Package: adductData Version: 1.17.0 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: 2b81b30552ea59d7921999fe15250d83 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: fc469d4 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/adductData_1.17.0.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: 97 Package: affycompData Version: 1.39.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp License: GPL (>= 2) MD5sum: 4572f644f06748b968b2ec61cce754d6 NeedsCompilation: no Title: affycomp data Description: Data needed by the affycomp package. biocViews: MicroarrayData Author: Rafael A. Irizarry and Zhijin Wu with contributions from Simon Cawley Maintainer: Harris Jaffee git_url: https://git.bioconductor.org/packages/affycompData git_branch: devel git_last_commit: 5605c1d git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/affycompData_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: affycomp dependencyCount: 7 Package: Affyhgu133A2Expr Version: 1.37.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 4f69b48f934c4d54c1890698c6a3f276 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: ad57489 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/Affyhgu133A2Expr_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: Affyhgu133aExpr Version: 1.39.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 2cc4c1186624a0668e66f22acf6aa886 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: d682cce git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/Affyhgu133aExpr_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: Affyhgu133Plus2Expr Version: 1.35.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: ef0144d3e4d8e53100c2e7eb76c58a64 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: ca0ef09 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/Affyhgu133Plus2Expr_1.35.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: AffymetrixDataTestFiles Version: 0.39.0 Depends: R (>= 2.5.0) License: LGPL-2.1 MD5sum: dc6470de28b5650ecd8e32543227ea9c 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: 167aaf3 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/AffymetrixDataTestFiles_0.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: affxparser, aroma.affymetrix dependencyCount: 0 Package: Affymoe4302Expr Version: 1.39.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 507972080d478d7ff615f63f0eec3d96 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: 5f6815f git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/Affymoe4302Expr_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSCA dependencyCount: 0 Package: airway Version: 1.21.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: knitr, GEOquery, markdown License: LGPL MD5sum: b50e1c992764529fbd5e5cce26f8dcde 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: b982585 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/airway_1.21.0.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 importsMe: consensusDE, NetActivity suggestsMe: apeglm, awst, biobroom, BioCor, BiocSet, CeTF, DelayedArray, DESeq2, EnhancedVolcano, EnrichmentBrowser, ExperimentSubset, ideal, IHW, InteractiveComplexHeatmap, iSEEu, OPWeight, pcaExplorer, PCAtools, progeny, runibic, SummarizedExperiment, TTMap, weitrix, IHWpaper, RegParallel, seqgendiff dependencyCount: 28 Package: ALL Version: 1.43.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Suggests: rpart License: Artistic-2.0 MD5sum: 58612f52a0a65894d04ed6f088697982 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: 42db0ce git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/ALL_1.43.0.tar.gz vignettes: vignettes/ALL/inst/doc/ALLintro.pdf vignetteTitles: ALL data intro hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ALL/inst/doc/ALLintro.R importsMe: ConsensusClusterPlus, dGAselID, scRNAtools suggestsMe: a4, a4Base, a4Classif, a4Preproc, Biobase, BioNet, Category, CellMapper, ChromHeatMap, clipper, EnrichmentBrowser, esetVis, genefilter, GeneSelectMMD, GOstats, graphite, GSAR, GSEAlm, MLInterfaces, npGSEA, pathRender, rScudo, SNAGEE, topGO, SNAGEEdata, MMDvariance, nlcv, SourceSet dependencyCount: 6 Package: AneuFinderData Version: 1.29.0 Depends: R (>= 3.3) License: file LICENSE MD5sum: 83648d1cefe7bf613cb5e3ac02d04a9e 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: 102e043 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/AneuFinderData_1.29.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: AneuFinder dependencyCount: 0 Package: antiProfilesData Version: 1.37.0 Depends: Biobase, Suggests: frma, GEOquery, GEOmetadb License: Artistic-2.0 MD5sum: ab5f8ea510c1492b0a2b87df50508884 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: 2e6b90b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/antiProfilesData_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: antiProfiles, epivizr, epivizrChart, messina dependencyCount: 6 Package: aracne.networks Version: 1.27.0 Depends: R (>= 3.3), viper License: file LICENSE MD5sum: 91ae5366b9bf99c3863d310e5eb86277 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: c9cb8e9 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/aracne.networks_1.27.0.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: 91 Package: ARRmData Version: 1.37.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: 2c91a87cb67d4cfaa46968745a357326 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: ad2011f git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/ARRmData_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ARRmNormalization dependencyCount: 0 Package: AshkenazimSonChr21 Version: 1.31.0 Suggests: knitr, VariantAnnotation License: Artistic-2.0 MD5sum: 59249f9b68cc5e6128434a1c94175b94 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: fc910f9 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/AshkenazimSonChr21_1.31.0.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: 1.21.0 Depends: R (>= 3.5) Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 92263b0fc7bfb03728be5019d29b16f1 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: 036b88b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/ASICSdata_1.21.0.tar.gz vignettes: vignettes/ASICSdata/inst/doc/ASICSdata.html vignetteTitles: ASICSdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ASICS dependencyCount: 0 Package: AssessORFData Version: 1.19.0 Depends: R (>= 3.5.0) Imports: DECIPHER, utils Suggests: AssessORF, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 5f778f14e9c59ae753227bdd9c1e1298 NeedsCompilation: no Title: Data and Files for the AssessORF Package Description: This package provides access to mapping and results objects generated by the AssessORF package, as well as the genome sequences for the strains corresponding to those objects. biocViews: OrganismData, Bacillus_subtilis_Data, Escherichia_coli_Data, Pseudomonas_aeruginosa_Data, Staphylococcus_aureus_Data, Genome, Proteome, SequencingData Author: Deepank Korandla [aut, cre] Maintainer: Deepank Korandla VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/AssessORFData git_branch: devel git_last_commit: 502e39a git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/AssessORFData_1.19.0.tar.gz vignettes: vignettes/AssessORFData/inst/doc/AssessORFDataGuide.pdf vignetteTitles: Using AssessORFData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/AssessORFData/inst/doc/AssessORFDataGuide.R suggestsMe: AssessORF dependencyCount: 36 Package: bcellViper Version: 1.37.0 Depends: R(>= 2.14.0), Biobase, methods License: GPL (>=2) MD5sum: 3036f75104299efe95224f55a2f1ed1a 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: fec0887 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/bcellViper_1.37.0.tar.gz vignettes: vignettes/bcellViper/inst/doc/bcellViper.pdf vignetteTitles: Using bcellViper hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bcellViper/inst/doc/bcellViper.R importsMe: dorothea suggestsMe: GenomicSuperSignature, iterClust, pageRank, viper dependencyCount: 6 Package: beadarrayExampleData Version: 1.39.0 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>= 2.0.0) License: GPL-2 MD5sum: 43563815bf84427ee21504f6f52b627a 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: c265f8c git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/beadarrayExampleData_1.39.0.tar.gz vignettes: vignettes/beadarrayExampleData/inst/doc/beadarrayExampleData.pdf vignetteTitles: beadarrayExampleData: example data for the beadarray package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/beadarrayExampleData/inst/doc/beadarrayExampleData.R suggestsMe: beadarray, MiRaGE, RobLoxBioC dependencyCount: 81 Package: BeadArrayUseCases Version: 1.39.0 Imports: beadarray (>= 2.3.18), limma, GEOquery Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db License: GPL-2 MD5sum: 2e58379a58401a78432c5cf3772539fd 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: 5cd1e36 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/BeadArrayUseCases_1.39.0.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: 1.9.0 Depends: R (>= 4.1), minfi(>= 1.36.0), ExperimentHub Suggests: knitr, rmarkdown License: GPL-3 MD5sum: b94f20c9de1b03e0c33e64fad1226611 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: c98f53c git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/BeadSorted.Saliva.EPIC_1.9.0.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: 171 Package: benchmarkfdrData2019 Version: 1.15.0 Depends: R (>= 3.6.0), SummarizedExperiment, ExperimentHub Imports: utils Suggests: rmarkdown, knitr, BiocStyle, testthat, SummarizedBenchmark, dplyr, ggplot2, rlang License: MIT + file LICENSE MD5sum: a7826fdd548d0dac2480a38b174d7ec8 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: a40d06b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/benchmarkfdrData2019_1.15.0.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: 106 Package: beta7 Version: 1.39.0 Depends: R (>= 2.4.0), marray License: LGPL MD5sum: 2c84ae84c28709075c48b7c383df2853 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: e248982 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/beta7_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: BioImageDbs Version: 1.9.0 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: 098263f02a8a7f7b09c5c61ebf3c7a65 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: e2b4f42 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/BioImageDbs_1.9.0.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: 113 Package: BioPlex Version: 1.7.0 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: c4f810cbd8c4f81151494748a8318297 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: c02a811 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/BioPlex_1.7.0.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: 83 Package: biotmleData Version: 1.25.0 Depends: R (>= 3.5.0) Suggests: Biobase, SummarizedExperiment License: file LICENSE MD5sum: 80452a5134cf7f7da68ac266ad60a51c 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: f3595b6 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/biotmleData_1.25.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: biotmle dependencyCount: 0 Package: bladderbatch Version: 1.39.0 Depends: Biobase License: Artistic-2.0 MD5sum: aca08c637c1b44228c9aa07fb2242679 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: 61e23d5 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/bladderbatch_1.39.0.tar.gz vignettes: vignettes/bladderbatch/inst/doc/bladderbatch.pdf vignetteTitles: bladderbatchTutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bladderbatch/inst/doc/bladderbatch.R importsMe: RUVcorr suggestsMe: Harman, sva dependencyCount: 6 Package: blimaTestingData Version: 1.21.0 Depends: R(>= 3.0.0) Suggests: blima, beadarray, illuminaHumanv4.db, BiocStyle License: GPL-3 MD5sum: fe6029790adeb5b547c2e66c54ebb72b 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: 4c1d549 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/blimaTestingData_1.21.0.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: 1.21.0 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: b46a9f2bbd3be42a903d8a63970baf8b 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: 936474b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/BloodCancerMultiOmics2017_1.21.0.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: 1.17.0 Depends: R (>= 3.6.0), SummarizedExperiment, ExperimentHub Imports: utils Suggests: rmarkdown, knitr, BiocStyle, testthat License: CC BY 4.0 MD5sum: e14cde65d45d4afc44a2c129cf84bddf 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: 2e20490 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/bodymapRat_1.17.0.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: 106 Package: breakpointRdata Version: 1.19.0 Depends: R (>= 3.5) Suggests: knitr, BiocStyle, License: file LICENSE MD5sum: 6af3fa80a0c8389a62d5452db996a226 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: 3471d55 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/breakpointRdata_1.19.0.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: 1.39.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 86f20eb9ee1611ecb896ebe838fbfd6a 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: 61786a2 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/breastCancerMAINZ_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: DART, genefu dependencyCount: 0 Package: breastCancerNKI Version: 1.39.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 5165e93d06ce64126a4b581f3f0c5969 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: a458843 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/breastCancerNKI_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, SigCheck dependencyCount: 0 Package: breastCancerTRANSBIG Version: 1.39.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 74b2c6582a7edf66ddda6ed22431bef2 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: 48ede50 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/breastCancerTRANSBIG_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, GSgalgoR dependencyCount: 0 Package: breastCancerUNT Version: 1.39.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 7dc273372d1524471177c5c9b17e1f62 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: a681a47 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/breastCancerUNT_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu dependencyCount: 0 Package: breastCancerUPP Version: 1.39.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: dcf46992f6b5459173f854218243c428 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: 4068357 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/breastCancerUPP_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, GSgalgoR, safe dependencyCount: 0 Package: breastCancerVDX Version: 1.39.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: f35eb180b949a8b68123f235d27eede7 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: 7c4725b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/breastCancerVDX_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: BAGS suggestsMe: AIMS, DART, genefu dependencyCount: 0 Package: bsseqData Version: 0.39.0 Depends: R (>= 3.5.0), bsseq (>= 1.16.0) License: Artistic-2.0 MD5sum: c9fd9da271a995811f9d9260dfa1ef73 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: 33cda4a git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/bsseqData_0.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: bsseq dependencyCount: 78 Package: cancerdata Version: 1.39.0 Depends: R (>= 2.10.1), Biobase License: GPL (>= 2) MD5sum: 7df87f57ffaea76fbab8274c07cdcf55 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: 079438d git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/cancerdata_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: cancerclass dependencyCount: 6 Package: CardinalWorkflows Version: 1.33.0 Depends: R (>= 2.10), Cardinal Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 9db120ade9e772a8815719e5d212166f 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: 9a34ba1 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/CardinalWorkflows_1.33.0.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: 76 Package: ccdata Version: 1.27.0 Depends: R (>= 3.3) License: MIT + file LICENSE MD5sum: 827a3072c4d2bbc0d56f982ddc8d8731 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: 5718a3c git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/ccdata_1.27.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE importsMe: ccmap suggestsMe: retriever dependencyCount: 0 Package: CCl4 Version: 1.39.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), limma License: Artistic-2.0 MD5sum: 945794c35807fb1f73bdb7e1b29d9e5f 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: 1c0971b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/CCl4_1.39.0.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 dependencyCount: 8 Package: celarefData Version: 1.19.0 Depends: R (>= 3.5.0) Suggests: ExperimentHub, knitr, rmarkdown License: GPL-3 MD5sum: ff5fb3fd2578bfa8272e39db2f93e8f6 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: b624eb7 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/celarefData_1.19.0.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: 1.11.1 Depends: SummarizedExperiment Imports: utils, ExperimentHub, AnnotationHub, AnnotationDbi, S4Vectors, DelayedArray, DelayedMatrixStats Suggests: testthat, knitr, rmarkdown, BiocStyle, DT, ensembldb License: GPL-3 MD5sum: 4ce04203d1eeb7954919674a20061e9f NeedsCompilation: no Title: Reference Index for Cell Types Description: Provides a collection of reference expression datasets with curated cell type labels, for use in procedures like automated annotation of single-cell data or deconvolution of bulk RNA-seq. biocViews: ExperimentHub, ExperimentData, ExpressionData, SequencingData, RNASeqData Author: Dvir Aran [aut], Aaron Lun [aut, cre, cph], Daniel Bunis [aut], Jared Andrews [aut], Friederike Dündar [aut] Maintainer: Aaron Lun URL: https://github.com/LTLA/celldex VignetteBuilder: knitr BugReports: https://support.bioconductor.org/ git_url: https://git.bioconductor.org/packages/celldex git_branch: devel git_last_commit: 69ceda1 git_last_commit_date: 2023-05-25 Date/Publication: 2023-05-25 source.ver: src/contrib/celldex_1.11.1.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 importsMe: singleCellTK suggestsMe: ontoProc, SingleR, tidySingleCellExperiment dependencyCount: 108 Package: CellMapperData Version: 1.27.0 Depends: ExperimentHub, CellMapper Suggests: BiocStyle License: Artistic-2.0 MD5sum: 4dbb9475c8489f819e26f20628812e05 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: 8039bc5 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/CellMapperData_1.27.0.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: 97 Package: ChAMPdata Version: 2.33.0 Depends: R (>= 3.5.0), GenomicRanges (>= 1.22.4), BiocGenerics (>= 0.16.1) License: GPL-3 MD5sum: f1c66ddc796e5ebb262b13c9d91be197 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: ccd7e35 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/ChAMPdata_2.33.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 16 Package: ChIC.data Version: 1.21.0 Depends: R (>= 3.5), genomeIntervals, randomForest Imports: caret (>= 6.0-78) License: GPL-2 MD5sum: de2b4195307bae5e8a5118292f17dbae NeedsCompilation: no Title: ChIC package data Description: This package contains annotation and metagene profile data for the ChIC package. biocViews: ExperimentData, ENCODE Author: Carmen Maria Livi [aut, cre, dtc], Endre Sebestyen [aut] Maintainer: Carmen Maria Livi git_url: https://git.bioconductor.org/packages/ChIC.data git_branch: devel git_last_commit: 868c653 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/ChIC.data_1.21.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 99 Package: chipenrich.data Version: 2.25.0 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: f7f4d1969d3540a6eb7f45e860ce7e57 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: 36fa232 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/chipenrich.data_2.25.0.tar.gz vignettes: vignettes/chipenrich.data/inst/doc/chipenrich.data-vignette.html vignetteTitles: chipenrich.data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/chipenrich.data/inst/doc/chipenrich.data-vignette.R importsMe: chipenrich dependencyCount: 88 Package: ChIPexoQualExample Version: 1.25.0 Depends: R (>= 3.3) Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 2da21ff14749c699a540c14668543987 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: c85f9d7 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/ChIPexoQualExample_1.25.0.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: 1.17.0 Imports: AnnotationHub, ExperimentHub, Rsamtools, S4Vectors Suggests: knitr, BiocStyle, rmarkdown License: CC BY 4.0 MD5sum: d2527b1ca75c0525f94f20411ef88bff 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: 7f11d62 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/chipseqDBData_1.17.0.