Package: ABAData Version: 1.14.0 Depends: R (>= 3.2) Suggests: BiocStyle, knitr, ABAEnrichment License: GPL (>= 2) MD5sum: 14527790b75fc139b5bbed7981c1a1ea NeedsCompilation: no Title: Averaged gene expression in human brain regions from Allen Brain Atlas Description: Provides the data for the gene expression enrichment analysis conducted in the package 'ABAEnrichment'. The package includes three datasets which are derived from the Allen Brain Atlas: (1) Gene expression data from Human Brain (adults) averaged across donors, (2) Gene expression data from the Developing Human Brain pooled into five age categories and averaged across donors and (3) a developmental effect score based on the Developing Human Brain expression data. All datasets are restricted to protein coding genes. biocViews: ExpressionData, Homo_sapiens_Data, MicroarrayData, RNASeqData Author: Steffi Grote Maintainer: Steffi Grote VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ABAData git_branch: RELEASE_3_9 git_last_commit: ed7460e git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ABAData_1.14.0.tar.gz vignettes: vignettes/ABAData/inst/doc/ABAData.html vignetteTitles: ABAData: gene expression data to use with enrichment analysis package ABAEnrichment hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ABAData/inst/doc/ABAData.R dependencyCount: 0 Package: adductData Version: 1.0.0 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: ee38a871976b2c0f4eba667771f3b3a0 NeedsCompilation: no Title: Data from untargeted MS of modifications to Cys34 of serum albumin Description: mzXML files from Grigoryan et al 2016 (Anal Chem). biocViews: ExperimentData,MassSpectrometryData,ExperimentHub Author: Josie Hayes Maintainer: Josie Hayes VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/adductData git_branch: RELEASE_3_9 git_last_commit: 40ebe7a git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/adductData_1.0.0.tar.gz vignettes: vignettes/adductData/inst/doc/adductData.html vignetteTitles: Raw mzXML data using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/adductData/inst/doc/adductData.R dependencyCount: 67 Package: affycompData Version: 1.22.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp License: GPL (>= 2) MD5sum: a334dbc9b6dc766a2f496d967de5e918 NeedsCompilation: no Title: affycomp data Description: Data needed by the affycomp package. biocViews: MicroarrayData Author: Rafael A. Irizarry and Zhijin Wu with contributions from Simon Cawley Maintainer: Harris Jaffee git_url: https://git.bioconductor.org/packages/affycompData git_branch: RELEASE_3_9 git_last_commit: 8ecda55 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/affycompData_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 8 Package: affydata Version: 1.32.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Imports: methods Suggests: hgu95av2cdf, hgu133acdf License: GPL (>= 2) MD5sum: a37af61d647439e98b7b03e7fe349ca1 NeedsCompilation: no Title: Affymetrix Data for Demonstration Purpose Description: Example datasets of a slightly large size. They represent 'real world examples', unlike the artificial examples included in the package affy. biocViews: ExperimentData, Tissue, MicroarrayData, TissueMicroarrayData Author: Laurent Gautier Maintainer: Harris Jaffee git_url: https://git.bioconductor.org/packages/affydata git_branch: RELEASE_3_9 git_last_commit: c7cef93 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/affydata_1.32.0.tar.gz vignettes: vignettes/affydata/inst/doc/affydata.pdf vignetteTitles: affydata primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/affydata/inst/doc/affydata.R dependencyCount: 13 Package: Affyhgu133A2Expr Version: 1.20.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 1eab8a17b6f940ee9d980b39ac66874b NeedsCompilation: no Title: Affymetrix Human Genome U133A 2.0 Array (GPL571) Expression Data Package Description: Contains pre-built human (GPL571) databases of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133A2Expr git_branch: RELEASE_3_9 git_last_commit: ada580f git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/Affyhgu133A2Expr_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: Affyhgu133aExpr Version: 1.22.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 39428013cde8719e8b487042fdea7f47 NeedsCompilation: no Title: Affymetrix Human hgu133a Array (GPL96) Expression Data Package Description: Contains pre-built human (GPL96) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133aExpr git_branch: RELEASE_3_9 git_last_commit: 2f8575c git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/Affyhgu133aExpr_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: Affyhgu133Plus2Expr Version: 1.18.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: f1d335aef3a0fb1371144a6f81e70fa4 NeedsCompilation: no Title: Affyhgu133Plus2Expr (GPL570) Expression Data Package Description: Contains pre-built human (GPL570) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133Plus2Expr git_branch: RELEASE_3_9 git_last_commit: c52433f git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/Affyhgu133Plus2Expr_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: AffymetrixDataTestFiles Version: 0.22.0 Depends: R (>= 2.5.0) License: LGPL-2.1 MD5sum: c2cdbf27e487b9877c00fb8c60e22959 NeedsCompilation: no Title: Affymetrix data files (CEL, CDF, CHP, EXP, PGF, PSI) for testing Description: This package contains annotation data files and sample data files of Affymetrix file formats. The files originate from the Affymetrix' Fusion SDK distribution and other official sources. biocViews: ExperimentData, MicroarrayData Author: Henrik Bengtsson [aut, cre], James Bullard [aut], Kasper Daniel Hansen [aut] Maintainer: Henrik Bengtsson git_url: https://git.bioconductor.org/packages/AffymetrixDataTestFiles git_branch: RELEASE_3_9 git_last_commit: 81ad2b3 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/AffymetrixDataTestFiles_0.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: Affymoe4302Expr Version: 1.22.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: f9c8f9273ae064ffc30074388b43f8ed NeedsCompilation: no Title: Affymetrix Mouse Genome 430 2.0 Array (GPL1261) Expression Data Package Description: Contains pre-built mouse (GPL1261) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Mus_musculus_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affymoe4302Expr git_branch: RELEASE_3_9 git_last_commit: fceb8ad git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/Affymoe4302Expr_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: airway Version: 1.4.0 Depends: R (>= 2.10), SummarizedExperiment Suggests: knitr, GEOquery License: LGPL MD5sum: ef609098c2893c759ddabbcb47cd4b6b NeedsCompilation: no Title: RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014 Description: This package provides a RangedSummarizedExperiment object of read counts in genes for an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. Details on the gene model and read counting procedure are provided in the package vignette. The citation for the experiment is: Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri R Jr, Tantisira KG, Weiss ST, Lu Q. 'RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells.' PLoS One. 2014 Jun 13;9(6):e99625. PMID: 24926665. GEO: GSE52778. biocViews: ExperimentData, SequencingData, RNASeqData, GEO Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/airway git_branch: RELEASE_3_9 git_last_commit: a4b513d git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/airway_1.4.0.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 suggestsMe: IHWpaper, RegParallel dependencyCount: 32 Package: ALL Version: 1.26.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Suggests: rpart License: Artistic-2.0 MD5sum: 10195f32f47c4af7bcb37ed7bdba04cb NeedsCompilation: no Title: A data package Description: Data of T- and B-cell Acute Lymphocytic Leukemia from the Ritz Laboratory at the DFCI (includes Apr 2004 versions) biocViews: ExperimentData, CancerData, LeukemiaCancerData Author: Xiaochun Li Maintainer: Robert Gentleman git_url: https://git.bioconductor.org/packages/ALL git_branch: RELEASE_3_9 git_last_commit: 7e3fee0 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ALL_1.26.0.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 suggestsMe: SNAGEEdata dependencyCount: 7 Package: allenpvc Version: 1.2.0 Depends: R (>= 3.5.0), AnnotationHub, ExperimentHub (>= 1.7.0), SingleCellExperiment Suggests: BiocStyle, knitr, rmarkdown License: CC0 MD5sum: 37da5faac1aeef26425a1f0ac4b3981c NeedsCompilation: no Title: GEO accession data GSE71585 as a SingleCellExperiment Description: Celular taxonomy of the primary visual cortex in adult mice based on single cell RNA-sequencing from a study performed by the Allen Institute for Brain Science. In said study 49 transcriptomic cell types are identified. biocViews: ExperimentData, ExpressionData, SingleCellData, RNASeqData Author: Diogo P. P. Branco Maintainer: Diogo P. P. Branco VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/allenpvc git_branch: RELEASE_3_9 git_last_commit: 2c7407f git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/allenpvc_1.2.0.tar.gz vignettes: vignettes/allenpvc/inst/doc/allenpvc.html vignetteTitles: Vignette Title hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/allenpvc/inst/doc/allenpvc.R dependencyCount: 86 Package: ALLMLL Version: 1.24.0 Depends: R (>= 2.10), affy (>= 1.23.4) License: GPL-2 MD5sum: 90b0a2dc8092018739e3c8b195888311 NeedsCompilation: no Title: A subset of arrays from a large acute lymphoblastic leukemia (ALL) study Description: This package provides probe-level data for 20 HGU133A and 20 HGU133B arrays which are a subset of arrays from a large ALL study. The data is for the MLL arrays. This data was published in Mary E. Ross, Xiaodong Zhou, Guangchun Song, Sheila A. Shurtleff, Kevin Girtman, W. Kent Williams, Hsi-Che Liu, Rami Mahfouz, Susana C. Raimondi, Noel Lenny, Anami Patel, and James R. Downing (2003) Classification of pediatric acute lymphoblastic leukemia by gene expression profiling Blood 102: 2951-2959 biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData Author: B. M. Bolstad git_url: https://git.bioconductor.org/packages/ALLMLL git_branch: RELEASE_3_9 git_last_commit: 742224b git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ALLMLL_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 13 Package: alpineData Version: 1.10.0 Depends: ExperimentHub, GenomicAlignments Imports: utils, AnnotationHub Suggests: GenomicAlignments, knitr License: GPL (>=2) MD5sum: b97dd0b4c0e4b0b3b55308ffe850740f NeedsCompilation: no Title: Data for the alpine package vignette Description: A small subset of paired-end RNA-seq reads from four samples of the GEUVADIS project. biocViews: SequencingData, RNASeqData, ExpressionData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/alpineData git_branch: RELEASE_3_9 git_last_commit: 18c85e8 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/alpineData_1.10.0.tar.gz vignettes: vignettes/alpineData/inst/doc/alpineData.html vignetteTitles: tximport hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/alpineData/inst/doc/alpineData.R dependencyCount: 89 Package: AmpAffyExample Version: 1.24.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Suggests: hgu133acdf License: LGPL (>= 2) MD5sum: 90cc999d9d645e4478c8ca9bee8900b3 NeedsCompilation: no Title: Example of Amplified Data Description: Six arrays. Three from amplified RNA, three from the typical procedure. biocViews: ExperimentData, MicroarrayData Author: Rafael A. Irizarry Maintainer: Rafael A. Irizarry git_url: https://git.bioconductor.org/packages/AmpAffyExample git_branch: RELEASE_3_9 git_last_commit: 52626ad git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/AmpAffyExample_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 13 Package: AneuFinderData Version: 1.12.0 Depends: R (>= 3.3) License: file LICENSE MD5sum: 1c7d8037814fe4ba56e13c74d85175c1 NeedsCompilation: no Title: WGSCS Data for Demonstration Purposes Description: Whole-genome single cell sequencing data for demonstration purposes in the AneuFinder package. biocViews: CopyNumberVariationData, LungCancerData, Homo_sapiens_Data, SequencingData Author: Aaron Taudt Maintainer: Aaron Taudt git_url: https://git.bioconductor.org/packages/AneuFinderData git_branch: RELEASE_3_9 git_last_commit: 7350f38 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/AneuFinderData_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: antiProfilesData Version: 1.20.0 Depends: Biobase, Suggests: frma, GEOquery, GEOmetadb License: Artistic-2.0 MD5sum: 939e6ebc361769f5198676a9502baba7 NeedsCompilation: no Title: Normal colon and cancer preprocessed affy data for antiProfile building. Description: Colon normal tissue and cancer samples used in Corrada Bravo, et al. gene expression anti-profiles paper: BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272. Measurements are z-scores obtained from the GeneExpression Barcode in the 'frma' package biocViews: ExperimentData, MicroarrayData, Tissue, CancerData, ColonCancerData Author: Hector Corrada Bravo, Matthew McCall and Rafael A. Irizarry Maintainer: Hector Corrada Bravo git_url: https://git.bioconductor.org/packages/antiProfilesData git_branch: RELEASE_3_9 git_last_commit: 6dbd190 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/antiProfilesData_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: aracne.networks Version: 1.10.0 Depends: R (>= 3.3), viper License: file LICENSE MD5sum: 3dafc172cee133222db156054e3bf6f9 NeedsCompilation: no Title: ARACNe-inferred gene networks from TCGA tumor datasets Description: This package contains ARACNe-inferred networks from TCGA tumor datasets. It also contains a function to export them into plain-text format. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData Author: Federico M. Giorgi Maintainer: Federico M. Giorgi , Mariano Alvarez git_url: https://git.bioconductor.org/packages/aracne.networks git_branch: RELEASE_3_9 git_last_commit: 14eef00 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/aracne.networks_1.10.0.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: 20 Package: ARRmData Version: 1.20.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: a31c9743207a9e6e802284323c235412 NeedsCompilation: no Title: Example dataset for normalization of Illumina 450k Methylation data Description: Raw Beta values from 36 samples across 3 groups from Illumina 450k methylation arrays biocViews: ExperimentData, MethylationArrayData Author: Jean-Philippe Fortin, Celia M.T. Greenwood, Aurelie Labbe Maintainer: Jean-Philippe Fortin git_url: https://git.bioconductor.org/packages/ARRmData git_branch: RELEASE_3_9 git_last_commit: 70a489d git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ARRmData_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: AshkenazimSonChr21 Version: 1.14.0 Suggests: knitr, VariantAnnotation License: Artistic-2.0 MD5sum: afcd79416fd2b6fb83f2ad1793dcbc2b NeedsCompilation: no Title: Annotated variants on the chromosome 21, human genome 19, Ashkenazim Trio son sample Description: SonVariantsChr21 is a dataset of annotated genomic variants coming from Complete Genomics whole genome sequencing. Data comes from GIAB project, Ashkenazim Trio, sample HG002 run 1. Both vcf and annotated data frame are provided. biocViews: GenomicVariation, Sequencing, WholeGenome Author: Tomasz Stokowy Maintainer: Who to complain to VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/AshkenazimSonChr21 git_branch: RELEASE_3_9 git_last_commit: 13d7b58 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/AshkenazimSonChr21_1.14.0.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: 1.4.0 Depends: R (>= 3.5) Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: c8a51bb2154a98248afedc0b926acd7d NeedsCompilation: no Title: Example of 1D NMR spectra data for ASICS package Description: 1D NMR example spectra and additional data for use with the ASICS package. Raw 1D Bruker spectral data files were found in the MetaboLights database (https://www.ebi.ac.uk/metabolights/, study MTBLS1). biocViews: ExperimentData, Homo_sapiens_Data Author: Gaëlle Lefort [aut, cre], Rémi Servien [aut], Nathalie Villa-Vialaneix [aut] Maintainer: Gaëlle Lefort VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ASICSdata git_branch: RELEASE_3_9 git_last_commit: 3e13c79 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ASICSdata_1.4.0.tar.gz vignettes: vignettes/ASICSdata/inst/doc/ASICSdata.html vignetteTitles: ASICSdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: AssessORFData Version: 1.2.0 Depends: R (>= 3.5.0) Imports: DECIPHER, utils Suggests: AssessORF, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: d8fb320aa512adb3b5c4656d7f2809b2 NeedsCompilation: no Title: Data and Files for the AssessORF Package Description: This package provides access to mapping and results objects generated by the AssessORF package, as well as the genome sequences for the strains corresponding to those objects. biocViews: OrganismData, Bacillus_subtilis_Data, Escherichia_coli_Data, Pseudomonas_aeruginosa_Data, Staphylococcus_aureus_Data, Genome, Proteome, SequencingData Author: Deepank Korandla [aut, cre] Maintainer: Deepank Korandla VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/AssessORFData git_branch: RELEASE_3_9 git_last_commit: 865a56b git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/AssessORFData_1.2.0.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 dependencyCount: 34 Package: bcellViper Version: 1.20.0 Depends: R(>= 2.14.0), Biobase, methods License: GPL (>=2) MD5sum: e0533eed79305a8a39db5051ba7fb9a5 NeedsCompilation: no Title: Human B-cell transcriptional interactome and normal human B-cell expression data Description: This package provides a human B-cell context-specific transcriptional regulatory network and a human normal B-cells dataset for the examples in package viper. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData Author: Mariano Javier Alvarez Maintainer: Mariano Javier Alvarez git_url: https://git.bioconductor.org/packages/bcellViper git_branch: RELEASE_3_9 git_last_commit: 83815b9 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/bcellViper_1.20.0.