Description: Contains default datasets used by the Bioconductor package SingleCellAlleleExperiment. The raw FASTQ files were sourced from publicly accessible datasets provided by 10x Genomics. Subsequently, our scIGD snakemake workflow was employed to process these FASTQ files. The resulting output from scIGD constitutes to the contents of this data package. biocViews: ExperimentHub, ExperimentData, Homo_sapiens_Data, SingleCellData Author: Ahmad Al Ajami [aut, cre] (), Jonas Schuck [aut] (), Federico Marini [aut] (), Katharina Imkeller [aut] () Maintainer: Ahmad Al Ajami URL: https://github.com/AGImkeller/scaeData VignetteBuilder: knitr BugReports: https://github.com/AGImkeller/scIGD/issues git_url: https://git.bioconductor.org/packages/scaeData git_branch: devel git_last_commit: 039d55a git_last_commit_date: 2024-05-02 Date/Publication: 2024-05-02 source.ver: src/contrib/scaeData_1.1.1.tar.gz vignettes: vignettes/scaeData/inst/doc/scaeData.html vignetteTitles: scaeData User Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/scaeData/inst/doc/scaeData.R suggestsMe: SingleCellAlleleExperiment dependencyCount: 67 Package: scanMiRData Version: 1.11.0 Depends: R (>= 4.0) Imports: scanMiR, utils Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 0a27914edeaa120316d470397ff3e778 NeedsCompilation: no Title: miRNA Affinity models for the scanMiR package Description: This package contains companion data to the scanMiR package. It contains `KdModel` (miRNA 12-mer binding affinity models) collections corresponding to all human, mouse and rat mirbase miRNAs. See the scanMiR package for details. biocViews: miRNAData, ExperimentData, Homo_sapiens_Data, Mus_musculus_Data, Rattus_norvegicus_Data Author: Pierre-Luc Germain [cre, aut] (), Michael Soutschek [aut], Fridolin Gross [aut] Maintainer: Pierre-Luc Germain VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/scanMiRData git_branch: devel git_last_commit: 4bb67d3 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/scanMiRData_1.11.0.tar.gz vignettes: vignettes/scanMiRData/inst/doc/scanMiRData.html vignetteTitles: scanMiRData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scanMiRData/inst/doc/scanMiRData.R importsMe: scanMiRApp dependencyCount: 71 Package: scATAC.Explorer Version: 1.11.0 Depends: R (>= 4.1), SingleCellExperiment, BiocFileCache, data.table, utils, S4Vectors Imports: methods, Matrix Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 0c8c6db26a225cdec5ee83c4119d37e1 NeedsCompilation: no Title: A Collection of Single-cell ATAC Sequencing Datasets and Corresponding Metadata Description: This package provides a tool to search and download a collection of publicly available single cell ATAC-seq datasets and their metadata. scATAC-Explorer aims to act as a single point of entry for users looking to study single cell ATAC-seq data. Users can quickly search available datasets using the metadata table and download datasets of interest for immediate analysis within R. biocViews: SingleCellData, SequencingData, ExpressionData, GEO, Tissue, Genome, PackageTypeData Author: Arrian Gibson-Khademi [aut, cre], Erik Christensen [aut], Parisa Shooshtari [aut] Maintainer: Arrian Gibson-Khademi VignetteBuilder: knitr BugReports: https://github.com/shooshtarilab/scATACseq/issues git_url: https://git.bioconductor.org/packages/scATAC.Explorer git_branch: devel git_last_commit: 223d242 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/scATAC.Explorer_1.11.0.tar.gz vignettes: vignettes/scATAC.Explorer/inst/doc/scATAC.Explorer.html vignetteTitles: scATAC.Explorer hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scATAC.Explorer/inst/doc/scATAC.Explorer.R dependencyCount: 70 Package: SCLCBam Version: 1.37.0 Depends: R(>= 2.10) Suggests: BiocStyle License: GPL-2 MD5sum: 8d481bf714a5dc8f8b97d5163023a316 NeedsCompilation: no Title: Sequence data from chromosome 4 of a small-cell lung tumor Description: Whole-exome sequencing data from a murine small-cell lung tumor; only contains data of chromosome 4. biocViews: SequencingData, LungCancerData Author: Thomas Kuilman Maintainer: Oscar Krijgsman git_url: https://git.bioconductor.org/packages/SCLCBam git_branch: devel git_last_commit: a9016dd git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/SCLCBam_1.37.0.tar.gz vignettes: vignettes/SCLCBam/inst/doc/SCLCBam.pdf vignetteTitles: SCLCBam hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SCLCBam/inst/doc/SCLCBam.R dependencyCount: 0 Package: scMultiome Version: 1.5.0 Depends: AnnotationHub, ExperimentHub (>= 2.8.1), MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment Imports: AzureStor, DelayedArray, GenomicRanges, HDF5Array, S4Vectors, checkmate, methods, rhdf5 Suggests: BiocGenerics, IRanges, Matrix, knitr, rmarkdown, rstudioapi, testthat (>= 3.0.0), devtools, BiocStyle, ExperimentHubData License: CC BY-SA 4.0 MD5sum: 716de1cde6d73df1e4ec03d62255e6bf NeedsCompilation: no Title: Collection of Public Single-Cell Multiome (scATAC + scRNAseq) Datasets Description: Single cell multiome data, containing chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) information analyzed with the ArchR package and presented as MultiAssayExperiment objects. biocViews: PackageTypeData, ExperimentHub, SingleCellData, ExpressionData, SequencingData, Homo_sapiens_Data, CellCulture, Tissue, GEO Author: Xiaosai Yao [cre, aut] (), Aleksander Chlebowski [aut], Aaron Lun [aut], Shiqi Xie [ctb], Tomasz Włodarczyk [aut] Maintainer: Xiaosai Yao VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/scMultiome git_branch: devel git_last_commit: c30ef4a git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/scMultiome_1.5.0.tar.gz vignettes: vignettes/scMultiome/inst/doc/scMultiome.html vignetteTitles: scMultiome tutorial hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scMultiome/inst/doc/scMultiome.R importsMe: epiregulon suggestsMe: epiregulon.extra dependencyCount: 95 Package: scpdata Version: 1.13.0 Depends: R (>= 4.2.0), QFeatures, ExperimentHub Imports: utils, AnnotationHub, SingleCellExperiment, S4Vectors Suggests: scp, magrittr, dplyr, knitr, BiocStyle, BiocCheck, rmarkdown, testthat License: GPL-2 MD5sum: 9a026357adcb402892f64764ad09a6a6 NeedsCompilation: no Title: Single-Cell Proteomics Data Package Description: The package disseminates mass spectrometry (MS)-based single-cell proteomics (SCP) datasets. The data were collected from published work and formatted using the `scp` data structure. The data sets contain quantitative information at spectrum, peptide and/or protein level for single cells or minute sample amounts. biocViews: ExperimentData, ExpressionData, ExperimentHub, ReproducibleResearch, MassSpectrometryData, Proteome, SingleCellData, PackageTypeData Author: Christophe Vanderaa [aut, cre] (), Laurent Gatto [aut] (), Enes Ayar [dtc] (), Samuel Grégoire [dtc] () Maintainer: Christophe Vanderaa VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/scpdata git_branch: devel git_last_commit: 5c8b368 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/scpdata_1.13.0.tar.gz vignettes: vignettes/scpdata/inst/doc/contribution_guidelines.html, vignettes/scpdata/inst/doc/scpdata.html vignetteTitles: Contribution guidelines, Data Package for Single Cell Proteomics hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scpdata/inst/doc/contribution_guidelines.R, vignettes/scpdata/inst/doc/scpdata.R suggestsMe: scp dependencyCount: 126 Package: scRNAseq Version: 2.19.0 Depends: SingleCellExperiment Imports: utils, methods, Matrix, BiocGenerics, S4Vectors, SparseArray, DelayedArray, GenomicRanges, SummarizedExperiment, ExperimentHub (>= 2.3.4), AnnotationHub (>= 3.3.6), AnnotationDbi, ensembldb, GenomicFeatures, alabaster.base, alabaster.matrix, alabaster.sce, gypsum, jsonlite, DBI, RSQLite Suggests: BiocStyle, knitr, rmarkdown, testthat, jsonvalidate, BiocManager License: CC0 MD5sum: b0ff0917d714199d3e0ab6cd7dcb77d5 NeedsCompilation: no Title: Collection of Public Single-Cell RNA-Seq Datasets Description: Gene-level counts for a collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata. biocViews: ExperimentHub, ExperimentData, ExpressionData, SequencingData, RNASeqData, SingleCellData Author: Davide Risso [aut, cph], Michael Cole [aut], Aaron Lun [ctb, cre], Alan O'Callaghan [ctb], Jens Preussner [ctb], Charlotte Soneson [ctb], Stephany Orjuela [ctb], Daniel Bunis [ctb], Milan Malfait [ctb] Maintainer: Aaron Lun VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/scRNAseq git_branch: devel git_last_commit: f7f1f70 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/scRNAseq_2.19.0.tar.gz vignettes: vignettes/scRNAseq/inst/doc/scRNAseq.html vignetteTitles: User's Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scRNAseq/inst/doc/scRNAseq.R dependsOnMe: OSCA.advanced, OSCA.basic, OSCA.intro, OSCA.workflows, SingleRBook importsMe: singleCellTK suggestsMe: APL, BASiCS, ClusterFoldSimilarity, Glimma, SingleCellExperiment, SingleR, UCell, batchelor, bluster, ccImpute, destiny, dittoSeq, iSEE, iSEEfier, iSEEhex, iSEEu, miQC, miloR, mumosa, scAnnotatR, scDblFinder, scFeatureFilter, scTreeViz, scater, scone, scran, scuttle, velociraptor, zellkonverter, zinbwave dependencyCount: 118 Package: scTHI.data Version: 1.17.0 Depends: R (>= 4.0) License: GPL-2 MD5sum: 7cf45efa258e60711492b1f3ca2b760d NeedsCompilation: no Title: The package contains examples of single cell data used in vignettes and examples of the scTHI package; data contain both tumor cells and immune cells from public dataset of glioma Description: Data for the vignette and tutorial of the package scTHI. biocViews: ExperimentData, SingleCellData Author: Francesca Pia Caruso [aut], Michele Ceccarelli [aut, cre] Maintainer: Michele Ceccarelli git_url: https://git.bioconductor.org/packages/scTHI.data git_branch: devel git_last_commit: b6a98fd git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/scTHI.data_1.17.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: scTHI dependencyCount: 0 Package: seq2pathway.data Version: 1.37.0 Depends: R (>= 3.6.2) License: GPL (>= 2) MD5sum: 8da6e2940ac391fb2575d75484836892 NeedsCompilation: no Title: data set for R package seq2pathway Description: Supporting data for the seq2patheway package. Includes modified gene sets from MsigDB and org.Hs.eg.db; gene locus definitions from GENCODE project. biocViews: ExperimentData Author: Bin Wang Maintainer: Arjun Kinstlick git_url: https://git.bioconductor.org/packages/seq2pathway.data git_branch: devel git_last_commit: 9a44316 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/seq2pathway.data_1.37.0.