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: 108 Package: ChIPXpressData Version: 1.39.0 Depends: bigmemory License: GPL (>=2) MD5sum: e7d4d0ed6078bf401bf7300849d1467c 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: d9d6ab5 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/ChIPXpressData_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: chromstaRData Version: 1.27.0 Depends: R (>= 3.3) License: GPL-3 MD5sum: 912b33df2c161a106036603dfb2da7d1 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: 72e9868 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/chromstaRData_1.27.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: chromstaR suggestsMe: epigraHMM dependencyCount: 0 Package: CLLmethylation Version: 1.21.0 Depends: R (>= 3.5.0) Imports: SummarizedExperiment, ExperimentHub Suggests: BiocStyle, ggplot2, knitr, rmarkdown License: LGPL MD5sum: 62d25adbb99ed5be949d64725752513e 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: 61e3393 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/CLLmethylation_1.21.0.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: 106 Package: CluMSIDdata Version: 1.17.0 Depends: R (>= 3.6) License: MIT + file LICENSE MD5sum: 4d77bf9de62528ef392086bc3c9cc78a 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: d9bc3d2 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/CluMSIDdata_1.17.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: clustifyrdatahub Version: 1.11.0 Depends: R (>= 4.0), ExperimentHub Imports: utils Suggests: clustifyr, Seurat, usethis, rmarkdown, knitr, tidyr, BiocStyle License: MIT + file LICENSE MD5sum: 1e7b415c921220b2987b93823ca03811 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: 89701c1 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/clustifyrdatahub_1.11.0.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: 96 Package: cMap2data Version: 1.37.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 84468edab1da97eb8635d6b459b06e6d 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: 59a5d9b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/cMap2data_1.37.0.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 dependencyCount: 0 Package: cnvGSAdata Version: 1.37.0 Depends: R (>= 2.10), cnvGSA License: LGPL MD5sum: a2af711c6342541bbddd799f8add35e5 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: 09db64c git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/cnvGSAdata_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: cnvGSA dependencyCount: 26 Package: COHCAPanno Version: 1.37.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 0d0ffe41ceb155c2cfc2357d847ffd5e 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: fe5728b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/COHCAPanno_1.37.0.tar.gz vignettes: vignettes/COHCAPanno/inst/doc/COHCAPanno.pdf vignetteTitles: COHCAPanno Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/COHCAPanno/inst/doc/COHCAPanno.R dependsOnMe: COHCAP dependencyCount: 0 Package: colonCA Version: 1.43.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: 269dd8381804928a5518af5faaed34bc 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: d1007ed git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/colonCA_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: clustComp, copa dependencyCount: 6 Package: CONFESSdata Version: 1.29.0 Depends: R (>= 3.3) License: GPL-2 MD5sum: 8823862f7e67f962c68ca149d8de688e 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: 27f77a6 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/CONFESSdata_1.29.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CONFESS dependencyCount: 0 Package: ConnectivityMap Version: 1.37.0 Depends: R (>= 2.15.1) Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 9566db7441215e19a4429953fb64e204 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: 42b66fd git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/ConnectivityMap_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: COPDSexualDimorphism.data Version: 1.37.0 License: LGPL-2.1 MD5sum: 9ce0e6be451cd849ad2d665589f73c5d 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: e0ec951 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/COPDSexualDimorphism.data_1.37.0.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: 1.33.0 Depends: R (>= 3.5.0) Suggests: BiocStyle License: GPL-2 MD5sum: d8a4ed9df08f514794be631479cd05a5 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: c4398e4 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/CopyhelpeR_1.33.0.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: 1.19.0 Depends: R (>= 3.5.0) Imports: ExperimentHub,Rdpack (>= 0.8) Suggests: BiocStyle,knitr,rmarkdown,minfi,conumee,minfiData License: Artistic-2.0 MD5sum: 435242bfc018a399eba022cc009fded0 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: 8f2e9aa git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/CopyNeutralIMA_1.19.0.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: 98 Package: CoSIAdata Version: 1.1.0 Depends: R (>= 4.3.0), ExperimentHub (>= 2.6.0), Suggests: BiocStyle (>= 2.26.0), utils (>= 4.3.0), AnnotationHub (>= 3.7.3), knitr (>= 1.42) License: MIT + file LICENSE MD5sum: 9808aef9810ef641fbe63e601a2a5c40 NeedsCompilation: no Title: VST normalized RNA-Sequencing data with annotations for multiple species samples from Bgee Description: Variance Stabilized Transformation of Read Counts derived from Bgee RNA-Seq Expression Data. Expression Data includes annotations and is across 6 species (Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Drosophila melanogaster, and Caenorhabditis elegans) and across more than 132 tissues. The data is represented as a RData files and is available in ExperimentHub. biocViews: ExperimentHub, RNASeqData, ExperimentData, PackageTypeData, OrganismData, Tissue,Caenorhabditis_elegans_Data, Danio_rerio_Data, Drosophila_melanogaster_Data, Homo_sapiens_Data, Mus_musculus_Data, Rattus_norvegicus_Data, SequencingData, ExpressionData Author: Anisha Haldar [aut] (), Vishal H. Oza [aut] (), Amanda D. Clark [cre, aut] (), Nathaniel S. DeVoss [aut] (), Brittany N. Lasseigne [aut] () Maintainer: Amanda D. Clark VignetteBuilder: knitr BugReports: https://github.com/lasseignelab/CoSIAdata/issues git_url: https://git.bioconductor.org/packages/CoSIAdata git_branch: devel git_last_commit: 3f3f229 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/CoSIAdata_1.1.0.tar.gz vignettes: vignettes/CoSIAdata/inst/doc/CoSIAdata_vignette.html vignetteTitles: CoSIAdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/CoSIAdata/inst/doc/CoSIAdata_vignette.R dependencyCount: 96 Package: COSMIC.67 Version: 1.37.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, SummarizedExperiment, VariantAnnotation Suggests: testthat, BiocStyle, knitr License: GPL-3 MD5sum: a7ccb1cc802ad53e85c5bdbc969502f5 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: ae5062d git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/COSMIC.67_1.37.0.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: 100 Package: CRCL18 Version: 1.21.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: b9936e883349befe704d7491326852d7 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: 3fad521 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/CRCL18_1.21.0.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: 1.5.0 Depends: ExperimentHub Imports: AnnotationHub, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: b8b5d13d3056ef803dd6c3efc2f19218 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: 9a8372f git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/crisprScoreData_1.5.0.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: 96 Package: curatedAdipoArray Version: 1.13.0 Depends: R (>= 4.0) Suggests: knitr, rmarkdown, ExperimentHub, SummarizedExperiment License: GPL-3 + file LICENSE MD5sum: 2ee5131b2a881f2ce906f74a81931c18 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: df065a5 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/curatedAdipoArray_1.13.0.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: 1.17.0 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: 4f8d89f203f398be07c6222788c619c2 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: 4b46f9a git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/curatedAdipoChIP_1.17.0.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: 106 Package: curatedAdipoRNA Version: 1.17.0 Depends: R (>= 3.6), SummarizedExperiment Suggests: knitr, rmarkdown, DESeq2, fastqcr, devtools, testthat, readr, dplyr, tidyr, ggplot2, S4Vectors License: GPL-3 MD5sum: 5cd0531b6eec9b58b28cdbd3b0c5bd26 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: 28c7992 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/curatedAdipoRNA_1.17.0.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: 28 Package: curatedBreastData Version: 2.29.0 Depends: R (>= 3.0.0), XML, ggplot2, impute, Biobase, BiocStyle Imports: methods, stats License: GPL (>= 2) MD5sum: d24b2e9f07707112ea684d6835d4f588 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: a1b336a git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/curatedBreastData_2.29.0.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: 67 Package: curatedCRCData Version: 2.33.0 Depends: R (>= 2.10.0), nlme Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle License: Artistic-2.0 MD5sum: 05c779c2579641fccb680422a776cbe1 NeedsCompilation: no Title: Colorectal Cancer Gene Expression Analysis Description: The curatedCRC package provides relevant functions and data for gene expression analysis in patients with colorectal cancer. biocViews: Colorectal, Cancer, TCGA, ExperimentData, RNAExpressionData Author: Princy Parsana, Markus Riester, Curtis Huttenhower, Levi Waldron Maintainer: Princy Parsana URL: https://bitbucket.org/biobakery/curatedcrcdata git_url: https://git.bioconductor.org/packages/curatedCRCData git_branch: devel git_last_commit: 098620a git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/curatedCRCData_2.33.0.tar.gz vignettes: vignettes/curatedCRCData/inst/doc/curatedCRCData_vignette.pdf vignetteTitles: curatedCRCData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedCRCData/inst/doc/curatedCRCData_vignette.R dependencyCount: 9 Package: curatedMetagenomicData Version: 3.9.0 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: 9b1f637ecf3a1c207d99b23f4b3a934f 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: efab363 git_last_commit_date: 2023-04-25 Date/Publication: 2023-05-23 source.ver: src/contrib/curatedMetagenomicData_3.9.0.tar.gz vignettes: vignettes/curatedMetagenomicData/inst/doc/curatedMetagenomicData.html vignetteTitles: curatedMetagenomicData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedMetagenomicData/inst/doc/curatedMetagenomicData.R suggestsMe: lefser dependencyCount: 187 Package: curatedTBData Version: 1.7.0 Depends: R (>= 4.1.0) Imports: AnnotationHub, ExperimentHub, MultiAssayExperiment, rlang, stats Suggests: BiocStyle, DT, dplyr, HGNChelper, knitr, methods, rmarkdown, SummarizedExperiment, sva, testthat License: MIT + file LICENSE MD5sum: a6652b369c1223247a8d6afb3d1991bd NeedsCompilation: no Title: Curation of existing 49 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: b633558 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/curatedTBData_1.7.0.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: 108 Package: curatedTCGAData Version: 1.23.4 Depends: R (>= 4.2.0), MultiAssayExperiment Imports: AnnotationHub, ExperimentHub, HDF5Array, methods, S4Vectors, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, RaggedExperiment, readr, rmarkdown, TCGAutils, testthat License: Artistic-2.0 MD5sum: 20c57356d8d3fe45deb163f7d57375a8 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: 4d04b47 git_last_commit_date: 2023-05-19 Date/Publication: 2023-05-23 source.ver: src/contrib/curatedTCGAData_1.23.4.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, glmSparseNet, IntOMICS, netDx, TCGAutils dependencyCount: 112 Package: depmap Version: 1.15.0 Depends: R (>= 3.6), methods, dplyr Imports: utils, ExperimentHub, AnnotationHub Suggests: knitr, rmarkdown, BiocStyle, viridis, gridExtra, ggplot2, readr, tibble, stringr, tidyr License: Artistic-2.0 MD5sum: a18dcc96879ec2f2182ac7eb639367dd 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: 9974ba3 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/depmap_1.15.0.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: mastR, BioPlex dependencyCount: 96 Package: derfinderData Version: 2.19.0 Depends: R (>= 3.5.0) Suggests: sessioninfo, knitr (>= 1.6), RefManageR, rmarkdown (>= 0.3.3), BiocStyle License: Artistic-2.0 MD5sum: de6e52b59dd588d27c1e72a9c7d50610 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: f8f848f git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/derfinderData_2.19.0.tar.gz vignettes: vignettes/derfinderData/inst/doc/derfinderData.html vignetteTitles: Introduction to derfinderData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/derfinderData/inst/doc/derfinderData.R suggestsMe: derfinder, derfinderPlot dependencyCount: 0 Package: DExMAdata Version: 1.9.0 Depends: R (>= 4.1) Imports: Biobase Suggests: BiocStyle License: GPL-2 MD5sum: f09a899860d72dbe417fd1af0810114e 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: 7b72a16 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/DExMAdata_1.9.0.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: 1.29.0 Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 8678839a6cfcaedf06704545b5ea6bb9 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: a989063 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/diffloopdata_1.29.0.tar.gz vignettes: vignettes/diffloopdata/inst/doc/diffloopdata.html vignetteTitles: diffloopdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: diggitdata Version: 1.33.0 Depends: R(>= 2.14.0), Biobase, methods Imports: viper License: GPL (>=2) MD5sum: b603e5b268d728e34af571f96e78a8cf 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: d43edba git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/diggitdata_1.33.0.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: 91 Package: DmelSGI Version: 1.33.0 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: 6acfbdd13bd556bd879a93819a71e95c 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: 22883f5 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/DmelSGI_1.33.0.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: 33 Package: DMRcatedata Version: 2.19.0 Depends: R (>= 3.6), ExperimentHub Imports: GenomicFeatures, Gviz, readxl, plyr, rtracklayer, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr License: GPL-3 MD5sum: 89011538c070e286d53b6ac77798d282 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: 08fd31d git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/DMRcatedata_2.19.0.tar.gz vignettes: vignettes/DMRcatedata/inst/doc/DMRcatedata.pdf vignetteTitles: The DMRcate package user's guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DMRcatedata/inst/doc/DMRcatedata.R dependencyCount: 211 Package: DNAZooData Version: 1.1.0 Depends: R (>= 4.2), HiCExperiment Imports: BiocFileCache, S4Vectors, rjson, utils, tools Suggests: dplyr, testthat, methods, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: d161193f619da2a3a271284122eae575 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: bcc0007 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/DNAZooData_1.1.0.tar.gz vignettes: vignettes/DNAZooData/inst/doc/DNAZooData.html vignetteTitles: DNAZooData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/DNAZooData/inst/doc/DNAZooData.R dependencyCount: 91 Package: DonaPLLP2013 Version: 1.39.0 Depends: EBImage, parallel License: Artistic-2.0 MD5sum: 7d6f72fb3eb0c9aa00b63a7aafe3b74d 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: 4c6b9a0 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/DonaPLLP2013_1.39.0.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: 51 Package: dorothea Version: 1.13.0 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: 4cbe8f636cff263ca83c3b751520de25 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: c004211 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/dorothea_1.13.0.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 dependencyCount: 37 Package: dressCheck Version: 0.39.0 Depends: R (>= 2.10.1), methods, Biobase (>= 2.5.5) Suggests: survival, chron License: Artistic-2.0 MD5sum: 61fb949295fccb94888bf7acfab7009c 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: 2986095 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/dressCheck_0.39.0.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: 1.11.0 Imports: utils, ExperimentHub, AnnotationHub, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, testthat, DropletUtils License: GPL-3 MD5sum: f7f96c18b7a70442bbecbf3c6e46ff10 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: 817c400 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/DropletTestFiles_1.11.0.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: 96 Package: DrugVsDiseasedata Version: 1.37.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: c13cdd995a5c84e2dad5cbc373e40658 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: 0622731 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/DrugVsDiseasedata_1.37.0.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 dependencyCount: 0 Package: DuoClustering2018 Version: 1.19.0 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: cc7139bda9935f7350a1cf6195c1b2c8 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: 8a88a62 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/DuoClustering2018_1.19.0.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, scellpam dependencyCount: 119 Package: DvDdata Version: 1.37.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 85ab893cbee0a9be87706876bf98a216 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: 0207400 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/DvDdata_1.37.0.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: 1.41.0 Depends: R (>= 1.4.1), marray, GEOquery Suggests: dyebias, convert, Biobase License: GPL-3 MD5sum: c75e5e3de91340e2c3f6e06e2758e386 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: fe706d1 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/dyebiasexamples_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: dyebias dependencyCount: 48 Package: easierData Version: 1.7.0 Depends: R (>= 4.1.0) Imports: ExperimentHub, AnnotationHub, utils, SummarizedExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 2ef1c2951a7ac959f83a3d83a738f631 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: 5a782c5 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/easierData_1.7.0.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: 106 Package: EatonEtAlChIPseq Version: 0.39.0 Depends: GenomicRanges (>= 1.5.42), ShortRead, rtracklayer License: Artistic 2.0 MD5sum: fed03e68b37b3ff4795c64df9e906f86 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: 8e8707f git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/EatonEtAlChIPseq_0.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 59 Package: EGSEAdata Version: 1.29.0 Depends: R (>= 3.4) Suggests: EGSEA License: file LICENSE MD5sum: c47d1fe2a85ae8e87f16e66e1489cb64 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: 65d0a7c git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/EGSEAdata_1.29.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: ELMER.data Version: 2.25.0 Depends: R (>= 3.5.0) Imports: GenomicRanges Suggests: BiocStyle, knitr, dplyr, devtools, DT, rmarkdown License: GPL-3 MD5sum: b68a2f23cfe85f2b5dfc7016b444174f 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: cf21e82 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/ELMER.data_2.25.0.tar.gz vignettes: vignettes/ELMER.data/inst/doc/vignettes.html vignetteTitles: ELMER.data: Supporting data for the ELMER package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ELMER.data/inst/doc/vignettes.R dependsOnMe: ELMER dependencyCount: 16 Package: emtdata Version: 1.9.0 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: e3b818b72e5863acb0729ea82168ca29 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: cfd5e57 git_last_commit_date: 2023-04-25 Date/Publication: 2023-05-23 source.ver: src/contrib/emtdata_1.9.0.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: 109 Package: epimutacionsData Version: 1.5.0 Depends: R (>= 4.2.0) Suggests: rmarkdown, BiocStyle, knitr, ExperimentHub, minfi License: MIT + file LICENSE MD5sum: 800dd4fda90f970c4a22cada8d86ba73 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: 19648bd git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/epimutacionsData_1.5.0.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: etec16s Version: 1.29.0 Depends: R (>= 3.3), Biobase, metagenomeSeq(>= 1.12.0) License: Artistic-2.0 MD5sum: f5974849193015167bd88ac75187610f 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: 5b6e2ea git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/etec16s_1.29.0.