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 dependencyCount: 7 Package: beadarrayExampleData Version: 1.22.0 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>= 2.0.0) License: GPL-2 MD5sum: ade87a63114d99fd5a48b24d7b08bfbb NeedsCompilation: no Title: Example data for the beadarray package Description: An small dataset that can be used to run examples from the beadarray vignette and examples biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/beadarrayExampleData git_branch: RELEASE_3_9 git_last_commit: 949f273 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/beadarrayExampleData_1.22.0.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 dependencyCount: 77 Package: BeadArrayUseCases Version: 1.22.0 Imports: beadarray (>= 2.3.18), limma, GEOquery Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db License: GPL-2 MD5sum: f137cb510837fa607e144c2c1290d846 NeedsCompilation: no Title: Analysing Illumina BeadArray expression data using Bioconductor Description: Example data files and use cases for processing Illumina BeadArray expression data using Bioconductor biocViews: MicroarrayData Author: Mark Dunning, Wei Shi, Andy Lynch, Mike Smith, Matt Ritchie Maintainer: Mike Smith git_url: https://git.bioconductor.org/packages/BeadArrayUseCases git_branch: RELEASE_3_9 git_last_commit: b1ff42b git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/BeadArrayUseCases_1.22.0.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: 91 Package: beta7 Version: 1.22.0 Depends: R (>= 2.4.0), marray License: LGPL MD5sum: 60b008e68244a7e355d290ac76aa0b04 NeedsCompilation: no Title: Rodriguez et al. (2004) Differential Gene Expression by Memory/Effector T Helper Cells Bearing the Gut-Homing Receptor Integrin alpha4 beta7. Description: Data from 6 gpr files aims to identify differential expressed genes between the beta 7+ and beta 7- memory T helper cells. biocViews: ExperimentData, Homo_sapiens_Data, CGHData, MicroarrayData Author: Jean Yang Maintainer: Jean Yang git_url: https://git.bioconductor.org/packages/beta7 git_branch: RELEASE_3_9 git_last_commit: 39bc1fa git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/beta7_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: biotmleData Version: 1.8.0 Depends: R (>= 3.0) Suggests: Biobase, SummarizedExperiment License: file LICENSE MD5sum: 81e38ef555e606146c1a7c8358a2f3a6 NeedsCompilation: no Title: Example experimental microarray data set for the "biotmle" R package Description: Microarray data (from the Illumina Ref-8 BeadChips platform) and phenotype-level data from an epidemiological investigation of benzene exposure, packaged using "SummarizedExperiemnt", for use as an example with the "biotmle" R package. biocViews: GeneExpression, DifferentialExpression, Sequencing, Microarray, RNASeq Author: Nima Hejazi [aut, cre] Maintainer: Nima Hejazi git_url: https://git.bioconductor.org/packages/biotmleData git_branch: RELEASE_3_9 git_last_commit: edbca6f git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/biotmleData_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: bladderbatch Version: 1.22.0 Depends: Biobase License: Artistic-2.0 MD5sum: 218fc2ffe79cb78448361adc8c9a3c2b NeedsCompilation: no Title: Bladder gene expression data illustrating batch effects Description: This package contains microarray gene expression data on 57 bladder samples from 5 batches. The data are used as an illustrative example for the sva package. biocViews: ExperimentData, CancerData, MicroarrayData Author: Jeffrey T. Leek Maintainer: Jeffrey T. Leek git_url: https://git.bioconductor.org/packages/bladderbatch git_branch: RELEASE_3_9 git_last_commit: 853cd46 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/bladderbatch_1.22.0.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 dependencyCount: 7 Package: blimaTestingData Version: 1.4.0 Depends: R(>= 3.0.0) Suggests: blima, beadarray, illuminaHumanv4.db, BiocStyle License: GPL-3 MD5sum: 0b979387eeedb8a9e0c32e120f2c6593 NeedsCompilation: no Title: Data for testing of the package blima. Description: Experiment data package. The set were prepared using microarray images of human mesenchymal cells treated with various supplements. This package is intended to provide example data to test functionality provided by blima. biocViews: MicroarrayData, ExperimentData, GEO Author: Vojtech Kulvait Maintainer: Vojtech Kulvait URL: https://bitbucket.org/kulvait/blima git_url: https://git.bioconductor.org/packages/blimaTestingData git_branch: RELEASE_3_9 git_last_commit: 0c8ed83 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/blimaTestingData_1.4.0.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 dependencyCount: 0 Package: BloodCancerMultiOmics2017 Version: 1.4.0 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, tidyverse, xtable License: LGPL (>= 3) MD5sum: 5836db39c714421d8cd32c63030483b9 NeedsCompilation: no Title: "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al. - experimental data and complete analysis Description: The package contains data of the Primary Blood Cancer Encyclopedia (PACE) project together with a complete executable transcript of the statistical analysis and reproduces figures presented in the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) 128(1):427-445. doi:10.1172/JCI93801. biocViews: ExperimentData, ReproducibleResearch, CancerData, LeukemiaCancerData Author: Malgorzata Oles, Sascha Dietrich, Junyan Lu, Britta Velten, Andreas Mock, Vladislav Kim, Wolfgang Huber Maintainer: Malgorzata Oles VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/BloodCancerMultiOmics2017 git_branch: RELEASE_3_9 git_last_commit: c793cbb git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/BloodCancerMultiOmics2017_1.4.0.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: 1.0.0 Depends: R (>= 3.6.0), SummarizedExperiment, ExperimentHub Imports: utils Suggests: knitr, BiocStyle, testthat License: CC BY 4.0 MD5sum: 828a327a3b634d6861595baea00c4ac3 NeedsCompilation: no Title: Experimental dataset from the rat BodyMap project Description: This package contains a SummarizedExperiment from the Yu et al. (2013) paper that performed the rat BodyMap across 11 organs and 4 developmental stages. Raw FASTQ files were downloaded and mapped using STAR. Data is available on ExperimentHub as a data package. biocViews: SequencingData, RNASeqData, ExpressionData, ExperimentData, ExperimentHub Author: Stephanie Hicks [aut, cre] (), Kwame Okrah [aut] Maintainer: Stephanie Hicks VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/bodymapRat git_branch: RELEASE_3_9 git_last_commit: b1c778a git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/bodymapRat_1.0.0.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 dependencyCount: 85 Package: brainImageRdata Version: 1.2.0 Depends: ExperimentHub Suggests: knitr License: CC BY-SA 4.0 MD5sum: 54c39516d8efa96d6404737c09bddb94 NeedsCompilation: no Title: Image masks and expression data for use with BrainImageR Description: brainImageRdata contains image masks for the developing human and the adult human brain. These masks can be used in conjunction with the gene expression data to generate spatial gene set enrichment plots. It also contains the expression data for the 15 pcw human brain, the adult human brain, and the developing human brain. biocViews: OrganismData, Homo_sapiens_Data, ExpressionData Author: Sara Linker Maintainer: Sara Linker VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/brainImageRdata git_branch: RELEASE_3_9 git_last_commit: b9444e2 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/brainImageRdata_1.2.0.tar.gz vignettes: vignettes/brainImageRdata/inst/doc/brainImageRdata.html vignetteTitles: brainImageRdata hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/brainImageRdata/inst/doc/brainImageRdata.R dependencyCount: 66 Package: breakpointRdata Version: 1.2.0 Depends: R (>= 3.5) Suggests: knitr, BiocStyle, License: file LICENSE MD5sum: 5bb31f8819f87705c211d99636af87eb NeedsCompilation: no Title: Strand-seq data for demonstration purposes Description: Strand-seq data to demonstrate functionalities of breakpointR package. biocViews: ExperimentData, Homo_sapiens_Data, SequencingData, DNASeqData, Genome, SingleCellData Author: David Porubsky, Aaron Taudt, Ashley Sanders Maintainer: David Porubsky URL: https://github.com/daewoooo/breakpointRdata VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/breakpointRdata git_branch: RELEASE_3_9 git_last_commit: 9da4a55 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/breakpointRdata_1.2.0.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 dependencyCount: 0 Package: breastCancerMAINZ Version: 1.22.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: f04819049e4092504c4f5a7c84f0ce4b NeedsCompilation: no Title: Gene expression dataset published by Schmidt et al. [2008] (MAINZ). Description: Gene expression data from the breast cancer study published by Schmidt et al. in 2008, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerMAINZ git_branch: RELEASE_3_9 git_last_commit: 41b8b64 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/breastCancerMAINZ_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: breastCancerNKI Version: 1.22.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 60ba238770e734f7995c540e52ced5d7 NeedsCompilation: no Title: Genexpression dataset published by van't Veer et al. [2002] and van de Vijver et al. [2002] (NKI). Description: Genexpression data from a breast cancer study published by van't Veer et al. in 2002 and van de Vijver et al. in 2002, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, CGHData, MicroarrayData, OneChannelData, ChipOnChipData Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerNKI git_branch: RELEASE_3_9 git_last_commit: 8330ef7 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/breastCancerNKI_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: seventyGeneData dependencyCount: 0 Package: breastCancerTRANSBIG Version: 1.22.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 1752abd0640ff2958d4b91752b68b28c NeedsCompilation: no Title: Gene expression dataset published by Desmedt et al. [2007] (TRANSBIG). Description: Gene expression data from a breast cancer study published by Desmedt et al. in 2007, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerTRANSBIG git_branch: RELEASE_3_9 git_last_commit: 39435ad git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/breastCancerTRANSBIG_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: breastCancerUNT Version: 1.22.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 4abb8ad6dee3b46bfe38e5712993418d NeedsCompilation: no Title: Gene expression dataset published by Sotiriou et al. [2007] (UNT). Description: Gene expression data from a breast cancer study published by Sotiriou et al. in 2007, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, TwoChannelData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerUNT git_branch: RELEASE_3_9 git_last_commit: 98a0847 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/breastCancerUNT_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: breastCancerUPP Version: 1.22.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 2c41fe7534c5a603b6aeef57e7b4600e NeedsCompilation: no Title: Gene expression dataset published by Miller et al. [2005] (UPP). Description: Gene expression data from a breast cancer study published by Miller et al. in 2005, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerUPP git_branch: RELEASE_3_9 git_last_commit: 7fc3032 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/breastCancerUPP_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: breastCancerVDX Version: 1.22.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: b437da5fd7abf3b1f10276dd6543217d NeedsCompilation: no Title: Gene expression datasets published by Wang et al. [2005] and Minn et al. [2007] (VDX). Description: Gene expression data from a breast cancer study published by Wang et al. in 2005 and Minn et al. in 2007, provided as an eSet. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData, BreastCancerData, LungCancerData, MicroarrayData, OneChannelData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerVDX git_branch: RELEASE_3_9 git_last_commit: fbe81eb git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/breastCancerVDX_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: brgedata Version: 1.6.0 Depends: R (>= 3.4), Biobase Imports: SummarizedExperiment Suggests: minfi, MultiAssayExperiment, knitr, rexposome License: MIT + file LICENSE MD5sum: cb1cdff76c21aabfa29e0004360532d8 NeedsCompilation: no Title: Exposures, Gene Expression and Methylation data for ilustration purpouses Description: This package contains several sets of omics data including Gene Expression (ExpressionSet), Methylation (GenomicRatioSet), Proteome and Exposome (ExposomeSet). This data is used in vignettes and exaples at MEAL, MultiDataSet and omicRexposome. biocViews: ExperimentData,Homo_sapiens_Data,MicroarrayData,MethylationArrayData Author: Carlos Ruiz-Arenas [aut, cre], Carles Hernandez-Ferrer [aut], Juan R. Gonzalez [aut] Maintainer: Carlos Ruiz-Arenas VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/brgedata git_branch: RELEASE_3_9 git_last_commit: c002547 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/brgedata_1.6.0.tar.gz vignettes: vignettes/brgedata/inst/doc/general_description.html vignetteTitles: brgedata -- data R package with three omic data-set and exposome data-set from the same Spanish pupulation hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/brgedata/inst/doc/general_description.R dependencyCount: 32 Package: bronchialIL13 Version: 1.22.0 Depends: R(>= 2.10.0), affy (>= 1.23.4) License: GPL-2 MD5sum: a7b5cbe220c3ad028b87560217dca192 NeedsCompilation: no Title: time course experiment involving il13 Description: derived from CNMC (pepr.cnmcresearch.org) http://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=95 Human Bronchial Cell line A549 biocViews: ExperimentData, MicroarrayData Author: Vince Carey Maintainer: Vince Carey URL: http://www.biostat.harvard.edu/~carey git_url: https://git.bioconductor.org/packages/bronchialIL13 git_branch: RELEASE_3_9 git_last_commit: 6ee6215 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/bronchialIL13_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 13 Package: bsseqData Version: 0.22.0 Depends: R (>= 2.15), bsseq (>= 1.16.0) License: Artistic-2.0 MD5sum: e7675043ef714d778044e826b0dd2b1d NeedsCompilation: no Title: Example whole genome bisulfite data for the bsseq package Description: Example whole genome bisulfite data for the bsseq package biocViews: Genome, CancerData, ColonCancerData, SequencingData Author: Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/bsseqData git_branch: RELEASE_3_9 git_last_commit: 059c1a5 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/bsseqData_0.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 61 Package: cancerdata Version: 1.22.0 Depends: R (>= 2.10.1), Biobase License: GPL (>= 2) MD5sum: e7527824c67a7dc60e2345b78ee01da7 NeedsCompilation: no Title: Development and validation of diagnostic tests from high-dimensional molecular data: Datasets Description: Dataset for the R package cancerclass biocViews: CancerData, MicroarrayData Author: Jan Budczies, Daniel Kosztyla Maintainer: Daniel Kosztyla git_url: https://git.bioconductor.org/packages/cancerdata git_branch: RELEASE_3_9 git_last_commit: b067ab3 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/cancerdata_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: CardinalWorkflows Version: 1.16.0 Depends: R (>= 2.10), Cardinal Suggests: BiocStyle License: Artistic-2.0 MD5sum: 1d61193cff92e95a54c8a79cf2148ba7 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 git_url: https://git.bioconductor.org/packages/CardinalWorkflows git_branch: RELEASE_3_9 git_last_commit: fa8a5df git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/CardinalWorkflows_1.16.0.tar.gz vignettes: vignettes/CardinalWorkflows/inst/doc/Workflows-classification.pdf, vignettes/CardinalWorkflows/inst/doc/Workflows-clustering.pdf vignetteTitles: Classification example workflow, Clustering example workflow hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CardinalWorkflows/inst/doc/Workflows-classification.R, vignettes/CardinalWorkflows/inst/doc/Workflows-clustering.R dependencyCount: 68 Package: ccdata Version: 1.10.0 Depends: R (>= 3.3) License: MIT + file LICENSE MD5sum: 5b120a35642d1ef94a586f18fc5fc7d5 NeedsCompilation: no Title: Data for Combination Connectivity Mapping (ccmap) Package Description: This package contains microarray gene expression data generated from the Connectivity Map build 02 and LINCS l1000. The data are used by the ccmap package to find drugs and drug combinations to mimic or reverse a gene expression signature. biocViews: ExperimentData, MicroarrayData, ExpressionData Author: Alex Pickering Maintainer: Alex Pickering git_url: https://git.bioconductor.org/packages/ccdata git_branch: RELEASE_3_9 git_last_commit: 50926dd git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ccdata_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: CCl4 Version: 1.22.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), limma License: Artistic-2.0 MD5sum: 465604e9af49594dd9bfdfe6c059edc1 NeedsCompilation: no Title: Carbon Tetrachloride (CCl4) treated hepatocytes Description: NChannelSet for rat hepatocytes treated with Carbon Tetrachloride (CCl4) data from LGC company. biocViews: ExperimentData, Genome, Rattus_norvegicus_Data, MicroarrayData Author: Audrey Kauffmann, Wolfgang Huber Maintainer: Audrey Kauffmann git_url: https://git.bioconductor.org/packages/CCl4 git_branch: RELEASE_3_9 git_last_commit: ce7cfcc git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/CCl4_1.22.0.