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: 1.39.0 Depends: R (>= 2.10) Imports: utils, Biobase License: GPL-3 MD5sum: 67a52257d19f0d68ff3167acd31d8222 NeedsCompilation: no Title: RNA-seq data generated from SEQC (MAQC-III) study Description: The SEQC/MAQC-III Consortium has produced benchmark RNA-seq data for the assessment of RNA sequencing technologies and data analysis methods (Nat Biotechnol, 2014). Billions of sequence reads have been generated from ten different sequencing sites. This package contains the summarized read count data for ~2000 sequencing libraries. It also includes all the exon-exon junctions discovered from the study. TaqMan RT-PCR data for ~1000 genes and ERCC spike-in sequence data are included in this package as well. biocViews: ExperimentData, RNASeqData, qPCRData, SequencingData Author: Yang Liao and Wei Shi with contributions from Gordon K Smyth and Steve Lianoglou. Maintainer: Yang Liao and Wei Shi URL: http://bioconductor.org/packages/release/data/experiment/html/seqc.html git_url: https://git.bioconductor.org/packages/seqc git_branch: devel git_last_commit: 6044d71 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/seqc_1.39.0.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: 6 Package: serumStimulation Version: 1.41.0 Depends: R (>= 2.10) License: GPL (>= 2) MD5sum: aed322171ba9125a56a7e539b86196a3 NeedsCompilation: no Title: serumStimulation is a data package which is used by examples in package pcaGoPromoter Description: Contains 13 micro array data results from a serum stimulation experiment biocViews: ExperimentData, MicroarrayData Author: Morten Hansen Maintainer: Morten Hansen, git_url: https://git.bioconductor.org/packages/serumStimulation git_branch: devel git_last_commit: 89ca15c git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/serumStimulation_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: sesameData Version: 1.23.0 Depends: R (>= 4.2.0), ExperimentHub, AnnotationHub Imports: utils, readr, stringr, GenomicRanges, S4Vectors, IRanges, GenomeInfoDb Suggests: BiocGenerics, sesame, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: 25ca345015427734efedd9882052a37b 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 URL: https://github.com/zwdzwd/sesame VignetteBuilder: knitr BugReports: https://github.com/zwdzwd/sesame/issue git_url: https://git.bioconductor.org/packages/sesameData git_branch: devel git_last_commit: 76fdafc git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/sesameData_1.23.0.tar.gz vignettes: vignettes/sesameData/inst/doc/sesameData.html vignetteTitles: sesameData User Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/sesameData/inst/doc/sesameData.R dependsOnMe: sesame importsMe: MethReg, knowYourCG, CytoMethIC suggestsMe: ELMER, iNETgrate dependencyCount: 75 Package: seventyGeneData Version: 1.41.0 Depends: R (>= 2.13.0) Suggests: Biobase, limma, breastCancerNKI, knitr, rmarkdown, readxl, BiocStyle License: Artistic-2.0 MD5sum: 07c23c4a2361a7834970a734f6de1da4 NeedsCompilation: no Title: ExpressionSets from the van't Veer and Van de Vijver breast cancer studies Description: Gene expression data for the two breast cancer cohorts published by van't Veer and Van de Vijver in 2002. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData Author: Luigi Marchionni [aut, cre] (), Claudio Zanettini [aut, ctb], Lucio Queiroz [aut, ctb] () Maintainer: Luigi Marchionni URL: https://bioconductor.org/packages/release/data/experiment/html/seventyGeneData.html VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/seventyGeneData git_branch: devel git_last_commit: 3828130 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/seventyGeneData_1.41.0.tar.gz vignettes: vignettes/seventyGeneData/inst/doc/seventyGeneData.html vignetteTitles: 1. Working with the seventyGeneData package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/seventyGeneData/inst/doc/seventyGeneData.R dependencyCount: 0 Package: SFEData Version: 1.7.0 Imports: BiocFileCache, AnnotationHub, ExperimentHub, utils Suggests: BiocStyle, knitr, rmarkdown, SeuratObject, SpatialFeatureExperiment, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: a50b1fab1160abe4705f08e1aad5431e NeedsCompilation: no Title: Example SpatialFeatureExperiment datasets Description: Example spatial transcriptomics datasets with Simple Feature annotations as SpatialFeatureExperiment objects. Technologies include Visium, slide-seq, Nanostring CoxMX, Vizgen MERFISH, and 10X Xenium. Tissues include mouse skeletal muscle, human melanoma metastasis, human lung, breast cancer, and mouse liver. biocViews: ExperimentHub, ExpressionData, Mus_musculus_Data, Homo_sapiens_Data, SpatialData, Tissue, SingleCellData Author: Lambda Moses [aut, cre] (), Alik Huseynov [aut] (), Kayla Jackson [aut] (), Lior Pachter [aut, ths] () Maintainer: Lambda Moses URL: https://github.com/pachterlab/SFEData VignetteBuilder: knitr BugReports: https://github.com/pachterlab/SFEData/issues git_url: https://git.bioconductor.org/packages/SFEData git_branch: devel git_last_commit: 5077703 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/SFEData_1.7.0.tar.gz vignettes: vignettes/SFEData/inst/doc/SFEData.html vignetteTitles: Example SpatialFeatureExperiment datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SFEData/inst/doc/SFEData.R suggestsMe: SpatialFeatureExperiment, Voyager dependencyCount: 67 Package: shinyMethylData Version: 1.25.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: 19a9e864f2c5f3735273e5c0848b3dc7 NeedsCompilation: no Title: Example dataset of input data for shinyMethyl Description: Extracted data from 369 TCGA Head and Neck Cancer DNA methylation samples. The extracted data serve as an example dataset for the package shinyMethyl. Original samples are from 450k methylation arrays, and were obtained from The Cancer Genome Atlas (TCGA). 310 samples are from tumor, 50 are matched normals and 9 are technical replicates of a control cell line. biocViews: Genome, CancerData Author: Jean-Philippe Fortin [cre, aut], Kasper Daniel Hansen [aut] Maintainer: Jean-Philippe Fortin git_url: https://git.bioconductor.org/packages/shinyMethylData git_branch: devel git_last_commit: dbd8808 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/shinyMethylData_1.25.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: shinyMethyl dependencyCount: 0 Package: signatureSearchData Version: 1.19.0 Depends: R (>= 3.6) Imports: ExperimentHub, utils, affy, limma, Biobase, magrittr, dplyr, R.utils, stats, rhdf5 Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 3df9106ada7b7cc84ba03c8e6f239ac7 NeedsCompilation: no Title: Datasets for signatureSearch package Description: CMAP/LINCS hdf5 databases and other annotations used for signatureSearch software package. biocViews: ExperimentHub, ExperimentData, ExpressionData Author: Yuzhu Duan , Brendan Gongol , Thomas Girke Maintainer: Brendan Gongol VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/signatureSearchData git_branch: devel git_last_commit: e04d777 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/signatureSearchData_1.19.0.tar.gz vignettes: vignettes/signatureSearchData/inst/doc/signatureSearchData.html vignetteTitles: signatureSearchData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/signatureSearchData/inst/doc/signatureSearchData.R importsMe: DFD suggestsMe: signatureSearch dependencyCount: 78 Package: SimBenchData Version: 1.13.0 Depends: ExperimentHub Imports: S4Vectors, utils Suggests: BiocStyle, knitr, rmarkdown, Seurat License: GPL-3 MD5sum: c8310245c0038c6c6cbe61194ceaf30d NeedsCompilation: no Title: SimBenchData: a collection of 35 single-cell RNA-seq data covering a wide range of data characteristics Description: The SimBenchData package contains a total of 35 single-cell RNA-seq datasets covering a wide range of data characteristics, including major sequencing protocols, multiple tissue types, and both human and mouse sources. biocViews: ExperimentHub, ExperimentData, SingleCellData, RNASeqData, Tissue, SequencingData Author: Yue Cao [aut, cre], Pengyi Yang [aut], Jean Yee Hwa Yang [aut] Maintainer: Yue Cao VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/SimBenchData git_branch: devel git_last_commit: 2ee332e git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/SimBenchData_1.13.0.tar.gz vignettes: vignettes/SimBenchData/inst/doc/SimBenchData-vignette.html vignetteTitles: SimBenchData: a collection of single-cell RNA-seq data covering a wide range of data characteristics hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SimBenchData/inst/doc/SimBenchData-vignette.R dependencyCount: 67 Package: simpIntLists Version: 1.41.0 License: GPL (>= 2) MD5sum: 3070d2b65b7bb8e5089129556794c369 NeedsCompilation: no Title: The package contains BioGRID interactions for various organisms in a simple format Description: The package contains BioGRID interactions for arabidopsis(thale cress), c.elegans, fruit fly, human, mouse, yeast( budding yeast ) and S.pombe (fission yeast) . Entrez ids, official names and unique ids can be used to find proteins. The format of interactions are lists. For each gene/protein, there is an entry in the list with "name" containing name of the gene/protein and "interactors" containing the list of genes/proteins interacting with it. biocViews: ExperimentData, Arabidopsis_thaliana_Data Author: Kircicegi Korkmaz, Volkan Atalay, Rengul Cetin-Atalay Maintainer: Kircicegi Korkmaz git_url: https://git.bioconductor.org/packages/simpIntLists git_branch: devel git_last_commit: 053540c git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/simpIntLists_1.41.0.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: 1.33.0 Depends: R (>= 3.5.0) Suggests: DESeq2, GenomicRanges, GenomicFeatures, genefilter, statmod, gdata, RColorBrewer, ggplot2, gplots, cluster, clue, grid, gridExtra, ggbio, Gviz, geneplotter, matrixStats, pheatmap, BiocStyle, knitr, BiocParallel License: LGPL MD5sum: 318383e047c541a1688e2b72cfbed39b NeedsCompilation: no Title: Single Cell Transcriptome Data and Analysis of Mouse mTEC cells Description: This data package contains the code used to analyse the single-cell RNA-seq and the bulk ATAC-seq data from the manuscript titled: Single-cell transcriptome analysis reveals coordinated ectopic-gene expression patterns in medullary thymic epithelial cells. This paper was published in Nature Immunology 16,933-941(2015). The data objects provided in this package has been pre-processed: the raw data files can be downloaded from ArrayExpress under the accession identifiers E-MTAB-3346 and E-MTAB-3624. The vignette of this data package provides a documented and reproducible workflow that includes the code that was used to generate each statistic and figure from the manuscript. biocViews: ExperimentData Author: Alejandro Reyes Maintainer: Alejandro Reyes VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/Single.mTEC.Transcriptomes git_branch: devel git_last_commit: 8f3e682 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/Single.mTEC.Transcriptomes_1.33.0.