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: 31 Package: ewceData Version: 1.9.0 Depends: R (>= 4.1), ExperimentHub Suggests: knitr, BiocStyle, ggplot2, cowplot, rmarkdown, markdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: e139f3932414c8588dd5515d81c9e29d 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: 3d4f10c git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/ewceData_1.9.0.tar.gz vignettes: vignettes/ewceData/inst/doc/ewceData.html vignetteTitles: Data package for Expression Weighted Celltype Enrichment EWCE hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ewceData/inst/doc/ewceData.R importsMe: EWCE dependencyCount: 96 Package: fabiaData Version: 1.39.0 Depends: R (>= 2.10.0), Biobase Imports: utils Suggests: fabia License: LGPL (>= 2.1) MD5sum: 15ce50776bccf137ea91f0b0073cd9c7 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: 2917be8 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/fabiaData_1.39.0.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: 1.37.0 Depends: R (>= 2.15.0) License: GPL-3 MD5sum: b06733c03b0ef6c4d44a94ab30a19e9e 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: 6691cfb git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/FANTOM3and4CAGE_1.37.0.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: fibroEset Version: 1.43.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: b8839d362cab6366d7a01478f9dc9b53 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: a15fa31 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/fibroEset_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: biocGraph, clusterStab, geneplotter dependencyCount: 6 Package: FieldEffectCrc Version: 1.11.0 Depends: utils Imports: BiocStyle, RUnit, SummarizedExperiment, ExperimentHub (>= 0.99.6), AnnotationHub, DESeq2 Suggests: knitr, rmarkdown, BiocGenerics, sva, BiocManager License: Artistic-2.0 MD5sum: 77ab8203708f1d4000c3b93a7253a369 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: 8c14cb2 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/FieldEffectCrc_1.11.0.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: 135 Package: FIs Version: 1.29.0 Depends: R (>= 3.3) License: GPL-3 MD5sum: 9a833a3945e8021440e966f32410e832 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: 3bf355d git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/FIs_1.29.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: splineTimeR dependencyCount: 0 Package: fission Version: 1.21.0 Depends: R (>= 2.10), SummarizedExperiment Suggests: knitr, markdown License: LGPL MD5sum: eb10458b34e37eb438613c99b07acd57 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: bb59ef8 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/fission_1.21.0.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 dependencyCount: 28 Package: Fletcher2013a Version: 1.37.0 Depends: R (>= 2.15), limma Imports: Biobase ,VennDiagram, gplots,grid License: GPL (>= 2) MD5sum: a6f5911a9e75adf4d31813440f0c3ce5 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: ed78487 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/Fletcher2013a_1.37.0.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: 19 Package: Fletcher2013b Version: 1.37.0 Depends: R (>= 2.15), Fletcher2013a, RTN (>= 1.1.2), RedeR (>= 1.8.1), igraph Imports: RColorBrewer License: GPL (>= 2) MD5sum: 30c1862c21f6eae2a94204c31d651e11 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: 73a53dd git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/Fletcher2013b_1.37.0.tar.gz vignettes: vignettes/Fletcher2013b/inst/doc/Fletcher2013b.pdf vignetteTitles: Main vignette:Fletcher2013b hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Fletcher2013b/inst/doc/Fletcher2013b.R suggestsMe: geneplast, RTNsurvival dependencyCount: 154 Package: flowPloidyData Version: 1.27.0 Suggests: knitr, rmarkdown, flowCore License: GPL-3 MD5sum: 127744f1c6df1da224cfe787f2e6bda6 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: 88a1df7 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/flowPloidyData_1.27.0.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: 1.39.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 5cbe9a725b9828b113b31162db89b350 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: 697df84 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/FlowSorted.Blood.450k_1.39.0.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 suggestsMe: mCSEA, minfi, FlowSorted.Blood.EPIC dependencyCount: 142 Package: FlowSorted.Blood.EPIC Version: 2.5.2 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: 24e7cdf9b7eaefc885540316755810dc 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: d7fe58f git_last_commit_date: 2023-05-18 Date/Publication: 2023-05-23 source.ver: src/contrib/FlowSorted.Blood.EPIC_2.5.2.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 suggestsMe: FlowSorted.CordBloodCombined.450k dependencyCount: 171 Package: FlowSorted.CordBlood.450k Version: 1.29.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: c04476c3477972e9ebe40c9661141181 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: 7e3662e git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/FlowSorted.CordBlood.450k_1.29.0.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: 142 Package: FlowSorted.CordBloodCombined.450k Version: 1.17.0 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: 08206216db3e0e2b1e9a4f0c1626f2ed 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: ae904e8 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/FlowSorted.CordBloodCombined.450k_1.17.0.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: 173 Package: FlowSorted.CordBloodNorway.450k Version: 1.27.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: c13852bd22980698c4709787aee36f24 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: be4a325 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/FlowSorted.CordBloodNorway.450k_1.27.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 142 Package: FlowSorted.DLPFC.450k Version: 1.37.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: c9017a01904f3586740fd3757751c521 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: ad1f5cf git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/FlowSorted.DLPFC.450k_1.37.0.tar.gz vignettes: vignettes/FlowSorted.DLPFC.450k/inst/doc/FlowSorted.DLPFC.450k.pdf vignetteTitles: FlowSorted DLPFC 450k Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.DLPFC.450k/inst/doc/FlowSorted.DLPFC.450k.R dependencyCount: 142 Package: flowWorkspaceData Version: 3.13.0 License: GPL-2 MD5sum: 31738ec55a2cad5f44790403fc26ae45 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: 308c871 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/flowWorkspaceData_3.13.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: COMPASS, CytoML, flowClust, flowCore, flowWorkspace, ggcyto, openCyto dependencyCount: 0 Package: fourDNData Version: 1.1.0 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: a223a0f169dc37d902196112b2134619 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: dd7173b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/fourDNData_1.1.0.tar.gz vignettes: vignettes/fourDNData/inst/doc/fourDNData.html vignetteTitles: fourDNData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/fourDNData/inst/doc/fourDNData.R dependencyCount: 90 Package: frmaExampleData Version: 1.37.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: c74b7d0452651f2661cfa94f0006dabb 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: d93eccf git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/frmaExampleData_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: furrowSeg Version: 1.29.0 Depends: R (>= 3.3), EBImage Imports: abind, dplyr, locfit, tiff Suggests: BiocStyle, ggplot2, knitr License: Artistic-2.0 MD5sum: 5f17a1c0c7ed6c763b05de196edc0a75 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: 3b6db8e git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/furrowSeg_1.29.0.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: 59 Package: gageData Version: 2.39.0 Depends: R (>= 2.10) Suggests: gage, pathview, genefilter License: GPL (>=2.0) MD5sum: 27a2db1cbd1f282f0f26bfbee9e80adf 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: e31228e git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/gageData_2.39.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: gage dependencyCount: 0 Package: gaschYHS Version: 1.39.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 59caae554d9cdc35a7f76fba994fc7d8 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: dde4a78 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/gaschYHS_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 6 Package: gcspikelite Version: 1.39.0 Depends: R (>= 2.5.0) License: LGPL MD5sum: 85a0c89a98354b9801a9e42a8e7ae663 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: d2f3daa git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/gcspikelite_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: gDNAinRNAseqData Version: 1.1.0 Depends: R (>= 4.3) Imports: RCurl, XML, ExperimentHub, BiocGenerics, Rsamtools Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 317518839bd47403e44a982832bcf49e 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: 47dd677 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/gDNAinRNAseqData_1.1.0.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 dependencyCount: 109 Package: geneLenDataBase Version: 1.37.0 Depends: R (>= 2.11.0) Imports: utils, rtracklayer, GenomicFeatures (>= 1.3.15) License: LGPL (>= 2) MD5sum: 8edbeb773b90ae82ad88af29c3507748 NeedsCompilation: no Title: Lengths of mRNA transcripts for a number of genomes Description: Length of mRNA transcripts for a number of genomes and gene ID formats, largely based on UCSC table browser biocViews: ExperimentData, Genome Author: Matthew Young Maintainer: Matthew Young , Nadia Davidson git_url: https://git.bioconductor.org/packages/geneLenDataBase git_branch: devel git_last_commit: e2510e7 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/geneLenDataBase_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: goseq importsMe: SMITE dependencyCount: 98 Package: genomationData Version: 1.33.0 Suggests: knitr License: GPL-3 MD5sum: 26c5e977814027f5e25088967e7d5113 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: 45fe5bc git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/genomationData_1.33.0.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: 1.9.0 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: 277e39544d7a03520308fec7a43c25ef 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: 0dd2c30 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/GenomicDistributionsData_1.9.0.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: 134 Package: GeuvadisTranscriptExpr Version: 1.29.0 Depends: R (>= 3.5.0) Suggests: limma, rtracklayer, GenomicRanges, Rsamtools, VariantAnnotation, tools, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: b890598743d95353db8688f3376ff282 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: dd5acd6 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/GeuvadisTranscriptExpr_1.29.0.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: 1.19.0 Depends: R (>= 3.5) Suggests: GIGSEA, knitr, rmarkdown License: LGPL-3 MD5sum: 5d4c8667471f394eeaaa7b77e26855b2 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: dcd7397 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/GIGSEAdata_1.19.0.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: 1.43.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: LGPL MD5sum: 3f9901effb2770aa0760a32709f60cee 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: c05c1d7 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/golubEsets_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: adSplit, Biobase, biosigner, GlobalAncova, globaltest, idiogram, MLInterfaces, RDRToolbox, twilight dependencyCount: 6 Package: gpaExample Version: 1.13.0 Depends: R (>= 4.0.0) License: GPL (>= 2) MD5sum: ec5ad774b71fa83a8d4325ba4d366301 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: 9285a40 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/gpaExample_1.13.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GPA dependencyCount: 0 Package: grndata Version: 1.33.0 Depends: R (>= 2.10) Suggests: RUnit, BiocGenerics, knitr License: GPL-3 MD5sum: fe61e09d32cae5344338bbed59679200 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: 4d8f960 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/grndata_1.33.0.tar.gz vignettes: vignettes/grndata/inst/doc/grndata.html vignetteTitles: GRNdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: GSBenchMark Version: 1.21.0 Depends: R (>= 2.13.1) License: GPL-2 MD5sum: d91ff75b6ddb4aaabb62a91f9b798a3a 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: eb8051a git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/GSBenchMark_1.21.0.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: 1.7.0 Depends: Biobase, GEOquery Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown, SummarizedExperiment, SingleCellExperiment License: Artistic-2.0 MD5sum: 8e8c1004ff0aa63f854ec4cc6c68b27e 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: 00317da git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/GSE103322_1.7.0.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: 47 Package: GSE13015 Version: 1.9.0 Depends: Biobase, GEOquery Imports: preprocessCore, SummarizedExperiment, GEOquery, Biobase Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown License: MIT License MD5sum: 28c5b7ffbb8cb070c5ac415f0259a772 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: bb10651 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/GSE13015_1.9.0.tar.gz vignettes: vignettes/GSE13015/inst/doc/GSE13015.html vignetteTitles: Expression data from GSE13015 using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/GSE13015/inst/doc/GSE13015.R dependencyCount: 67 Package: GSE159526 Version: 1.7.0 Suggests: ExperimentHub, BiocStyle, RefManageR, knitr, rmarkdown, testthat, minfi, tibble, sessioninfo License: MIT + file LICENSE MD5sum: 6cbe8b1c92183c56ee05d052ac2554a2 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: 09900f3 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/GSE159526_1.7.0.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: GSVAdata Version: 1.37.0 Depends: R (>= 3.5), Biobase, GSEABase, hgu95a.db License: Artistic-2.0 MD5sum: 713a62227701e63e48aaa2a15d459551 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: 479835c git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/GSVAdata_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: singleCellTK, RVA suggestsMe: GSAR, GSVA dependencyCount: 53 Package: h5vcData Version: 2.21.0 Suggests: h5vc License: GPL (>= 3) MD5sum: 35bf05428e6f1c932eb3870098729fb5 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: 858ff7c git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/h5vcData_2.21.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: h5vc suggestsMe: HDF5Array dependencyCount: 0 Package: hapmap100khind Version: 1.43.0 Suggests: oligo License: GPL MD5sum: 2eaaf01a10b6c1e8b2ab30a728a4bf3f 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: db792fc git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/hapmap100khind_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmap100kxba Version: 1.43.0 Suggests: oligo License: GPL MD5sum: 31367084812f1fb133b000fa4d046ec8 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: 98aaecd git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/hapmap100kxba_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligo dependencyCount: 0 Package: hapmap500knsp Version: 1.43.0 Suggests: oligo License: GPL MD5sum: d069376878f698d76990873ed2cc90af 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: a482324 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/hapmap500knsp_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmap500ksty Version: 1.43.0 Suggests: oligo License: GPL MD5sum: 3e8b5dc9de9f9eb492128060778bee42 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: 3e813d0 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/hapmap500ksty_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmapsnp5 Version: 1.43.0 Suggests: oligo License: GPL MD5sum: a87ea0c43938d5a1369c0175034147d5 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: 3dc8148 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/hapmapsnp5_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligoClasses dependencyCount: 0 Package: hapmapsnp6 Version: 1.43.0 Depends: R (>= 2.15) Suggests: oligo, oligoClasses License: GPL MD5sum: a67dc2dc14a1c647c732a4a53c58c757 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: e4e01ea git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/hapmapsnp6_1.43.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: crlmm, oligoClasses dependencyCount: 0 Package: harbChIP Version: 1.39.0 Depends: R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5), Biostrings Imports: methods, stats License: Artistic-2.0 MD5sum: bed555f6879c961b7f887cab92b1c593 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: a001d97 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/harbChIP_1.39.0.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: 19 Package: HarmanData Version: 1.29.0 Depends: R (>= 3.5.0) Suggests: BiocGenerics, BiocStyle, knitr, rmarkdown, Harman (>= 1.23.3) License: GPL-3 MD5sum: 78d6f2b747ebe9c993e2b8d949634eac 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: 242a18b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/HarmanData_1.29.0.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: 1.23.0 Depends: R (>= 3.4.0) Imports: ExperimentHub Suggests: AnnotationHub, knitr, rmarkdown, igraph, survival, ANF, stats, testthat License: GPL-3 MD5sum: 2ae3e1f1e7f23d9205282cf538bf0e72 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: 641e642 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/HarmonizedTCGAData_1.23.0.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: 96 Package: HCAData Version: 1.17.0 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: 11c95bd668f4f096123678b812f6e7fc 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: 5fd8fd3 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/HCAData_1.17.0.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: 111 Package: HD2013SGI Version: 1.41.0 Depends: R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots, limma, vcd, LSD,EBImage Suggests: BiocStyle License: Artistic-2.0 MD5sum: 31a6a7e899d43a540534af26f5d6c8f3 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: 1d2d272 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/HD2013SGI_1.41.0.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: 92 Package: HDCytoData Version: 1.21.0 Depends: ExperimentHub, SummarizedExperiment, flowCore Imports: utils, methods Suggests: BiocStyle, knitr, rmarkdown, Rtsne, umap, ggplot2, FlowSOM, mclust License: MIT + file LICENSE MD5sum: 48c5286ec9e69bc64ed51ab496829b56 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: 4cc0693 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/HDCytoData_1.21.0.tar.gz vignettes: vignettes/HDCytoData/inst/doc/Contribution_guidelines.html, vignettes/HDCytoData/inst/doc/Examples_and_use_cases.html, vignettes/HDCytoData/inst/doc/HDCytoData_package.html vignetteTitles: 3. Contribution guidelines, 2. Examples and use cases, 1. HDCytoData package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HDCytoData/inst/doc/Contribution_guidelines.R, vignettes/HDCytoData/inst/doc/Examples_and_use_cases.R, vignettes/HDCytoData/inst/doc/HDCytoData_package.R dependsOnMe: cytofWorkflow suggestsMe: diffcyt dependencyCount: 111 Package: healthyControlsPresenceChecker Version: 1.5.0 Depends: R (>= 4.0.0) Imports: xml2, GEOquery, geneExpressionFromGEO, magrittr Suggests: RUnit, BiocGenerics, markdown, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 0ef1ce8816ae5e755cfe69aff7db64da 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: f49a3c7 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/healthyControlsPresenceChecker_1.5.0.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: 1.39.0 Depends: R (>= 2.15.0), flowCore Imports: methods License: Artistic-2.0 MD5sum: c590602d0df56a7ad2e5b791dfdd4dd1 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: 8dd3328 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/healthyFlowData_1.39.0.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: 1.39.0 License: LGPL MD5sum: a2922b98ea7a6ae2909ada4869d5d275 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: e72e07b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/HEEBOdata_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQuality dependencyCount: 0 Package: HelloRangesData Version: 1.27.0 Suggests: BiocStyle License: GPL (>= 2) MD5sum: 2cc890994331ab258cd9d24ab60158b0 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: e2f644b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/HelloRangesData_1.27.0.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: plyranges dependencyCount: 0 Package: hgu133abarcodevecs Version: 1.39.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: ee31ecbbd2dbbea850e31c4a8e881e83 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: ffdade5 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/hgu133abarcodevecs_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hgu133plus2barcodevecs Version: 1.39.