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: 9 Package: ccTutorial Version: 1.22.0 Depends: R (>= 2.10), Ringo(>= 1.9.8), affy(>= 1.23.4), topGO(>= 1.13.1) Imports: Biobase Suggests: biomaRt, Biobase(>= 2.5.5), xtable License: Artistic-2.0 MD5sum: 9a7ab28f231b5b046e61a1fa80385ef3 NeedsCompilation: no Title: Data package for ChIP-chip tutorial Description: This is a data package that accompanies a ChIP-chip tutorial, which has been published in PLoS Computational Biology. The data and source code in this package allow the reader to completely reproduce the steps in the tutorial. biocViews: ExperimentData, Mus_musculus_Data, MicroarrayData, ChipOnChipData Author: Joern Toedling, Wolfgang Huber Maintainer: Joern Toedling git_url: https://git.bioconductor.org/packages/ccTutorial git_branch: RELEASE_3_9 git_last_commit: b691159 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ccTutorial_1.22.0.tar.gz vignettes: vignettes/ccTutorial/inst/doc/ccTutorial.pdf, vignettes/ccTutorial/inst/doc/ccTutorialSupplement.pdf vignetteTitles: A tutorial on how to analyze ChIP-chip readouts using Bioconductor, Supplement to A tutorial on how to analyze ChIP-chip readouts using Bioconductor hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ccTutorial/inst/doc/ccTutorial.R, vignettes/ccTutorial/inst/doc/ccTutorialSupplement.R dependencyCount: 81 Package: celarefData Version: 1.2.0 Depends: R (>= 3.5.0) Suggests: ExperimentHub, knitr, rmarkdown License: GPL-3 MD5sum: 45c742f3a1047a409cc2ab112c2712e7 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 Author: Sarah Williams [aut, cre] Maintainer: Sarah Williams VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/celarefData git_branch: RELEASE_3_9 git_last_commit: 3eb3f32 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/celarefData_1.2.0.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: CellMapperData Version: 1.10.0 Depends: ExperimentHub, CellMapper Suggests: BiocStyle License: Artistic-2.0 MD5sum: ad6ececf308dc29a5ebc1e56a6bf7632 NeedsCompilation: no Title: Pre-processed data for use with the CellMapper package Description: Experiment data package. Contains microarray data from several large expression compendia that have been pre-processed for use with the CellMapper package. This pre-processed data is recommended for routine searches using the CellMapper package. biocViews: ExperimentData, MicroarrayData, ExpressionData Author: Brad Nelms Maintainer: Brad Nelms git_url: https://git.bioconductor.org/packages/CellMapperData git_branch: RELEASE_3_9 git_last_commit: 336ea09 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/CellMapperData_1.10.0.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 dependencyCount: 67 Package: ceu1kg Version: 0.22.0 Depends: R (>= 2.12.0), GGBase (>= 3.9.0), GGtools, Biobase Suggests: SNPlocs.Hsapiens.dbSNP.20101109 License: Artistic-2.0 MD5sum: c755c9ed3fded070eb1c8acb518e3d15 NeedsCompilation: no Title: CEU (N=60) genotypes from 1000 genomes pilot phase I Description: CEU genotypes from 1000 genomes "low coverage" pilot phase I (approx 8 million SNP calls released July 2010); includes Wellcome trust GENEVAR expression for 43 indiv biocViews: SNPData, HapMap, Project1000genomes Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/ceu1kg git_branch: RELEASE_3_9 git_last_commit: 546ac40 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ceu1kg_0.22.0.tar.gz vignettes: vignettes/ceu1kg/inst/doc/ceu1kg.pdf vignetteTitles: ceu1kg overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ceu1kg/inst/doc/ceu1kg.R dependencyCount: 151 Package: ceu1kgv Version: 0.26.0 Depends: R (>= 3.0), GGBase Imports: Biobase License: Artistic-2.0 MD5sum: 287b778e75815512fa403979131b628d NeedsCompilation: no Title: expression + genotype on 79 unrelated CEU individuals Description: expression + genotype on 79 unrelated CEU individuals biocViews: ArrayExpress Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/ceu1kgv git_branch: RELEASE_3_9 git_last_commit: e29663c git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ceu1kgv_0.26.0.tar.gz vignettes: vignettes/ceu1kgv/inst/doc/ceu1kgv.pdf vignetteTitles: ceu1kgv -- genotype plus expression for HapMap CEU hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ceu1kgv/inst/doc/ceu1kgv.R dependencyCount: 61 Package: ceuhm3 Version: 0.22.0 Depends: R (>= 2.12.0), GGBase, Biobase Imports: GGtools License: Artistic-2.0 MD5sum: c3036effe82163927a9658279be42c81 NeedsCompilation: no Title: ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort Description: ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort biocViews: SNPData, HapMap Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/ceuhm3 git_branch: RELEASE_3_9 git_last_commit: dd0d042 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ceuhm3_0.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 151 Package: cgdv17 Version: 0.22.0 Depends: R (>= 2.15), methods, VariantAnnotation (>= 1.15.15) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biobase Suggests: parallel, GGtools, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, illuminaHumanv1.db License: Artistic-2.0 MD5sum: f7d6c5564f18afe12623a4b6f184e787 NeedsCompilation: no Title: Complete Genomics Diversity Panel, chr17 on 46 individuals Description: Complete Genomics Diversity Panel, chr17 on 46 individuals biocViews: SequencingData, SNPData, BiocViews Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/cgdv17 git_branch: RELEASE_3_9 git_last_commit: c8617e8 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/cgdv17_0.22.0.tar.gz vignettes: vignettes/cgdv17/inst/doc/cgdv.pdf vignetteTitles: cgdv17: extract from Complete Genomics diversity panel hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cgdv17/inst/doc/cgdv.R dependencyCount: 75 Package: ChAMPdata Version: 2.16.0 Depends: GenomicRanges (>= 1.22.4),BiocGenerics(>= 0.16.1),R (>= 3.3) License: GPL-3 MD5sum: 41023a6402403275016b865f07eba6a5 NeedsCompilation: no Title: Data Packages for ChAMP package Description: Provides datasets needed for ChAMP including a test dataset and blood controls for CNA analysis. biocViews: ExperimentData Author: Yuan Tian [ctb,aut], Tiffany Morris [cre,aut], Lee Stirling [ctb] and Andrew Teschendorff [ctb] Maintainer: Yuan Tian git_url: https://git.bioconductor.org/packages/ChAMPdata git_branch: RELEASE_3_9 git_last_commit: cf2dc5e git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ChAMPdata_2.16.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 16 Package: charmData Version: 1.19.0 Depends: R(>= 2.11.0), charm, pd.charm.hg18.example License: LGPL (>= 2) MD5sum: b01273cf14a402015dc5a26f6b3780ef NeedsCompilation: no Title: An example dataset for use with the charm package Description: An example dataset for use with the charm package biocViews: ExperimentData, MicroarrayData Author: Martin Aryee Maintainer: Martin Aryee git_url: https://git.bioconductor.org/packages/charmData git_branch: master git_last_commit: fffa8cd git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/charmData_1.19.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 93 Package: ChIC.data Version: 1.4.0 Depends: R (>= 3.5) Imports: caret (>= 6.0-78) License: GPL-2 MD5sum: 363188008f53ea5cab5ae873be14365a NeedsCompilation: no Title: ChIC package data Description: This package contains annotation and metagene profile data for the ChIC package. biocViews: ExperimentData, ENCODE Author: Carmen Maria Livi [aut, cre, dtc], Endre Sebestyen [aut] Maintainer: Carmen Maria Livi git_url: https://git.bioconductor.org/packages/ChIC.data git_branch: RELEASE_3_9 git_last_commit: 6bcc832 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ChIC.data_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 74 Package: ChimpHumanBrainData Version: 1.22.0 Depends: affy,qvalue,limma,hexbin,statmod License: MIT MD5sum: d7a381464a431897c78431f93a64998d NeedsCompilation: no Title: Chimp and human brain data package Description: This data package contains chimp and human brain data extracted from the ArrayExpress accession E-AFMX-2. Both human and chimp RNAs were run on human hgu95av2 Affymetrix arrays. It is a useful dataset for tutorials. biocViews: Tissue, Homo_sapiens_Data, Pan_troglodytes_Data, MicroarrayData, TissueMicroarrayData, GEO Author: Roman Jaksik, Naomi Altman, and Sean Davis Maintainer: Sean Davis git_url: https://git.bioconductor.org/packages/ChimpHumanBrainData git_branch: RELEASE_3_9 git_last_commit: 8ecebd2 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ChimpHumanBrainData_1.22.0.tar.gz vignettes: vignettes/ChimpHumanBrainData/inst/doc/DiffExpressVignette.pdf vignetteTitles: DiffExpressVignette.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ChimpHumanBrainData/inst/doc/DiffExpressVignette.R dependencyCount: 57 Package: chipenrich.data Version: 2.8.0 Depends: R (>= 3.4.0) 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: 26d744a980e0698a991565fb0beea5a1 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, cre], Laura J. Scott [ths], Maureen A. Sartor [ths] Maintainer: Raymond G. Cavalcante VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/chipenrich.data git_branch: RELEASE_3_9 git_last_commit: e1c56d3 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/chipenrich.data_2.8.0.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 dependencyCount: 68 Package: ChIPexoQualExample Version: 1.8.0 Depends: R (>= 3.3) License: GPL (>= 2) MD5sum: 991058493c34afddf1ea08c093d52206 NeedsCompilation: no Title: Example data for the ChIPexoQual package, which implements a quality control pipeline for ChIP-exo data Description: Data for the ChIPexoQual package, consisting of (3) chromosome 1 aligned reads from a ChIP-exo experiment for FoxA1 in mouse liver cell lines aligned to the mm9 genome. biocViews: ExperimentData, Genome Author: Rene Welch, Dongjun Chung, Sunduz Keles Maintainer: Rene Welch URL: http://www.github.com/keleslab/ChIPexoQualExample VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ChIPexoQualExample git_branch: RELEASE_3_9 git_last_commit: 2ad3ea8 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ChIPexoQualExample_1.8.0.tar.gz vignettes: vignettes/ChIPexoQualExample/inst/doc/vignette.html vignetteTitles: Vignette Title hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ChIPexoQualExample/inst/doc/vignette.R dependencyCount: 0 Package: chipseqDBData Version: 1.0.0 Imports: AnnotationHub, ExperimentHub, S4Vectors Suggests: knitr, BiocStyle, Rsamtools License: CC BY 4.0 MD5sum: 89f8ca03e19a3107510d93bb3a082625 NeedsCompilation: no Title: Data for the chipseqDB Workflow Description: Sorted and indexed BAM files for ChIP-seq libraries, for use in the chipseqDB workflow. BAM indices are also included. biocViews: SequencingData, ChIPSeqData, ExperimentHub Author: Aaron Lun [aut, cre] Maintainer: Aaron Lun VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/chipseqDBData git_branch: RELEASE_3_9 git_last_commit: bc95bba git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/chipseqDBData_1.0.0.tar.gz vignettes: vignettes/chipseqDBData/inst/doc/chipseqDBData.html vignetteTitles: File manifest and statistics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/chipseqDBData/inst/doc/chipseqDBData.R dependencyCount: 66 Package: ChIPXpressData Version: 1.22.0 Depends: bigmemory License: GPL (>=2) MD5sum: 4dc8f6accadaa504672e7f40d144460a NeedsCompilation: no Title: ChIPXpress Pre-built Databases Description: Contains pre-built mouse (GPL1261) and human (GPL570) database of gene expression profiles to be used for ChIPXpress ranking. biocViews: Homo_sapiens_Data, Mus_musculus_Data, GEO Author: George Wu Maintainer: George Wu git_url: https://git.bioconductor.org/packages/ChIPXpressData git_branch: RELEASE_3_9 git_last_commit: 30cbcec git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ChIPXpressData_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 6 Package: chromstaRData Version: 1.10.0 Depends: R (>= 3.3) License: GPL-3 MD5sum: 10d6c6236f90681d268ddb75e36f8549 NeedsCompilation: no Title: ChIP-seq data for Demonstration Purposes Description: ChIP-seq data for demonstration purposes in the chromstaR package. biocViews: Mus_musculus_Data, StemCell, ChIPSeqData Author: Aaron Taudt Maintainer: Aaron Taudt git_url: https://git.bioconductor.org/packages/chromstaRData git_branch: RELEASE_3_9 git_last_commit: 9370d29 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/chromstaRData_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: CLL Version: 1.24.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: LGPL MD5sum: c7e9da38377b6a30c1a4969b4175a543 NeedsCompilation: no Title: A Package for CLL Gene Expression Data Description: The CLL package contains the chronic lymphocytic leukemia (CLL) gene expression data. The CLL data had 24 samples that were either classified as progressive or stable in regards to disease progression. The data came from Dr. Sabina Chiaretti at Division of Hematology, Department of Cellular Biotechnologies and Hematology, University La Sapienza, Rome, Italy and Dr. Jerome Ritz at Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts. biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData Author: Elizabeth Whalen Maintainer: Robert Gentleman git_url: https://git.bioconductor.org/packages/CLL git_branch: RELEASE_3_9 git_last_commit: fa8c2f5 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/CLL_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 13 Package: CLLmethylation Version: 1.4.0 Depends: R (>= 3.5.0) Imports: SummarizedExperiment, ExperimentHub Suggests: BiocStyle, ggplot2, knitr, rmarkdown License: LGPL MD5sum: 2b2496c6f9a26e10a55c87b5a1087859 NeedsCompilation: no Title: Methylation data of primary CLL samples in PACE project Description: The package includes DNA methylation data for the primary Chronic Lymphocytic Leukemia samples included in the Primary Blood Cancer Encyclopedia (PACE) project. Raw data from the 450k DNA methylation arrays is stored in the European Genome-Phenome Archive (EGA) under accession number EGAS0000100174. For more information concerning the project please refer to the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) and R/Bioconductor package BloodCancerMultiOmics2017. biocViews: ExperimentData, DiseaseModel, CancerData, LeukemiaCancerData Author: Malgorzata Oles, Andreas Mock Maintainer: Malgorzata Oles , Andreas Mock VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/CLLmethylation git_branch: RELEASE_3_9 git_last_commit: 8adba07 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/CLLmethylation_1.4.0.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: 85 Package: CluMSIDdata Version: 1.0.0 Depends: R (>= 3.6) License: MIT + file LICENSE MD5sum: a9ba9176bf862de81836a3b74f60af5e NeedsCompilation: no Title: Data for the CluMSID package Description: This package contains various LC-MS/MS and GC-MS data that is used in vignettes and examples in the CluMSID package. biocViews: ExperimentData, MassSpectrometryData Author: Tobias Depke [aut, cre] Maintainer: Tobias Depke git_url: https://git.bioconductor.org/packages/CluMSIDdata git_branch: RELEASE_3_9 git_last_commit: 89a652d git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/CluMSIDdata_1.0.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: cMap2data Version: 1.20.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 5a816640a2b0fbe93e9398b460320ed7 NeedsCompilation: no Title: Connectivity Map (version 2) Data Description: Data package which provides default drug profiles for the DrugVsDisease package as well as associated gene lists and data clusters used by the DrugVsDisease package. biocViews: Homo_sapiens_Data, MicroarrayData, GEO Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/cMap2data git_branch: RELEASE_3_9 git_last_commit: 6b98623 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/cMap2data_1.20.0.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: 1.20.0 Depends: R (>= 2.10), cnvGSA License: LGPL MD5sum: 084bb4dde34828a90051aec087948cf1 NeedsCompilation: no Title: Data used in the vignette of the cnvGSA package Description: This package contains the data used in the vignette of the cnvGSA package. biocViews: ExperimentData, Genome, CopyNumberVariationData Author: Joseph Lugo Maintainer: Joseph Lugo git_url: https://git.bioconductor.org/packages/cnvGSAdata git_branch: RELEASE_3_9 git_last_commit: 0c43447 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/cnvGSAdata_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 25 Package: COHCAPanno Version: 1.20.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 7372e4f9927b5c9b1060be2105a3e3f4 NeedsCompilation: no Title: Annotations for City of Hope CpG Island Analysis Pipeline Description: Provides genomic location, nearby CpG island and nearby gene information for common Illumina methylation array platforms biocViews: Homo_sapiens_Data, MicroarrayData, MethylationArrayData, CpGIslandData, GEO, ArrayExpress Author: Charles Warden Maintainer: Charles Warden git_url: https://git.bioconductor.org/packages/COHCAPanno git_branch: RELEASE_3_9 git_last_commit: cc8df8a git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/COHCAPanno_1.20.0.tar.gz vignettes: vignettes/COHCAPanno/inst/doc/COHCAPanno.pdf vignetteTitles: COHCAPanno Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/COHCAPanno/inst/doc/COHCAPanno.R dependencyCount: 0 Package: colonCA Version: 1.26.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: 26823f01a5ba01edf9e744c98dcb74b3 NeedsCompilation: no Title: exprSet for Alon et al. (1999) colon cancer data Description: exprSet for Alon et al. (1999) colon cancer data biocViews: ExperimentData, Tissue, CancerData, ColonCancerData, MicroarrayData, TissueMicroarrayData Author: Sylvia Merk Maintainer: W Sylvia Merk git_url: https://git.bioconductor.org/packages/colonCA git_branch: RELEASE_3_9 git_last_commit: 1a3dea9 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/colonCA_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: CONFESSdata Version: 1.12.0 Depends: R (>= 3.3) License: GPL-2 MD5sum: 5a94a77fec0407c04bc72f89934775a1 NeedsCompilation: no Title: Example dataset for CONFESS package Description: Example text-converted C01 image files for use in the CONFESS Bioconductor package. biocViews: HighThroughputImagingData,CellCulture,Homo_sapiens_Data,ExpressionData Author: Diana LOW and Efthimios MOTAKIS Maintainer: Diana LOW git_url: https://git.bioconductor.org/packages/CONFESSdata git_branch: RELEASE_3_9 git_last_commit: 54b3a96 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/CONFESSdata_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: ConnectivityMap Version: 1.20.0 Depends: R (>= 2.15.1) Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 0556684e97c094a8206e314400bb5165 NeedsCompilation: no Title: Functional connections between drugs, genes and diseases as revealed by common gene-expression changes Description: The Broad Institute's Connectivity Map (cmap02) is a "large reference catalogue of gene-expression data from cultured human cells perturbed with many chemicals and genetic reagents", containing more than 7000 gene expression profiles and 1300 small molecules. biocViews: ExperimentData, CancerData, MicroarrayData Author: Paul Shannon Maintainer: Paul Shannon git_url: https://git.bioconductor.org/packages/ConnectivityMap git_branch: RELEASE_3_9 git_last_commit: 8531cf8 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ConnectivityMap_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: COPDSexualDimorphism.data Version: 1.20.0 License: LGPL-2.1 MD5sum: 47555d52e02a3b6d87bbe39a18174531 NeedsCompilation: no Title: Data to support sexually dimorphic and COPD differential analysis for gene expression and methylation. Description: Datasets to support COPDSexaulDimorphism Package. biocViews: ExperimentData, Tissue, COPDData Author: J Fah Sathirapongsasuti Maintainer: J Fah Sathirapongsasuti git_url: https://git.bioconductor.org/packages/COPDSexualDimorphism.data git_branch: RELEASE_3_9 git_last_commit: 38ac21b git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/COPDSexualDimorphism.data_1.20.0.