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: 1.17.3 Depends: R (>= 4.2.0), MultiAssayExperiment Imports: AnnotationHub, BiocBaseUtils, BiocFileCache, ExperimentHub, graphics, HDF5Array, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, Matrix, methods, utils Suggests: BiocStyle, ggplot2, knitr, RaggedExperiment, rmarkdown, scater, scran, UpSetR, uwot License: Artistic-2.0 MD5sum: 2d5b6186dbdf63b40ddd3efcd25d4deb NeedsCompilation: no Title: Integrating Multi-modal Single Cell Experiment datasets Description: SingleCellMultiModal is an ExperimentHub package that serves multiple datasets obtained from GEO and other sources and represents them as MultiAssayExperiment objects. We provide several multi-modal datasets including scNMT, 10X Multiome, seqFISH, CITEseq, SCoPE2, and others. The scope of the package is is to provide data for benchmarking and analysis. To cite, use the 'citation' function and see . biocViews: ExperimentData, SingleCellData, ReproducibleResearch, ExperimentHub, GEO Author: Marcel Ramos [aut, cre] (), Ricard Argelaguet [aut], Al Abadi [ctb], Dario Righelli [aut], Christophe Vanderaa [ctb], Kelly Eckenrode [aut], Ludwig Geistlinger [aut], Levi Waldron [aut] Maintainer: Marcel Ramos VignetteBuilder: knitr BugReports: https://github.com/waldronlab/SingleCellMultiModal/issues git_url: https://git.bioconductor.org/packages/SingleCellMultiModal git_branch: devel git_last_commit: 1ac9a1f git_last_commit_date: 2024-06-18 Date/Publication: 2024-06-20 source.ver: src/contrib/SingleCellMultiModal_1.17.3.tar.gz vignettes: vignettes/SingleCellMultiModal/inst/doc/CITEseq.html, vignettes/SingleCellMultiModal/inst/doc/ECCITEseq.html, vignettes/SingleCellMultiModal/inst/doc/GTseq.html, vignettes/SingleCellMultiModal/inst/doc/scMultiome.html, vignettes/SingleCellMultiModal/inst/doc/scNMT.html, vignettes/SingleCellMultiModal/inst/doc/SCoPE2.html, vignettes/SingleCellMultiModal/inst/doc/seqFISH.html, vignettes/SingleCellMultiModal/inst/doc/SingleCellMultiModal.html vignetteTitles: CITEseq Cord Blood, ECCITEseq Peripheral Blood, GT-seq Mouse Embryo, scMultiome 10x PBMC, scNMT Mouse Gastrulation, SCoPE2: macrophage vs monocytes, seqFISH Mouse Visual Cortex, SingleCellMultiModal Introduction hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SingleCellMultiModal/inst/doc/CITEseq.R, vignettes/SingleCellMultiModal/inst/doc/ECCITEseq.R, vignettes/SingleCellMultiModal/inst/doc/GTseq.R, vignettes/SingleCellMultiModal/inst/doc/scMultiome.R, vignettes/SingleCellMultiModal/inst/doc/scNMT.R, vignettes/SingleCellMultiModal/inst/doc/SCoPE2.R, vignettes/SingleCellMultiModal/inst/doc/seqFISH.R, vignettes/SingleCellMultiModal/inst/doc/SingleCellMultiModal.R suggestsMe: MuData, decontX dependencyCount: 89 Package: SingleMoleculeFootprintingData Version: 1.13.0 Imports: ExperimentHub, utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 35797d79f13abbf42f9346fd38011683 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: devel git_last_commit: cf95b18 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/SingleMoleculeFootprintingData_1.13.0.tar.gz vignettes: vignettes/SingleMoleculeFootprintingData/inst/doc/SingleMoleculeFootprintingData.html vignetteTitles: SingleMoleculeFootprintingData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/SingleMoleculeFootprintingData/inst/doc/SingleMoleculeFootprintingData.R suggestsMe: SingleMoleculeFootprinting dependencyCount: 67 Package: smokingMouse Version: 1.3.0 Suggests: ExperimentHub, AnnotationHubData, BiocStyle, covr, ExperimentHubData, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: f93496676a78283ac634fe95b32c7701 NeedsCompilation: no Title: Provides access to smokingMouse project data Description: This is an ExperimentHub package that provides access to the data at the gene, exon, transcript and junction level used in the analyses of the smokingMouse project. See https://github.com/LieberInstitute/smokingMouse_Indirects. This datasets contain the expression counts of genes, transcripts, exons and exon-exon junctions across 208 mice samples from pup and adult brains and adult blood. They also contain relevant information of these samples and features, such as conditions, QC metrics and if they were used after filtering steps and also if the features were differently expressed in the different experiments. biocViews: ExperimentHub, ExpressionData, Mus_musculus_Data, RNASeqData Author: Daianna Gonzalez-Padilla [aut, cre] () Maintainer: Daianna Gonzalez-Padilla URL: https://github.com/LieberInstitute/smokingMouse VignetteBuilder: knitr BugReports: https://support.bioconductor.org/t/smokingMouse git_url: https://git.bioconductor.org/packages/smokingMouse git_branch: devel git_last_commit: 29d1457 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/smokingMouse_1.3.0.tar.gz vignettes: vignettes/smokingMouse/inst/doc/smokingMouse.html vignetteTitles: Introduction to smokingMouse hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/smokingMouse/inst/doc/smokingMouse.R dependencyCount: 0 Package: SNAData Version: 1.51.0 Depends: R (>= 2.4.0), graph Suggests: Rgraphviz License: LGPL MD5sum: 233ac2bdaaf517fe107e5afca7cae940 NeedsCompilation: no Title: Social Networks Analysis Data Examples Description: Data from Wasserman & Faust (1999) "Social Network Analysis" biocViews: ExperimentData Author: Denise Scholtens Maintainer: Denise Scholtens git_url: https://git.bioconductor.org/packages/SNAData git_branch: devel git_last_commit: bd8c16b git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/SNAData_1.51.0.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: 7 Package: SNAGEEdata Version: 1.41.0 Depends: R (>= 2.6.0) Suggests: ALL, hgu95av2.db, SNAGEE License: Artistic-2.0 MD5sum: 1716ff61ce8f8600c37f90b5fe0df73b NeedsCompilation: no Title: SNAGEE data Description: SNAGEE data - gene list and correlation matrix biocViews: MicroarrayData Author: David Venet Maintainer: David Venet URL: http://fleming.ulb.ac.be/SNAGEE git_url: https://git.bioconductor.org/packages/SNAGEEdata git_branch: devel git_last_commit: 5f2245d git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/SNAGEEdata_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: SNAGEE dependencyCount: 0 Package: SNPhoodData Version: 1.35.0 Depends: R (>= 3.2) Suggests: BiocStyle,knitr,rmarkdown License: LGPL (>= 3) MD5sum: 50527ef2fecb9e5753aa90a78db0855a NeedsCompilation: no Title: Additional and more complex example data for the SNPhood package Description: This companion package for SNPhood provides some example datasets of a larger size than allowed for the SNPhood package. They include full and real-world examples for performing analyses with the SNPhood package. biocViews: ExperimentData Author: Christian Arnold, Judith Zaugg Maintainer: Christian Arnold VignetteBuilder: knitr BugReports: christian.arnold@embl.de git_url: https://git.bioconductor.org/packages/SNPhoodData git_branch: devel git_last_commit: f6d7a91 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/SNPhoodData_1.35.0.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: 1.43.0 Depends: R (>= 2.14) License: Artistic-2.0 MD5sum: 6012998f2635857808c7f67ff31ab8c7 NeedsCompilation: no Title: An example cancer whole genome sequencing data for the SomatiCA package Description: An example cancer whole genome sequencing data for the SomatiCA package biocViews: ExperimentData, Genome, CancerData, SequencingData Author: Mengjie Chen Maintainer: Mengjie Chen git_url: https://git.bioconductor.org/packages/SomatiCAData git_branch: devel git_last_commit: 7239164 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/SomatiCAData_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: SomaticCancerAlterations Version: 1.41.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, IRanges, S4Vectors Suggests: testthat, ggbio, ggplot2, knitr License: GPL-3 MD5sum: 9080e2f5accbddff79583de79ae22372 NeedsCompilation: no Title: Somatic Cancer Alterations Description: Collection of somatic cancer alteration datasets biocViews: ExperimentData, Genome, CancerData, Project1000genomes, NCI Author: Julian Gehring Maintainer: Julian Gehring VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/SomaticCancerAlterations git_branch: devel git_last_commit: 8bec1f2 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/SomaticCancerAlterations_1.41.0.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: 23 Package: SpatialDatasets Version: 1.3.0 Depends: ExperimentHub, SpatialExperiment, Imports: utils Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 97b43fa4f49b3d241a65bc0c16163645 NeedsCompilation: no Title: Collection of spatial omics datasets Description: This is a collection of publically available spatial omics datasets. Where possible we have curated these datasets as either SpatialExperiments, MoleculeExperiments or CytoImageLists and included annotations of the sample characteristics. biocViews: ExperimentData, ExperimentHub, ReproducibleResearch, SingleCellData, SpatialData, Homo_sapiens_Data, Mus_musculus_Data Author: Farhan Ameen [aut], Nick Robertson [aut], Alex Qin [aut], Elijah Willie [aut], Ellis Patrick [aut, cre] Maintainer: Ellis Patrick URL: https://github.com/SydneyBioX/SpatialDatasets VignetteBuilder: knitr BugReports: https://github.com/SydneyBioX/SpatialDatasets/issues git_url: https://git.bioconductor.org/packages/SpatialDatasets git_branch: devel git_last_commit: 146590f git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/SpatialDatasets_1.3.0.tar.gz vignettes: vignettes/SpatialDatasets/inst/doc/SpatialDatasets_overview.html vignetteTitles: The SpatialDataset package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SpatialDatasets/inst/doc/SpatialDatasets_overview.R dependencyCount: 83 Package: spatialDmelxsim Version: 1.11.0 Depends: R (>= 4.1), ExperimentHub, SummarizedExperiment Imports: utils Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: ed7d6f4d2459766c497ae9e661b1d12a NeedsCompilation: no Title: Spatial allelic expression counts for fly cross embryo Description: Spatial allelic expression counts from Combs & Fraser (2018), compiled into a SummarizedExperiment object. This package contains data of allelic expression counts of spatial slices of a fly embryo, a Drosophila melanogaster x Drosophila simulans cross. See the CITATION file for the data source, and the associated script for how the object was constructed from publicly available data. biocViews: ExperimentHub, SequencingData, RNASeqData, ExpressionData, Drosophila_melanogaster_Data, GEO Author: Michael Love [aut, cre] Maintainer: Michael Love URL: https://github.com/mikelove/spatialDmelxsim VignetteBuilder: knitr BugReports: https://github.com/mikelove/spatialDmelxsim/issues git_url: https://git.bioconductor.org/packages/spatialDmelxsim git_branch: devel git_last_commit: 36d040d git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/spatialDmelxsim_1.11.0.tar.gz vignettes: vignettes/spatialDmelxsim/inst/doc/spatialDmelxsim.html vignetteTitles: spatialDmelxsim hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/spatialDmelxsim/inst/doc/spatialDmelxsim.R dependencyCount: 78 Package: spatialLIBD Version: 1.17.2 Depends: SpatialExperiment (>= 1.3.3), R (>= 3.6) Imports: shiny, golem, ggplot2, cowplot, plotly, viridisLite, shinyWidgets, sessioninfo, grid, grDevices, methods, AnnotationHub, utils, png, scater, DT, ExperimentHub, RColorBrewer, SummarizedExperiment, stats, graphics, S4Vectors, IRanges, fields, benchmarkme, SingleCellExperiment, BiocFileCache, jsonlite, tibble, rtracklayer, Matrix, BiocGenerics, GenomicRanges, magick, paletteer, scuttle, edgeR, limma, statmod, MatrixGenerics, rlang Suggests: knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager, lobstr, DropletUtils License: Artistic-2.0 MD5sum: 1f73cd85d92ebb131bc91b562edec7e5 