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: f380055e3716913f8fa3592d27ee96ed 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: f6524ec git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/hgu133plus2barcodevecs_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hgu133plus2CellScore Version: 1.21.0 Depends: R (>= 3.5.0) Imports: Biobase (>= 2.39.1) Suggests: knitr License: GPL-3 MD5sum: 3cbc6266aadaed163cb5c76ca8356102 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: 9b796de git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/hgu133plus2CellScore_1.21.0.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: 1.41.0 Depends: R (>= 2.0.0) License: Artistic-2.0 MD5sum: 3a08a31a5c79f3f8cfe6f780eab64649 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: 3b1c0f4 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/hgu2beta7_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: HiCDataHumanIMR90 Version: 1.21.0 Depends: R (>= 3.5.0) Suggests: HiTC License: GPL-3 MD5sum: 9f1aecd8bba414927330c4549e045668 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: 4adfe78 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/HiCDataHumanIMR90_1.21.0.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: 1.37.0 Suggests: ShortRead License: GPL-3 MD5sum: b90f5bd27aab4b431e0cab5ba2db1706 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: 31608d8 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/HiCDataLymphoblast_1.37.0.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: 1.3.0 Depends: ExperimentHub Imports: BiocFileCache, AnnotationHub Suggests: testthat, methods, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 738f437b807b9043ea2369b5f1aab145 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: e1855f1 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/HiContactsData_1.3.0.tar.gz vignettes: vignettes/HiContactsData/inst/doc/HiContactsData.html vignetteTitles: HiContactsData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HiContactsData/inst/doc/HiContactsData.R suggestsMe: HiCExperiment, HiContacts, HiCool dependencyCount: 96 Package: HighlyReplicatedRNASeq Version: 1.13.0 Depends: SummarizedExperiment, ExperimentHub Imports: S4Vectors Suggests: BiocStyle, BiocFileCache, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 18447967f4474aca1fc3bf568b78a4a1 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: dd0cc1a git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/HighlyReplicatedRNASeq_1.13.0.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: 106 Package: HIVcDNAvantWout03 Version: 1.41.0 License: GPL (>= 2) MD5sum: af2ac865584920795c5b29615b571f8f 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: 9ba620d git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/HIVcDNAvantWout03_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: HMP16SData Version: 1.21.0 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: 494a3b0d94448a78cda6c6a14baec3fd 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: 7a6ee31 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/HMP16SData_1.21.0.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: 132 Package: HMP2Data Version: 1.15.0 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: d32f08b0a63b9afcdc162f3dd7126292 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: 3e5a0b6 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/HMP2Data_1.15.0.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: 164 Package: HSMMSingleCell Version: 1.21.0 Depends: R (>= 2.10) License: Artistic-2.0 MD5sum: 4affaebdaf8a20999e8798f277e3a422 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: 85f2bc4 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/HSMMSingleCell_1.21.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: monocle dependencyCount: 0 Package: HumanAffyData Version: 1.27.0 Depends: ExperimentHub, Biobase, R (>= 3.3) Suggests: BiocStyle License: Artistic-2.0 MD5sum: f9552d1ec4352acc79d2c61fb748f58b 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: cb28196 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/HumanAffyData_1.27.0.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: 96 Package: humanStemCell Version: 0.41.0 Depends: Biobase (>= 2.5.5), hgu133plus2.db License: Artistic-2.0 MD5sum: 9d333ceb696836df8b67331a3d9411ec 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: cf94ecb git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/humanStemCell_0.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MiRaGE, rtracklayer dependencyCount: 48 Package: IHWpaper Version: 1.29.0 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: d4873852dbaae1005efb3d66457475a3 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: 581ee96 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/IHWpaper_1.29.0.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: 1.37.0 Depends: R (>= 3.0.1) License: GPL-3 MD5sum: 5e71b40c825286bb45bc88f729abbcb0 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: ff63d3d git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/Illumina450ProbeVariants.db_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: IlluminaDataTestFiles Version: 1.39.0 License: Artistic-2.0 MD5sum: c95a8d8f58acf457599a2b15a13082a9 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: e0ceba4 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/IlluminaDataTestFiles_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: illuminaio dependencyCount: 0 Package: imcdatasets Version: 1.9.0 Depends: R (>= 4.3.0), SingleCellExperiment, SpatialExperiment, cytomapper, Imports: methods, utils, ExperimentHub, S4Vectors, DelayedArray, HDF5Array Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat License: GPL-3 + file LICENSE MD5sum: 1b294c3e29e30aac22f084d0a8c3eca7 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: e26cae4 git_last_commit_date: 2023-04-25 Date/Publication: 2023-05-25 source.ver: src/contrib/imcdatasets_1.9.0.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: 169 Package: ITALICSData Version: 2.39.0 Depends: R (>= 2.0.0) License: GPL MD5sum: 1607bcdea0b96aff3a13d60248dc600b 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: 55d969b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/ITALICSData_2.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ITALICS dependencyCount: 0 Package: Iyer517 Version: 1.43.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: bd57e96d776b0f4b41b4723193caa418 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: 3135d68 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/Iyer517_1.43.0.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: 1.37.0 Depends: R (>= 3.0.1), methods, Biostrings (>= 2.29.19) License: GPL-2 MD5sum: e51f0844775417b3dd4e70ead454d032 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: ab0e75b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/JASPAR2014_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MatrixRider, TFBSTools dependencyCount: 18 Package: JASPAR2016 Version: 1.29.0 Depends: R (>= 3.2.2), methods License: GPL-2 MD5sum: 6f55fb9be0d9e6b3d4e2d17696beb9da 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: 6649fa5 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/JASPAR2016_1.29.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: chromVAR, TFBSTools, CAGEWorkflow dependencyCount: 1 Package: KEGGandMetacoreDzPathwaysGEO Version: 1.21.0 Depends: R (>= 2.15.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: b0d6d800f6340823c6b74678bb70407a 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: 85fc81b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/KEGGandMetacoreDzPathwaysGEO_1.21.0.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: 1.39.0 Depends: R (>= 2.13.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: 41622b01183c621a3933540e4a485179 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: 23e919f git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/KEGGdzPathwaysGEO_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: PADOG importsMe: GSEABenchmarkeR dependencyCount: 6 Package: kidpack Version: 1.43.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5) License: GPL-2 MD5sum: f82666604a3c70611db89d9c34f53903 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: b68ce27 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/kidpack_1.43.0.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: 1.27.0 Depends: R (>= 3.3.0) License: MIT + file LICENSE MD5sum: 4a0cfe66bab25d5b95c947364fe86ea0 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: a62ddd9 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/KOdata_1.27.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: KEGGlincs dependencyCount: 0 Package: leeBamViews Version: 1.37.0 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: 5cb98aaade452456fd3be0aee8cca8b5 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: 27d75cf git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/leeBamViews_1.37.0.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: 49 Package: leukemiasEset Version: 1.37.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 4b4484a7750a969dedbbbab3123f41be 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: e990333 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/leukemiasEset_1.37.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: geNetClassifier, mCSEA, multiclassPairs dependencyCount: 6 Package: LiebermanAidenHiC2009 Version: 0.39.0 Depends: KernSmooth, IRanges License: LGPL MD5sum: 144e44bc5bdadd0b5515157dfca23dbc 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: 6e3f3ce git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/LiebermanAidenHiC2009_0.39.0.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: 1.33.1 Depends: R (>= 3.1.1), methylPipe Suggests: BSgenome.Hsapiens.UCSC.hg18 License: Artistic 2.0 MD5sum: c908fe94a419742017e59ab360f8aecc 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: b3809ac git_last_commit_date: 2023-05-01 Date/Publication: 2023-05-02 source.ver: src/contrib/ListerEtAlBSseq_1.33.1.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 162 Package: LRcellTypeMarkers Version: 1.9.0 Depends: R (>= 4.1) Imports: ExperimentHub Suggests: LRcell, BiocStyle, knitr, rmarkdown, roxygen2, testthat License: MIT + file LICENSE MD5sum: 51c67cb0ef35a2e16046e535c5f485fa 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: 33c22c5 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/LRcellTypeMarkers_1.9.0.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: 96 Package: LungCancerACvsSCCGEO Version: 1.37.0 Depends: R (>= 2.15.0) License: GPL-2 MD5sum: b44df8f9578f6e009ecfeb39b398a37e 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: 6173b8d git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/LungCancerACvsSCCGEO_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: LungCancerLines Version: 0.39.0 Imports: Rsamtools License: Artistic-2.0 MD5sum: 0bc464182f726fd5fb4f6adc51e84d4d NeedsCompilation: no Title: Reads from Two Lung Cancer Cell Lines Description: Reads from an RNA-seq experiment between two lung cancer cell lines: H1993 (met) and H2073 (primary). The reads are stored as Fastq files and are meant for use with the TP53Genome object in the gmapR package. biocViews: ExperimentData, Genome, CancerData, LungCancerData, RNASeqData Author: Cory Barr, Michael Lawrence Maintainer: Cory Barr git_url: https://git.bioconductor.org/packages/LungCancerLines git_branch: devel git_last_commit: adb067a git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/LungCancerLines_0.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: gmapR dependencyCount: 31 Package: lungExpression Version: 0.39.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 48aee7c62dbd4b8a950d10da94d4746f 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: 35130cf git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/lungExpression_0.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: globaltest dependencyCount: 6 Package: lydata Version: 1.27.0 License: MIT + file LICENSE MD5sum: 79abd46e0358ed14c3e7689e9d7073e6 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: fc073d1 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/lydata_1.27.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: ccmap dependencyCount: 0 Package: M3DExampleData Version: 1.27.0 Depends: R (>= 3.3) License: GPL (>=2) MD5sum: c3d10824745eebcecf786c7a2b7f246f 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: 283b812 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/M3DExampleData_1.27.0.tar.gz hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: celda, M3Drop dependencyCount: 0 Package: macrophage Version: 1.17.0 Depends: R (>= 3.5.0) Suggests: knitr, markdown License: GPL (>= 2) MD5sum: 4bfc22e70922e6a9ff61f307ba6ae8e9 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: 04d741e git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/macrophage_1.17.0.tar.gz vignettes: vignettes/macrophage/inst/doc/macrophage.html vignetteTitles: Salmon quantifications for human macrophage immune response experiment hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/macrophage/inst/doc/macrophage.R suggestsMe: fishpond, GeneTonic, quantiseqr, fluentGenomics dependencyCount: 0 Package: MACSdata Version: 1.9.0 License: file LICENSE MD5sum: cbd7302e1b6bdcf9f81a610ab7b0dc6f 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: b1509ae git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/MACSdata_1.9.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: MACSr dependencyCount: 0 Package: mammaPrintData Version: 1.37.0 Depends: R (>= 2.13.0) Suggests: Biobase, readxl, limma License: Artistic-2.0 MD5sum: 312538726709969c33390e15478e4307 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: a594e09 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/mammaPrintData_1.37.0.tar.gz vignettes: vignettes/mammaPrintData/inst/doc/mammaPrintData.pdf vignetteTitles: Working with the mammaPrintData package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mammaPrintData/inst/doc/mammaPrintData.R dependencyCount: 0 Package: mAPKLData Version: 1.33.0 Depends: R (>= 3.2.0) Suggests: Biobase License: Artistic-2.0 MD5sum: 3a9ce34c91ee88cdc833e0786c9a5e88 NeedsCompilation: no Title: Gene expression data for testing of the package mAPKL. Description: Gene expression data from a breast cancer study published by Turashvili et al. in 2007, provided as an eSet. biocViews: ExperimentData, ExpressionData, Cancer, Breast Author: Argiris Sakellariou Maintainer: Argiris Sakellariou git_url: https://git.bioconductor.org/packages/mAPKLData git_branch: devel git_last_commit: 55dd16c git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/mAPKLData_1.33.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: maqcExpression4plex Version: 1.45.0 Suggests: oligo, pdInfoBuilder License: GPL MD5sum: 494e9ea6625cd33c7b008071d454945e 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: c9d6ced git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/maqcExpression4plex_1.45.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oligo dependencyCount: 0 Package: marinerData Version: 1.1.0 Imports: utils, ExperimentHub Suggests: knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0) License: GPL-3 MD5sum: 78c08014ad7808d9e0107fcfc249fa32 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: 16d6a90 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/marinerData_1.1.0.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: 96 Package: MEDIPSData Version: 1.37.0 Depends: R (>= 3.5.0) License: GPL (>= 2) MD5sum: 0708c9efe87a4a62c63ac4ef58e5cc01 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: 2c80e21 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/MEDIPSData_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MEDIPS, qsea dependencyCount: 0 Package: MEEBOdata Version: 1.39.0 License: LGPL MD5sum: f0b9f0976ae3b86f58d9447f79b47f63 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: 181cfa7 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/MEEBOdata_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: arrayQuality dependencyCount: 0 Package: MerfishData Version: 1.3.0 Depends: R (>= 4.2.0), EBImage, SpatialExperiment Imports: grDevices, AnnotationHub, BumpyMatrix, ExperimentHub, S4Vectors, SingleCellExperiment, SummarizedExperiment Suggests: grid, ggplot2, ggpubr, knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: 01034a5b4176231fc2529c3a3149afe5 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: 695448b git_last_commit_date: 2023-04-25 Date/Publication: 2023-05-25 source.ver: src/contrib/MerfishData_1.3.0.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: 142 Package: MetaGxBreast Version: 1.21.0 Depends: R (>= 3.6.0), Biobase, AnnotationHub, ExperimentHub Imports: stats, lattice, impute, SummarizedExperiment Suggests: testthat, xtable, tinytex License: Apache License (>= 2) MD5sum: ab0ad24735a7c5fae7d093f8e6ca489a 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: 120f28b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/MetaGxBreast_1.21.0.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: 107 Package: MetaGxOvarian Version: 1.21.0 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: 756ecb15d725588e8cd781801eaffada 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: 5546607 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/MetaGxOvarian_1.21.0.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: 107 Package: MetaGxPancreas Version: 1.21.0 Depends: SummarizedExperiment, ExperimentHub, R (>= 3.6.0) Imports: stats, impute, S4Vectors, AnnotationHub Suggests: testthat, knitr, BiocStyle, rmarkdown, markdown License: Artistic-2.0 MD5sum: 4b3ae200a882938c45fdd7ceb92bd269 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: ca046b8 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/MetaGxPancreas_1.21.0.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: 107 Package: metaMSdata Version: 1.37.0 License: GPL (>= 2) MD5sum: 1ce7d5823a36f43d33bbcc1620d38fbf 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: ce1124e git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/metaMSdata_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: MetaScope Version: 1.1.0 Depends: R (>= 4.2.0) Imports: BiocFileCache, Biostrings, data.table, dplyr, ggplot2, magrittr, Matrix, MultiAssayExperiment, qlcMatrix, R.utils, Rbowtie2, readr, rlang, Rsamtools, S4Vectors, stringr, SummarizedExperiment, taxize, tidyr, tools Suggests: BiocStyle, biomformat, knitr, lintr, plyr, rmarkdown, Rsubread, spelling, sys, testthat, usethis Enhances: BiocParallel License: GPL (>= 3) MD5sum: c93c6a0edd2c5396f5cbd838bd3abf42 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 partly an R translation of the PathoScope 2.0 pipeline. biocViews: MicrobiomeData, ReproducibleResearch, SequencingData Author: Aubrey Odom-Mabey [aut, cre] (), Rahul Varki [aut], W. Evan Johnson [aut] (), Howard Fan [ctb] Maintainer: Aubrey Odom-Mabey URL: https://github.com/compbiomed/metascope https://compbiomed.github.io/metascope-docs/ VignetteBuilder: knitr BugReports: https://github.com/compbiomed/MetaScope/issues git_url: https://git.bioconductor.org/packages/MetaScope git_branch: devel git_last_commit: fb9daba git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/MetaScope_1.1.0.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: 179 Package: MethylAidData Version: 1.33.0 Depends: MethylAid, R (>= 3.2) Suggests: BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC License: GPL (>= 2) MD5sum: 6a2ea009e1a79f028a203806b02891b8 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: 2814751 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/MethylAidData_1.33.0.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: 169 Package: MethylSeqData Version: 1.11.0 Depends: SummarizedExperiment Imports: ExperimentHub, HDF5Array, rhdf5, GenomeInfoDb, S4Vectors, GenomicRanges, stats, IRanges, utils Suggests: BiocFileCache, BiocStyle, data.table, knitr, rmarkdown License: CC0 MD5sum: 325b2efd19d388b5cfe2ad11778bf9a3 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: eeadb3d git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/MethylSeqData_1.11.0.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: 110 Package: MicrobiomeBenchmarkData Version: 1.3.0 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: 55387521225f0a5bb340c913235e75e0 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: 09bd29e git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/MicrobiomeBenchmarkData_1.3.0.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: 88 Package: microbiomeDataSets Version: 1.9.0 Depends: R (>= 4.1), SummarizedExperiment, TreeSummarizedExperiment, MultiAssayExperiment Imports: methods, utils, BiocGenerics, ExperimentHub, Biostrings, ape Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, testthat License: CC0 MD5sum: 75765152f2f60b5d4786701947c57cf6 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: d29e94a git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/microbiomeDataSets_1.9.0.tar.gz vignettes: vignettes/microbiomeDataSets/inst/doc/microbiomeDataSets.html vignetteTitles: microbiomeDataSets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/microbiomeDataSets/inst/doc/microbiomeDataSets.R suggestsMe: mia, miaViz dependencyCount: 124 Package: microRNAome Version: 1.23.