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: 1.16.0 Depends: R(>= 2.10) Suggests: BiocStyle License: GPL-2 MD5sum: d2c50c7ac853e6f631111da79fe7bc03 NeedsCompilation: no Title: Helper files for CopywriteR Description: This package contains the helper files that are required to run the Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content and mappability files for the reference genomes hg18, hg19, hg38, mm9 and mm10. In addition, it contains a blacklist filter to remove regions that display CNV. Files are stored as GRanges objects from the GenomicRanges Bioconductor package. biocViews: Homo_sapiens, GenomicSequence Author: Thomas Kuilman Maintainer: Oscar Krijgsman git_url: https://git.bioconductor.org/packages/CopyhelpeR git_branch: RELEASE_3_9 git_last_commit: 3bfb2aa git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/CopyhelpeR_1.16.0.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: 1.2.0 Depends: R (>= 3.5.0) Imports: ExperimentHub,Rdpack (>= 0.8) Suggests: BiocStyle,knitr,rmarkdown,minfi,conumee,minfiData License: Artistic-2.0 MD5sum: 99b9b248b03ad09a1b274a986d0a6b54 NeedsCompilation: no Title: Copy Neutral Illumina Methylation Arrays Description: Provides a set of genomic copy neutral samples hybridized using Illumina Methylation arrays (450k and EPIC). biocViews: ExperimentData,Homo_sapiens_Data,MicroarrayData,TwoChannelData,MethylationArrayData,GEO Author: Xavier Pastor Hostench [aut, cre], Moritz Przybilla [aut] Maintainer: Xavier Pastor Hostench VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/CopyNeutralIMA git_branch: RELEASE_3_9 git_last_commit: 7a9e052 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/CopyNeutralIMA_1.2.0.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: 71 Package: COSMIC.67 Version: 1.20.0 Depends: R (>= 3.0.2) Imports: GenomicRanges, SummarizedExperiment, VariantAnnotation Suggests: testthat, BiocStyle, knitr License: GPL-3 MD5sum: 4ddee996e33164a4f0d0034c438b7783 NeedsCompilation: no Title: COSMIC.67 Description: COSMIC: Catalogue Of Somatic Mutations In Cancer, version 67 (2013-10-24) biocViews: ExperimentData, Genome, CancerData Author: Julian Gehring Maintainer: Julian Gehring VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/COSMIC.67 git_branch: RELEASE_3_9 git_last_commit: 87d8e5e git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/COSMIC.67_1.20.0.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 dependencyCount: 75 Package: CRCL18 Version: 1.4.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: acaf9fea6a3b3fc312d3fe77a0157e93 NeedsCompilation: no Title: CRC cell line dataset Description: colorectal cancer mRNA and miRNA on 18 cell lines biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/CRCL18 git_branch: RELEASE_3_9 git_last_commit: 2c8a27f git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/CRCL18_1.4.0.tar.gz vignettes: vignettes/CRCL18/inst/doc/CRCL18Vignette.pdf vignetteTitles: CRCL18 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CRCL18/inst/doc/CRCL18Vignette.R dependencyCount: 7 Package: curatedAdipoChIP Version: 1.0.0 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: bd1152653faf9424562c638ea8fc1ded NeedsCompilation: no Title: A Curated ChIP-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Description: A curated dataset of publicly available ChIP-sequencing of transcription factors, chromatin remodelers and histone modifications in the 3T3-L1 pre-adipocyte cell line. The package document the data collection, pre-processing and processing of the data. In addition to the documentation, the package contains the scripts that was used to generated the data. biocViews: ExperimentData, ExperimentHub, GEO, ChIPSeqData, SequencingData Author: Mahmoud Ahmed [aut, cre] () Maintainer: Mahmoud Ahmed URL: https://github.com/MahShaaban/curatedAdipoChIP VignetteBuilder: knitr BugReports: https://github.com/MahShaaban/curatedAdipoChIP/issues git_url: https://git.bioconductor.org/packages/curatedAdipoChIP git_branch: RELEASE_3_9 git_last_commit: ae7aa64 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/curatedAdipoChIP_1.0.0.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: 85 Package: curatedAdipoRNA Version: 1.0.0 Depends: R (>= 3.6), SummarizedExperiment Suggests: knitr, rmarkdown, DESeq2, fastqcr, devtools, testthat, readr, dplyr, tidyr, ggplot2, S4Vectors License: GPL-3 MD5sum: 4424c4af38fa09e6d09b81c4d485c830 NeedsCompilation: no Title: A Curated RNA-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Description: A curated dataset of RNA-Seq samples. The samples are MDI-induced pre-phagocytes (3T3-L1) at different time points/stage of differentiation. The package document the data collection, pre-processing and processing. In addition to the documentation, the package contains the scripts that was used to generated the data. biocViews: ExperimentData, GEO, RNASeqData, SequencingData Author: Mahmoud Ahmed [aut, cre] () Maintainer: Mahmoud Ahmed URL: https://github.com/MahShaaban/curatedAdipoRNA VignetteBuilder: knitr BugReports: https://github.com/MahShaaban/curatedAdipoRNA/issues git_url: https://git.bioconductor.org/packages/curatedAdipoRNA git_branch: RELEASE_3_9 git_last_commit: 5a4c61d git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/curatedAdipoRNA_1.0.0.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: 32 Package: curatedBladderData Version: 1.20.0 Depends: R (>= 2.10.0), affy Suggests: BiocStyle, survival, xtable, sva, genefilter, logging License: Artistic-2.0 MD5sum: e81603412d05d4aeef774fb278648872 NeedsCompilation: no Title: Bladder Cancer Gene Expression Analysis Description: The curatedBladderData package provides relevant functions and data for gene expression analysis in patients with bladder cancer. biocViews: ExperimentData, CancerData, OvarianCancerData, MicroarrayData, ExpressionData Author: Markus Riester Maintainer: Markus Riester URL: https://github.com/lima1/curatedBladderData git_url: https://git.bioconductor.org/packages/curatedBladderData git_branch: RELEASE_3_9 git_last_commit: 22ca1a3 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/curatedBladderData_1.20.0.tar.gz vignettes: vignettes/curatedBladderData/inst/doc/curatedBladderData_vignette.pdf vignetteTitles: curatedBladderData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedBladderData/inst/doc/curatedBladderData_vignette.R dependencyCount: 13 Package: curatedBreastData Version: 2.12.0 Depends: R (>= 3.0.0), XML, ggplot2, impute, Biobase, BiocStyle Imports: methods, stats License: GPL (>= 2) MD5sum: 945c48e2f40b55c017fcb7acf33c86d8 NeedsCompilation: no Title: Curated breast cancer gene expression data with survival and treatment information Description: Curated human breast cancer tissue S4 ExpresionSet datasets from over 16 clinical trials comprising over 2,000 patients. All datasets contain at least one type of outcomes variable and treatment information (minimum level: whether they had chemotherapy and whether they had hormonal therapy). Includes code to post-process these datasets. biocViews: ExperimentData, ExpressionData, CancerData, Tissue, BreastCancerData, qPCRData, MicroarrayData, TissueMicroarrayData, GEO Author: Katie Planey Maintainer: Katie Planey git_url: https://git.bioconductor.org/packages/curatedBreastData git_branch: RELEASE_3_9 git_last_commit: 4086734 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/curatedBreastData_2.12.0.tar.gz vignettes: vignettes/curatedBreastData/inst/doc/curatedBreastData-manual.pdf vignetteTitles: Manual hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedBreastData/inst/doc/curatedBreastData-manual.R dependencyCount: 65 Package: curatedCRCData Version: 2.16.0 Depends: R (>= 2.10.0), nlme Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle License: Artistic-2.0 MD5sum: e9df2a3ae6a0b51c081cc3a653045805 NeedsCompilation: no Title: Colorectal Cancer Gene Expression Analysis Description: The curatedCRC package provides relevant functions and data for gene expression analysis in patients with colorectal cancer. biocViews: Colorectal, Cancer, TCGA, ExperimentData, RNAExpressionData Author: Princy Parsana, Markus Riester, Curtis Huttenhower, Levi Waldron Maintainer: Princy Parsana URL: https://bitbucket.org/biobakery/curatedcrcdata git_url: https://git.bioconductor.org/packages/curatedCRCData git_branch: RELEASE_3_9 git_last_commit: a5624de git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/curatedCRCData_2.16.0.tar.gz vignettes: vignettes/curatedCRCData/inst/doc/curatedCRCData_vignette.pdf vignetteTitles: curatedCRCData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedCRCData/inst/doc/curatedCRCData_vignette.R dependencyCount: 10 Package: curatedMetagenomicData Version: 1.14.1 Depends: R (>= 3.6.0), AnnotationHub (>= 2.9.0), Biobase (>= 2.37.0), dplyr (>= 0.5.0), ExperimentHub (>= 1.3.0) Imports: magrittr, methods, S4Vectors, tidyr, utils Suggests: ape, covr, BiocCheck, BiocManager, BiocParallel, BiocStyle, devtools, ggplot2, knitr, metagenomeSeq, phyloseq, readr, RISmed, rmarkdown, roxygen2, testthat License: Artistic-2.0 MD5sum: 8d83fed3572f0f4c679a974c8e2c031c NeedsCompilation: no Title: Curated Metagenomic Data of the Human Microbiome Description: The curatedMetagenomicData package provides microbial taxonomic, functional, and gene marker abundance for samples collected from different bodysites. biocViews: Homo_sapiens_Data, ReproducibleResearch, MicrobiomeData, ExperimentHub Author: Lucas Schiffer , Edoardo Pasolli , Levi Waldron , Faizan Malik , Nicola Segata , Valerie Obenchain , Morgan Martin Maintainer: Lucas Schiffer URL: https://github.com/waldronlab/curatedMetagenomicData VignetteBuilder: knitr BugReports: https://github.com/waldronlab/curatedMetagenomicData/issues git_url: https://git.bioconductor.org/packages/curatedMetagenomicData git_branch: RELEASE_3_9 git_last_commit: d33ca60 git_last_commit_date: 2019-05-21 Date/Publication: 2019-05-23 source.ver: src/contrib/curatedMetagenomicData_1.14.1.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: HMP16SData dependencyCount: 69 Package: curatedOvarianData Version: 1.22.0 Depends: R (>= 2.10.0), affy Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle License: Artistic-2.0 MD5sum: 1af5517292618a6a05871dbf02953866 NeedsCompilation: no Title: Clinically Annotated Data for the Ovarian Cancer Transcriptome Description: The curatedOvarianData package provides data for gene expression analysis in patients with ovarian cancer. biocViews: ExperimentData, RNASeqData, CancerData, OvarianCancerData, MicroarrayData Author: Benjamin F. Ganzfried, Markus Riester, Steve Skates, Victoria Wang, Thomas Risch, Benjamin Haibe-Kains, Svitlana Tyekucheva, Jie Ding, Ina Jazic, Michael Birrer, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron Maintainer: Levi Waldron URL: http://bcb.dfci.harvard.edu/ovariancancer git_url: https://git.bioconductor.org/packages/curatedOvarianData git_branch: RELEASE_3_9 git_last_commit: 9fb600b git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/curatedOvarianData_1.22.0.tar.gz vignettes: vignettes/curatedOvarianData/inst/doc/curatedOvarianData_vignette.pdf vignetteTitles: curatedOvarianData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedOvarianData/inst/doc/curatedOvarianData_vignette.R dependencyCount: 13 Package: curatedTCGAData Version: 1.6.0 Depends: R (>= 3.5.0), MultiAssayExperiment Imports: AnnotationHub, ExperimentHub, HDF5Array, S4Vectors, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, readr, rmarkdown, TCGAutils, testthat License: Artistic-2.0 MD5sum: 3389cf6624a52501366bbccdcf9d2534 NeedsCompilation: no Title: Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects Description: This package provides publicly available data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects. MultiAssayExperiment integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. It also links assay barcodes with patient identifiers, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-'omics experiment. biocViews: Homo_sapiens_Data, ReproducibleResearch, CancerData, ExperimentHub Author: Marcel Ramos [aut, cre], Levi Waldron [ctb], Lucas Schiffer [ctb], Ludwig Geistlinger [ctb], Valerie Obenchain [ctb], Martin Morgan [ctb] Maintainer: Marcel Ramos VignetteBuilder: knitr BugReports: https://github.com/waldronlab/curatedTCGAData/issues git_url: https://git.bioconductor.org/packages/curatedTCGAData git_branch: RELEASE_3_9 git_last_commit: 0a31a05 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/curatedTCGAData_1.6.0.tar.gz vignettes: vignettes/curatedTCGAData/inst/doc/curatedTCGAData.html vignetteTitles: curatedTCGAData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedTCGAData/inst/doc/curatedTCGAData.R dependencyCount: 92 Package: DAPARdata Version: 1.14.0 Depends: R (>= 3.5) Imports: utils, knitr, MSnbase Suggests: DAPAR, Prostar License: GPL-2 MD5sum: 4807b95a2b0aea5cc46adb360a165383 NeedsCompilation: no Title: Data accompanying the DAPAR and Prostar packages Description: Mass-spectrometry based UPS proteomics data sets from Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssie D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianferani S, Ferro M, Dorssaeler AV, Burlet-Schiltz O, Schaeffer C, Coute Y, Gonzalez de Peredo A. Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods. Data Brief. 2015 Dec 17;6:286-94 and Giai Gianetto, Q., Combes, F., Ramus, C., Bruley, C., Coute, Y., Burger, T. (2016). Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments. Proteomics, 16(1), 29-32. biocViews: ExperimentData, MassSpectrometryData Author: Samuel Wieczorek and Florence Combes Maintainer: Samuel Wieczorek git_url: https://git.bioconductor.org/packages/DAPARdata git_branch: RELEASE_3_9 git_last_commit: d5c9e25 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/DAPARdata_1.14.0.tar.gz vignettes: vignettes/DAPARdata/inst/doc/Exp1_R2_pept.pdf, vignettes/DAPARdata/inst/doc/Exp1_R2_prot.pdf, vignettes/DAPARdata/inst/doc/Exp1_R25_pept.pdf, vignettes/DAPARdata/inst/doc/Exp1_R25_prot.pdf, vignettes/DAPARdata/inst/doc/Exp2_R10_pept.pdf, vignettes/DAPARdata/inst/doc/Exp2_R10_prot.pdf, vignettes/DAPARdata/inst/doc/Exp2_R100_pept.pdf, vignettes/DAPARdata/inst/doc/Exp2_R100_prot.pdf, vignettes/DAPARdata/inst/doc/Exp2_R2_pept.pdf, vignettes/DAPARdata/inst/doc/Exp2_R2_prot.pdf vignetteTitles: Exp1_R2_pept.pdf, Exp1_R2_prot.pdf, Exp1_R25_pept.pdf, Exp1_R25_prot.pdf, Exp2_R10_pept.pdf, Exp2_R10_prot.pdf, Exp2_R100_pept.pdf, Exp2_R100_prot.pdf, Exp2_R2_pept.pdf, Exp2_R2_prot.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 86 Package: davidTiling Version: 1.24.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db License: LGPL MD5sum: fc322c673362b180aacb0e2f381db62c NeedsCompilation: no Title: Data and analysis scripts for David, Huber et al. yeast tiling array paper Description: This package contains the data for the paper by L. David et al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix genechips, an ExpressionSet object with the raw feature data, a probe annotation data structure for the chip and the yeast genome annotation (GFF file) that was used. In addition, some custom-written analysis functions are provided, as well as R scripts in the scripts directory. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, MicroarrayData, ReproducibleResearch Author: Wolfgang Huber , Joern Toedling Maintainer: Wolfgang Huber URL: http://www.ebi.ac.uk/huber git_url: https://git.bioconductor.org/packages/davidTiling git_branch: RELEASE_3_9 git_last_commit: 0730807 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/davidTiling_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 81 Package: derfinderData Version: 2.2.1 Depends: R(>= 3.1.1) Suggests: sessioninfo, knitcitations (>= 1.0.1), knitr (>= 1.6), knitrBootstrap (>= 0.9.0), RefManageR, rmarkdown (>= 0.3.3), License: Artistic-2.0 MD5sum: c915d3e6f24850f3c49294539796035b NeedsCompilation: no Title: Processed BigWigs from BrainSpan for examples Description: Processed 22 samples from BrainSpan keeping only the information for chromosome 21. Data is stored in the BigWig format and is used for examples in other packages. biocViews: ExperimentData, Homo_sapiens_Data, RNASeqData Author: Leonardo Collado-Torres [aut, cre], Andrew Jaffe [aut], Jeffrey Leek [aut, ths] Maintainer: Leonardo Collado-Torres URL: https://github.com/leekgroup/derfinderData VignetteBuilder: knitr BugReports: https://github.com/leekgroup/derfinderData/issues git_url: https://git.bioconductor.org/packages/derfinderData git_branch: RELEASE_3_9 git_last_commit: 0a6fc68 git_last_commit_date: 2019-05-22 Date/Publication: 2019-05-23 source.ver: src/contrib/derfinderData_2.2.1.