NeedsCompilation: no Title: spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data Description: Inspect interactively the spatially-resolved transcriptomics data from the 10x Genomics Visium platform as well as data from the Maynard, Collado-Torres et al, Nature Neuroscience, 2021 project analyzed by Lieber Institute for Brain Development (LIBD) researchers and collaborators. biocViews: Homo_sapiens_Data, ExperimentHub, SequencingData, SingleCellData, ExpressionData, Tissue, PackageTypeData, SpatialData Author: Leonardo Collado-Torres [aut, cre] (), Kristen R. Maynard [ctb] (), Andrew E. Jaffe [ctb] (), Brenda Pardo [ctb] (), Abby Spangler [ctb] (), Jesús Vélez Santiago [ctb] (), Lukas M. Weber [ctb] (), Louise Huuki-Myers [ctb] (), Nicholas Eagles [ctb] () Maintainer: Leonardo Collado-Torres URL: https://github.com/LieberInstitute/spatialLIBD VignetteBuilder: knitr BugReports: https://support.bioconductor.org/tag/spatialLIBD git_url: https://git.bioconductor.org/packages/spatialLIBD git_branch: devel git_last_commit: e0947a2 git_last_commit_date: 2024-05-24 Date/Publication: 2024-05-28 source.ver: src/contrib/spatialLIBD_1.17.2.tar.gz vignettes: vignettes/spatialLIBD/inst/doc/guide_to_spatial_registration.html, vignettes/spatialLIBD/inst/doc/multi_gene_plots.html, vignettes/spatialLIBD/inst/doc/spatialLIBD.html, vignettes/spatialLIBD/inst/doc/TenX_data_download.html vignetteTitles: Guide to Spatial Registration, Guide to Multi-Gene Plots, Introduction to spatialLIBD, Using spatialLIBD with 10x Genomics public datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/spatialLIBD/inst/doc/guide_to_spatial_registration.R, vignettes/spatialLIBD/inst/doc/multi_gene_plots.R, vignettes/spatialLIBD/inst/doc/spatialLIBD.R, vignettes/spatialLIBD/inst/doc/TenX_data_download.R suggestsMe: Banksy, BayesSpace, DESpace dependencyCount: 202 Package: SpikeIn Version: 1.47.0 Depends: R (>= 2.10), affy (>= 1.23.4) License: Artistic-2.0 MD5sum: 2f66166df2c9bcb513fce571f9882f9f NeedsCompilation: no Title: Affymetrix Spike-In Experiment Data Description: Contains the HGU133 and HGU95 spikein experiment data. biocViews: ExperimentData, MicroarrayData Author: Rafael Irizarry Maintainer: Robert D Shear URL: https://bioconductor.org/packages/SpikeIn BugReports: https://github.com/rafalab/SpikeIn/issues git_url: https://git.bioconductor.org/packages/SpikeIn git_branch: devel git_last_commit: dc75e9b git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/SpikeIn_1.47.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PECA dependencyCount: 12 Package: SpikeInSubset Version: 1.45.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5), affy (>= 1.23.4) License: LGPL MD5sum: 96b7b6d59121cdc4698b726494236ed6 NeedsCompilation: no Title: Part of Affymetrix's Spike-In Experiment Data Description: Includes probe-level and expression data for the HGU133 and HGU95 spike-in experiments biocViews: ExperimentData, MicroarrayData Author: Rafael Irizarry and Zhijin Wu Maintainer: Robert D Shear URL: https://bioconductor.org/packages/SpikeInSubset BugReports: https://github.com/rafalab/SpikeInSubset/issues git_url: https://git.bioconductor.org/packages/SpikeInSubset git_branch: devel git_last_commit: 09a987f git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/SpikeInSubset_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 12 Package: spqnData Version: 1.17.0 Depends: R (>= 4.0), SummarizedExperiment License: Artistic-2.0 MD5sum: 374374d1af61223af459a1a5f2ead1b5 NeedsCompilation: no Title: Data for the spqn package Description: Bulk RNA-seq from GTEx on 4,000 randomly selected, expressed genes. Data has been processed for co-expression analysis. biocViews: Homo_sapiens_Data, ExpressionData, Tissue, RNASeqData Author: Yi Wang [cre, aut], Kasper Daniel Hansen [aut] Maintainer: Yi Wang git_url: https://git.bioconductor.org/packages/spqnData git_branch: devel git_last_commit: f809fa2 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/spqnData_1.17.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: spqn dependencyCount: 36 Package: stemHypoxia Version: 1.41.0 Depends: R (>= 2.14.1) License: GPL (>=2) MD5sum: ca8e6d021a61b883ae8cddbf183d9440 NeedsCompilation: no Title: Differentiation of Human Embryonic Stem Cells under Hypoxia gene expression dataset by Prado-Lopez et al. (2010) Description: Expression profiling using microarray technology to prove if 'Hypoxia Promotes Efficient Differentiation of Human Embryonic Stem Cells to Functional Endothelium' by Prado-Lopez et al. (2010) Stem Cells 28:407-418. Full data available at Gene Expression Omnibus series GSE37761. biocViews: ExperimentData, Tissue, StemCell, Homo_sapiens_Data, CancerData, MicroarrayData, TissueMicroarrayData, GEO Author: Cristobal Fresno and Elmer A. Fernandez Maintainer: Cristobal Fresno URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37761, http://onlinelibrary.wiley.com/doi/10.1002/stem.295/abstract git_url: https://git.bioconductor.org/packages/stemHypoxia git_branch: devel git_last_commit: eb92fce git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/stemHypoxia_1.41.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: lmdme dependencyCount: 0 Package: STexampleData Version: 1.13.3 Depends: ExperimentHub, SingleCellExperiment, SpatialExperiment Imports: utils Suggests: BiocStyle, knitr, rmarkdown, BumpyMatrix, HDF5Array License: MIT + file LICENSE MD5sum: 2227ea68b2f8de48a9889178ffcdec04 NeedsCompilation: no Title: Collection of spatial transcriptomics datasets in SpatialExperiment Bioconductor format Description: Collection of spatial transcriptomics datasets stored in SpatialExperiment Bioconductor format, for use in examples, demonstrations, and tutorials. The datasets are from several different platforms and have been sourced from various publicly available sources. Several datasets include images and/or reference annotation labels. biocViews: ExperimentData, ExperimentHub, ReproducibleResearch, ExpressionData, SingleCellData, SpatialData, Homo_sapiens_Data, Mus_musculus_Data Author: Lukas M. Weber [aut, cre] (), Yixing E. Dong [aut] () Maintainer: Lukas M. Weber URL: https://github.com/lmweber/STexampleData VignetteBuilder: knitr BugReports: https://github.com/lmweber/STexampleData/issues git_url: https://git.bioconductor.org/packages/STexampleData git_branch: devel git_last_commit: 463a2b1 git_last_commit_date: 2024-05-17 Date/Publication: 2024-05-21 source.ver: src/contrib/STexampleData_1.13.3.tar.gz vignettes: vignettes/STexampleData/inst/doc/STexampleData_overview.html vignetteTitles: STexampleData overview hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/STexampleData/inst/doc/STexampleData_overview.R suggestsMe: SpotSweeper, escheR, ggsc, ggspavis, nnSVG, smoothclust, spoon, tpSVG dependencyCount: 83 Package: SubcellularSpatialData Version: 1.1.0 Depends: R (>= 4.4) Imports: dplyr, hexbin, Matrix, SpatialExperiment, stats Suggests: BiocStyle, ExperimentHub, ggplot2, knitr, prettydoc, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: 81402cdf50462c67acb0ddd2cb712fc5 NeedsCompilation: no Title: Annotated spatial transcriptomics datasets from 10x Xenium, NanoString CosMx and BGI STOmics. Description: This is a data package that hosts annotated sub-cellular localised datasets from the STOmics, Xenium and CosMx platforms. Specifically, it hosts datasets analysed in the publication Bhuva et. al, 2024 titled "Library size confounds biology in spatial transcriptomics data". Raw transcript detections are hosted and functions to convert them to SpatialExperiment objects have been implemented. biocViews: ExperimentHub, SpatialData, Homo_sapiens_Data, Mus_musculus_Data, LungCancerData Author: Dharmesh D. Bhuva [aut, cre] () Maintainer: Dharmesh D. Bhuva URL: https://davislaboratory.github.io/SubcellularSpatialData VignetteBuilder: knitr BugReports: https://github.com/DavisLaboratory/SubcellularSpatialData/issues git_url: https://git.bioconductor.org/packages/SubcellularSpatialData git_branch: devel git_last_commit: 300308b git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/SubcellularSpatialData_1.1.0.tar.gz vignettes: vignettes/SubcellularSpatialData/inst/doc/SubcellularSpatialData.html vignetteTitles: SubcellularSpatialData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SubcellularSpatialData/inst/doc/SubcellularSpatialData.R dependencyCount: 74 Package: SVM2CRMdata Version: 1.37.0 Depends: R(>= 3.2.0) License: LGPL (>= 2) MD5sum: ce295652f3f4f1c08b3b3ae2bdf2e9aa NeedsCompilation: no Title: An example dataset for use with the SVM2CRM package Description: An example dataset for use with the SVM2CRM package. biocViews: ExperimentData, ChIPSeq, HistoneModification, Preprocessing, DataImport Author: Guidantonio Malagoli Tagliazucchi Maintainer: Guidantonio Malagoli Tagliazucchi git_url: https://git.bioconductor.org/packages/SVM2CRMdata git_branch: devel git_last_commit: 32e1bce git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/SVM2CRMdata_1.37.0.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: 1.43.0 Depends: R (>= 2.10), synapter (>= 1.99.2) Imports: utils License: GPL-2 MD5sum: e3da11a739230c7874feb2ea54755e2f NeedsCompilation: no Title: Data accompanying the synapter package Description: Data independant acquisition of UPS1 protein mix in an E. coli background obtained on a Waters Synapt G2 instrument. biocViews: ExperimentData, MassSpectrometryData Author: Laurent Gatto, Sebastian Gibb and Pavel V. Shliaha Maintainer: Laurent Gatto git_url: https://git.bioconductor.org/packages/synapterdata git_branch: devel git_last_commit: 0f9cf4e git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/synapterdata_1.43.