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: BiocGenerics, RUnit License: GPL (>= 2) MD5sum: 3509881175f3d70915c72f9ed4be196c 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: 62f59eb git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/microRNAome_1.23.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 28 Package: minfiData Version: 0.47.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2), IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 License: Artistic-2.0 MD5sum: 8eb9c5b4f2ffafd7cff7f284070fd59c 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: 343e3c3 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/minfiData_0.47.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: conumee, ENmix, funtooNorm, Harman, mCSEA, MEAL, MethylAid, minfi, missMethyl, MultiDataSet, recountmethylation, shinyepico, shinyMethyl, MethylAidData dependencyCount: 144 Package: minfiDataEPIC Version: 1.27.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2), IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: Artistic-2.0 MD5sum: 6844d3aafb10b7825fb9953bad13e740 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: e236f1b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/minfiDataEPIC_1.27.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MethylAid, minfi, recountmethylation, REMP, MethylAidData dependencyCount: 144 Package: minionSummaryData Version: 1.31.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 38356b950a7750c7b890737aab73289c 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: d53ba24 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/minionSummaryData_1.31.0.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: 1.31.0 Depends: R (>= 3.2), Imports: utils License: GPL-3 | file LICENSE MD5sum: 22693d3407cfc8656ac2a30b548847d2 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: f64b03d git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/miRcompData_1.31.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: miRcomp dependencyCount: 1 Package: miRNATarget Version: 1.39.0 Depends: R (>= 2.10), Biobase License: GPL MD5sum: 34dd2bdbcce1aa688f29ee1e8c808573 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: 6684143 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/miRNATarget_1.39.0.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: MMAPPR2data Version: 1.15.0 Depends: R (>= 3.6.0) Imports: Rsamtools Suggests: knitr, rmarkdown, BiocStyle, roxygen2, seqinr, readr Enhances: MMAPPR2 License: GPL-3 MD5sum: be3546aecfb42389de4a88fb7b63f51d NeedsCompilation: no Title: Sample Data for MMAPPR2 Description: Contains data for illustration purposes in the MMAPPR2 package, namely simulated BAM files containing RNA-Seq data for a mutation in the slc24a5 gene, taken from the GRCz11 genome. Also contains reference sequence and annotation files for the region. biocViews: RNASeqData, Danio_rerio_Data, SequencingData, Genome Author: Kyle Johnsen [aut], Jonathon Hill [cre] Maintainer: Jonathon Hill URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3613585/, https://github.com/kjohnsen/MMAPPR2 VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MMAPPR2data git_branch: devel git_last_commit: 0f8b81c git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/MMAPPR2data_1.15.0.tar.gz vignettes: vignettes/MMAPPR2data/inst/doc/MMAPPR2data.html vignetteTitles: Using MMAPPR2data Resources hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MMAPPR2data/inst/doc/MMAPPR2data.R dependencyCount: 31 Package: MMDiffBamSubset Version: 1.37.0 Suggests: MMDiff2 License: LGPL MD5sum: 5e5f6adaedcc769ae3e1c5543bbd7b5d 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: bf3718a git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/MMDiffBamSubset_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MMDiff2 dependencyCount: 0 Package: mosaicsExample Version: 1.39.0 Depends: R (>= 2.11.1) License: GPL (>= 2) MD5sum: 91f538f5593c179ef9094a83f69396f5 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: 4cb411b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/mosaicsExample_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: mosaics dependencyCount: 0 Package: mouse4302barcodevecs Version: 1.39.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 48405287f8172c8edfda9c7718e524aa 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: a4de666 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/mouse4302barcodevecs_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: MouseGastrulationData Version: 1.15.0 Depends: R (>= 4.1), SingleCellExperiment, SummarizedExperiment, SpatialExperiment Imports: methods, ExperimentHub, BiocGenerics, S4Vectors, BumpyMatrix Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 4af28fc032adcddf8829661719c19207 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: 2876263 git_last_commit_date: 2023-04-25 Date/Publication: 2023-05-25 source.ver: src/contrib/MouseGastrulationData_1.15.0.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: 137 Package: MouseThymusAgeing Version: 1.9.0 Depends: SingleCellExperiment, SummarizedExperiment Imports: ExperimentHub, methods, BiocGenerics, S4Vectors Suggests: knitr, scuttle, rmarkdown, BiocStyle License: GPL-3 MD5sum: 90d611c52d37adcac0b7ae8863773e88 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: d4dd616 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/MouseThymusAgeing_1.9.0.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: 107 Package: msd16s Version: 1.21.0 Depends: R (>= 2.10), Biobase, metagenomeSeq, License: Artistic-2.0 MD5sum: 7a533467ad219568cdc09eacdd49b893 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: 433d292 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/msd16s_1.21.0.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: 31 Package: msdata Version: 0.41.0 Depends: R (>= 3.5.0) Suggests: xcms, mzR, MSnbase License: GPL (>= 2) MD5sum: e2c2a1f23acc594b7b1a57d39b0a0b0e 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: 2c35c94 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/msdata_0.41.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MetaboAnnotation, MsBackendSql, MsExperiment, msqrob2, MsQuality, mzR, PSMatch, QFeatures, Spectra, TargetDecoy dependencyCount: 0 Package: msigdb Version: 1.9.0 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: 155756b2df8d89c448bb1b3553d10046 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: c0d9655 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/msigdb_1.9.0.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: 102 Package: MSMB Version: 1.19.0 Depends: R (>= 3.5), tibble Suggests: knitr, BiocStyle License: LGPL MD5sum: 2191585aef741eaf0dd892fe8aed1a00 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: 200d45e git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/MSMB_1.19.0.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: 1.29.0 Suggests: knitr License: GPL (>= 2) MD5sum: e7be182a45c49d2dced3287921f5e121 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: b04f457 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/msPurityData_1.29.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: msPurity dependencyCount: 0 Package: msqc1 Version: 1.29.0 Depends: R (>= 3.6), lattice, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, specL (>= 1.2) License: GPL MD5sum: 96f67fdbd380fa07854748575424af3c 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: 73381e6 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/msqc1_1.29.0.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: 1.31.0 Depends: R (>= 2.10) Suggests: xcms (>= 3.13.8), CAMERA, Risa (>= 1.0.0), knitr, Heatplus, pcaMethods, sp, rmarkdown License: CC0 MD5sum: ae289adc4e0349b12e7431c82d3fc2db 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: 3302d9b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/mtbls2_1.31.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: yamss dependencyCount: 0 Package: MUGAExampleData Version: 1.21.0 Depends: R (>= 2.10.0) License: GPL-3 MD5sum: 8fd6d4950a07c23f1ea10506825b43d7 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: 024fd0b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/MUGAExampleData_1.21.0.tar.gz vignettes: vignettes/MUGAExampleData/inst/doc/MUGAExampleData.pdf vignetteTitles: User Manual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MUGAExampleData/inst/doc/MUGAExampleData.R dependencyCount: 0 Package: muscData Version: 1.15.0 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: ef653fc344ac551d07e09d20696580eb 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: 18942c8 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/muscData_1.15.0.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: 107 Package: NanoporeRNASeq Version: 1.11.0 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: 3ff92e68b18aa83a187c61635fda22de 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: fd31502 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/NanoporeRNASeq_1.11.0.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: 96 Package: nanotubes Version: 1.17.0 Depends: R (>= 3.6) Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, rtracklayer, CAGEfightR License: GPL-3 MD5sum: 6aa5838cbd7d719a1c849e952f033911 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: dda3fa3 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/nanotubes_1.17.0.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: 1.37.0 Depends: R (>= 2.10.0) Suggests: Rgraphviz License: GPL-3 MD5sum: 26362e3174c7705150cf85fce7958827 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: 0aa919c git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/NCIgraphData_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: NestLink Version: 1.17.0 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: 6d446cc3209b403849bc684cae010217 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: 66f66c7 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/NestLink_1.17.0.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: 132 Package: NetActivityData Version: 1.3.0 Depends: R (>= 4.2.0) Suggests: BiocStyle, knitr License: MIT + file LICENSE MD5sum: 01b3803c04daca7e3fcf79c875394fba 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: 3e646bf git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/NetActivityData_1.3.0.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: 0.39.0 Depends: R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0), hgu133a.db, annotate License: Artistic-2.0 MD5sum: b33e48267776dcc3bceba0be9357f06d 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: 0c529b8 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/Neve2006_0.39.0.tar.gz vignettes: vignettes/Neve2006/inst/doc/neve06notes.pdf vignetteTitles: Neve 2006: combined CGH and expression data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Neve2006/inst/doc/neve06notes.R dependencyCount: 51 Package: NGScopyData Version: 1.21.0 License: GPL (>=2) MD5sum: 6c4e9e5c534970759dd0c1a6ba68f04b 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: 1652024 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/NGScopyData_1.21.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: nullrangesData Version: 1.7.0 Depends: R (>= 4.1.0), ExperimentHub, GenomicRanges, InteractionSet Imports: utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 73898c3f0d9401b5b99dc9e894ca386a 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: b5eff00 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/nullrangesData_1.7.0.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: nullranges dependencyCount: 107 Package: NxtIRFdata Version: 1.7.0 Imports: ExperimentHub, BiocFileCache, rtracklayer, R.utils Suggests: testthat (>= 3.0.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: 03f61471f994d853877432162a10cd20 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: 8408e1e git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/NxtIRFdata_1.7.0.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: 126 Package: ObMiTi Version: 1.9.0 Depends: R (>= 4.1), SummarizedExperiment, ExperimentHub Suggests: knitr, rmarkdown, BiocManager, GenomicFeatures, S4Vectors, devtools, testthat License: GPL-3 MD5sum: b8b87b1fce2b02d0d37e4373b4b80e4d 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: 569d594 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/ObMiTi_1.9.0.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: 106 Package: oct4 Version: 1.17.0 Suggests: knitr, markdown License: GPL (>= 2) MD5sum: 089d881fd3300b7c9e6a1e2f70067b1a 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: 236bc10 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/oct4_1.17.0.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: 1.3.0 Depends: R (>= 4.2.0), ExperimentHub Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 577d710014206381737423112b5dee06 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: 50b05dd git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/octad.db_1.3.0.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: 96 Package: OMICsPCAdata Version: 1.19.0 Depends: R (>= 3.5.0), MultiAssayExperiment Suggests: knitr, kableExtra, rmarkdown License: GPL-3 MD5sum: 2a7ae113c3dc05fc023fe7395dd7f7d0 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: 43bd34b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/OMICsPCAdata_1.19.0.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 dependencyCount: 51 Package: OnassisJavaLibs Version: 1.23.0 Depends: R (>= 3.4) Imports: rJava Suggests: BiocStyle, rmarkdown, knitr License: GPL-2 MD5sum: 5efff14e41dbcb834dcecda5c1d56292 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: 59940e0 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/OnassisJavaLibs_1.23.0.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: 1.13.0 Depends: R (>= 4.0) Suggests: knitr, BiocStyle, rmarkdown, magick License: Artistic-2.0 MD5sum: ee010c819617b3593b65ce499f40d28a 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: fcbc5fc git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/optimalFlowData_1.13.0.tar.gz vignettes: vignettes/optimalFlowData/inst/doc/optimalFlowData_vignette.html vignetteTitles: optimalFlow: optimal-transport approach to Flow Cytometry analysis hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/optimalFlowData/inst/doc/optimalFlowData_vignette.R dependsOnMe: optimalFlow dependencyCount: 0 Package: parathyroidSE Version: 1.39.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: Rsamtools, GenomicAlignments, GEOquery, SRAdb, GenomicFeatures, BiocStyle License: LGPL MD5sum: 6987318710fdccd58e342b9975112927 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: 3bb0dc4 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/parathyroidSE_1.39.0.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 dependencyCount: 28 Package: pasillaBamSubset Version: 0.39.0 Suggests: pasilla License: LGPL MD5sum: c064ec01e1149d4fc166202fb5ff4b0b 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: b788c0a git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/pasillaBamSubset_0.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: APAlyzer, GenomicAlignments, GenomicFeatures, GenomicRanges, gmoviz, IRanges, karyoploteR, plyranges, TransView dependencyCount: 0 Package: PasillaTranscriptExpr Version: 1.29.0 Depends: R (>= 3.3.0) Suggests: rtracklayer, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: a6e264cec803348c218fe33acf392921 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: 9ba0865 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/PasillaTranscriptExpr_1.29.0.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: 1.37.0 Depends: R (>= 1.14.0) License: GPL-3 MD5sum: c73fb66ef4d3bc09e31649e8a6973eba 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: 9fb465b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/PathNetData_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PathNet dependencyCount: 0 Package: PCHiCdata Version: 1.29.0 Depends: R (>= 3.2), Chicago Suggests: testthat, BiocStyle, knitr License: Artistic-2.0 MD5sum: 788436714796e795bc4f5ef1637c889c 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: b5a7b5a git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/PCHiCdata_1.29.0.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: pcxnData Version: 2.23.0 Depends: R (>= 3.4) Suggests: pcxn License: MIT + file LICENSE MD5sum: 8353bd3f97ad82c9db4e75553bfe8596 NeedsCompilation: no Title: Correlation coefficients and p values between pre-defined pathway/gene sets Description: PCxN database contains correlation coefficients and p values between pre-defined gene sets within MSigDB H hallmark gene sets, MSigDB C2 CP (Canonical pathways), MSigDB C5 GO BP gene sets and Pathprint respectively, as well as adjusted pathway correlations to account for the shared genes between pathway pairs. biocViews: ExperimentData, ExpressionData, MicroarrayData, GEO, Homo_sapiens_Data, OneChannelData, PathwayInteractionDatabase Author: Sokratis Kariotis, Yered Pita-Juarez, Wenbin Wei, Winston Hide Maintainer: Sokratis Kariotis git_url: https://git.bioconductor.org/packages/pcxnData git_branch: devel git_last_commit: cabff0a git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/pcxnData_2.23.0.tar.gz vignettes: vignettes/pcxnData/inst/doc/usingpcxnData.pdf vignetteTitles: pcxnData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/pcxnData/inst/doc/usingpcxnData.R dependsOnMe: pcxn dependencyCount: 0 Package: pd.atdschip.tiling Version: 0.39.0 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: 11edfaa21bc7655147e1061f8b4bce28 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: 1c90aca git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/pd.atdschip.tiling_0.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 56 Package: pepDat Version: 1.21.0 Depends: R (>= 3.5.0) Imports: GenomicRanges Suggests: knitr License: Artistic-2.0 MD5sum: f30417400f479d604194984c2eefa117 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: ee526f4 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/pepDat_1.21.0.tar.gz vignettes: vignettes/pepDat/inst/doc/pepDat.pdf vignetteTitles: The pepDat users guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pepDat/inst/doc/pepDat.R suggestsMe: pepStat, Pviz dependencyCount: 16 Package: PepsNMRData Version: 1.19.0 Depends: R (>= 3.5) Suggests: knitr, markdown, rmarkdown, BiocStyle License: GPL-2 | file LICENSE MD5sum: 6704b523adaddb1ef72b1ceb482c8640 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: 4df4bf3 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/PepsNMRData_1.19.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE suggestsMe: PepsNMR dependencyCount: 0 Package: PhyloProfileData Version: 1.15.0 Depends: R (>= 4.1.0) Imports: ExperimentHub, Biostrings, BiocStyle Suggests: knitr, rmarkdown, markdown License: MIT + file LICENSE MD5sum: d13bb6643f14eaea63123850ef21b026 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: fe70b4c git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/PhyloProfileData_1.15.0.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: 98 Package: plotgardenerData Version: 1.7.0 Depends: R (>= 4.1.0) Suggests: rmarkdown, knitr License: MIT + file LICENSE MD5sum: 95a6604aad28e93e5f64009aedb7c38d 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: 7110020 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/plotgardenerData_1.7.0.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: 1.37.0 Depends: R (>= 2.14.0) License: Artistic-2.0 MD5sum: 527b57ae50f1cdecabf122949cdee342 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: 8cdbb8a git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/prebsdata_1.37.0.tar.gz vignettes: vignettes/prebsdata/inst/doc/prebsdata.pdf vignetteTitles: prebsdata User Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: SigFuge dependencyCount: 0 Package: preciseTADhub Version: 1.9.0 Depends: R (>= 4.1) Imports: ExperimentHub Suggests: knitr, rmarkdown, markdown, BiocStyle, preciseTAD License: MIT + file LICENSE MD5sum: 8d04d69a550653b3ab854f9aa0f7cffb 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: d1d1b69 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/preciseTADhub_1.9.0.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: 96 Package: ProData Version: 1.39.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL MD5sum: 3577f6126bc7b5b299ac547ced5d583c 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: 1158707 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/ProData_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: CorrectedFDR dependencyCount: 6 Package: prostateCancerCamcap Version: 1.29.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 3dddd023ae85c66408387b7b5bc14948 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: fb1b2ac git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/prostateCancerCamcap_1.29.0.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: 1.29.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: f67b60186d0c542d4a946e757808e65e 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: a630e2c git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/prostateCancerGrasso_1.29.0.