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 dependencyCount: 0 Package: DeSousa2013 Version: 1.20.0 Depends: R (>= 2.15), Imports: affy, frma, frmaTools, hgu133plus2.db, hgu133plus2frmavecs, sva, rgl, ConsensusClusterPlus, cluster, siggenes, ROCR, pamr, survival, gplots, AnnotationDbi, Biobase License: Artistic-2.0 MD5sum: 6772bbad387e983a0f1ba536055635ca NeedsCompilation: no Title: Poor prognosis colon cancer is defined by a molecularly distinct subtype and precursor lesion Description: This package reproduces the main pipeline to analyze the AMC-AJCCII-90 microarray data set in De Sousa et al. accepted by Nature Medicine in 2013. biocViews: CancerData, ColonCancerData, MicroarrayData Author: Xin Wang Maintainer: Xin Wang git_url: https://git.bioconductor.org/packages/DeSousa2013 git_branch: RELEASE_3_9 git_last_commit: e943a7e git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/DeSousa2013_1.20.0.tar.gz vignettes: vignettes/DeSousa2013/inst/doc/DeSousa2013-Vignette.pdf vignetteTitles: Main vignette:Poor prognosis colon cancer is defined by a molecular distinct subtype and develops from serrated precursor lesions hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DeSousa2013/inst/doc/DeSousa2013-Vignette.R dependencyCount: 139 Package: diffloopdata Version: 1.12.0 Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: eb6194f78579441878992b842aa3cbea NeedsCompilation: no Title: Example ChIA-PET Datasets for the diffloop Package Description: ChIA-PET example datasets and additional data for use with the diffloop package. biocViews: ExperimentData, SequencingData Author: Caleb Lareau [aut], Martin Aryee [aut, cre] Maintainer: Caleb Lareau VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/diffloopdata git_branch: RELEASE_3_9 git_last_commit: 34f1e23 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/diffloopdata_1.12.0.tar.gz vignettes: vignettes/diffloopdata/inst/doc/diffloopdata.html vignetteTitles: diffloopdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: diggitdata Version: 1.16.0 Depends: R(>= 2.14.0), Biobase, methods Imports: viper License: GPL (>=2) MD5sum: a16c7ace0ba38076d549222dc0afb374 NeedsCompilation: no Title: Example data for the diggit package Description: This package provides expression profile and CNV data for glioblastoma from TCGA, and transcriptional and post-translational regulatory networks assembled with the ARACNe and MINDy algorithms, respectively. biocViews: ExperimentData, Cancer Author: Mariano Javier Alvarez Maintainer: Mariano Javier Alvarez git_url: https://git.bioconductor.org/packages/diggitdata git_branch: RELEASE_3_9 git_last_commit: 4f58611 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/diggitdata_1.16.0.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 dependencyCount: 20 Package: DLBCL Version: 1.24.0 Depends: R(>= 2.11.0), Biobase License: GPL (>=2) MD5sum: 730b96fa17675ada97131b40a2466c94 NeedsCompilation: no Title: Diffuse large B-cell lymphoma expression data Description: This package provides additional expression data on diffuse large B-cell lymphomas for the BioNet package. biocViews: ExperimentData, CancerData, MicroarrayData, ChipOnChipData Author: Marcus Dittrich and Daniela Beisser Maintainer: Marcus Dittrich URL: http://bionet.bioapps.biozentrum.uni-wuerzburg.de/ git_url: https://git.bioconductor.org/packages/DLBCL git_branch: RELEASE_3_9 git_last_commit: 4f2400b git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/DLBCL_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: DmelSGI Version: 1.16.0 Depends: R (>= 3.0) Imports: grid, TSP, limma, rhdf5, knitr, abind, gplots, igraph Suggests: BiocStyle, EBImage, RColorBrewer, RNAinteractMAPK, RSVGTipsDevice, cgdsr, hwriter, xtable, beeswarm License: Artistic-2.0 MD5sum: 42c76634466b104f1c93c49d14757b49 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 Maintainer: Bernd Fischer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DmelSGI git_branch: RELEASE_3_9 git_last_commit: c11de1b git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/DmelSGI_1.16.0.tar.gz vignettes: vignettes/DmelSGI/inst/doc/DmelSGI.pdf vignetteTitles: DmelSGI hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DmelSGI/inst/doc/DmelSGI.R dependencyCount: 36 Package: DMRcatedata Version: 1.20.0 Depends: R (>= 3.2.2), GenomicRanges Suggests: knitr License: GPL-3 MD5sum: 4401fe1a28b3d313d4ec38d5ca48b7fe NeedsCompilation: no Title: Data Package for DMRcate package Description: This package contains 8 data objects supporting functionality and examples of the Bioconductor package DMRcate. biocViews: ExperimentData, SNPData Author: Tim Peters Maintainer: Tim Peters VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DMRcatedata git_branch: RELEASE_3_9 git_last_commit: 19c2a98 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/DMRcatedata_1.20.0.tar.gz vignettes: vignettes/DMRcatedata/inst/doc/DMRcatedata.pdf vignetteTitles: The DMRcate package user's guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DMRcatedata/inst/doc/DMRcatedata.R dependencyCount: 16 Package: DonaPLLP2013 Version: 1.22.0 Depends: EBImage, parallel License: Artistic-2.0 MD5sum: dc254e899f0e9368fea3d2543408970c NeedsCompilation: no Title: Supplementary data package for Dona et al. (2013) containing example images and tables Description: An experiment data package associated with the publication Dona et al. (2013). Package contains runnable vignettes showing an example image segmentation for one posterior lateral line primordium, and also the data table and code used to analyze tissue-scale lifetime-ratio statistics. biocViews: ExperimentData, Tissue Author: Erika Dona, Joseph D. Barry, Guillaume Valentin, Charlotte Quirin, Anton Khmelinskii, Andreas Kunze, Sevi Durdu, Lionel R. Newton, Ana Fernandez-Minan, Wolfgang Huber, Michael Knop, Darren Gilmour Maintainer: Joseph D. Barry git_url: https://git.bioconductor.org/packages/DonaPLLP2013 git_branch: RELEASE_3_9 git_last_commit: 026f809 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/DonaPLLP2013_1.22.0.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: 25 Package: DREAM4 Version: 1.20.0 Depends: R (>= 2.15.1), SummarizedExperiment Suggests: RUnit, networkBMA License: GPL MD5sum: 00d929e1410ebea22bae8e2f9b15ea6e NeedsCompilation: no Title: Synthetic Expression Data for Gene Regulatory Network Inference from the 2009 DREAM4 challenge Description: Simulated expression data for five 10-node, and five 100-node networks, with associated data (including solutions) from the 2009 DREAM4 challenge. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, SequencingData Author: Paul Shannon Maintainer: Paul Shannon git_url: https://git.bioconductor.org/packages/DREAM4 git_branch: RELEASE_3_9 git_last_commit: fd21593 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/DREAM4_1.20.0.tar.gz vignettes: vignettes/DREAM4/inst/doc/DREAM4_InSilico_Description.pdf, vignettes/DREAM4/inst/doc/DREAM4.pdf vignetteTitles: DREAM4_InSilico_Description.pdf, DREAM4 Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DREAM4/inst/doc/DREAM4.R dependencyCount: 32 Package: dressCheck Version: 0.22.0 Depends: R (>= 2.10.1), methods, Biobase (>= 2.5.5) Suggests: survival, chron License: Artistic-2.0 MD5sum: 7584cc6c48fa1c394fe41c524f7b3854 NeedsCompilation: no Title: data and software for checking Dressman JCO 25(5) 2007 Description: data and software for checking Dressman JCO 25(5) 2007 biocViews: ExperimentData, Genome Author: Vincent Carey Maintainer: Vincent Carey git_url: https://git.bioconductor.org/packages/dressCheck git_branch: RELEASE_3_9 git_last_commit: 891d418 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/dressCheck_0.22.0.tar.gz vignettes: vignettes/dressCheck/inst/doc/short.pdf vignetteTitles: short review of dressCheck contents hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/dressCheck/inst/doc/short.R dependencyCount: 7 Package: DrugVsDiseasedata Version: 1.20.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 70457ffd167a803e7b9572c3ee8de757 NeedsCompilation: no Title: Drug versus Disease Data Description: Data package which provides default disease expression profiles, clusters and annotation information for use with the DrugVsDisease package. biocViews: Homo_sapiens_Data, MicroarrayData Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/DrugVsDiseasedata git_branch: RELEASE_3_9 git_last_commit: b01b969 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/DrugVsDiseasedata_1.20.0.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: dsQTL Version: 0.22.0 Depends: R (>= 2.15.0), utils, Biobase, SummarizedExperiment, GGBase (>= 3.31.1) Suggests: GGtools, rtracklayer License: Artistic-2.0 MD5sum: 832fc2afb33890374a5efa553fe276ab NeedsCompilation: no Title: dsQTL, data excerpt from Degner et al. 2012 Nature letter Description: dsQTL, excerpt from Degner et al. 2012 Nature letter on DNA variants associated with DnaseI hypersensitivity biocViews: ExperimentData, Genome, SequencingData, DNASeqData, NCI, Project1000genomes, BiocViews Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/dsQTL git_branch: RELEASE_3_9 git_last_commit: 2a1e6fa git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/dsQTL_0.22.0.tar.gz vignettes: vignettes/dsQTL/inst/doc/dsq.pdf vignetteTitles: dsQTL,, data excerpt from Degner et al. 2012 Nature letter hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/dsQTL/inst/doc/dsq.R importsMe: yriMulti dependencyCount: 61 Package: DuoClustering2018 Version: 1.2.0 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: 49e45aac011f59a54755d13f314949c3 NeedsCompilation: no Title: Data, Clustering Results and Visualization Functions From Duò et al (2018) Description: Preprocessed experimental and simulated scRNA-seq data sets used for evaluation of clustering methods for scRNA-seq data in Duò et al (2018). Also contains results from applying several clustering methods to each of the data sets, and functions for plotting method performance. biocViews: SingleCellData, ExperimentData Author: Angelo Duò, Charlotte Soneson Maintainer: Angelo Duò VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DuoClustering2018 git_branch: RELEASE_3_9 git_last_commit: 20a9b0b git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/DuoClustering2018_1.2.0.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 dependencyCount: 93 Package: DvDdata Version: 1.20.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 532227658b29e36af2d13ba3d27c4ae5 NeedsCompilation: no Title: Drug versus Disease Data Description: Data package which provides default drug and disease expression profiles for the DvD package. biocViews: GEO Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/DvDdata git_branch: RELEASE_3_9 git_last_commit: 0a2b2c8 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/DvDdata_1.20.0.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: 1.24.0 Depends: R (>= 1.4.1), marray, GEOquery Suggests: dyebias, convert, Biobase License: GPL-3 MD5sum: 5b5ecedcc8fc4ec91f6180788357b69a NeedsCompilation: no Title: Example data for the dyebias package, which implements the GASSCO method. Description: Data for the dyebias package, consisting of 4 self-self hybrizations of self-spotted yeast slides, as well as data from Array Express accession E-MTAB-32 biocViews: ExperimentData, SAGEData, CGHData, MicroarrayData, TwoChannelData, ArrayExpress Author: Philip Lijnzaad and Thanasis Margaritis Maintainer: Philip Lijnzaad URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad git_url: https://git.bioconductor.org/packages/dyebiasexamples git_branch: RELEASE_3_9 git_last_commit: 681955d git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/dyebiasexamples_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 49 Package: EatonEtAlChIPseq Version: 0.22.0 Depends: GenomicRanges (>= 1.5.42), ShortRead, rtracklayer License: Artistic 2.0 MD5sum: e6375a109bfe89cab8a89d343dd1105c NeedsCompilation: no Title: ChIP-seq data of ORC-binding sites in Yeast excerpted from Eaton et al. 2010 Description: ChIP-seq analysis subset from "Conserved nucleosome positioning defines replication origins" (PMID 20351051) biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, ChIPSeqData, GEO Author: Patrick Aboyoun Maintainer: Patrick Aboyoun git_url: https://git.bioconductor.org/packages/EatonEtAlChIPseq git_branch: RELEASE_3_9 git_last_commit: 833fff2 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/EatonEtAlChIPseq_0.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 42 Package: ecoliLeucine Version: 1.24.0 Depends: R (>= 1.9.0), affy (>= 1.23.4), ecolicdf License: GPL (>= 2) MD5sum: 6b94fceec7ba510c24754b9fcd8c6ac5 NeedsCompilation: no Title: Experimental data with Affymetrix E. coli chips Description: Experimental data with Affymetrix E. coli chips, as reported in She-pin Hung, Pierre Baldi, and G. Wesley Hatfield, J. Biol. Chem., Vol. 277, Issue 43, 40309-40323, October 25, 2002 biocViews: ExperimentData, MicroarrayData Author: Laurent Gautier Maintainer: Laurent Gautier git_url: https://git.bioconductor.org/packages/ecoliLeucine git_branch: RELEASE_3_9 git_last_commit: e47a2db git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ecoliLeucine_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 39 Package: EGSEAdata Version: 1.12.0 Depends: R (>= 3.4) Suggests: EGSEA License: file LICENSE MD5sum: 66cb1885c1cc1a378884e34c41ef2e25 NeedsCompilation: no Title: Gene set collections for the EGSEA package Description: This package includes gene set collections that are used for the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. It includes Human and Mouse versions of the MSidDB (Subramanian, et al. (2005) PNAS, 102(43):15545-15550) and GeneSetDB (Araki, et al. (2012) FEBS Open Bio, 2:76-82) collections. biocViews: ExperimentData, Homo_sapiens_Data, Mus_musculus_Data, Rattus_norvegicus_Data Author: Monther Alhamdoosh, Yifang Hu and Gordon K. Smyth Maintainer: Monther Alhamdoosh git_url: https://git.bioconductor.org/packages/EGSEAdata git_branch: RELEASE_3_9 git_last_commit: 1ab7caf git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/EGSEAdata_1.12.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: ELMER.data Version: 2.8.1 Depends: R (>= 3.5.0) Imports: GenomicRanges Suggests: BiocStyle, knitr, dplyr, devtools, DT License: GPL-3 MD5sum: 281860a50661cdf5feacd800b43969d0 NeedsCompilation: no Title: Data for the ELMER package Description: Supporting data for the ELMER package. It includes: - elmer.data.example.promoter: mae.promoter - elmer.data.example: data - EPIC.hg38.manifest - EPIC.hg19.manifest - hm450.hg38.manifest - hm450.hg19.manifest - hocomoco.table - human.TF - LUSC_meth_refined: Meth - LUSC_RNA_refined: GeneExp - Probes.motif.hg19.450K - Probes.motif.hg19.EPIC - Probes.motif.hg38.450K - Probes.motif.hg38.EPIC - TF.family - TF.subfamily - Human_genes__GRCh37_p13 - Human_genes__GRCh38_p12 - Human_genes__GRCh37_p13__tss - Human_genes__GRCh38_p12__tss biocViews: AssayDomainData, TechnologyData, OrganismData Author: Tiago Chedraoui Silva, Lijing Yao Simon Coetzee, Benjamin P. Berman Maintainer: Tiago Chedraoui Silva VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ELMER.data git_branch: RELEASE_3_9 git_last_commit: 6d3e1da git_last_commit_date: 2019-07-29 Date/Publication: 2019-07-30 source.ver: src/contrib/ELMER.data_2.8.1.tar.gz vignettes: vignettes/ELMER.data/inst/doc/vignettes.html vignetteTitles: ELMER.data: Supporting data for the ELMER package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ELMER.data/inst/doc/vignettes.R dependencyCount: 16 Package: estrogen Version: 1.30.0 Suggests: affy, hgu95av2, hgu95av2cdf, vsn, knitr License: LGPL MD5sum: fe5ddaafa6641e710a5cf76fb47a9989 NeedsCompilation: no Title: Microarray dataset that can be used as example for 2x2 factorial designs Description: Data from 8 Affymetrix genechips, looking at a 2x2 factorial design (with 2 repeats per level). biocViews: ExperimentData, MicroarrayData Author: Wolfgang Huber, Robert Gentleman Maintainer: Wolfgang Huber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/estrogen git_branch: RELEASE_3_9 git_last_commit: 21704c1 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/estrogen_1.30.0.tar.gz vignettes: vignettes/estrogen/inst/doc/estrogen.pdf vignetteTitles: estrogen hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/estrogen/inst/doc/estrogen.R dependencyCount: 0 Package: etec16s Version: 1.12.0 Depends: R (>= 3.3), Biobase, metagenomeSeq(>= 1.12.0) License: Artistic-2.0 MD5sum: d59c6663c4df8f745e0b326cb712137b NeedsCompilation: no Title: Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment Description: 16S rRNA gene sequencing data to study changes in the faecal microbiota of 12 volunteers during a human challenge study with ETEC (H10407) and subsequent treatment with ciprofloxacin. biocViews: ExperimentData, SequencingData, MicrobiomeData Author: Joseph N. Paulson Maintainer: Joseph N. Paulson git_url: https://git.bioconductor.org/packages/etec16s git_branch: RELEASE_3_9 git_last_commit: f6ceff9 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/etec16s_1.12.0.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: faahKO Version: 1.24.0 Depends: xcms License: LGPL MD5sum: c2d5a234c32448986696671867e5fbca NeedsCompilation: no Title: Saghatelian et al. (2004) FAAH knockout LC/MS data Description: Positive ionization mode data in NetCDF file format. Centroided subset from 200-600 m/z and 2500-4500 seconds. Data originally reported in "Assignment of Endogenous Substrates to Enzymes by Global Metabolite Profiling" Biochemistry; 2004; 43(45). Also includes detected peaks in an xcmsSet. biocViews: ExperimentData, MassSpectrometryData Author: Colin A. Smith Maintainer: Colin A. Smith URL: http://dx.doi.org/10.1021/bi0480335 git_url: https://git.bioconductor.org/packages/faahKO git_branch: RELEASE_3_9 git_last_commit: 7672af2 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/faahKO_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 87 Package: fabiaData Version: 1.22.0 Depends: R (>= 2.10.0), Biobase Imports: utils Suggests: fabia License: LGPL (>= 2.1) MD5sum: ebba780603b8886835107e4653c27d6d NeedsCompilation: no Title: Data sets for FABIA (Factor Analysis for Bicluster Acquisition) Description: Supplying gene expression data sets for the demos of the biclustering method "Factor Analysis for Bicluster Acquisition" (FABIA). The following three data sets are provided: A) breast cancer (van't Veer, Nature, 2002), B) multiple tissues (Su, PNAS, 2002), and C) diffuse large-B-cell lymphoma (Rosenwald, N Engl J Med, 2002). biocViews: CancerData, BreastCancerData, MicroarrayData Author: Sepp Hochreiter Maintainer: Sepp Hochreiter URL: http://www.bioinf.jku.at/software/fabia/fabia.html git_url: https://git.bioconductor.org/packages/fabiaData git_branch: RELEASE_3_9 git_last_commit: 46ad142 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/fabiaData_1.22.0.tar.gz vignettes: vignettes/fabiaData/inst/doc/fabiaData.pdf vignetteTitles: fabiaData: Manual for the R Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/fabiaData/inst/doc/fabiaData.R dependencyCount: 7 Package: facopy.annot Version: 1.4.