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: synapter dependencyCount: 152 Package: systemPipeRdata Version: 2.9.0 Imports: methods, Biostrings, BiocGenerics, jsonlite, remotes Suggests: GenomicFeatures, GenomicRanges, IRanges, Rsamtools, ShortRead, rtracklayer, RUnit, BiocStyle, knitr, rmarkdown, systemPipeR License: Artistic-2.0 MD5sum: 8448068c31db8ce5175f050fed11fcdb 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, https://systempipe.org/ VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/systemPipeRdata git_branch: devel git_last_commit: 49a9fce git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/systemPipeRdata_2.9.0.tar.gz vignettes: vignettes/systemPipeRdata/inst/doc/SPblast.html, vignettes/systemPipeRdata/inst/doc/SPcheminfo.html, vignettes/systemPipeRdata/inst/doc/SPscrna.html, vignettes/systemPipeRdata/inst/doc/systemPipeChIPseq.html, vignettes/systemPipeRdata/inst/doc/systemPipeRdata.html, vignettes/systemPipeRdata/inst/doc/systemPipeRIBOseq.html, vignettes/systemPipeRdata/inst/doc/systemPipeRNAseq.html, vignettes/systemPipeRdata/inst/doc/systemPipeVARseq.html vignetteTitles: WF: BLAST Template, WF: Cheminformatics Drug Similarity Template, WF: Basic Single Cell Template, WF: ChIP-Seq Workflow Template, systemPipeRdata: Workflow templates and sample data, WF: RIBO-Seq Workflow Template, WF: RNA-Seq Workflow Template, WF: VAR-Seq Template hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/systemPipeRdata/inst/doc/SPblast.R, vignettes/systemPipeRdata/inst/doc/SPcheminfo.R, vignettes/systemPipeRdata/inst/doc/SPscrna.R, vignettes/systemPipeRdata/inst/doc/systemPipeChIPseq.R, vignettes/systemPipeRdata/inst/doc/systemPipeRdata.R, vignettes/systemPipeRdata/inst/doc/systemPipeRIBOseq.R, vignettes/systemPipeRdata/inst/doc/systemPipeRNAseq.R, vignettes/systemPipeRdata/inst/doc/systemPipeVARseq.R suggestsMe: systemPipeR, systemPipeShiny dependencyCount: 26 Package: TabulaMurisData Version: 1.23.0 Depends: R (>= 3.5) Imports: ExperimentHub, utils Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran, scater, iSEE, testthat License: MIT + file LICENSE MD5sum: 89d39f825fe94f4cefb8211917022871 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: devel git_last_commit: 688f5a3 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/TabulaMurisData_1.23.0.tar.gz vignettes: vignettes/TabulaMurisData/inst/doc/TabulaMurisData.html vignetteTitles: Tabula Muris data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TabulaMurisData/inst/doc/TabulaMurisData.R dependencyCount: 67 Package: TabulaMurisSenisData Version: 1.11.0 Imports: ExperimentHub, SingleCellExperiment, HDF5Array, SummarizedExperiment, gdata, AnnotationHub Suggests: ggplot2, testthat, knitr, rmarkdown, iSEE, BiocStyle License: MIT + file LICENSE MD5sum: e88bc5906aacc44f88ae3d6400baa914 NeedsCompilation: no Title: Bulk and single-cell RNA-seq data from the Tabula Muris Senis project Description: This package provides access to RNA-seq data generated by the Tabula Muris Senis project via the Bioconductor project. The data is made available without restrictions by the Chan Zuckerberg Biohub. It is provided here without further processing, collected in the form of SingleCellExperiment objects. biocViews: SingleCellData, ExperimentData, RNASeqData, ExperimentHub Author: Charlotte Soneson [aut, cre] (), Dania Machlab [aut] (), Federico Marini [aut] (), Stefania Astrologo [aut] () Maintainer: Charlotte Soneson URL: https://github.com/fmicompbio/TabulaMurisSenisData VignetteBuilder: knitr BugReports: https://github.com/fmicompbio/TabulaMurisSenisData/issues git_url: https://git.bioconductor.org/packages/TabulaMurisSenisData git_branch: devel git_last_commit: 4928e4c git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/TabulaMurisSenisData_1.11.0.tar.gz vignettes: vignettes/TabulaMurisSenisData/inst/doc/TabulaMurisSenisData.html vignetteTitles: TabulaMurisSenisData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TabulaMurisSenisData/inst/doc/TabulaMurisSenisData.R suggestsMe: SPOTlight dependencyCount: 85 Package: TargetScoreData Version: 1.41.0 Suggests: TargetScore, gplots License: GPL-2 MD5sum: 2a01d42a6cb66d96c7da6f456dbc53e7 NeedsCompilation: no Title: TargetScoreData Description: Precompiled and processed miRNA-overexpression fold-changes from 84 Gene Expression Omnibus (GEO) series corresponding to 6 platforms, 77 human cells or tissues, and 113 distinct miRNAs. Accompanied with the data, we also included in this package the sequence feature scores from TargetScanHuman 6.1 including the context+ score and the probabilities of conserved targeting for each miRNA-mRNA interaction. Thus, the user can use these static sequence-based scores together with user-supplied tissue/cell-specific fold-change due to miRNA overexpression to predict miRNA targets using the package TargetScore (download separately) biocViews: ExperimentData, RNASeqData, miRNAData Author: Yue Li Maintainer: Yue Li git_url: https://git.bioconductor.org/packages/TargetScoreData git_branch: devel git_last_commit: 999f7ec git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/TargetScoreData_1.41.0.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: 1.43.0 License: GPL (>= 2) MD5sum: 34b650624fdbec90105f702dd2599ca4 NeedsCompilation: no Title: Example GC-MS data for TargetSearch Package Description: Example files of GC-MS data for the TargetSearch Package. The package contains raw NetCDF files from a E.coli salt stress experiment, extracted peak lists, and sample metadata required for a GC-MS analysis. The raw data has been restricted for demonstration purposes. biocViews: ExperimentData, Escherichia_coli_Data Author: Alvaro Cuadros-Inostroza [aut, cre], Jan Lisec [aut], Henning Redestig [aut], Matt Hannah [aut] Maintainer: Alvaro Cuadros-Inostroza URL: https://github.com/acinostroza/TargetSearchData BugReports: https://github.com/acinostroza/TargetSearchData/issues git_url: https://git.bioconductor.org/packages/TargetSearchData git_branch: devel git_last_commit: af8c5d3 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/TargetSearchData_1.43.0.tar.gz vignettes: vignettes/TargetSearchData/inst/doc/TargetSearchData.pdf vignetteTitles: The TargetSearchData Package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TargetSearchData/inst/doc/TargetSearchData.R suggestsMe: TargetSearch dependencyCount: 0 Package: tartare Version: 1.19.0 Depends: R (>= 4.1), AnnotationHub (>= 2.16), ExperimentHub (>= 1.0) Imports: utils Suggests: BiocStyle, knitr, rmarkdown, testthat, tools License: GPL-3 MD5sum: 222a776b29367effb3ebccb444e6bde0 NeedsCompilation: no Title: Raw ground spectra recorded on Thermo Fisher Scientific mass spectrometers Description: Provides raw files recorded on different Liquid Chromatography Mass Spectrometry (LC-MS) instruments. All included MS instruments are manufactured by Thermo Fisher Scientific and belong to the Orbitrap Tribrid or Q Exactive Orbitrap family of instruments. Despite their common origin and shared hardware components, e.g., Orbitrap mass analyser, the above instruments tend to write data in different "dialects" in a shared binary file format (.raw). The intention behind tartare is to provide complex but slim real-world files that can be used to make code robust with respect to this diversity. In other words, it is intended for enhanced unit testing. The package is considered to be used with the rawrr package and the Spectra MsBackends. biocViews: ExperimentData, MassSpectrometryData, ExperimentHub Author: Christian Panse [aut, cre] (), 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: devel git_last_commit: 0759d8c git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/tartare_1.19.0.tar.gz vignettes: vignettes/tartare/inst/doc/tartare.html vignetteTitles: make and use tartare data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tartare/inst/doc/tartare.R suggestsMe: MsBackendRawFileReader, rawDiag, rawrr dependencyCount: 67 Package: TBX20BamSubset Version: 1.41.0 Depends: Rsamtools (>= 1.9.8) Imports: xtable License: LGPL MD5sum: 5a4bfe12c5cce903b71fa4599f6cfbd5 NeedsCompilation: no Title: Subset of BAM files from the "TBX20" experiment Description: Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. A subset of the RNA-Seq data. biocViews: ExperimentData, SequencingData, RNASeqData Author: D. Bindreither Maintainer: D. Bindreither git_url: https://git.bioconductor.org/packages/TBX20BamSubset git_branch: devel git_last_commit: 6dd8cea git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/TBX20BamSubset_1.41.0.tar.gz vignettes: vignettes/TBX20BamSubset/inst/doc/TBX20BamSubset.pdf vignetteTitles: TBX20 RNA-Seq data subset hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TBX20BamSubset/inst/doc/TBX20BamSubset.R importsMe: Rmmquant suggestsMe: APAlyzer, magpie dependencyCount: 40 Package: TCGAbiolinksGUI.data Version: 1.25.0 Depends: R (>= 3.5.0) Suggests: BiocStyle, knitr, rmarkdown, readr, DT License: GPL-3 MD5sum: ec8c734d70c1173f8fd0ba854986cf48 NeedsCompilation: no Title: Data for the TCGAbiolinksGUI package Description: Supporting data for the TCGAbiolinksGUI package. biocViews: AssayDomainData, TechnologyData, OrganismData Author: Tiago Chedraoui Silva Maintainer: Tiago Chedraoui Silva URL: https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data VignetteBuilder: knitr BugReports: https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data/issues git_url: https://git.bioconductor.org/packages/TCGAbiolinksGUI.data git_branch: devel git_last_commit: d5092e9 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/TCGAbiolinksGUI.data_1.25.0.tar.gz vignettes: vignettes/TCGAbiolinksGUI.data/inst/doc/vignettes.html vignetteTitles: Supporting data for the TCGAbiolinksGUI package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TCGAbiolinksGUI.data/inst/doc/vignettes.R importsMe: TCGAbiolinks dependencyCount: 0 Package: TCGAcrcmiRNA Version: 1.25.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: fe2e3c82363ef8467a9244832246f6e2 NeedsCompilation: no Title: TCGA CRC 450 miRNA dataset Description: colorectal cancer miRNA profile provided by TCGA biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/TCGAcrcmiRNA git_branch: devel git_last_commit: b5837e4 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/TCGAcrcmiRNA_1.25.0.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: 6 Package: TCGAcrcmRNA Version: 1.25.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: d387f3b80a9cb422248ae287760020e0 NeedsCompilation: no Title: TCGA CRC 450 mRNA dataset Description: colorectal cancer mRNA profile provided by TCGA biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/TCGAcrcmRNA git_branch: devel git_last_commit: 6999e36 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/TCGAcrcmRNA_1.25.0.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: 6 Package: TCGAMethylation450k Version: 1.41.0 License: GPL-2 MD5sum: fceec44567d02f666c8cdd0c81288788 NeedsCompilation: no Title: The Cancer Genome Atlas Illumina 450k methylation example data Description: The Cancer Genome Atlas (TCGA) is applying genomics technologies to over 20 different types of cancer. This package contains a small set of 450k array data in idat format. biocViews: Genome, CancerData, MethylationArrayData Author: Sean Davis Maintainer: Sean Davis git_url: https://git.bioconductor.org/packages/TCGAMethylation450k git_branch: devel git_last_commit: 3e404fe git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/TCGAMethylation450k_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: methylumi dependencyCount: 0 Package: TCGAWorkflowData Version: 1.29.0 Depends: R (>= 3.5.0) Imports: SummarizedExperiment Suggests: knitr, rmarkdown, pander, testthat, BiocStyle License: GPL-3 MD5sum: d77e6785d485b8447a49673ec00c663e NeedsCompilation: no Title: Data for TCGA Workflow Description: This experimental data package contains 11 data sets necessary to follow the "TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages". biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData, CancerData Author: Tiago Chedraoui Silva Maintainer: Tiago Chedraoui Silva URL: https://f1000research.com/articles/5-1542/v2 VignetteBuilder: knitr BugReports: https://github.com/BioinformaticsFMRP/TCGAWorkflow/issues git_url: https://git.bioconductor.org/packages/TCGAWorkflowData git_branch: devel git_last_commit: 2ead8a5 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/TCGAWorkflowData_1.29.0.