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: 1.29.0 Depends: Biobase , R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: fc22288f17e41b6443ce67494e4ca297 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: 9023cf3 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/prostateCancerStockholm_1.29.0.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: 1.29.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery, org.Hs.eg.db License: Artistic-2.0 MD5sum: cb42021b3aa077ffcc4f14d4dfe7accd 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: eac1ba0 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/prostateCancerTaylor_1.29.0.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: 1.29.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 1d9de440028fa80ea00b3df4e5ec4cf6 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: 965f6e0 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/prostateCancerVarambally_1.29.0.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: 1.9.0 Imports: rhdf5, signal, stats, graphics Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 73b421222848d4e82ddcc1532dc73526 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: e3a5716 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/ptairData_1.9.0.tar.gz vignettes: vignettes/ptairData/inst/doc/ptairData_vignette.html vignetteTitles: PTR-TOF-MS dataset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ptairData/inst/doc/ptairData_vignette.R dependencyCount: 10 Package: PWMEnrich.Dmelanogaster.background Version: 4.35.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: 64d97215f128dfbc1791099f1cc8ebdc 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: e2b254e git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/PWMEnrich.Dmelanogaster.background_4.35.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 24 Package: PWMEnrich.Hsapiens.background Version: 4.35.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: 94951b5e99c75b6bf0aec676d1501bea 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: 8daaca9 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/PWMEnrich.Hsapiens.background_4.35.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 24 Package: PWMEnrich.Mmusculus.background Version: 4.35.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: f8fcad08133800ebf74f4be671108404 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: b37c6c1 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/PWMEnrich.Mmusculus.background_4.35.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PWMEnrich dependencyCount: 24 Package: QDNAseq.hg19 Version: 1.31.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: ba38acd740a045fa966a6e57249fcb77 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: 44940c0 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/QDNAseq.hg19_1.31.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: QDNAseq dependencyCount: 50 Package: QDNAseq.mm10 Version: 1.31.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: 0c36f9e0f45392854e85259e05c9e4c0 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: 201abaa git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/QDNAseq.mm10_1.31.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: QDNAseq dependencyCount: 50 Package: QUBICdata Version: 1.29.0 Depends: R (>= 3.1) Suggests: knitr, rmarkdown License: Unlimited | file LICENSE MD5sum: 57293a7ab3e3cc41f5b0e6fe9cdf4d1a 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: 21fbbcc git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/QUBICdata_1.29.0.tar.gz vignettes: vignettes/QUBICdata/inst/doc/qubic_data_vignette.pdf vignetteTitles: QUBIC Data Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/QUBICdata/inst/doc/qubic_data_vignette.R suggestsMe: QUBIC dependencyCount: 0 Package: rcellminerData Version: 2.23.0 Depends: R (>= 3.5.0), Biobase Suggests: knitr, testthat, BiocStyle, rcellminer, rmarkdown License: LGPL-3 + file LICENSE MD5sum: d270af53bb8429bf1a810e938c805d73 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: df7d18d git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/rcellminerData_2.23.0.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: 1.21.0 Depends: R (>= 3.3) Imports: data.table License: GPL-3 MD5sum: 992f6332c21fa3d4dc811e495ea4b57f 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: 954f18e git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.21.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 2 Package: RegParallel Version: 1.19.0 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: 373d1512b165ec0733ad29004a0b4867 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: 103f20c git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RegParallel_1.19.0.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: 61 Package: RGMQLlib Version: 1.21.0 Depends: R(>= 3.4.2) Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 0794c23eec3c6b0bf5d873359551e895 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: bc7c616 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RGMQLlib_1.21.0.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: 1.39.0 Depends: R (>= 2.10.0) Suggests: genefilter, Biobase, hgu133plus2.db License: Artistic-2.0 MD5sum: 9f9dbfdda0cd7aa1e424734437ad95ef 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: f20470a git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/rheumaticConditionWOLLBOLD_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: RMassBankData Version: 1.39.0 Suggests: RMassBank License: Artistic-2.0 MD5sum: 159a8b78f7a61ef7047d76fcf43e1782 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: 9dd0370 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RMassBankData_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: RNAmodR.Data Version: 1.15.0 Depends: R (>= 3.6), ExperimentHub, ExperimentHubData (>= 1.9.2) Imports: utils Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, sessioninfo, testthat License: Artistic-2.0 MD5sum: 507545aa7bd61e276c6278e0e619c012 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: 52ad137 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RNAmodR.Data_1.15.0.tar.gz vignettes: vignettes/RNAmodR.Data/inst/doc/RNAmodR.Data.html vignetteTitles: RNAmodR.Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RNAmodR.Data/inst/doc/RNAmodR.Data.R suggestsMe: RNAmodR, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq dependencyCount: 139 Package: RNAseqData.HNRNPC.bam.chr14 Version: 0.39.0 Suggests: GenomicAlignments, BiocManager License: LGPL MD5sum: 3fb4bbab7f46964ed34e49b83446751b 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: 3914c22 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RNAseqData.HNRNPC.bam.chr14_0.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: sequencing suggestsMe: BiocParallel, GenomicAlignments, GenomicFiles, GenomicRanges, roar, Rsamtools, SplicingGraphs dependencyCount: 0 Package: RnaSeqSampleSizeData Version: 1.33.0 Depends: edgeR,R (>= 2.10) Suggests: BiocStyle, knitr License: GPL (>= 2) MD5sum: 0ab03c60e331a38e975280af3e1d1eb2 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: 6676376 git_last_commit_date: 2023-04-25 Date/Publication: 2023-05-23 source.ver: src/contrib/RnaSeqSampleSizeData_1.33.0.tar.gz vignettes: vignettes/RnaSeqSampleSizeData/inst/doc/RnaSeqSampleSizeData.pdf vignetteTitles: RnaSeqSampleSizeData: Read counts and dispersion distribution from real data for sample size estimation of RNA-seq experiments hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RnaSeqSampleSizeData/inst/doc/RnaSeqSampleSizeData.R dependsOnMe: RnaSeqSampleSize dependencyCount: 11 Package: RnBeads.hg19 Version: 1.33.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: df17ff556c2ac1f5c3b4ee28bc5d4928 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: 881910f git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RnBeads.hg19_1.33.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: MAGAR suggestsMe: RnBeads dependencyCount: 16 Package: RnBeads.hg38 Version: 1.33.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 685eb84e8bc359f592ca884208c2ee21 NeedsCompilation: no Title: RnBeads.hg38 Description: Automatically generated RnBeads annotation package for the assembly hg38. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.hg38 git_branch: devel git_last_commit: 41dbfd5 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RnBeads.hg38_1.33.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 16 Package: RnBeads.mm10 Version: 2.9.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 7b7dc2ad4c8c8a6e6a713afdef9dc90c 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: e6bf81b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RnBeads.mm10_2.9.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 16 Package: RnBeads.mm9 Version: 1.33.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: c73308f3774ca8c53c662f1fb60a5883 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: 1e14e52 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RnBeads.mm9_1.33.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RnBeads dependencyCount: 16 Package: RnBeads.rn5 Version: 1.33.0 Depends: R (>= 3.5.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 860d87622a34b36a30aebfdc736d3f83 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: b28453c git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RnBeads.rn5_1.33.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 16 Package: RRBSdata Version: 1.21.0 Depends: R (>= 3.5.0), BiSeq (>= 1.9.2) License: LGPL-3 MD5sum: 1d327857436014dd90d0d8b340363d8f 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: 773242b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RRBSdata_1.21.0.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: 90 Package: rRDPData Version: 1.21.0 Depends: rRDP License: GPL-2 MD5sum: fa77f2577d5efe55f7a619bed1f7f778 NeedsCompilation: no Title: Database for the Default RDP Classifier Description: Database used by the default RDP Classifier biocViews: SequencingData, MicrobiomeData Author: Michael Hahsler, Anurag Nagar Maintainer: Michael Hahsler SystemRequirements: Java git_url: https://git.bioconductor.org/packages/rRDPData git_branch: devel git_last_commit: bc358ad git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/rRDPData_1.21.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: rRDP dependencyCount: 19 Package: RTCGA.clinical Version: 20151101.31.0 Depends: R (>= 3.2.0), RTCGA Suggests: rmarkdown, knitr License: GPL-2 MD5sum: ef0d55bf31dd2370e8cf87458085ca28 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: 2017559 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RTCGA.clinical_20151101.31.0.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: 138 Package: RTCGA.CNV Version: 1.29.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: cc49b44691d0d8a238263a729cfd7d3c 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: d21ca09 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RTCGA.CNV_1.29.0.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: 138 Package: RTCGA.methylation Version: 1.29.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 6706702b57d0831266cee1f291a1cd4b 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: a4b95f3 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RTCGA.methylation_1.29.0.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: 138 Package: RTCGA.miRNASeq Version: 1.29.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 0db3261fb2545777e4e012e7eb7a8734 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: 676fe60 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RTCGA.miRNASeq_1.29.0.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: 138 Package: RTCGA.mRNA Version: 1.29.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: da896f115fbfb23596f0e1213061d2bd 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: 8b82137 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RTCGA.mRNA_1.29.0.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: 138 Package: RTCGA.mutations Version: 20151101.31.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 12be445a5a958da482b1bf006832739c 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: 8e330c0 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RTCGA.mutations_20151101.31.0.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: 138 Package: RTCGA.PANCAN12 Version: 1.29.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: f0834e7d2e7a78d29681ea4945353b85 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: 44008df git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RTCGA.PANCAN12_1.29.0.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: 138 Package: RTCGA.rnaseq Version: 20151101.31.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 371a206eb7e7c24757b33a577bb4fc1d 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: 467bc66 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RTCGA.rnaseq_20151101.31.0.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: 138 Package: RTCGA.RPPA Version: 1.29.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 859e0d8eb0a5613a63b837ac69e8694f 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: e609fa8 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RTCGA.RPPA_1.29.0.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: 138 Package: RUVnormalizeData Version: 1.21.0 Depends: R (>= 2.10.0), Biobase License: GPL-3 MD5sum: fd37b31fb5e59fbd2148538a76632c1d 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: 9281bd6 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/RUVnormalizeData_1.21.0.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: 1.25.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: BiocStyle License: Artistic-2.0 MD5sum: af7e4670518eea56775ece8e96b4882e 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: 9f2e488 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/sampleClassifierData_1.25.0.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: 28 Package: SBGNview.data Version: 1.15.0 Depends: R (>= 3.6) Imports: knitr, rmarkdown, bookdown Suggests: SummarizedExperiment License: AGPL-3 MD5sum: c69b17dfa2958d90e56476ab8c02b283 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: 8dfe9ac git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/SBGNview.data_1.15.0.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: 37 Package: scanMiRData Version: 1.7.0 Depends: R (>= 4.0) Imports: scanMiR, utils Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 5794a5a087001c22b62f8f31db1a9fa6 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 [aut] (), Michael Soutschek [aut], Fridolin Gross [cre, aut] Maintainer: Fridolin Gross VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/scanMiRData git_branch: devel git_last_commit: 2220051 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/scanMiRData_1.7.0.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: 64 Package: scATAC.Explorer Version: 1.7.0 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: d527d19bdfea0b56970f4c4fa810e595 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: cec4d25 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/scATAC.Explorer_1.7.0.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: 1.33.0 Depends: R(>= 2.10) Suggests: BiocStyle License: GPL-2 MD5sum: 1e696d8eba25292d614e98dbd1e72052 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: 12b8063 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/SCLCBam_1.33.0.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: 1.1.0 Depends: R (>= 4.3.0), AnnotationHub, ExperimentHub, 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: 33b99cd7fcbb27513f39693aad24390e 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 Wlodarczyk [aut], Natalie Fox [aut] Maintainer: Xiaosai Yao VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/scMultiome git_branch: devel git_last_commit: a940a1e git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/scMultiome_1.1.0.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 dependencyCount: 123 Package: scpdata Version: 1.9.1 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: 9c2cd100f442116fb893a7247f54ca55 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] () Maintainer: Christophe Vanderaa VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/scpdata git_branch: devel git_last_commit: e7e1a8a git_last_commit_date: 2023-05-12 Date/Publication: 2023-05-16 source.ver: src/contrib/scpdata_1.9.1.tar.gz vignettes: vignettes/scpdata/inst/doc/scpdata.html vignetteTitles: Data Package for Single Cell Proteomics hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scpdata/inst/doc/scpdata.R dependencyCount: 132 Package: scRNAseq Version: 2.15.0 Depends: SingleCellExperiment Imports: utils, methods, BiocGenerics, S4Vectors, GenomicRanges, SummarizedExperiment, ExperimentHub (>= 2.3.4), AnnotationHub (>= 3.3.6), AnnotationDbi, ensembldb, GenomicFeatures Suggests: BiocStyle, knitr, rmarkdown, BiocFileCache, testthat, rappdirs, tools License: CC0 MD5sum: cec367655a6d6577964945c5a23e1d8a 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: 9dc7009 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/scRNAseq_2.15.0.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 importsMe: singleCellTK suggestsMe: APL, BASiCS, batchelor, bluster, ccImpute, destiny, dittoSeq, Glimma, iSEE, iSEEhex, iSEEu, miQC, mumosa, scAnnotatR, scater, scDblFinder, scFeatureFilter, scone, scran, scTreeViz, scuttle, SingleCellExperiment, SingleR, SummarizedBenchmark, UCell, velociraptor, zellkonverter, zinbwave dependencyCount: 133 Package: scTHI.data Version: 1.13.0 Depends: R (>= 4.0) License: GPL-2 MD5sum: 235d480688d1710e3e904104f7cab091 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: 565e477 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/scTHI.data_1.13.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: scTHI dependencyCount: 0 Package: seq2pathway.data Version: 1.33.0 Depends: R (>= 3.6.2) License: GPL (>= 2) MD5sum: 363220bbc798b1841aa3dfd252435554 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: c914b13 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/seq2pathway.data_1.33.0.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: 1.35.0 Depends: R (>= 2.10) Imports: utils, Biobase License: GPL-3 MD5sum: 58d8eb76599a9b10a708586a3c5bcecf 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: f10fcbc git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/seqc_1.35.0.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: seqCNA.annot Version: 1.37.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: f6a6561a3eafbfa5a46a5e8ffb46c6f7 NeedsCompilation: no Title: Annotation for the copy number analysis of deep sequencing cancer data with seqCNA Description: Provides annotation on GC content, mappability and genomic features for various genomes biocViews: Genome, CopyNumberVariationData Author: David Mosen-Ansorena Maintainer: David Mosen-Ansorena git_url: https://git.bioconductor.org/packages/seqCNA.annot git_branch: devel git_last_commit: cc4ec4b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/seqCNA.annot_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: seqCNA dependencyCount: 0 Package: serumStimulation Version: 1.37.0 Depends: R (>= 2.10) License: GPL (>= 2) MD5sum: cdd44ebd93e94bdc5dff86cece689d5f 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: 11acd62 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/serumStimulation_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: sesameData Version: 1.19.0 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: 514a64be2ee94c2f9cd337560319ee81 NeedsCompilation: no Title: Supporting Data for SeSAMe Package Description: Provides supporting annotation and test data for SeSAMe package. This includes chip tango addresses, mapping information, performance annotation, and trained predictor for Infinium array data. This package provides user access to essential annotation data for working with many generations of the Infinium DNA methylation array. Current we support human array (HM27, HM450, EPIC), mouse array (MM285) and the HorvathMethylChip40 (Mammal40) array. biocViews: ExperimentData, MicroarrayData, Genome, ExperimentHub, MethylationArrayData Author: Wanding Zhou [aut, cre] (), Hui Shen [aut], Timothy Triche [ctb] Maintainer: Wanding Zhou VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/sesameData git_branch: devel git_last_commit: 9b20ad5 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/sesameData_1.19.0.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 suggestsMe: ELMER dependencyCount: 104 Package: SFEData Version: 1.3.0 Imports: BiocFileCache, AnnotationHub, ExperimentHub Suggests: BiocStyle, knitr, rmarkdown, SpatialFeatureExperiment, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 9db668bc81a302624899cf15aa1d6d7a 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] (), 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: cfff90c git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/SFEData_1.3.0.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: 96 Package: shinyMethylData Version: 1.21.