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 5a332eb0a856a4bd83e8d6e2236fabc4 NeedsCompilation: no Title: Annotation for the copy number alteration association and enrichment analyses with facopy Description: Provides facopy with genome annotation on chromosome arms, genomic features and copy number alterations. biocViews: Genome Author: David Mosen-Ansorena Maintainer: David Mosen-Ansorena git_url: https://git.bioconductor.org/packages/facopy.annot git_branch: RELEASE_3_9 git_last_commit: 1477787 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/facopy.annot_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: facsDorit Version: 1.26.0 Depends: R (>= 1.9.1), prada (>= 1.0.5) License: GPL-2 MD5sum: dcf6e4b99ee9e013e30ebd0f8ec678d0 NeedsCompilation: no Title: DKFZ FACS example data Description: FACS example data for cell-based assays. This data is used in the examples and vignettes of the package prada. biocViews: ExperimentData, MicrotitrePlateAssayData Author: Florian Hahne Maintainer: Florian Hahne URL: http://www.dkfz.de/mga git_url: https://git.bioconductor.org/packages/facsDorit git_branch: RELEASE_3_9 git_last_commit: b446230 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/facsDorit_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 20 Package: FANTOM3and4CAGE Version: 1.20.0 Depends: R (>= 2.15.0) License: GPL-3 MD5sum: bfadfb9fe266c14e13c78de6887e8270 NeedsCompilation: no Title: CAGE data from FANTOM3 and FANTOM4 projects Description: CAGE (Cap Analysis Gene Expression) data from FANTOM3 and FANTOM4 projects produced by RIKEN Omics Science Center. biocViews: ExperimentData, Tissue Author: Vanja Haberle, Department of Biology, University of Bergen, Norway Maintainer: Vanja Haberle git_url: https://git.bioconductor.org/packages/FANTOM3and4CAGE git_branch: RELEASE_3_9 git_last_commit: 3dc7ff3 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/FANTOM3and4CAGE_1.20.0.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 dependencyCount: 0 Package: ffpeExampleData Version: 1.22.0 Depends: R (>= 2.10.0), lumi Suggests: genefilter, affy License: GPL (>2) MD5sum: cc909cc2b13a7cc9a8238bdab9f68d08 NeedsCompilation: no Title: Illumina DASL example microarray data Description: A subset of GSE17565 (April et al. 2009) containing 32 FFPE samples of Burkitts Lymphoma and Breast Adenocarcinoma, with a dilution series in technical duplicate. biocViews: Tissue, Genome, MicroarrayData, TissueMicroarrayData, GEO Author: Levi Waldron Maintainer: Levi Waldron git_url: https://git.bioconductor.org/packages/ffpeExampleData git_branch: RELEASE_3_9 git_last_commit: 25dc5a0 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ffpeExampleData_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 145 Package: fibroEset Version: 1.26.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: cb7df36fe536a6bdbefeddf2086ec477 NeedsCompilation: no Title: exprSet for Karaman et al. (2003) fibroblasts data Description: exprSet for Karaman et al. (2003) human, bonobo and gorilla fibroblasts data biocViews: ExperimentData, Genome, Homo_sapiens_Data, MicroarrayData, ChipOnChipData Author: Sylvia Merk Maintainer: Sylvia Merk git_url: https://git.bioconductor.org/packages/fibroEset git_branch: RELEASE_3_9 git_last_commit: ebc1bed git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/fibroEset_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: FIs Version: 1.12.0 Depends: R (>= 3.3) License: GPL-3 MD5sum: 26a808973c479d338754411a994a3df9 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 git_url: https://git.bioconductor.org/packages/FIs git_branch: RELEASE_3_9 git_last_commit: 85fa39e git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/FIs_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: fission Version: 1.4.0 Depends: R (>= 2.10), SummarizedExperiment Suggests: knitr License: LGPL MD5sum: 9e37bceecdb13c6f82799730387e02d0 NeedsCompilation: no Title: RangedSummarizedExperiment for time course RNA-Seq of fission yeast in response to stress, by Leong et al., Nat Commun 2014. Description: This package provides a RangedSummarizedExperiment object of read counts in genes for a time course RNA-Seq experiment of fission yeast (Schizosaccharomyces pombe) in response to oxidative stress (1M sorbitol treatment) at 0, 15, 30, 60, 120 and 180 mins. The samples are further divided between a wild-type group and a group with deletion of atf21. The read count matrix was prepared and provided by the author of the study: Leong HS, Dawson K, Wirth C, Li Y, Connolly Y, Smith DL, Wilkinson CR, Miller CJ. "A global non-coding RNA system modulates fission yeast protein levels in response to stress". Nat Commun 2014 May 23;5:3947. PMID: 24853205. GEO: GSE56761. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData, GEO Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/fission git_branch: RELEASE_3_9 git_last_commit: 66b6e72 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/fission_1.4.0.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 dependencyCount: 32 Package: Fletcher2013a Version: 1.20.0 Depends: R (>= 2.15), limma Imports: Biobase ,VennDiagram, gplots,grid License: GPL (>= 2) MD5sum: 3e34329457960bd66816855ecaba1584 NeedsCompilation: no Title: Gene expression data from breast cancer cells under FGFR2 signalling perturbation Description: The package Fletcher2013a contains time-course gene expression data from MCF-7 cells treated under different experimental systems in order to perturb FGFR2 signalling. The data comes from Fletcher et al. (Nature Comms 4:2464, 2013) where further details about the background and the experimental design of the study can be found. biocViews: ExperimentData, ExpressionData, CancerData, BreastCancerData, MicroarrayData Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin Meyer. Maintainer: Mauro Castro URL: http://dx.doi.org/10.1038/ncomms3464 git_url: https://git.bioconductor.org/packages/Fletcher2013a git_branch: RELEASE_3_9 git_last_commit: e282310 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/Fletcher2013a_1.20.0.tar.gz vignettes: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.pdf vignetteTitles: Main vignette:Fletcher2013a hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.R dependsOnMe: Fletcher2013b dependencyCount: 21 Package: Fletcher2013b Version: 1.20.0 Depends: R (>= 2.15), Fletcher2013a, RTN (>= 1.1.2), RedeR (>= 1.8.1), igraph Imports: RColorBrewer License: GPL (>= 2) MD5sum: 5da665ab15174d34747bfea5b972d48b NeedsCompilation: no Title: Master regulators of FGFR2 signalling and breast cancer risk Description: This package reproduces the systems biology analysis for the data in package Fletcher2013a using RTN. biocViews: ExperimentData, ChIPSeqData, CancerData, BreastCancerData, SNPData Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin Meyer. Maintainer: Mauro Castro URL: http://dx.doi.org/10.1038/ncomms3464 git_url: https://git.bioconductor.org/packages/Fletcher2013b git_branch: RELEASE_3_9 git_last_commit: 1b5771f git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/Fletcher2013b_1.20.0.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 dependencyCount: 57 Package: flowFitExampleData Version: 1.20.0 Depends: R (>= 2.12.2), flowCore Imports: methods License: Artistic-2.0 MD5sum: d5627c525cb0ab48377638d0af2e8c3c NeedsCompilation: no Title: Example data for the flowFit package Description: Two dataset that can be used to run examples from the flowFit vignette and examples biocViews: FlowCytometryData Author: davide Rambaldi Maintainer: Davide Rambaldi git_url: https://git.bioconductor.org/packages/flowFitExampleData git_branch: RELEASE_3_9 git_last_commit: 25b0755 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/flowFitExampleData_1.20.0.tar.gz vignettes: vignettes/flowFitExampleData/inst/doc/flowFitExampleData.pdf vignetteTitles: flowFitExampleData: example data for the beadarray package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowFitExampleData/inst/doc/flowFitExampleData.R dependencyCount: 24 Package: flowPloidyData Version: 1.10.0 Suggests: knitr, rmarkdown, flowCore License: GPL-3 MD5sum: e207b89cdef6679d0ee10063a582c930 NeedsCompilation: no Title: Example Flow Cytometry Data Description: A collection of raw flow cytometry data for use in vignettes for the flowPloidy package. biocViews: FlowCytometryData Author: Tyler Smith Maintainer: Tyler Smith VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/flowPloidyData git_branch: RELEASE_3_9 git_last_commit: 34668be git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/flowPloidyData_1.10.0.tar.gz vignettes: vignettes/flowPloidyData/inst/doc/flowPloidyData.html vignetteTitles: flowPloidy Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: flowQBData Version: 1.10.0 Depends: R (>= 3.2.0) Suggests: flowQB License: Artistic License 2.0 MD5sum: e5d94c8fb66f811c34a7a92ef607f20d NeedsCompilation: no Title: flowQB test and example data files Description: The flowQBData package provides data files used as examples and for testing of the software provided in the flowQB package. biocViews: ExperimentData, FlowCytometryData Author: Josef Spidlen, Wayne Moore, David Parks, Faysal El Khettabi, Ryan Brinkman Maintainer: Josef Spidlen PackageStatus: Deprecated git_url: https://git.bioconductor.org/packages/flowQBData git_branch: RELEASE_3_9 git_last_commit: 4982e93 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/flowQBData_1.10.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: FlowSorted.Blood.450k Version: 1.22.0 Depends: R (>= 2.13.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: d2a79cbca36828a67db9655e7e23e059 NeedsCompilation: no Title: Illumina HumanMethylation data on sorted blood cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays, and an object depicting which CpGs on the array are associated with cell type. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Andrew E Jaffe Maintainer: Andrew E Jaffe git_url: https://git.bioconductor.org/packages/FlowSorted.Blood.450k git_branch: RELEASE_3_9 git_last_commit: bd8b649 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/FlowSorted.Blood.450k_1.22.0.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 suggestsMe: FlowSorted.Blood.EPIC dependencyCount: 125 Package: FlowSorted.Blood.EPIC Version: 1.2.0 Depends: R (>= 3.5), minfi (>= 1.21.2), SummarizedExperiment, genefilter, quadprog, nlme, S4Vectors, graphics, stats, utils, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, ExperimentHub Suggests: knitr, rmarkdown, EpiDISH, FlowSorted.Blood.450k(>= 1.0.1), FlowSorted.CordBlood.450k, FlowSorted.CordBloodNorway.450k, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: GPL-3 MD5sum: 4e6f8a48f8d8504c3027429fb164eb98 NeedsCompilation: no Title: Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells Description: Raw data objects to be used for blood cell proportion estimation in minfi and similar packages. The FlowSorted.Blood.EPIC object is based in samples assayed by Brock Christensen and colleagues; for details see Salas et al. 2018. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, Genome, TissueMicroarrayData, MethylationArrayData Author: Lucas A. Salas [cre, aut], Devin C. Koestler [aut], Rondi A. Butler [ctb], Helen M. Hansen [ctb], John K. Wiencke [ctb], Karl T. Kelsey [ctb], Brock C. Christensen [ctb], Kasper Daniel Hansen [ctb] (author and maintainer of the original minfi estimateCellCounts and internal functions), Jean-Philippe Fortin [ctb] (contributor in the original minfi estimateCellCounts and internal functions), Shan V. Andrews [ctb] (contributor in the original minfi estimateCellCounts and internal functions), E. Andres Houseman [ctb] (author of the original quadratic programming function used for cell projection), Andrew E Jaffe [ctb] (author of the original estimateCellCounts and internal functions within minfi) Maintainer: Lucas A. Salas URL: https://github.com/immunomethylomics/FlowSorted.Blood.EPIC VignetteBuilder: knitr BugReports: https://github.com/immunomethylomics/FlowSorted.Blood.EPIC/issues. git_url: https://git.bioconductor.org/packages/FlowSorted.Blood.EPIC git_branch: RELEASE_3_9 git_last_commit: e92856a git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/FlowSorted.Blood.EPIC_1.2.0.tar.gz vignettes: vignettes/FlowSorted.Blood.EPIC/inst/doc/FlowSorted.Blood.EPIC.html vignetteTitles: FlowSorted.Blood.EPIC hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.Blood.EPIC/inst/doc/FlowSorted.Blood.EPIC.R dependsOnMe: FlowSorted.CordBloodCombined.450k dependencyCount: 141 Package: FlowSorted.CordBlood.450k Version: 1.12.0 Depends: R (>= 3.2.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 35c1420b23f1016c0953af3f67a48e07 NeedsCompilation: no Title: Illumina 450k data on sorted cord blood cells Description: Raw data objects to be used for cord blood cell proportion estimation in minfi. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Shan V. Andrews [cre, aut], Kelly M. Bakulski [aut] Maintainer: Shan V. Andrews git_url: https://git.bioconductor.org/packages/FlowSorted.CordBlood.450k git_branch: RELEASE_3_9 git_last_commit: 11697e4 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/FlowSorted.CordBlood.450k_1.12.0.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: 125 Package: FlowSorted.CordBloodCombined.450k Version: 1.0.0 Depends: R (>= 3.6), minfi (>= 1.21.2), SummarizedExperiment, IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b4.hg19, ExperimentHub(>= 1.9.1), FlowSorted.Blood.EPIC, utils Suggests: knitr, rmarkdown, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: GPL-3 MD5sum: 526f5a9879e6ae163dcbea71951cd91c NeedsCompilation: no Title: Illumina 450k/EPIC data on FACS and MACS umbilical blood cells Description: Raw data objects to be used for umbilical cord blood cell proportion estimation in minfi and similar packages. The FlowSorted.CordBloodCombined.450k object is based in samples assayed by Bakulski et al, Gervin et al., de Goede et al., and Lin et al. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, Genome, TissueMicroarrayData, MethylationArrayData, ExperimentHub Author: Lucas A. Salas [cre, aut], Kristina Gervin [aut], Meaghan C. Jones [aut], Kelly M. Bakulski [ctb], Devin C. Koestler [ctb], John K. Wiencke [ctb], Karl T. Kelsey [ctb], Robert Lyle [ctb], Brock C. Christensen [ctb], Janine Felix [ctb] Maintainer: Lucas A. Salas URL: https://github.com/immunomethylomics/FlowSorted.CordBloodCombined.450k VignetteBuilder: knitr BugReports: https://github.com/immunomethylomics/FlowSorted.CordBloodCombined.450k/issues. git_url: https://git.bioconductor.org/packages/FlowSorted.CordBloodCombined.450k git_branch: RELEASE_3_9 git_last_commit: 7c4280e git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/FlowSorted.CordBloodCombined.450k_1.0.0.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: 143 Package: FlowSorted.CordBloodNorway.450k Version: 1.10.0 Depends: R (>= 3.2.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 83e0a618318a466dbb7df19db7340909 NeedsCompilation: no Title: Illumina HumanMethylation data on sorted cord blood cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays, for cell type composition estimation. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: kristina gervin [cre, aut], Kasper Daniel Hansen [aut] Maintainer: kristina gervin URL: https://bitbucket.com/kasperdanielhansen/Illumina_CordBlood git_url: https://git.bioconductor.org/packages/FlowSorted.CordBloodNorway.450k git_branch: RELEASE_3_9 git_last_commit: 1a31ff6 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/FlowSorted.CordBloodNorway.450k_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: FlowSorted.Blood.EPIC dependencyCount: 125 Package: FlowSorted.DLPFC.450k Version: 1.20.0 Depends: R (>= 2.13.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 2079268ebe8b094cc960b96c9ab94876 NeedsCompilation: no Title: Illumina HumanMethylation data on sorted frontal cortex cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Andrew E Jaffe, Zachary A. Kaminsky Maintainer: Andrew E Jaffe git_url: https://git.bioconductor.org/packages/FlowSorted.DLPFC.450k git_branch: RELEASE_3_9 git_last_commit: f44dc85 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/FlowSorted.DLPFC.450k_1.20.0.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: 125 Package: flowWorkspaceData Version: 2.20.0 License: GPL-2 MD5sum: c729e940217ce7298e58ddb4b654b85a NeedsCompilation: no Title: A data package containing two flowJo, one diva xml workspace and the associated fcs files as well as three GatingSets for testing the flowWorkspace, openCyto and CytoML packages. Description: The necessary external data to run the flowWorkspace and openCyto vignette is found in this package. biocViews: ExperimentData, FlowCytometryData Author: Greg Finak Maintainer: Mike Jiang git_url: https://git.bioconductor.org/packages/flowWorkspaceData git_branch: RELEASE_3_9 git_last_commit: c83f53e git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/flowWorkspaceData_2.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: frmaExampleData Version: 1.20.