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: 36 Package: TENxBrainData Version: 1.25.0 Depends: SingleCellExperiment, HDF5Array Imports: AnnotationHub (>= 2.9.22), ExperimentHub Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel, data.table, rmarkdown License: CC BY 4.0 MD5sum: 31ad672547aabbb1f0f8f764a5bb6a8e NeedsCompilation: no Title: Data from the 10X 1.3 Million Brain Cell Study Description: Single-cell RNA-seq data for 1.3 million brain cells from E18 mice, generated by 10X Genomics. biocViews: SequencingData, RNASeqData, ExpressionData, SingleCellData Author: Aaron Lun [aut], Martin Morgan [aut], Bioconductor Package Maintainer [cre] Maintainer: Bioconductor Package Maintainer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TENxBrainData git_branch: devel git_last_commit: 38cb82b git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/TENxBrainData_1.25.0.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 dependsOnMe: OSCA.advanced suggestsMe: HDF5Array dependencyCount: 83 Package: TENxBUSData Version: 1.19.0 Imports: ExperimentHub, AnnotationHub, utils, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle License: BSD_2_clause + file LICENSE MD5sum: 85c75e97ff64424d02abcddae3d72b05 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: devel git_last_commit: 671ba77 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/TENxBUSData_1.19.0.tar.gz vignettes: vignettes/TENxBUSData/inst/doc/downloading-10x-hgmm-data.html vignetteTitles: Downloading BUS data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TENxBUSData/inst/doc/downloading-10x-hgmm-data.R suggestsMe: BUSpaRse dependencyCount: 67 Package: TENxPBMCData Version: 1.23.0 Depends: SingleCellExperiment, HDF5Array Imports: AnnotationHub, ExperimentHub Suggests: rmarkdown, knitr, BiocStyle, snow, BiocFileCache, BiocParallel License: CC BY 4.0 MD5sum: 3ff368be92380059b327796c2e661471 NeedsCompilation: no Title: PBMC data from 10X Genomics Description: Single-cell RNA-seq data for on PBMC cells, generated by 10X Genomics. biocViews: SequencingData, RNASeqData, ExpressionData, ExperimentHub, ExperimentData, SingleCellData Author: Kasper D. Hansen [aut], Davide Risso [aut], Milan Malfait [ctb], Jeroen Gilis [ctb], Theodore Killian [ctb], Murat Cem Kose [ctb], Chong Tang [ctb], Teun van den Brand [ctb], Dania Machlab [ctb], Stephanie Hicks [aut, cre] Maintainer: Stephanie Hicks VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TENxPBMCData git_branch: devel git_last_commit: 585a645 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/TENxPBMCData_1.23.0.tar.gz vignettes: vignettes/TENxPBMCData/inst/doc/TENxPBMCData.html vignetteTitles: Obtaining scRNA-seq data on PBMCs from 10X Genomics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TENxPBMCData/inst/doc/TENxPBMCData.R dependsOnMe: OSCA.multisample, SingleRBook importsMe: singleCellTK suggestsMe: ASURAT, ExperimentSubset, adverSCarial, celda, concordexR, decontX, glmGamPoi, iSEE, mbkmeans, schex, scone, scry, sketchR, transformGamPoi dependencyCount: 83 Package: TENxVisiumData Version: 1.13.0 Depends: ExperimentHub, SpatialExperiment Imports: utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: efbf8314204253ce880426200677c653 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: devel git_last_commit: 94ec7cb git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/TENxVisiumData_1.13.0.tar.gz vignettes: vignettes/TENxVisiumData/inst/doc/vignette.html vignetteTitles: TENxVisiumData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TENxVisiumData/inst/doc/vignette.R suggestsMe: SPOTlight dependencyCount: 83 Package: TENxXeniumData Version: 1.1.0 Depends: ExperimentHub Imports: SpatialExperiment, SpatialFeatureExperiment, BumpyMatrix, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: ab70dd3361b22e6b1830362b4f966f80 NeedsCompilation: no Title: Collection of Xenium spatial data by 10X genomics Description: Collection of Xenium spatial transcriptomics datasets provided by 10x Genomics, formatted into the Bioconductor classes, the SpatialExperiment or SpatialFeatureExperiment (SFE), to facilitate seamless integration into various applications, including examples, demonstrations, and tutorials. The constructed data objects include gene expression profiles, per-transcript location data, centroid, segmentation boundaries (e.g., cell or nucleus boundaries), and image. biocViews: ExperimentData, ExperimentHub, SpatialData Author: Matineh Rahmatbakhsh [aut, cre], Monica Ge [aut] Maintainer: Matineh Rahmatbakhsh URL: https://github.com/mrbakhsh/TENxXeniumData VignetteBuilder: knitr BugReports: https://github.com/mrbakhsh/TENxXeniumData/issues git_url: https://git.bioconductor.org/packages/TENxXeniumData git_branch: devel git_last_commit: 9801c74 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-21 source.ver: src/contrib/TENxXeniumData_1.1.0.tar.gz vignettes: vignettes/TENxXeniumData/inst/doc/TENxXeniumData.html vignetteTitles: TENxXeniumData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TENxXeniumData/inst/doc/TENxXeniumData.R dependencyCount: 155 Package: timecoursedata Version: 1.15.0 Depends: R (>= 4.0), SummarizedExperiment Suggests: testthat (>= 1.0.0), knitr, rmarkdown, markdown, covr, BiocStyle License: BSD 3-clause License + file LICENSE MD5sum: e9a98eb46be8522686411178574104e3 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: devel git_last_commit: e75e529 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/timecoursedata_1.15.0.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: 36 Package: TimerQuant Version: 1.35.0 Depends: shiny Imports: ggplot2, grid, gridExtra, deSolve, dplyr, locfit Suggests: BiocStyle, reshape2, knitr, shinyBS License: Artistic-2.0 MD5sum: d347340584744c95e061c9893b744a1c NeedsCompilation: no Title: Timer Quantification Description: Supplementary Data package for tandem timer methods paper by Barry et al. (2015) including TimerQuant shiny applications. biocViews: ExperimentData, Danio_rerio_Data, HighThroughputImagingData, Tissue Author: Joseph Barry Maintainer: Joseph Barry VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TimerQuant git_branch: devel git_last_commit: bfc85cf git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/TimerQuant_1.35.0.tar.gz vignettes: vignettes/TimerQuant/inst/doc/genPaperFigures.pdf, vignettes/TimerQuant/inst/doc/mathematicalDerivations.pdf vignetteTitles: Supplementary Methods - automatic generation of paper figures, Supplementary Methods - mathematical derivations hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TimerQuant/inst/doc/genPaperFigures.R, vignettes/TimerQuant/inst/doc/mathematicalDerivations.R dependencyCount: 65 Package: tinesath1cdf Version: 1.43.0 License: Artistic-2.0 MD5sum: 4ca821a375a7b489f12c5289081a248c NeedsCompilation: no Title: tinesath1cdf Description: A package containing an environment represeting the newcdf/tinesATH1.cdf.cdf file. biocViews: Arabidopsis_thaliana_Data, ChipOnChipData Author: Tine Casneuf Maintainer: Tine Casneuf git_url: https://git.bioconductor.org/packages/tinesath1cdf git_branch: devel git_last_commit: 8ccea20 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/tinesath1cdf_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: XhybCasneuf dependencyCount: 0 Package: tinesath1probe Version: 1.43.0 Depends: R (>= 1.6), AnnotationDbi (>= 1.11.9) License: LGPL MD5sum: 625ac295ebd2c1ca5c6202fd9580ec15 NeedsCompilation: no Title: Probe sequence data for microarrays of type tinesath1 Description: This package was automatically created by package matchprobes version 1.4.0. The probe sequence data was obtained from http://www.affymetrix.com. biocViews: Arabidopsis_thaliana_Data, SequencingData, MicroarrayData Author: The Bioconductor Project www.bioconductor.org Maintainer: Tine Casneuf git_url: https://git.bioconductor.org/packages/tinesath1probe git_branch: devel git_last_commit: cce5143 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/tinesath1probe_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 45 Package: tissueTreg Version: 1.25.0 Depends: R (>= 3.5) Suggests: BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq, SummarizedExperiment, ggplot2, reshape2 License: GPL (>= 2) MD5sum: ab519bfcd5466777d10f14775f6085b4 NeedsCompilation: no Title: TWGBS and RNA-seq data from tissue T regulatory cells from mice Description: The package provides ready to use epigenomes (obtained from TWGBS) and transcriptomes (RNA-seq) from various tissues as obtained in the study (Delacher and Imbusch 2017, PMID: 28783152). Regulatory T cells (Treg cells) perform two distinct functions: they maintain self-tolerance, and they support organ homeostasis by differentiating into specialized tissue Treg cells. The underlying dataset characterises the epigenetic and transcriptomic modifications for specialized tissue Treg cells. biocViews: ExperimentData, Tissue, Mus_musculus_Data, SequencingData, RNASeqData Author: Charles Imbusch [aut, cre], Michael Delacher [aut], Markus Feuerer [aut], Benedikt Brors [aut] Maintainer: Charles Imbusch URL: https://github.com/cimbusch/tissueTreg VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tissueTreg git_branch: devel git_last_commit: 1cb7ca1 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/tissueTreg_1.25.0.tar.gz vignettes: vignettes/tissueTreg/inst/doc/tissueTreg.html vignetteTitles: tissueTreg hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tissueTreg/inst/doc/tissueTreg.R suggestsMe: DMRcate dependencyCount: 0 Package: TMExplorer Version: 1.15.0 Depends: R (>= 4.1), SingleCellExperiment, BiocFileCache Imports: methods, Matrix Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: ebfe7dda316e67609b8cf9572600a591 NeedsCompilation: no Title: A Collection of Tumour Microenvironment Single-cell RNA Sequencing Datasets and Corresponding Metadata Description: This package provides a tool to search and download a collection of tumour microenvironment single-cell RNA sequencing datasets and their metadata. TMExplorer aims to act as a single point of entry for users looking to study the tumour microenvironment at the single cell level. Users can quickly search available datasets using the metadata table and then download the ones they are interested in for analysis. biocViews: CancerData, SingleCellData, RNASeqData, SequencingData, ExpressionData, GEO, PackageTypeData Author: Erik Christensen [aut, cre], Alaine Naidas [aut], David Chen [aut], Parisa Shooshtari [aut] Maintainer: Erik Christensen VignetteBuilder: knitr BugReports: https://github.com/shooshtarilab/TMExplorer/issues git_url: https://git.bioconductor.org/packages/TMExplorer git_branch: devel git_last_commit: 010b3aa git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/TMExplorer_1.15.0.tar.gz vignettes: vignettes/TMExplorer/inst/doc/TMExplorer.html vignetteTitles: TMExplorer hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TMExplorer/inst/doc/TMExplorer.R dependencyCount: 69 Package: tofsimsData Version: 1.33.0 Depends: R (>= 3.2.0) Suggests: knitr, rmarkdown, tools License: GPL-3 MD5sum: b05fe15dd999b6a2f719b1266f0f6670 NeedsCompilation: no Title: Import, process and analysis of ToF-SIMS imaging data Description: This packages contains data to be used with the 'tofsims' package. biocViews: ExperimentData, MassSpectrometry, ImagingMassSpectrometry, DataImport Author: Lorenz Gerber, Viet Mai Hoang Maintainer: Lorenz Gerber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tofsimsData git_branch: devel git_last_commit: cf64520 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/tofsimsData_1.33.