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: 3a48d6d6b4604cab1b9ed1bd61fb7432 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: b3e8bda git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/shinyMethylData_1.21.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: shinyMethyl dependencyCount: 0 Package: SimBenchData Version: 1.9.0 Depends: ExperimentHub Imports: S4Vectors, utils Suggests: BiocStyle, knitr, rmarkdown, Seurat License: GPL-3 MD5sum: d8e0b651d5ec4ed20975e04b8b330496 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: 0a8248c git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/SimBenchData_1.9.0.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: 96 Package: simpIntLists Version: 1.37.0 License: GPL (>= 2) MD5sum: 128c99015820ca404a6b88aaf5010cb6 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: d609dfc git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/simpIntLists_1.37.0.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: 1.29.0 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: fa7d595155a0dad577234a041d52d3c8 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: f2c3b32 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/Single.mTEC.Transcriptomes_1.29.0.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: 1.13.8 Depends: R (>= 4.2.0), MultiAssayExperiment Imports: AnnotationHub, BiocBaseUtils, BiocFileCache, ExperimentHub, HDF5Array, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, Matrix, methods, utils Suggests: BiocStyle, ggplot2, knitr, RaggedExperiment, rmarkdown, scater, scran, UpSetR, uwot License: Artistic-2.0 MD5sum: 49433f7b5ddaca20c1f3c7d8efe2506b NeedsCompilation: no Title: Integrating Multi-modal Single Cell Experiment datasets Description: SingleCellMultiModal is an ExperimentHub package that serves multiple datasets obtained from GEO and other sources and represents them as MultiAssayExperiment objects. We provide several multi-modal datasets including scNMT, 10X Multiome, seqFISH, CITEseq, SCoPE2, and others. The scope of the package is is to provide data for benchmarking and analysis. biocViews: ExperimentData, SingleCellData, ReproducibleResearch, ExperimentHub, GEO Author: Marcel Ramos [aut, cre] (), Ricard Argelaguet [aut], 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: 72b6bd9 git_last_commit_date: 2023-05-22 Date/Publication: 2023-05-25 source.ver: src/contrib/SingleCellMultiModal_1.13.8.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 dependencyCount: 138 Package: SingleMoleculeFootprintingData Version: 1.9.0 Imports: ExperimentHub, utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 3ebefbf05615a4cd0cbc3c41930188e9 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: fa514c7 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/SingleMoleculeFootprintingData_1.9.0.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: 96 Package: SNAData Version: 1.47.0 Depends: R (>= 2.4.0), graph Suggests: Rgraphviz License: LGPL MD5sum: e702e8f65d97f39c1fb2ff7f9b07d72e 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: f396726 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/SNAData_1.47.0.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: 1.37.0 Depends: R (>= 2.6.0) Suggests: ALL, hgu95av2.db, SNAGEE License: Artistic-2.0 MD5sum: 2a135a08795ba0f380be9b222e12e65e 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: 8be44e7 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/SNAGEEdata_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: SNAGEE dependencyCount: 0 Package: SNPhoodData Version: 1.31.0 Depends: R (>= 3.2) Suggests: BiocStyle,knitr,rmarkdown License: LGPL (>= 3) MD5sum: 29b795611cce616bfe51dcedc7f2713c 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: 0444b9f git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/SNPhoodData_1.31.0.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: 1.39.0 Depends: R (>= 2.14) License: Artistic-2.0 MD5sum: 44bc5628f9f37d208885e80987f68ed3 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: 69cbab6 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/SomatiCAData_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: SomaticCancerAlterations Version: 1.37.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, IRanges, S4Vectors Suggests: testthat, ggbio, ggplot2, knitr License: GPL-3 MD5sum: dbc5e3b996bf27009bc4b488333f3aae 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: 1242777 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/SomaticCancerAlterations_1.37.0.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: 16 Package: spatialLIBD Version: 1.13.4 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 Suggests: knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager, lobstr License: Artistic-2.0 MD5sum: ce04856a64e262857cf708de58570400 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: edc8b72 git_last_commit_date: 2023-05-24 Date/Publication: 2023-05-25 source.ver: src/contrib/spatialLIBD_1.13.4.tar.gz vignettes: vignettes/spatialLIBD/inst/doc/guide_to_spatial_registration.html, vignettes/spatialLIBD/inst/doc/spatialLIBD.html, vignettes/spatialLIBD/inst/doc/TenX_data_download.html vignetteTitles: Guide to Spatial Registration, 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/spatialLIBD.R, vignettes/spatialLIBD/inst/doc/TenX_data_download.R suggestsMe: BayesSpace, DESpace dependencyCount: 216 Package: spqnData Version: 1.13.0 Depends: R (>= 4.0), SummarizedExperiment License: Artistic-2.0 MD5sum: ac67300dde4a4b76af7242f66c56e18b 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: 14e51ed git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/spqnData_1.13.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: spqn dependencyCount: 28 Package: stemHypoxia Version: 1.37.0 Depends: R (>= 2.14.1) License: GPL (>=2) MD5sum: a2395e639ab5ae82663a380b45c530e7 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: cf05c32 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/stemHypoxia_1.37.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: lmdme dependencyCount: 0 Package: STexampleData Version: 1.9.0 Depends: ExperimentHub, SpatialExperiment Imports: utils Suggests: BiocStyle, knitr, rmarkdown, BumpyMatrix License: MIT + file LICENSE MD5sum: 3332266bb9e63a6df1e87b5e7e94d4ae NeedsCompilation: no Title: Collection of spatially-resolved transcriptomics datasets in SpatialExperiment Bioconductor format Description: Collection of spatially-resolved transcriptomics (SRT) datasets in SpatialExperiment Bioconductor format, for use in examples, demonstrations, and tutorials. The datasets are from several different SRT platforms and have been sourced from various publicly available sources. Several datasets include images and/or ground truth annotation labels. biocViews: ExperimentData, ExperimentHub, ReproducibleResearch, ExpressionData, SingleCellData, SpatialData, Homo_sapiens_Data, Mus_musculus_Data Author: Lukas M. Weber [aut, cre] () Maintainer: Lukas M. Weber URL: https://github.com/lmweber/STexampleData VignetteBuilder: knitr BugReports: https://github.com/lmweber/STexampleData/issues git_url: https://git.bioconductor.org/packages/STexampleData git_branch: devel git_last_commit: 2f51f01 git_last_commit_date: 2023-04-25 Date/Publication: 2023-05-25 source.ver: src/contrib/STexampleData_1.9.0.tar.gz vignettes: vignettes/STexampleData/inst/doc/STexampleData_overview.html vignetteTitles: STexampleData package overview hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/STexampleData/inst/doc/STexampleData_overview.R suggestsMe: escheR, ggspavis, nnSVG dependencyCount: 136 Package: stjudem Version: 1.41.0 Depends: R (>= 2.10), utils License: LGPL (>= 2) MD5sum: 95300a10330f2ef8a3fbab04fb771c5d NeedsCompilation: no Title: Microarray Data from Yeoh et al. in MACAT format Description: This is a microarray data set on acute lymphoblastic leukemia, published in 2002 (Yeoh et al.Cancer Cell 2002). The experiments were conducted in the St.Jude Children's Research Hospital, Memphis, Tenessee, USA. The raw data was preprocessed by variance stabilizing normalization (Huber et al.) on probe and subsequent summarization of probe expression values into probe set expression values using median polish. biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData, ChipOnChipData Author: Benjamin Georgi, Matthias Heinig, Sebastian Schmeier, Joern Toedling Maintainer: Joern Toedling git_url: https://git.bioconductor.org/packages/stjudem git_branch: devel git_last_commit: 1b29752 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/stjudem_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: macat dependencyCount: 1 Package: SVM2CRMdata Version: 1.33.0 Depends: R(>= 3.2.0) License: LGPL (>= 2) MD5sum: d4948ef67255d5b9b45e8b3d87e8c16a 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: 2523af6 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/SVM2CRMdata_1.33.0.tar.gz vignettes: vignettes/SVM2CRMdata/inst/doc/SVM2CRMdata.pdf vignetteTitles: The \Rpackage{SVM2CRMdata} Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SVM2CRMdata/inst/doc/SVM2CRMdata.R dependencyCount: 0 Package: systemPipeRdata Version: 2.5.0 Imports: methods, Biostrings, BiocGenerics, jsonlite, remotes Suggests: GenomicFeatures, GenomicRanges, IRanges, Rsamtools, ShortRead, rtracklayer, RUnit, BiocStyle, knitr, rmarkdown, systemPipeR License: Artistic-2.0 MD5sum: e96f20bc8f6cf4cf3dc581204a6be317 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: 0042d78 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/systemPipeRdata_2.5.0.tar.gz vignettes: vignettes/systemPipeRdata/inst/doc/systemPipeChIPseq.html, vignettes/systemPipeRdata/inst/doc/systemPipeRdata.html, vignettes/systemPipeRdata/inst/doc/systemPipeRIBOseq.html, vignettes/systemPipeRdata/inst/doc/systemPipeRNAseq.html, vignettes/systemPipeRdata/inst/doc/systemPipeVARseq.html vignetteTitles: WF: ChIP-Seq Workflow Template, systemPipeRdata: Workflow templates and sample data, WF: RIBO-Seq Workflow Template, WF: RNA-Seq Workflow Template, WF: VAR-Seq Template hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/systemPipeRdata/inst/doc/systemPipeChIPseq.R, vignettes/systemPipeRdata/inst/doc/systemPipeRdata.R, vignettes/systemPipeRdata/inst/doc/systemPipeRIBOseq.R, vignettes/systemPipeRdata/inst/doc/systemPipeRNAseq.R, vignettes/systemPipeRdata/inst/doc/systemPipeVARseq.R suggestsMe: systemPipeR, systemPipeShiny dependencyCount: 20 Package: TabulaMurisData Version: 1.19.0 Depends: R (>= 3.5) Imports: ExperimentHub, utils Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran, scater, iSEE, testthat License: MIT + file LICENSE MD5sum: 19fdded4dbe705804d1845ef95bffd6a 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: 6cd177b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/TabulaMurisData_1.19.0.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: 96 Package: TabulaMurisSenisData Version: 1.7.0 Imports: ExperimentHub, SingleCellExperiment, HDF5Array, SummarizedExperiment, gdata, AnnotationHub Suggests: ggplot2, testthat, knitr, rmarkdown, iSEE, BiocStyle License: MIT + file LICENSE MD5sum: 8ab4af9fc499b1df88ed3753ddc5488e 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: 0190a07 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/TabulaMurisSenisData_1.7.0.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: 113 Package: TargetScoreData Version: 1.37.0 Suggests: TargetScore, gplots License: GPL-2 MD5sum: c6df0e3cff6eb725fe9b3112d49972e3 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: fbe6b3d git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/TargetScoreData_1.37.0.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: 1.39.0 License: GPL (>= 2) MD5sum: 1aaa504afdab598a8da0dca7d02c1738 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: 6b3eb51 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/TargetSearchData_1.39.0.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: 1.15.0 Depends: R (>= 4.1), AnnotationHub (>= 2.16), ExperimentHub (>= 1.0) Imports: utils Suggests: BiocStyle, knitr, rmarkdown, testthat, tools License: GPL-3 MD5sum: 744eb016017012f40d9d4ef8be5e7f7d 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: 0da93f4 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/tartare_1.15.0.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, rawrr dependencyCount: 96 Package: TBX20BamSubset Version: 1.37.0 Depends: Rsamtools (>= 1.9.8) Imports: xtable License: LGPL MD5sum: 293219f19feafbf51b434ef89abe625b 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: 9bd3963 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/TBX20BamSubset_1.37.0.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: 32 Package: TCGAbiolinksGUI.data Version: 1.21.0 Depends: R (>= 3.5.0) Suggests: BiocStyle, knitr, rmarkdown, readr, DT License: GPL-3 MD5sum: 17aaf28f6ab172b1e4bcf5094f45dafd 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: e0c1ea4 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/TCGAbiolinksGUI.data_1.21.0.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: 1.21.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: bdeba7cae5ce74855b693d4d84a1f533 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: 8211cc2 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/TCGAcrcmiRNA_1.21.0.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: 1.21.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 96c9a0e4ad2ca3af04627c8b8abdc2c0 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: 0e96035 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/TCGAcrcmRNA_1.21.0.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: 1.37.0 License: GPL-2 MD5sum: 5287eeaddc2ea6caa789b82daff4c38c 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: facdea4 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/TCGAMethylation450k_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: methylumi dependencyCount: 0 Package: TENxBrainData Version: 1.21.0 Depends: SingleCellExperiment, HDF5Array Imports: AnnotationHub (>= 2.9.22), ExperimentHub Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel, data.table, rmarkdown License: CC BY 4.0 MD5sum: 09644b760067953367e927086cc4027d 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: bb758d9 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/TENxBrainData_1.21.0.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: 111 Package: TENxBUSData Version: 1.15.0 Imports: ExperimentHub, AnnotationHub, utils, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle License: BSD_2_clause + file LICENSE MD5sum: b46820f9e309b794c3c0217fcd8a86da 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: 716a1c9 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/TENxBUSData_1.15.0.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: 96 Package: TENxPBMCData Version: 1.19.0 Depends: SingleCellExperiment, HDF5Array Imports: AnnotationHub, ExperimentHub Suggests: rmarkdown, knitr, BiocStyle, snow, BiocFileCache, BiocParallel License: CC BY 4.0 MD5sum: c05468c2f044c7a39ae723966ffc4bde 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: d6dc9a7 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/TENxPBMCData_1.19.0.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 importsMe: singleCellTK suggestsMe: ASURAT, celda, concordexR, ExperimentSubset, glmGamPoi, iSEE, mbkmeans, schex, scone, scry, transformGamPoi dependencyCount: 111 Package: TENxVisiumData Version: 1.9.0 Depends: ExperimentHub, SpatialExperiment Imports: utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 63ac210c5bc873ef27e6789e3ebc6ca6 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: 5e268f6 git_last_commit_date: 2023-04-25 Date/Publication: 2023-05-25 source.ver: src/contrib/TENxVisiumData_1.9.0.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: 136 Package: timecoursedata Version: 1.11.0 Depends: R (>= 4.0), SummarizedExperiment Suggests: testthat (>= 1.0.0), knitr, rmarkdown, markdown, covr, BiocStyle License: BSD 3-clause License + file LICENSE MD5sum: 00002db615beeda069d86db353b4a01c 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: 0de5804 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/timecoursedata_1.11.0.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: 28 Package: TimerQuant Version: 1.31.0 Depends: shiny Imports: ggplot2, grid, gridExtra, deSolve, dplyr, locfit Suggests: BiocStyle, reshape2, knitr, shinyBS License: Artistic-2.0 MD5sum: 87e7e5f10f44689657685c3698e78590 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: 28466f7 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/TimerQuant_1.31.0.tar.gz vignettes: vignettes/TimerQuant/inst/doc/genPaperFigures.pdf, vignettes/TimerQuant/inst/doc/mathematicalDerivations.pdf vignetteTitles: Supplementary Methods - automatic generation of paper figures, Supplementary Methods - mathematical derivations hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TimerQuant/inst/doc/genPaperFigures.R, vignettes/TimerQuant/inst/doc/mathematicalDerivations.R dependencyCount: 66 Package: tinesath1cdf Version: 1.39.0 License: Artistic-2.0 MD5sum: cbe81a1deb47fdc1915e2777e9db7b4f 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: 501f0a0 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/tinesath1cdf_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: tinesath1probe Version: 1.39.0 Depends: R (>= 1.6), AnnotationDbi (>= 1.11.9) License: LGPL MD5sum: e4955fbb7f6ac507cef8f3a246950b3c 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: ee86a8a git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/tinesath1probe_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 46 Package: TMExplorer Version: 1.11.0 Depends: R (>= 4.1), SingleCellExperiment, BiocFileCache Imports: methods, Matrix Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 96ee82abfc06d6489bdc19fc1a444909 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: 936bf20 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/TMExplorer_1.11.0.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: 1.29.0 Depends: R (>= 3.2.0) Suggests: knitr, rmarkdown, tools License: GPL-3 MD5sum: 69a71301f9c5944f194098aa18d51996 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: 2f35cf0 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/tofsimsData_1.29.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: tuberculosis Version: 1.7.0 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: b584f83bcf517fcf9f76227fd30dc96f 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: 75842cb git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/tuberculosis_1.7.0.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: 106 Package: tweeDEseqCountData Version: 1.39.0 Depends: Biobase, R (>= 2.10) License: GPL (>=2) MD5sum: 3e0b8a7049fe6cc9729c7c5ac683af02 NeedsCompilation: no Title: RNA-seq count data employed in the vignette of the tweeDEseq package Description: RNA-seq count data from Pickrell et al. (2010) employed to illustrate the use of the Poisson-Tweedie family of distributions with the tweeDEseq package. biocViews: Genome, Homo_sapiens_Data, RNASeqData Author: Juan R Gonzalez and Mikel Esnaola (with contributions from Robert Castelo ) Maintainer: Juan R Gonzalez URL: http://www.creal.cat/jrgonzalez/software.htm git_url: https://git.bioconductor.org/packages/tweeDEseqCountData git_branch: devel git_last_commit: fb4a2bd git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/tweeDEseqCountData_1.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: GSAR, missMethyl dependencyCount: 6 Package: tximportData Version: 1.29.0 Suggests: knitr, markdown License: GPL (>= 2) MD5sum: b8cd106531d986f326920c3668929846 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: 864ac16 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/tximportData_1.29.0.tar.gz vignettes: vignettes/tximportData/inst/doc/tximportData.html vignetteTitles: Sample output files for tximport hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tximportData/inst/doc/tximportData.R importsMe: TDbasedUFE suggestsMe: DESeq2, eds, fishpond, HumanTranscriptomeCompendium, tximeta, tximport dependencyCount: 0 Package: VariantToolsData Version: 1.25.0 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: 794ab075c02536592e6d9e2681805e4f 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: 015d69a git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/VariantToolsData_1.25.0.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: 100 Package: VectraPolarisData Version: 1.5.0 Depends: ExperimentHub, SpatialExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, dplyr License: Artistic-2.0 MD5sum: 509a62d1edfb5b1e938ea052930a5447 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: 151fd25 git_last_commit_date: 2023-04-25 Date/Publication: 2023-05-25 source.ver: src/contrib/VectraPolarisData_1.5.0.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: 136 Package: vulcandata Version: 1.23.0 Imports: utils License: LGPL-3 MD5sum: 915e744090e57f492fcdc99ce2bfe8a0 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: 2370bb9 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/vulcandata_1.23.0.