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 3eb2349bbcc2b56bc60f2f7911e6d7cc NeedsCompilation: no Title: Frma Example Data Description: Data files used by the examples in frma and frmaTools packages biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/frmaExampleData git_branch: RELEASE_3_9 git_last_commit: 7218b7f git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/frmaExampleData_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: FunciSNP.data Version: 1.20.0 Depends: R (>= 2.14.0), IRanges Imports: rtracklayer License: GPL-3 MD5sum: 693316a2d7cea94fbf95e20e011ae1be NeedsCompilation: no Title: Various data sets for use with the FunciSNP package Description: Data sets needed for FunciSNP to integrate information from GWAS, 1000genomes and chromatin feature, in order to identify functional SNP in coding or non-coding regions. biocViews: SNPData, Project1000genomes, ENCODE Author: Simon G. Coetzee and Houtan Noushmehr, PhD Maintainer: Simon G. Coetzee URL: http://coetzeeseq.usc.edu/publication/Coetzee_SG_et_al_2012/ git_url: https://git.bioconductor.org/packages/FunciSNP.data git_branch: RELEASE_3_9 git_last_commit: 209fe30 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/FunciSNP.data_1.20.0.tar.gz vignettes: vignettes/FunciSNP.data/inst/doc/FunciSNP.data.pdf vignetteTitles: FunciSNP Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FunciSNP.data/inst/doc/FunciSNP.data.R dependencyCount: 38 Package: furrowSeg Version: 1.12.0 Depends: R (>= 3.3), EBImage Imports: abind, dplyr, locfit, tiff Suggests: BiocStyle, ggplot2, knitr License: Artistic-2.0 MD5sum: ce4d21cb772147f45976e3e47612cfb0 NeedsCompilation: no Title: Furrow Segmentation Description: Image feature data and analysis codes for the Guglielmi, Barry et al. paper describing the application of an optogenetics tools to disrupt Drosophila embryo furrowing. biocViews: ExperimentData, Drosophila_melanogaster_Data, Tissue, ReproducibleResearch Author: Joseph Barry Maintainer: Joseph Barry VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/furrowSeg git_branch: RELEASE_3_9 git_last_commit: e7aae18 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/furrowSeg_1.12.0.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: 46 Package: gageData Version: 2.22.0 Depends: R (>= 2.10) Suggests: gage, pathview, genefilter License: GPL (>=2.0) MD5sum: b20e038013ae19b70c5dc543fea69efe NeedsCompilation: no Title: Auxillary data for gage package Description: This is a supportive data package for the software package, gage. However, the data supplied here are also useful for gene set or pathway analysis or microarray data analysis in general. In this package, we provide two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and BMP6 (originally published as an demo dataset for GAGE, also registered as GSE13604 in GEO). This package also includes commonly used gene set data based on KEGG pathways and GO terms for major research species, including human, mouse, rat and budding yeast. Mapping data between common gene IDs for budding yeast are also included. biocViews: ExperimentData, StemCell, CancerData, BreastCancerData, MicroarrayData, GEO Author: Weijun Luo Maintainer: Weijun Luo git_url: https://git.bioconductor.org/packages/gageData git_branch: RELEASE_3_9 git_last_commit: 72ed234 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/gageData_2.22.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: gaschYHS Version: 1.22.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 640ea3dc1bccf57861211b0f6395ec1b NeedsCompilation: no Title: ExpressionSet for response of yeast to heat shock and other environmental stresses Description: Data from PMID 11102521 biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data Author: Audrey Gasch and colleagues Maintainer: Vince Carey URL: http://genome-www.stanford.edu/yeast_stress/data/rawdata/complete_dataset.txt git_url: https://git.bioconductor.org/packages/gaschYHS git_branch: RELEASE_3_9 git_last_commit: 1e3ca7a git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/gaschYHS_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: gatingMLData Version: 2.24.0 Depends: R (>= 1.9.0) Suggests: flowUtils License: GPL MD5sum: 8738620aac52004fefa9a3af7194df75 NeedsCompilation: no Title: Data and XML files for Gating-ML Test suite Description: Test data and XML files for testing compliance of the flowUtils/flowCore packages with Gating-ML (1.5 and 2.0) standards. biocViews: ExperimentData, FlowCytometryData Author: J. Spidlen, N. Gopalakrishnan Maintainer: J. Spidlen git_url: https://git.bioconductor.org/packages/gatingMLData git_branch: RELEASE_3_9 git_last_commit: 6887569 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/gatingMLData_2.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: gcspikelite Version: 1.22.0 Depends: R (>= 2.5.0) License: LGPL MD5sum: 008f920fa946568d0e31d4333e2fe28c NeedsCompilation: no Title: Spike-in data for GC/MS data and methods within flagme Description: Spike-in data for GC/MS data and methods within flagme biocViews: MassSpectrometryData Author: Mark Robinson Maintainer: Mark Robinson git_url: https://git.bioconductor.org/packages/gcspikelite git_branch: RELEASE_3_9 git_last_commit: 058b7b1 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/gcspikelite_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: geneLenDataBase Version: 1.20.0 Depends: R (>= 2.11.0) Imports: utils, rtracklayer, GenomicFeatures (>= 1.3.15) License: LGPL (>= 2) MD5sum: 53df16996486e637bf7a98b5498525ff NeedsCompilation: no Title: Lengths of mRNA transcripts for a number of genomes Description: Length of mRNA transcripts for a number of genomes and gene ID formats, largely based on UCSC table browser biocViews: ExperimentData, Genome Author: Matthew Young Maintainer: Matthew Young , Nadia Davidson git_url: https://git.bioconductor.org/packages/geneLenDataBase git_branch: RELEASE_3_9 git_last_commit: 70a1abe git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/geneLenDataBase_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 73 Package: genomationData Version: 1.16.0 Suggests: knitr License: GPL-3 MD5sum: e9b054305d2ce85aeb1bca338eb07b66 NeedsCompilation: no Title: Experimental data for showing functionalities of the genomation package Description: The package contains Chip Seq, Methylation and Cage data, downloaded from Encode biocViews: ExperimentData, Genome, StemCell, SequencingData, ChIPSeqData, ChipOnChipData, ENCODE Author: Altuna Akalin, Vedran Franke Maintainer: Vedran Franke VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/genomationData git_branch: RELEASE_3_9 git_last_commit: ed76790 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/genomationData_1.16.0.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 dependencyCount: 0 Package: GeuvadisTranscriptExpr Version: 1.12.0 Depends: R (>= 3.3.0) Suggests: limma, rtracklayer, GenomicRanges, Rsamtools, VariantAnnotation, tools, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: ece1f0f2d431b75bca527b79f319c9a0 NeedsCompilation: no Title: Data package with transcript expression and bi-allelic genotypes from the GEUVADIS project Description: Provides transcript expression and bi-allelic genotypes corresponding to the chromosome 19 for CEU individuals from the GEUVADIS project, Lappalainen et al. biocViews: Homo_sapiens_Data, SNPData, Genome, RNASeqData, SequencingData, ExpressionData Author: Malgorzata Nowicka [aut, cre] Maintainer: Malgorzata Nowicka VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GeuvadisTranscriptExpr git_branch: RELEASE_3_9 git_last_commit: 01b5838 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/GeuvadisTranscriptExpr_1.12.0.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 dependencyCount: 0 Package: geuvPack Version: 1.16.0 Depends: R (>= 2.10), SummarizedExperiment License: Artistic-2.0 MD5sum: ab9980646eee0afbfb64f8009fc0862e NeedsCompilation: no Title: summarized experiment with expression data from GEUVADIS Description: FPKM from GEUVADIS, annotated to gencode regions biocViews: ExperimentData, Genome, SequencingData, MicroarrayData, ArrayExpress Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/geuvPack git_branch: RELEASE_3_9 git_last_commit: a3d0d88 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/geuvPack_1.16.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: yriMulti suggestsMe: yriMulti dependencyCount: 32 Package: geuvStore2 Version: 1.14.0 Depends: BatchJobs, GenomicRanges Imports: methods, gQTLBase Suggests: Homo.sapiens, knitr (>= 1.7), rmarkdown License: Artistic-2.0 MD5sum: ca0b70a5e2a1b47dd19f9e9566dc8411 NeedsCompilation: no Title: demonstrate storage discipline for eQTL enumerations, revised Description: demonstrate storage discipline for eQTL enumerations and analyses based on a selection of GEUVADIS results biocViews: ExperimentData, SequencingData, MicroarrayData Author: VJ Carey Maintainer: VJ Carey VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/geuvStore2 git_branch: RELEASE_3_9 git_last_commit: e66409f git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/geuvStore2_1.14.0.tar.gz vignettes: vignettes/geuvStore2/inst/doc/geuvStore2.pdf vignetteTitles: geuvStore: sharded storage for cis-association statistics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/geuvStore2/inst/doc/geuvStore2.R dependencyCount: 91 Package: GGdata Version: 1.22.0 Depends: R (>= 2.12.0), methods, Biobase (>= 2.5.5), GGBase, snpStats, illuminaHumanv1.db, AnnotationDbi Enhances: GGtools License: LGPL MD5sum: afba50713e07d019b729a86fda04580e NeedsCompilation: no Title: all 90 hapmap CEU samples, 47K expression, 4mm SNP Description: data exemplars dealing with hapmap SNP reports, GWAS, etc. biocViews: ExperimentData, HapMap, Genome, SequencingData, MicroarrayData, SNPData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/GGdata git_branch: RELEASE_3_9 git_last_commit: ba63ef3 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/GGdata_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 63 Package: GIGSEAdata Version: 1.2.0 Depends: R (>= 3.5) Suggests: GIGSEA, knitr, rmarkdown License: LGPL-3 MD5sum: 9179864b9233f0010eb2f0fb58317ae5 NeedsCompilation: no Title: Gene set collections for the GIGSEA package Description: The gene set collection used for the GIGSEA package. biocViews: ExperimentData, Homo_sapiens_Data Author: Shijia Zhu Maintainer: Shijia Zhu VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GIGSEAdata git_branch: RELEASE_3_9 git_last_commit: e9730cb git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/GIGSEAdata_1.2.0.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: 1.26.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: LGPL MD5sum: 3e7e78f951be8c6542fd6de61eabd92e NeedsCompilation: no Title: exprSets for golub leukemia data Description: representation of public golub data with some covariate data of provenance unknown to the maintainer at present; now employs ExpressionSet format biocViews: ExperimentData, Genome, CancerData, LeukemiaCancerData Author: Todd Golub Maintainer: Vince Carey git_url: https://git.bioconductor.org/packages/golubEsets git_branch: RELEASE_3_9 git_last_commit: f358b9f git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/golubEsets_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: grndata Version: 1.16.0 Depends: R (>= 2.10) Suggests: RUnit, BiocGenerics, knitr License: GPL-3 MD5sum: f68d2293bf9ad882ff9f061266f63fd1 NeedsCompilation: no Title: Synthetic Expression Data for Gene Regulatory Network Inference Description: Simulated expression data for five large Gene Regulatory Networks from different simulators biocViews: ExperimentData, NetworkInference, GeneExpression, Microarray, GeneRegulation, Network Author: Pau Bellot, Catharina Olsen, Patrick E Meyer Maintainer: Pau Bellot VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/grndata git_branch: RELEASE_3_9 git_last_commit: 60f4443 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/grndata_1.16.0.tar.gz vignettes: vignettes/grndata/inst/doc/grndata.html vignetteTitles: GRNdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: GSBenchMark Version: 1.4.0 Depends: R (>= 2.13.1) License: GPL-2 MD5sum: a59a7b4328531cb827db30a0cabe0c5f NeedsCompilation: no Title: Gene Set Benchmark Description: Benchmarks for Machine Learning Analysis of the Gene Sets. The package contains a list of pathways and gene expression data sets used in "Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)" (2010) by Eddy et al. biocViews: MicroarrayData Author: Bahman Afsari , Elana J. Fertig Maintainer: Bahman Afsari git_url: https://git.bioconductor.org/packages/GSBenchMark git_branch: RELEASE_3_9 git_last_commit: ae0db3b git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/GSBenchMark_1.4.0.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 dependencyCount: 0 Package: GSE62944 Version: 1.12.0 Depends: Biobase, GEOquery Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle License: Artistic-2.0 MD5sum: 817f3700ad4889d79e78336b42bd802b NeedsCompilation: no Title: GEO accession data GSE62944 as a SummarizedExperiment Description: TCGA processed RNA-Seq data for 9264 tumor and 741 normal samples across 24 cancer types and made them available as GEO accession [GSE62944](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944). GSE62944 data have been parsed into a SummarizedExperiment object available in ExperimentHub. biocViews: ExperimentData, Genome, DNASeqData, RNASeqData Author: Sonali Arora Maintainer: Bioconductor Package Maintainer URL: http://bioconductor.org/packages/release/bioc/html/GSE62944.html VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GSE62944 git_branch: RELEASE_3_9 git_last_commit: e68e6f9 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/GSE62944_1.12.0.tar.gz vignettes: vignettes/GSE62944/inst/doc/GSE62944.html vignetteTitles: Raw TCGA data using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GSE62944/inst/doc/GSE62944.R dependencyCount: 48 Package: gskb Version: 1.16.0 Depends: R (>= 3.2.0) Suggests: PGSEA License: Artistic-2.0 MD5sum: b6a505908c6339c2cc3e5f9b937737aa NeedsCompilation: no Title: Gene Set data for pathway analysis in mouse Description: Gene Set Knowledgebase (GSKB) is a comprehensive knowledgebase for pathway analysis in mouse. Interpretation of high-throughput genomics data based on biological pathways constitutes a constant challenge, partly because of the lack of supporting pathway database. We created a functional genomics knowledgebase in mouse, which includes 33,261 pathways and gene sets compiled from 40 sources such as Gene Ontology, KEGG, GeneSetDB, PANTHER, microRNA and transcription factor target genes, etc. In addition, we also manually collected and curated 8,747 lists of differentially expressed genes from 2,526 published gene expression studies to enable the detection of similarity to previously reported gene expression signatures. These two types of data constitute a comprehensive Gene Set Knowledgebase (GSKB), which can be readily used by various pathway analysis software such as gene set enrichment analysis (GSEA). As a first step, we gathered annotation information from 40 existing databases for mouse-related gene sets. These gene sets are divided into 7 categories, namely, Gene Ontology, Curated pathways, Metabolic Pathways, Transcription Factor (TF) and microRNA target genes, location (cytogenetics band), and others. We used information in GeneSetDB for some of the databases. Detailed information on these 40 sources and the citations is available http://ge-lab.org/gskb/Table%201-sources.pdf . The gene lists from literature were retrieved manually from individual gene expression studies through a process similar to the one used to create AraPath, a similar resource for Arabidopsis[12]. As most expression studies upload raw data to repositories like GEO and ArrayExpress, we used the meta-data in these databases to search for publications. We scanned all datasets we can found and retrieved 4,313 potentially useful papers reporting gene expression studies in mouse. These papers were individually read by curators to identify lists of differentially expressed genes in various conditions. We compiled a total of 8,747 lists of differently expressed genes from 2,518 of papers. Each gene list was annotated with a unique name, brief description, and publication information, similar to the protocol used in MSigDB and Arapath. These gene lists constitute a large collection of published gene expression signatures that form a foundation for interpret new gene lists and expression profiles. More information about this data is available here http://ge-lab.org/gskb/. There is also a paper describing these data are currently in revision by Database: The Journal of Biological Databases and Curation. biocViews: ExperimentData, Mus_musculus Author: Valerie Bares, Xijin Ge Maintainer: Valerie Bares git_url: https://git.bioconductor.org/packages/gskb git_branch: RELEASE_3_9 git_last_commit: a641aae git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/gskb_1.16.0.tar.gz vignettes: vignettes/gskb/inst/doc/gskb.pdf vignetteTitles: gskb: mouse data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/gskb/inst/doc/gskb.R dependencyCount: 0 Package: GSVAdata Version: 1.20.0 Depends: R (>= 2.10), Biobase, GSEABase, hgu95a.db License: GPL (>= 2) MD5sum: 484d17c3ba9983370f7d91f8db3899e7 NeedsCompilation: no Title: Data employed in the vignette of the GSVA package Description: This package stores the data employed in the vignette of the GSVA package. These data belong to the following publications: Armstrong et al. Nat Genet 30:41-47, 2002; Cahoy et al. J Neurosci 28:264-278, 2008; Carrel and Willard, Nature, 434:400-404, 2005; Huang et al. PNAS, 104:9758-9763, 2007; Pickrell et al. Nature, 464:768-722, 2010; Skaletsky et al. Nature, 423:825-837; Verhaak et al. Cancer Cell 17:98-110, 2010 biocViews: ExperimentData, RNASeqData, Homo_sapiens_Data, CancerData, LeukemiaCancerData Author: Robert Castelo Maintainer: Robert Castelo git_url: https://git.bioconductor.org/packages/GSVAdata git_branch: RELEASE_3_9 git_last_commit: d0ff76f git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/GSVAdata_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 41 Package: GWASdata Version: 1.22.0 Depends: GWASTools License: Artistic-2.0 MD5sum: 4e1c2ce5dfcb6411e5b6d6690aeeb369 NeedsCompilation: no Title: Data used in the examples and vignettes of the GWASTools package Description: Selected Affymetrix and Illlumina SNP data for HapMap subjects. Data provided by the Center for Inherited Disease Research at Johns Hopkins University and the Broad Institute of MIT and Harvard University. biocViews: ExperimentData, MicroarrayData, SNPData, HapMap Author: Stephanie Gogarten Maintainer: Stephanie Gogarten , Adrienne Stilp git_url: https://git.bioconductor.org/packages/GWASdata git_branch: RELEASE_3_9 git_last_commit: d763d19 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/GWASdata_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 86 Package: h5vcData Version: 2.4.0 Suggests: h5vc License: GPL (>= 3) MD5sum: cd3b929b2cde6716aa26ffd790f350da NeedsCompilation: no Title: Example data for the h5vc package Description: This package contains the data used in the vignettes and examples of the 'h5vc' package biocViews: CancerData Author: Paul Theodor Pyl Maintainer: Paul Theodor Pyl git_url: https://git.bioconductor.org/packages/h5vcData git_branch: RELEASE_3_9 git_last_commit: 12c6927 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/h5vcData_2.