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: topdownrdata Version: 1.27.0 Depends: topdownr License: GPL (>= 3) MD5sum: 3007929743ec510ff38d48f08249ba88 NeedsCompilation: no Title: Example Files for the topdownr R Package Description: Example data for the topdownr package generated on a Thermo Orbitrap Fusion Lumos MS device. biocViews: ExperimentData, MassSpectrometryData Author: Sebastian Gibb [aut, cre], Pavel Shliaha [aut], Ole Nørregaard Jensen [aut] Maintainer: Sebastian Gibb URL: https://github.com/sgibb/topdownrdata/ BugReports: https://github.com/sgibb/topdownrdata/issues/ git_url: https://git.bioconductor.org/packages/topdownrdata git_branch: devel git_last_commit: 36f7489 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/topdownrdata_1.27.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: topdownr dependencyCount: 139 Package: TransOmicsData Version: 1.1.0 Imports: S4Vectors, utils Suggests: BiocStyle, knitr, rmarkdown, RefManageR, sessioninfo, testthat, ExperimentHub License: GPL-3 + file LICENSE MD5sum: 2ba1eb13fa740400357e5bfc9dd09db1 NeedsCompilation: no Title: A collection of trans-omics datasets across various biological systems Description: Contains a collection of trans-omics datasets generated using various sequencing technologies such as RNA-seq, Mass spectrometry and ChIP-seq. Modalities include the bulk profiling of the phosphoproteome, proteome, transcriptome and epigenome. Data reflects the timecourses of different developmental systems from the mouse or human. biocViews: ExperimentHub, MassSpectrometryData, RNASeqData, ChIPSeqData, Tissue, SequencingData Author: Carissa Chen [aut] (), Di Xiao [aut, cre] (), Pengyi Yang [aut] () Maintainer: Di Xiao URL: https://github.com/PYangLab/TransOmicsData VignetteBuilder: knitr BugReports: https://support.bioconductor.org/t/TransOmicsData git_url: https://git.bioconductor.org/packages/TransOmicsData git_branch: devel git_last_commit: ebb0047 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/TransOmicsData_1.1.0.tar.gz vignettes: vignettes/TransOmicsData/inst/doc/TransOmicsData-vignette.html vignetteTitles: TransOmicsData: A collection of trans-omics datasets across various biological systems hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TransOmicsData/inst/doc/TransOmicsData-vignette.R dependencyCount: 7 Package: tuberculosis Version: 1.11.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: AnnotationHub, ExperimentHub, S4Vectors, dplyr, magrittr, purrr, rlang, stringr, tibble, tidyr Suggests: BiocStyle, ggplot2, hrbrthemes, knitr, readr, rmarkdown, scater, usethis, utils License: Artistic-2.0 MD5sum: f8bd5062c34fd7f7abc4cf822e7289da NeedsCompilation: no Title: Tuberculosis Gene Expression Data for Machine Learning Description: The tuberculosis R/Bioconductor package features tuberculosis gene expression data for machine learning. All human samples from GEO that did not come from cell lines, were not taken postmortem, and did not feature recombination have been included. The package has more than 10,000 samples from both microarray and sequencing studies that have been processed from raw data through a hyper-standardized, reproducible pipeline. biocViews: ExperimentHub, ExpressionData, Homo_sapiens_Data, MicroarrayData, SequencingData, ReproducibleResearch Author: Lucas Schiffer [aut, cre] () Maintainer: Lucas Schiffer URL: https://github.com/schifferl/tuberculosis VignetteBuilder: knitr BugReports: https://github.com/schifferl/tuberculosis/issues git_url: https://git.bioconductor.org/packages/tuberculosis git_branch: devel git_last_commit: 3cdffab git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/tuberculosis_1.11.0.tar.gz vignettes: vignettes/tuberculosis/inst/doc/tuberculosis.html vignetteTitles: tuberculosis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tuberculosis/inst/doc/tuberculosis.R dependencyCount: 78 Package: TumourMethData Version: 1.3.0 Depends: R (>= 4.2), SummarizedExperiment Imports: ExperimentHub, GenomicRanges, HDF5Array, R.utils, rhdf5 Suggests: ggplot2, knitr, rmarkdown License: Artistic-2.0 MD5sum: 33c0ff42d0fbc47bb824bd29b06c34f2 NeedsCompilation: no Title: A Collection of DNA Methylation Datasets for Human Tumour Samples and Matching Normal Samples Description: TumourMethData collects tumour methylation data from a variety of different tumour types (and also matching normal samples where available) and produced with different technologies (e.g. WGBS, RRBS and methylation arrays) and provides them as RangedSummarizedExperiments. This facilitates easy extraction of methylation data for regions of interest across different tumour types and studies. biocViews: ExperimentData, ExperimentHub, MethylSeqData, CancerData, Homo_sapiens_Data, Author: Richard Heery [aut, cre] () Maintainer: Richard Heery URL: https://github.com/richardheery/TumourMethData VignetteBuilder: knitr BugReports: https://support.bioconductor.org/tag/TumourMethData git_url: https://git.bioconductor.org/packages/TumourMethData git_branch: devel git_last_commit: 5a8934f git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/TumourMethData_1.3.0.tar.gz vignettes: vignettes/TumourMethData/inst/doc/getting_tumour_methylation_from_TumourMethData.html vignetteTitles: getting_tumour_methylation_from_TumourMethData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TumourMethData/inst/doc/getting_tumour_methylation_from_TumourMethData.R suggestsMe: methodical dependencyCount: 85 Package: tweeDEseqCountData Version: 1.43.0 Depends: Biobase, R (>= 4.3.0) Suggests: knitr, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: b41ae75be88abfd53b4913ba54ed50aa NeedsCompilation: no Title: RNA-seq count data employed in the vignette of the tweeDEseq package Description: RNA-seq count data from Pickrell et al. (2010) employed to illustrate the use of the Poisson-Tweedie family of distributions with the tweeDEseq package. biocViews: Genome, Homo_sapiens_Data, RNASeqData Author: Dolors Pelegri-Siso [aut, cre] (), Juan R. Gonzalez [aut] (), Mikel Esnaola [aut], Robert Castelo [aut] Maintainer: Dolors Pelegri-Siso URL: https://github.com/isglobal-brge/tweeDEseqCountData/ VignetteBuilder: knitr BugReports: https://github.com/isglobal-brge/tweeDEseqCountData/issues git_url: https://git.bioconductor.org/packages/tweeDEseqCountData git_branch: devel git_last_commit: 626c04b git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/tweeDEseqCountData_1.43.0.tar.gz vignettes: vignettes/tweeDEseqCountData/inst/doc/tweeDEseqCountData.html vignetteTitles: RNA-seq count data employed in the vignette of the tweeDEseq package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tweeDEseqCountData/inst/doc/tweeDEseqCountData.R suggestsMe: GSAR, missMethyl, tweeDEseq, zenith dependencyCount: 6 Package: tximportData Version: 1.33.0 Suggests: knitr, markdown License: GPL (>= 2) MD5sum: dbb60e5b13f77684699300deff1413be NeedsCompilation: no Title: tximportData Description: This package provides the output of running various transcript abundance quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project. The quantifiers were Cufflinks, RSEM, kallisto, Salmon and Sailfish. alevin example output is also included. Forr details on version numbers, sample information, and details on calls, see the package vignette. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tximportData git_branch: devel git_last_commit: d049e08 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/tximportData_1.33.0.tar.gz vignettes: vignettes/tximportData/inst/doc/tximportData.html vignetteTitles: Sample output files for tximport hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tximportData/inst/doc/tximportData.R importsMe: TDbasedUFE suggestsMe: DESeq2, HumanTranscriptomeCompendium, eds, fishpond, tximeta, tximport, variancePartition dependencyCount: 0 Package: VariantToolsData Version: 1.29.0 Depends: R (>= 3.5.0), VariantAnnotation (>= 1.7.35) Imports: BiocGenerics, GenomicRanges Suggests: VariantTools (>= 1.3.4), gmapR (>= 1.3.3), BiocStyle License: Artistic-2.0 MD5sum: 95d8b940a45ed25b52f08d57a0144e87 NeedsCompilation: no Title: Data for the VariantTools tutorial Description: Data from the sequencing of a 50/50 mixture of HapMap trio samples NA12878 (CEU) and NA19240 (YRI), subset to the TP53 region. biocViews: ExperimentData, SequencingData, HapMap, SNPData Author: Michael Lawrence Maintainer: Michael Lawrence git_url: https://git.bioconductor.org/packages/VariantToolsData git_branch: devel git_last_commit: ac2dec0 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/VariantToolsData_1.29.0.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: 79 Package: VectraPolarisData Version: 1.9.0 Depends: ExperimentHub, SpatialExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, dplyr License: Artistic-2.0 MD5sum: 33efc8df8dfa7f01ccbdd20221822564 NeedsCompilation: no Title: Vectra Polaris and Vectra 3 multiplex single-cell imaging data Description: Provides two multiplex imaging datasets collected on Vectra instruments at the University of Colorado Anschutz Medical Campus. Data are provided as a Spatial Experiment objects. Data is provided in tabular form and has been segmented and phenotyped using Inform software. Raw .tiff files are not included. biocViews: ExperimentHub, ExperimentData, SpatialData, SingleCellData, Homo_sapiens_Data, ReproducibleResearch Author: Wrobel Julia [aut, cre] (), Tusharkanti Ghosh [aut] Maintainer: Wrobel Julia URL: https://github.com/julia-wrobel/VectraPolarisData VignetteBuilder: knitr BugReports: https://support.bioconductor.org/t/VectraPolarisData git_url: https://git.bioconductor.org/packages/VectraPolarisData git_branch: devel git_last_commit: dadee3d git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/VectraPolarisData_1.9.0.tar.gz vignettes: vignettes/VectraPolarisData/inst/doc/VectraPolarisData.html vignetteTitles: VectraPolarisData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/VectraPolarisData/inst/doc/VectraPolarisData.R dependencyCount: 83 Package: vulcandata Version: 1.27.0 Imports: utils Suggests: viper License: LGPL-3 MD5sum: 1f0267856b15f8c293f5c49dbaf322ab NeedsCompilation: no Title: VirtUaL ChIP-Seq data Analysis using Networks, dummy dataset Description: This package provides a dummy regulatory network and ChIP-Seq dataset for running examples in the vulcan package biocViews: ExperimentData, Homo_sapiens_Data, CancerData, ChIPSeqData Author: Federico M. Giorgi, Andrew N. Holding, Florian Markowetz Maintainer: Federico M. Giorgi git_url: https://git.bioconductor.org/packages/vulcandata git_branch: devel git_last_commit: 1893d62 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/vulcandata_1.27.0.tar.gz vignettes: vignettes/vulcandata/inst/doc/vulcandata.pdf vignetteTitles: Vulcan: VirtUaL ChIP-Seq Analysis through Networks,, dummy datasets hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/vulcandata/inst/doc/vulcandata.R suggestsMe: vulcan dependencyCount: 1 Package: WeberDivechaLCdata Version: 1.7.0 Depends: ExperimentHub, SpatialExperiment, SingleCellExperiment Imports: utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 0fef4d194b5da8892b740221fbfd6450 NeedsCompilation: no Title: Spatially-resolved transcriptomics and single-nucleus RNA-sequencing data from the locus coeruleus (LC) in postmortem human brain samples Description: Spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from the locus coeruleus (LC) in postmortem human brain samples. Data were generated with the 10x Genomics Visium SRT and 10x Genomics Chromium snRNA-seq platforms. Datasets are stored in SpatialExperiment and SingleCellExperiment formats. biocViews: ExperimentData, ExperimentHub, ReproducibleResearch, ExpressionData, SequencingData, RNASeqData, SingleCellData, SpatialData, Homo_sapiens_Data Author: Lukas M. Weber [aut, cre] (), Heena R. Divecha [aut] () Maintainer: Lukas M. Weber URL: https://github.com/lmweber/WeberDivechaLCdata VignetteBuilder: knitr BugReports: https://github.com/lmweber/WeberDivechaLCdata/issues git_url: https://git.bioconductor.org/packages/WeberDivechaLCdata git_branch: devel git_last_commit: fb4f3bd git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/WeberDivechaLCdata_1.7.0.tar.gz vignettes: vignettes/WeberDivechaLCdata/inst/doc/WeberDivechaLCdata.html vignetteTitles: WeberDivechaLCdata package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/WeberDivechaLCdata/inst/doc/WeberDivechaLCdata.R suggestsMe: nnSVG dependencyCount: 83 Package: WES.1KG.WUGSC Version: 1.37.0 License: GPL-2 MD5sum: 7dbd76218db8343c87c89d1937e3a1d2 NeedsCompilation: no Title: Whole Exome Sequencing (WES) of chromosome 22 401st to 500th exon from the 1000 Genomes (1KG) Project by the Washington University Genome Sequencing Center (WUGSC). Description: The assembled .bam files of whole exome sequencing data from the 1000 Genomes Project. 46 samples sequenced by the Washington University Genome Sequencing Center are included. biocViews: ExperimentData, Project1000genomes, SequencingData, DNASeqData, Homo_sapiens_Data Author: Yuchao Jiang, Nancy R. Zhang Maintainer: Yuchao Jiang git_url: https://git.bioconductor.org/packages/WES.1KG.WUGSC git_branch: devel git_last_commit: 781e013 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/WES.1KG.WUGSC_1.37.0.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: 1.17.0 Depends: R (>= 3.6.0), GenomicRanges License: GPL-2 MD5sum: 029d5098cd6d6516ba48c746c53268a8 NeedsCompilation: no Title: Mappability tracks of Whole-genome Sequencing from the ENCODE Project Description: This package provides whole-genome mappability tracks on human hg19/hg38 assembly. We employed the 100-mers mappability track from the ENCODE Project and computed weighted average of the mappability scores if multiple ENCODE regions overlap with the same bin. “Blacklist” bins, including segmental duplication regions and gaps in reference assembly from telomere, centromere, and/or heterochromatin regions are included. The dataset consists of three assembled .bam files of single-cell whole genome sequencing from 10X for illustration purposes. biocViews: ExperimentData, SequencingData, DNASeqData, SingleCellData, Homo_sapiens_Data, Genome, ENCODE Author: Rujin Wang Maintainer: Rujin Wang git_url: https://git.bioconductor.org/packages/WGSmapp git_branch: devel git_last_commit: ae6708f git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/WGSmapp_1.17.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: SCOPE dependencyCount: 23 Package: xcoredata Version: 1.9.0 Depends: R (>= 4.2) Imports: ExperimentHub (>= 2.2.0), utils (>= 4.2.0) Suggests: BiocGenerics (>= 0.40.0), data.table (>= 1.14.2), GenomeInfoDb (>= 1.30.0), GenomicRanges (>= 1.46.1), IRanges (>= 2.28.0), knitr (>= 1.37), rmarkdown (>= 2.11), Matrix (>= 1.3.4), stringr (>= 1.4.0), S4Vectors (>= 0.32.3), TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.14.0), xcore License: GPL-2 MD5sum: 53ec49ce3a7443d2084a808913e83096 NeedsCompilation: no Title: data package for xcore Description: Provides data to use with xcore package. biocViews: ExperimentHub, ExperimentData, Homo_sapiens_Data Author: Maciej Migdał [aut, cre] (), Bogumił Kaczkowski [aut] () Maintainer: Maciej Migdał VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/xcoredata git_branch: devel git_last_commit: 3f2a072 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/xcoredata_1.9.0.tar.gz vignettes: vignettes/xcoredata/inst/doc/xcoredata.html vignetteTitles: xcoredata hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/xcoredata/inst/doc/xcoredata.R suggestsMe: xcore dependencyCount: 67 Package: XhybCasneuf Version: 1.43.0 Depends: R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf , RColorBrewer , methods, grid License: Artistic-2.0 MD5sum: 1d3b9c587c239217b5c40cc643e48f56 NeedsCompilation: no Title: EBI/PSB cross-hybridisation study package Description: Cross-hybridisation study on the ATH1 Affymetrix GeneChip biocViews: ExperimentData, Tissue, MicroarrayData, TissueMicroarrayData Author: Tineke Casneuf Maintainer: Tineke Casneuf git_url: https://git.bioconductor.org/packages/XhybCasneuf git_branch: devel git_last_commit: 695eef4 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/XhybCasneuf_1.43.0.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: 53 Package: yeastCC Version: 1.45.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: d2a8493d096d1b6b8745340d8299de6b NeedsCompilation: no Title: Spellman et al. (1998) and Pramila/Breeden (2006) yeast cell cycle microarray data Description: ExpressionSet for Spellman et al. (1998) yeast cell cycle microarray experiment biocViews: ExperimentData, CellCulture, Saccharomyces_cerevisiae_Data, CancerData, MicroarrayData, OneChannelData, GEO Author: Sandrine Dudoit Maintainer: Sandrine Dudoit git_url: https://git.bioconductor.org/packages/yeastCC git_branch: devel git_last_commit: 74d534e git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/yeastCC_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: LiquidAssociation suggestsMe: fastLiquidAssociation, ibh dependencyCount: 6 Package: yeastExpData Version: 0.51.0 Depends: R (>= 2.4), graph (>= 1.9.26) Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db License: GPL MD5sum: fe316102ef121b34d255213c153478a9 NeedsCompilation: no Title: Yeast Experimental Data Description: A collection of different sets of experimental data from yeast. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data Author: R. Gentleman Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/yeastExpData git_branch: devel git_last_commit: 8c506f5 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/yeastExpData_0.51.0.tar.gz vignettes: vignettes/yeastExpData/inst/doc/yeastExample.pdf vignetteTitles: Yeast PPI Example hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/yeastExpData/inst/doc/yeastExample.R dependsOnMe: PPInfer suggestsMe: ClusterJudge dependencyCount: 7 Package: yeastGSData Version: 0.43.0 License: Artistic-2.0 MD5sum: 4dda6a05bfda75807e61c4ac4732b4f3 NeedsCompilation: no Title: Yeast Gold Standard Data Description: A collection of so-called gold (and other) standard data sets biocViews: ExperimentData, Saccharomyces_cerevisiae_Data Author: R. Gentleman Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/yeastGSData git_branch: devel git_last_commit: bc9b565 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/yeastGSData_0.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: yeastNagalakshmi Version: 1.41.0 License: Artistic-2.0 MD5sum: ada47978c81448f5888b4251a127538c NeedsCompilation: no Title: Yeast genome RNA sequencing data based on Nagalakshmi et. al. Description: The yeast genome data was retrieved from the sequence read archive, aligned with bwa, and converted to BAM format with samtools. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, SequencingData, BiocViews, ChIPSeqData Author: Martin Morgan Maintainer: Bioconductor Package Maintainer git_url: https://git.bioconductor.org/packages/yeastNagalakshmi git_branch: devel git_last_commit: 2d25d56 git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/yeastNagalakshmi_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ShortRead dependencyCount: 0 Package: yeastRNASeq Version: 0.43.0 Depends: R (>= 2.4) Suggests: Biobase, ShortRead, IRanges License: GPL MD5sum: 8338e63f7fa1018b7895eb9531fa9660 NeedsCompilation: no Title: Yeast RNA-Seq Experimental Data from Lee et al. 2008 Description: A selection of RNA-Seq data from a yeast transcriptome experiment. biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData Author: James H. Bullard and Kasper D. Hansen Maintainer: J. Bullard git_url: https://git.bioconductor.org/packages/yeastRNASeq git_branch: devel git_last_commit: f0d3b6a git_last_commit_date: 2024-04-30 Date/Publication: 2024-05-02 source.ver: src/contrib/yeastRNASeq_0.43.0.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: 1.25.1 Depends: R (>= 2.10) Suggests: BiocStyle, knitr License: GPL MD5sum: 143aace1b9d043cefdaf4492660f61c8 NeedsCompilation: no Title: Zebrafish RNA-Seq Experimental Data from Ferreira et al. (2014) Description: Gene-level read counts from RNA-Seq for gallein-treated and control zebrafish. biocViews: ExperimentData, Danio_rerio_Data, RNASeqData Author: Davide Risso Maintainer: Davide Risso VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/zebrafishRNASeq git_branch: devel git_last_commit: ad13a44 git_last_commit_date: 2024-06-07 Date/Publication: 2024-06-11 source.ver: src/contrib/zebrafishRNASeq_1.25.1.tar.gz vignettes: vignettes/zebrafishRNASeq/inst/doc/preprocessing.html vignetteTitles: Pre-Processing for the Zebrafish RNA-Seq Gene-Level Counts hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/zebrafishRNASeq/inst/doc/preprocessing.R suggestsMe: RUVSeq, sva dependencyCount: 0 Package: curatedCRCData Version: 2.37.0 Depends: R (>= 2.10.0), nlme Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle License: Artistic-2.0 Title: Colorectal Cancer Gene Expression Analysis Description: The curatedCRC package provides relevant functions and data for gene expression analysis in patients with colorectal cancer. biocViews: Colorectal, Cancer, TCGA, ExperimentData, RNAExpressionData Author: Princy Parsana, Markus Riester, Curtis Huttenhower, Levi Waldron Maintainer: Princy Parsana URL: https://bitbucket.org/biobakery/curatedcrcdata Package: AssessORFData Version: 1.23.0 Depends: R (>= 3.5.0) Imports: DECIPHER, utils Suggests: AssessORF, BiocStyle, knitr, rmarkdown License: GPL-3 NeedsCompilation: no Title: Data and Files for the AssessORF Package Description: This package provides access to mapping and results objects generated by the AssessORF package, as well as the genome sequences for the strains corresponding to those objects. biocViews: OrganismData, Bacillus_subtilis_Data, Escherichia_coli_Data, Pseudomonas_aeruginosa_Data, Staphylococcus_aureus_Data, Genome, Proteome, SequencingData Author: Deepank Korandla [aut, cre] Maintainer: Deepank Korandla VignetteBuilder: knitr