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: 1.3.0 Depends: ExperimentHub, SpatialExperiment, SingleCellExperiment Imports: utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 08fc174dbcbd63ecf23cbeea1990d09e 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: e28f433 git_last_commit_date: 2023-04-25 Date/Publication: 2023-05-25 source.ver: src/contrib/WeberDivechaLCdata_1.3.0.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: 136 Package: WES.1KG.WUGSC Version: 1.33.0 License: GPL-2 MD5sum: 0598e0b1b64c6810cafea556b0801bca 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: f19d524 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/WES.1KG.WUGSC_1.33.0.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: 1.13.0 Depends: R (>= 3.6.0), GenomicRanges License: GPL-2 MD5sum: a5764283aac55e147bab5a5ab2a9979d 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: a73f4d6 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/WGSmapp_1.13.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: SCOPE dependencyCount: 16 Package: xcoredata Version: 1.5.0 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: e0e49b73599825310299277cf44e29f3 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: 2219ea0 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/xcoredata_1.5.0.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: 96 Package: yeastCC Version: 1.41.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 150aa5dd77fc80b1524fbbec5aec2bd5 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: 2f74389 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/yeastCC_1.41.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: LiquidAssociation suggestsMe: fastLiquidAssociation, ibh dependencyCount: 6 Package: yeastExpData Version: 0.47.0 Depends: R (>= 2.4), graph (>= 1.9.26) Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db License: GPL MD5sum: 0ac9a9aa498206ed0761db8d3894a976 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: 357d143 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/yeastExpData_0.47.0.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: 0.39.0 License: Artistic-2.0 MD5sum: 73dfefdaf5287abc1e351b565b8950d1 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: bf11bdd git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/yeastGSData_0.39.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: yeastNagalakshmi Version: 1.37.0 License: Artistic-2.0 MD5sum: 8bfe72852064c54e6e71ca0a591229c3 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: 5ebaa2b git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/yeastNagalakshmi_1.37.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ShortRead dependencyCount: 0 Package: yeastRNASeq Version: 0.39.0 Depends: R (>= 2.4) Suggests: Biobase, ShortRead, IRanges License: GPL MD5sum: 791dfa7ec87936f95f9f70755fb7efaa 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: b4e15e7 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/yeastRNASeq_0.39.0.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: 1.21.0 Depends: R (>= 2.10) Suggests: BiocStyle, knitr License: GPL MD5sum: 71860f9ab7d116f89b0a4c0b1780f878 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: bf04b89 git_last_commit_date: 2023-04-25 Date/Publication: 2023-04-27 source.ver: src/contrib/zebrafishRNASeq_1.21.0.tar.gz vignettes: vignettes/zebrafishRNASeq/inst/doc/preprocessing.pdf vignetteTitles: Pre-Processing for the Zebrafish RNA-Seq Gene-Level Counts hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/zebrafishRNASeq/inst/doc/preprocessing.R suggestsMe: RUVSeq, sva dependencyCount: 0 Package: affydata Version: 1.49.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Imports: methods Suggests: hgu95av2cdf, hgu133acdf License: GPL (>= 2) Title: Affymetrix Data for Demonstration Purpose Description: Example datasets of a slightly large size. They represent 'real world examples', unlike the artificial examples included in the package affy. biocViews: ExperimentData, Tissue, MicroarrayData, TissueMicroarrayData Author: Laurent Gautier Maintainer: Harris Jaffee Package: ALLMLL Version: 1.41.0 Depends: R (>= 2.10), affy (>= 1.23.4) License: GPL-2 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 Package: AmpAffyExample Version: 1.41.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Suggests: hgu133acdf License: LGPL (>= 2) Title: Example of Amplified Data Description: Six arrays. Three from amplified RNA, three from the typical procedure. biocViews: ExperimentData, MicroarrayData Author: Rafael A. Irizarry Maintainer: Rafael A. Irizarry Package: bronchialIL13 Version: 1.39.0 Depends: R(>= 2.10.0), affy (>= 1.23.4) License: GPL-2 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 Package: CLL Version: 1.41.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: LGPL 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 Package: davidTiling Version: 1.41.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db License: LGPL 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 Package: ecoliLeucine Version: 1.41.0 Depends: R (>= 1.9.0), affy (>= 1.23.4), ecolicdf License: GPL (>= 2) 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 Package: estrogen Version: 1.47.0 Suggests: affy, hgu95av2.db, hgu95av2cdf, vsn, knitr License: LGPL 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 Package: faahKO Version: 1.41.0 Depends: R (>= 2.10), xcms (>= 3.4.0) License: LGPL 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 Package: MAQCsubset Version: 1.39.0 Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), lumi, methods Suggests: genefilter, codelink License: Artistic-2.0 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 Package: SpikeIn Version: 1.43.0 Depends: R (>= 1.6), affy (>= 1.23.4) License: Artistic-2.0 Title: Affymetrix Spike-In Experiment Data Description: Contains the HGU133 and HGU95 spikein experiment data. biocViews: ExperimentData, MicroarrayData Author: Rafael Irizarry Maintainer: Rafael A. Irizarry Package: SpikeInSubset Version: 1.41.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5), affy (>= 1.23.4) License: LGPL Title: Part of Affymetrix's Spike-In Experiment Data Description: Includes probe-level and expression data for the HGU133 and HGU95 spike-in experiments biocViews: ExperimentData, MicroarrayData Author: Rafael Irizarry and Zhijin Wu Maintainer: Rafael A. Irizarry Package: lumiBarnes Version: 1.41.0 Depends: R (>= 2.0), Biobase (>= 2.5.5), lumi (>= 1.1.0) License: LGPL 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 Package: pumadata Version: 2.37.0 Depends: R (>= 3.2.0), Biobase (>= 2.5.5),puma, oligo(>= 1.32.0) License: LGPL 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: master git_last_commit: f5c2c48 git_last_commit_date: 2019-09-04 Date/Publication: 2019-09-04 Package: XhybCasneuf Version: 1.39.0 Depends: R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf , RColorBrewer , methods, grid License: Artistic-2.0 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 Package: MAQCsubsetILM Version: 1.39.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), lumi License: Artistic-2.0 Title: MAQC data subset for the Illumina platform Description: MAQC data subset for the Illumina platform biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData Author: Laurent Gatto Maintainer: Laurent Gatto Package: ccTutorial Version: 1.39.0 Depends: R (>= 2.10), Ringo(>= 1.9.8), affy(>= 1.23.4), topGO(>= 1.13.1) Imports: Biobase Suggests: biomaRt, Biobase(>= 2.5.5), xtable License: Artistic-2.0 Title: Data package for ChIP-chip tutorial Description: This is a data package that accompanies a ChIP-chip tutorial, which has been published in PLoS Computational Biology. The data and source code in this package allow the reader to completely reproduce the steps in the tutorial. biocViews: ExperimentData, Mus_musculus_Data, MicroarrayData, ChipOnChipData Author: Joern Toedling, Wolfgang Huber Maintainer: Joern Toedling Package: mvoutData Version: 1.37.0 Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4), lumi License: Artistic-2.0 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 Package: DLBCL Version: 1.41.0 Depends: R(>= 2.11.0), Biobase License: GPL (>=2) 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/ Package: pasilla Version: 1.29.0 Depends: R (>= 3.5.0), DEXSeq Suggests: rmarkdown, BiocStyle, knitr License: LGPL Title: Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011. Description: This package provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in the article "Conservation of an RNA regulatory map between Drosophila and mammals" by Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR, Genome Res. 2011 Feb;21(2):193-202, Epub 2010 Oct 4, PMID: 20921232. The experiment studied the effect of RNAi knockdown of Pasilla, the Drosophila melanogaster ortholog of mammalian NOVA1 and NOVA2, on the transcriptome. The package vignette describes how the data provided here were derived from the RNA-Seq read sequence data that are provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. biocViews: ExperimentData, Genome, Drosophila_melanogaster_Data, RNASeqData Author: Wolfgang Huber, Alejandro Reyes Maintainer: Alejandro Reyes VignetteBuilder: knitr Package: PREDAsampledata Version: 0.41.0 Depends: R (>= 2.10.0), methods, PREDA, Biobase, affy, annotate Suggests: hgu133plus2.db, hgu133plus2cdf License: Artistic-2.0 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 Package: GWASdata Version: 1.39.0 Depends: GWASTools License: Artistic-2.0 Title: Data used in the examples and vignettes of the GWASTools package Description: Selected Affymetrix and Illlumina SNP data for HapMap subjects. Data provided by the Center for Inherited Disease Research at Johns Hopkins University and the Broad Institute of MIT and Harvard University. biocViews: ExperimentData, MicroarrayData, SNPData, HapMap Author: Stephanie Gogarten Maintainer: Stephanie Gogarten , Adrienne Stilp Package: ffpeExampleData Version: 1.39.0 Depends: R (>= 2.10.0), lumi Suggests: genefilter, affy License: GPL (>2) 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 Package: synapterdata Version: 1.39.0 Depends: R (>= 2.10), synapter (>= 1.99.2) Imports: utils License: GPL-2 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 Package: pRolocdata Version: 1.39.0 Depends: R (>= 3.6.3), MSnbase Imports: Biobase, utils Suggests: pRoloc (>= 1.13.8), testthat, SummarizedExperiment License: GPL-2 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 Package: RforProteomics Version: 1.39.1 Depends: R (>= 3.5), MSnbase (>= 2.5.3) Imports: R.utils, biocViews, BiocManager Suggests: AnnotationDbi, rpx (>= 2.0.3), DT, knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, 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 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 Package: curatedOvarianData Version: 1.39.0 Depends: R (>= 2.10.0), affy Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle License: Artistic-2.0 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 Package: Hiiragi2013 Version: 1.37.0 Depends: R (>= 3.0.0), affy, Biobase, boot, clue, cluster, genefilter, geneplotter, gplots, gtools, KEGGREST, MASS, mouse4302.db, RColorBrewer, xtable Imports: grid, lattice, latticeExtra Suggests: ArrayExpress, BiocStyle License: Artistic-2.0 Title: Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages Description: This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881." biocViews: ExperimentData, MicroarrayData, qPCRData, ReproducibleResearch Author: Andrzej Oles, Wolfgang Huber Maintainer: Andrzej Oles Package: DeSousa2013 Version: 1.37.0 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 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 Package: seventyGeneData Version: 1.37.3 Depends: R (>= 2.13.0) Suggests: Biobase, readxls, limma, breastCancerNKI License: Artistic-2.0 Title: ExpressionSets from the van't Veer and Van de Vijver breast cancer studies Description: Gene expression data for the two breast cancer cohorts published by van't Veer and Van de Vijver in 2002 biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData Author: Luigi Marchionni Maintainer: Luigi Marchionni URL: http://luigimarchionni.org/breastTSP.html Package: curatedBladderData Version: 1.37.0 Depends: R (>= 2.10.0), affy Suggests: BiocStyle, survival, xtable, sva, genefilter, logging License: Artistic-2.0 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 Package: ChimpHumanBrainData Version: 1.39.0 Depends: affy,qvalue,limma,hexbin,statmod License: MIT 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 Package: GSE62944 Version: 1.29.0 Depends: Biobase, GEOquery Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown License: Artistic-2.0 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 Package: DAPARdata Version: 1.31.0 Depends: R (>= 4.2.0), MSnbase Imports: utils Suggests: knitr, DAPAR License: GPL-2 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: Florence Combes [aut], Samuel Wieczorek [cre, aut] Maintainer: Samuel Wieczorek URL: http://www.prostar-proteomics.org/ VignetteBuilder: knitr BugReports: https://github.com/prostarproteomics/DAPARdata/issues Package: PtH2O2lipids Version: 1.27.0 Depends: R (>= 3.3), xcms, CAMERA, LOBSTAHS, methods, utils Suggests: gplots, RColorBrewer, cluster, vegan License: MIT + file LICENSE 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 Package: MIGSAdata Version: 1.25.0 Depends: R (>= 3.4) Suggests: BiocGenerics License: GPL (>= 2) Title: MIGSA vignette data Description: MIGSA vignette data. The MIGSAdata package provides several data objects needed by MIGSA package to correctly generate its vignette, and follow it step by step. biocViews: ExperimentData, RepositoryData, ReproducibleResearch, CancerData, BreastCancerData, MicroarrayData Author: Juan C. Rodriguez, Cristobal Fresno, Andrea S. Llera and Elmer A. Fernandez Maintainer: Juan C. Rodriguez URL: http://www.bdmg.com.ar/ Package: TCGAWorkflowData Version: 1.25.0 Depends: R (>= 3.4.0) Imports: SummarizedExperiment Suggests: knitr, rmarkdown, pander, testthat License: GPL-3 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 Package: restfulSEData Version: 1.23.0 Depends: R (>= 3.4), SummarizedExperiment, ExperimentHub, DelayedArray (>= 0.21.2), HDF5Array (>= 1.23.2) Imports: utils, methods Suggests: knitr, rmarkdown License: Artistic-2.0 Title: Example metadata for the "restfulSE" R package Description: Metadata RangedSummarizedExperiment shell for use with restfulSE. biocViews: ExperimentData, Mus_musculus_Data, Homo_sapiens_Data, ExpressionData, SequencingData Author: Vincent Carey [aut], Shweta Gopaulakrishnan [cre, aut] Maintainer: Bioconductor Package Maintainer VignetteBuilder: knitr Package: topdownrdata Version: 1.23.0 Depends: topdownr License: GPL (>= 3) 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/ Package: mCSEAdata Version: 1.21.0 Depends: R (>= 3.5) Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 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 Package: tissueTreg Version: 1.21.0 Depends: R (>= 3.5) Suggests: BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq, SummarizedExperiment License: GPL (>= 2) 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 Package: qPLEXdata Version: 1.19.0 Depends: R (>= 3.5), qPLEXanalyzer Imports: utils, knitr, MSnbase, dplyr License: GPL-2 NeedsCompilation: no Title: Data accompanying qPLEXanalyzer package Description: qPLEX-RIME and Full proteome TMT mass spectrometry datasets. biocViews: ExperimentData, MassSpectrometryData, Proteome Author: Kamal Kishore Developer [aut, cre] Maintainer: Kamal Kishore Developer VignetteBuilder: knitr Package: mcsurvdata Version: 1.19.0 Depends: R (>= 3.5), ExperimentHub Imports: AnnotationHub, Biobase Suggests: knitr License: GPL (>=2) 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 Package: MOFAdata Version: 1.17.0 Depends: R (>= 3.5) Suggests: knitr, MultiAssayExperiment, rmarkdown License: LGPL-3 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 Package: ReactomeGSA.data Version: 1.15.0 Depends: R (>= 3.6), limma, edgeR, ReactomeGSA, Seurat License: Artistic-2.0 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 Package: pwrEWAS.data Version: 1.15.0 Imports: ExperimentHub Suggests: knitr, RUnit, BiocGenerics License: Artistic-2.0 Title: pwrEWAS.data: Reference data accompanying pwrEWAS Description: This package provides reference data required for pwrEWAS. pwrEWAS is a user-friendly tool to estimate power in EWAS as a function of sample and effect size for two-group comparisons of DNAm (e.g., case vs control, exposed vs non-exposed, etc.). biocViews: ExperimentHub, MethylationArrayData, MicroarrayData, TissueMicroarrayData, Tissue Author: Stefan Graw Maintainer: Stefan Graw VignetteBuilder: knitr Package: biscuiteerData Version: 1.15.2 Depends: R (>= 4.1.0), ExperimentHub Imports: AnnotationHub, utils, curl, GenomicRanges Suggests: knitr, rmarkdown, markdown License: GPL-3 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 Package: signatureSearchData Version: 1.15.0 Depends: R (>= 3.6) Imports: ExperimentHub, utils, affy, limma, Biobase, magrittr, dplyr, R.utils, stats, rhdf5 Suggests: knitr, rmarkdown License: Artistic-2.0 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 Package: SCATEData Version: 1.11.0 Depends: ExperimentHub, GenomicAlignments, GenomicRanges, base Imports: utils Suggests: knitr, rmarkdown License: MIT + file LICENSE Title: Data for SCATE (Single-cell ATAC-seq Signal Extraction and Enhancement) Description: SCATEData is an ExperimentHub package for SCATE which is a software tool for extracting and enhancing the sparse and discrete Single-cell ATAC-seq Signal. biocViews: ExperimentHub, ExperimentData Author: Zhicheng Ji [aut], Weiqiang Zhou [aut], Wenpin Hou [cre, aut] (), Hongkai Ji [aut] Maintainer: Wenpin Hou VignetteBuilder: knitr BugReports: https://github.com/Winnie09/SCATEData/issues Package: RNAinteractMAPK Version: 1.39.0 Depends: R (>= 2.12.0), sparseLDA, RNAinteract Imports: grid, gdata, MASS, genefilter, methods, fields, utils, lattice, Biobase Suggests: qvalue License: Artistic-2.0 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 Package: methylclockData Version: 1.9.0 Imports: ExperimentHubData, ExperimentHub, utils Suggests: knitr, rmarkdown License: MIT + file LICENSE 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 Package: brgedata Version: 1.23.0 Depends: R (>= 3.4), Biobase Imports: SummarizedExperiment Suggests: minfi, MultiAssayExperiment, knitr, rmarkdown, rexposome License: MIT + file LICENSE Title: Exposures, Gene Expression and Methylation data for ilustration purpouses Description: This package contains several sets of omics data including Gene Expression (ExpressionSet), Methylation (GenomicRatioSet), Proteome and Exposome (ExposomeSet). This data is used in vignettes and exaples at MEAL, MultiDataSet and omicRexposome. biocViews: ExperimentData,Homo_sapiens_Data,MicroarrayData,MethylationArrayData Author: Dolors Pelegri-Siso [aut, cre], Carlos Ruiz-Arenas [aut], Carles Hernandez-Ferrer [aut], Juan R. Gonzalez [aut] Maintainer: Dolors Pelegri-Siso VignetteBuilder: knitr Package: spatialDmelxsim Version: 1.7.0 Depends: R (>= 4.1), ExperimentHub, SummarizedExperiment Imports: utils Suggests: knitr, rmarkdown License: GPL-3 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 Package: RLHub Version: 1.7.0 Imports: AnnotationHub, ExperimentHub, utils Suggests: knitr, DT, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE Title: An ExperimentHub package for accessing processed RLSuite data sets Description: | RLHub provides a convenient interface to the processed data provided within RLSuite, a tool-chain for analyzing R-loop-mapping data sets. The primary purpose of RLHub is to serve the processed data sets required by the RLSeq R package and the RLBase web service. Additionally, RLHub provides a stand-alone R interface to these data, benefiting users who are addressing questions related to R-loop regions (RL-Regions), R-loop-binding proteins (RLBPs), R-loop co-localizing factors, and the differences between R-loop-mapping methods. The full data-generating protocol is found here: https://github.com/Bishop-Laboratory/RLBase-data. biocViews: ExperimentData, ExperimentHub, ExpressionData, ReproducibleResearch, SequencingData, Genome, ChIPSeqData, RNASeqData, GEO, PackageTypeData, DNASeqData, ENCODE Author: Henry Miller [aut, cre, cph] (), Alexander Bishop [ths, cph] () Maintainer: Henry Miller URL: https://github.com/Bishop-Laboratory/RLHub, https://bishop-laboratory.github.io/RLHub/ VignetteBuilder: knitr BugReports: https://github.com/Bishop-Laboratory/RLHub/issues Package: RITANdata Version: 1.25.0 Depends: R (>= 3.4) License: file LICENSE NeedsCompilation: no Title: This package contains the annotation and network data sets Description: Data such as is contained in these two R data files in this package are required for the RITAN package examples. Users may use their own or additional resources in conjunction with RITANdata. See the RITAN vignettes for more information, such as gathering more up-to-date annotation data. biocViews: AnnotationData, Homo_sapiens Author: Michael Zimmermann Maintainer: Michael Zimmermann VignetteBuilder: knitr Package: EpiMix.data Title: ERROR Maintainer: ERROR