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmap100khind Version: 1.26.0 Suggests: oligo License: GPL MD5sum: a5072491e91e762e1ec95fe998413f77 NeedsCompilation: no Title: Sample data - Hapmap 100K HIND Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap100khind git_branch: RELEASE_3_9 git_last_commit: 57d9db4 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/hapmap100khind_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmap100kxba Version: 1.26.0 Suggests: oligo License: GPL MD5sum: 11ec72b847b929a9697461cb7143ecc1 NeedsCompilation: no Title: Sample data - Hapmap 100K XBA Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap100kxba git_branch: RELEASE_3_9 git_last_commit: be11131 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/hapmap100kxba_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmap500knsp Version: 1.26.0 Suggests: oligo License: GPL MD5sum: c78f3012d3aee6bcfe793a7f14cdac6d NeedsCompilation: no Title: Sample data - Hapmap 500K NSP Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap500knsp git_branch: RELEASE_3_9 git_last_commit: c7a23b0 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/hapmap500knsp_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmap500ksty Version: 1.26.0 Suggests: oligo License: GPL MD5sum: c9c6bd3acf4e2ab7e7beb7ad6a9dbb8f NeedsCompilation: no Title: Sample data - Hapmap 500K STY Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap500ksty git_branch: RELEASE_3_9 git_last_commit: 8a1338e git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/hapmap500ksty_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmapsnp5 Version: 1.26.0 Suggests: oligo License: GPL MD5sum: 0ca43c40b0ef668b56edefa059dead89 NeedsCompilation: no Title: Sample data - Hapmap SNP 5.0 Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData, SNPData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmapsnp5 git_branch: RELEASE_3_9 git_last_commit: ac04dbb git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/hapmapsnp5_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hapmapsnp6 Version: 1.26.0 Depends: R (>= 2.15) Suggests: oligo, oligoClasses License: GPL MD5sum: df63dbabc0405f8f09ca76aecd6077b8 NeedsCompilation: no Title: Sample data - Hapmap SNP 6.0 Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, SNPData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmapsnp6 git_branch: RELEASE_3_9 git_last_commit: 96dfef7 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/hapmapsnp6_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: harbChIP Version: 1.22.0 Depends: R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5), Biostrings Imports: methods, stats License: Artistic-2.0 MD5sum: 8b019087317d308012e39effa61094d7 NeedsCompilation: no Title: Experimental Data Package: harbChIP Description: data from a yeast ChIP-chip experiment biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/harbChIP git_branch: RELEASE_3_9 git_last_commit: 074c896 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/harbChIP_1.22.0.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: 14 Package: HarmanData Version: 1.12.0 Depends: R (>= 3.2.3) Suggests: BiocGenerics, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: e556ea2db6907201425241a1251c4149 NeedsCompilation: no Title: Data for the Harman package Description: Datasets of accompany Harman, a PCA and constrained optimisation based technique. Contains three datasets: IMR90, Human lung fibroblast cells exposed to nitric oxide; NPM, an experiment to test skin penetration of metal oxide nanoparticles following topical application of sunscreens in non-pregnant mice; OLF; an experiment to gauge the response of human olfactory neurosphere-derived (hONS) cells to ZnO nanoparticles. biocViews: ExpressionData, MicroarrayData, ExperimentData, Homo_sapiens_Data, Mus_musculus_Data Author: Josh Bowden [aut], Jason Ross [aut, cre], Yalchin Oytam [aut] Maintainer: Jason Ross URL: http://www.bioinformatics.csiro.au/harman/ VignetteBuilder: knitr BugReports: https://github.com/JasonR055/Harman/issues git_url: https://git.bioconductor.org/packages/HarmanData git_branch: RELEASE_3_9 git_last_commit: 347e15d git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/HarmanData_1.12.0.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 dependencyCount: 0 Package: HarmonizedTCGAData Version: 1.6.0 Depends: R (>= 3.4.0) Imports: ExperimentHub Suggests: AnnotationHub, knitr, rmarkdown, igraph, survival, ANF, stats, testthat License: GPL-3 MD5sum: 90382d0b019354adb9ec7253737a1a5b NeedsCompilation: no Title: Processed Harmonized TCGA Data of Five Selected Cancer Types Description: This package contains the processed harmonized TCGA data of five cancer types used in "Tianle Ma and Aidong Zhang, Integrate Multi-omic Data Using Affinity Network Fusion (ANF) for Cancer Patient Clustering". biocViews: CancerData, ReproducibleResearch Author: Tianle Ma Maintainer: Tianle Ma VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/HarmonizedTCGAData git_branch: RELEASE_3_9 git_last_commit: 33184a7 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/HarmonizedTCGAData_1.6.0.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: 66 Package: HCAData Version: 1.0.0 Depends: R (>= 3.6), SingleCellExperiment Imports: ExperimentHub, AnnotationHub, HDF5Array, utils Suggests: knitr, rmarkdown, BiocStyle, scran (>= 1.11.4), scater, igraph, iSEE, testthat License: MIT + file LICENSE MD5sum: 1a28dbab85f7d88dc4d525dbdb7f6757 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 VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/HCAData git_branch: RELEASE_3_9 git_last_commit: 83c8a6a git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/HCAData_1.0.0.tar.gz vignettes: vignettes/HCAData/inst/doc/hcadata.html vignetteTitles: Accessing the Human Cell Atlas datasets hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HCAData/inst/doc/hcadata.R dependencyCount: 89 Package: HD2013SGI Version: 1.24.0 Depends: R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots, limma, vcd, LSD,EBImage Suggests: BiocStyle License: Artistic-2.0 MD5sum: bc5df4cfc33cf00def4c05aa6f6d78c9 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: Bernd Fischer SystemRequirements: GNU make git_url: https://git.bioconductor.org/packages/HD2013SGI git_branch: RELEASE_3_9 git_last_commit: f77d36a git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/HD2013SGI_1.24.0.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 dependencyCount: 66 Package: HDCytoData Version: 1.4.0 Depends: ExperimentHub, SummarizedExperiment, flowCore Imports: utils, methods Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 7e6294543c192c0a089c6eb1c6c406ce NeedsCompilation: no Title: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats Description: Data package containing a collection of high-dimensional cytometry benchmark datasets saved in SummarizedExperiment and flowSet Bioconductor object formats, including row and column metadata describing samples, cell populations (clusters), and protein markers. biocViews: ExperimentHub, ExperimentData, ExpressionData, FlowCytometryData, Homo_sapiens_Data, ImmunoOncologyData Author: Lukas M. Weber [aut, cre], Charlotte Soneson [aut] Maintainer: Lukas M. Weber URL: https://github.com/lmweber/HDCytoData VignetteBuilder: knitr BugReports: https://github.com/lmweber/HDCytoData/issues git_url: https://git.bioconductor.org/packages/HDCytoData git_branch: RELEASE_3_9 git_last_commit: 15c25d6 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/HDCytoData_1.4.0.tar.gz vignettes: vignettes/HDCytoData/inst/doc/HDCytoData.html vignetteTitles: HDCytoData data package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HDCytoData/inst/doc/HDCytoData.R dependencyCount: 95 Package: healthyFlowData Version: 1.22.0 Depends: R (>= 2.15.0), flowCore Imports: methods License: Artistic-2.0 MD5sum: e68c9638bbe2a477a0d8cf2b99d7fd3c NeedsCompilation: no Title: Healthy dataset used by the flowMatch package Description: A healthy dataset with 20 flow cytometry samples used by the flowMatch package. biocViews: FlowCytometryData Author: Ariful Azad Maintainer: Ariful Azad git_url: https://git.bioconductor.org/packages/healthyFlowData git_branch: RELEASE_3_9 git_last_commit: 2cef520 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/healthyFlowData_1.22.0.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 dependencyCount: 24 Package: HEEBOdata Version: 1.22.0 License: LGPL MD5sum: 76163c616e6f8e975962b0b0ad45da7f NeedsCompilation: no Title: HEEBO set and HEEBO controls. Description: R objects describing the HEEBO oligo set. biocViews: ExperimentData Author: Agnes Paquet Maintainer: Agnes Paquet URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/ git_url: https://git.bioconductor.org/packages/HEEBOdata git_branch: RELEASE_3_9 git_last_commit: fd6a824 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/HEEBOdata_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: HelloRangesData Version: 1.10.0 Suggests: BiocStyle License: GPL (>= 2) MD5sum: 25607b151c01f459bf0673a7a1fe6ea7 NeedsCompilation: no Title: Data for the HelloRanges tutorial vignette Description: Provides the data that were used in the bedtools tutorial by Aaron Quinlan (http://quinlanlab.org/tutorials/bedtools/bedtools.html). Includes a subset of the DnaseI hypersensitivity data from "Maurano et al. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA. Science. 2012. Vol. 337 no. 6099 pp. 1190-1195." The rest of the tracks were originally downloaded from the UCSC table browser. See the HelloRanges vignette for a port of the bedtools tutorial to R. biocViews: ExperimentData, SequencingData Author: Michael Lawrence Maintainer: Michael Lawrence git_url: https://git.bioconductor.org/packages/HelloRangesData git_branch: RELEASE_3_9 git_last_commit: 1226463 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/HelloRangesData_1.10.0.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 dependencyCount: 0 Package: hgu133abarcodevecs Version: 1.22.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: c3a80fbd654d19c76355f818e4e19b24 NeedsCompilation: no Title: hgu133a data for barcode Description: Data used by the barcode package for microarrays of type hgu133a. biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/hgu133abarcodevecs git_branch: RELEASE_3_9 git_last_commit: 21fa378 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/hgu133abarcodevecs_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hgu133plus2barcodevecs Version: 1.22.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 48c436478b8b6da87385b0d4f8d3e205 NeedsCompilation: no Title: hgu133plus2 data for barcode Description: Data used by the barcode package for microarrays of type hgu133plus2. biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/hgu133plus2barcodevecs git_branch: RELEASE_3_9 git_last_commit: 29d57d8 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/hgu133plus2barcodevecs_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: hgu133plus2CellScore Version: 1.4.0 Depends: R (>= 3.5.0) Imports: Biobase (>= 2.39.1) Suggests: knitr License: GPL-3 MD5sum: db5ad2756c518d14e1f2ed55e3794d16 NeedsCompilation: no Title: CellScore Standard Cell Types Expression Dataset [hgu133plus2] Description: The CellScore Standard Dataset contains expression data from a wide variety of human cells and tissues, which should be used as standard cell types in the calculation of the CellScore. All data was curated from public databases such as Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) or ArrayExpress (https://www.ebi.ac.uk/arrayexpress/). This standard dataset only contains data from the Affymetrix GeneChip Human Genome U133 Plus 2.0 microarrays. Samples were manually annotated using the database information or consulting the publications in which the datasets originated. The sample annotations are stored in the phenoData slot of the expressionSet object. Raw data (CEL files) were processed with the affy package to generate present/absent calls (mas5calls) and background-subtracted values, which were then normalized by the R-package yugene to yield the final expression values for the standard expression matrix. The annotation table for the microarray was retrieved from the BioC annotation package hgu133plus2. All data are stored in an expressionSet object. biocViews: ExpressionData, MicroarrayData, GEO, ExperimentData, Homo_sapiens_Data, Genome, ArrayExpress Author: Nancy Mah, Katerina Taskova Maintainer: Nancy Mah VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/hgu133plus2CellScore git_branch: RELEASE_3_9 git_last_commit: bedff70 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/hgu133plus2CellScore_1.4.0.tar.gz vignettes: vignettes/hgu133plus2CellScore/inst/doc/hgu133plus2Vignette.pdf vignetteTitles: R packages: hgu133plus2CellScore hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/hgu133plus2CellScore/inst/doc/hgu133plus2Vignette.R dependencyCount: 7 Package: hgu2beta7 Version: 1.24.0 Depends: R (>= 2.0.0) License: Artistic-2.0 MD5sum: 26d4ad63ca4429968dbdd8d981436c13 NeedsCompilation: no Title: A data package containing annotation data for hgu2beta7 Description: Annotation data file for hgu2beta7 assembled using data from public data repositories biocViews: Genome Author: Chenwei Lin Maintainer: Bioconductor Package Maintainer git_url: https://git.bioconductor.org/packages/hgu2beta7 git_branch: RELEASE_3_9 git_last_commit: ccf1553 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/hgu2beta7_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: HiCDataHumanIMR90 Version: 1.4.0 Depends: R (>= 2.10) Suggests: HiTC License: GPL-3 MD5sum: d7687765d6d2bee5988b52c927a1c6c3 NeedsCompilation: no Title: Human IMR90 Fibroblast HiC data from Dixon et al. 2012 Description: The HiC data from Human Fibroblast IMR90 cell line (HindIII restriction) was retrieved from the GEO website, accession number GSE35156 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35156). The raw reads were processed as explained in Dixon et al. (Nature 2012). biocViews: ExperimentData, Genome, Homo_sapiens_Data, GEO Author: Nicolas Servant Maintainer: Nicolas Servant git_url: https://git.bioconductor.org/packages/HiCDataHumanIMR90 git_branch: RELEASE_3_9 git_last_commit: ee3261b git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/HiCDataHumanIMR90_1.4.0.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 dependencyCount: 0 Package: HiCDataLymphoblast Version: 1.20.0 Suggests: GOTHiC, ShortRead License: GPL-3 MD5sum: 6b12b6d3851d638acdab1a15a9225b92 NeedsCompilation: no Title: Human lymphoblastoid HiC data from Lieberman-Aiden et al. 2009 Description: The HiC data from human lymphoblastoid cell line (HindIII restriction) was retrieved from the sequence read archive and two ends of the paired reads were aligned separately with bowtie. biocViews: ExperimentData, Homo_sapiens_Data Author: Borbala Mifsud Maintainer: Borbala Mifsud git_url: https://git.bioconductor.org/packages/HiCDataLymphoblast git_branch: RELEASE_3_9 git_last_commit: 8dd6cc1 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/HiCDataLymphoblast_1.20.0.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 dependencyCount: 0 Package: Hiiragi2013 Version: 1.20.0 Depends: R (>= 3.0.0), affy, Biobase, boot, clue, cluster, genefilter, geneplotter, gplots, gtools, KEGGREST, MASS, mouse4302.db, RColorBrewer, xtable Imports: grid, lattice, latticeExtra Suggests: ArrayExpress, BiocStyle License: Artistic-2.0 MD5sum: c8382abd59d8f36b4ab89b63d0a7a438 NeedsCompilation: no Title: Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages Description: This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881." biocViews: ExperimentData, MicroarrayData, qPCRData, ReproducibleResearch Author: Andrzej Oles, Wolfgang Huber Maintainer: Andrzej Oles git_url: https://git.bioconductor.org/packages/Hiiragi2013 git_branch: RELEASE_3_9 git_last_commit: be529e0 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/Hiiragi2013_1.20.0.tar.gz vignettes: vignettes/Hiiragi2013/inst/doc/Hiiragi2013.pdf vignetteTitles: Hiiragi2013 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Hiiragi2013/inst/doc/Hiiragi2013.R dependencyCount: 75 Package: HIVcDNAvantWout03 Version: 1.24.0 License: GPL (>= 2) MD5sum: 3978039dba5000fa5456c7fac8082002 NeedsCompilation: no Title: T cell line infections with HIV-1 LAI (BRU) Description: The expression levels of approximately 4600 cellular RNA transcripts were assessed in CD4+ T cell lines at different times after infection with HIV-1BRU using DNA microarrays. This data corresponds to the first block of a 12 block array image (001030_08_1.GEL) in the first data set (2000095918 A) in the first experiment (CEM LAI vs HI-LAI 24hr). There are two data sets, which are part of a dye-swap experiment with replicates, representing the Cy3 (green) absorption intensities for channel 1 (hiv1raw) and the Cy5 (red) absorption intensities for channel 2 (hiv2raw). biocViews: ExperimentData, MicroarrayData, TwoChannelData, HIVData Author: Dr. Angelique van't Wout, Department of Microbiology, University of Washington Maintainer: Chris Fraley URL: http://expression.microslu.washington.edu/expression/vantwoutjvi2002.html git_url: https://git.bioconductor.org/packages/HIVcDNAvantWout03 git_branch: RELEASE_3_9 git_last_commit: 79b5295 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/HIVcDNAvantWout03_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: HMP16SData Version: 1.4.1 Depends: R (>= 3.6.0), SummarizedExperiment Imports: AnnotationHub, assertthat, dplyr, ExperimentHub, kableExtra, knitr, magrittr, methods, readr, S4Vectors, tibble, utils Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, circlize, covr, cowplot, curatedMetagenomicData, dendextend, devtools, ggplot2, gridExtra, haven, phyloseq, rmarkdown, roxygen2, stats, testthat License: Artistic-2.0 MD5sum: a0bd3005be9fff33b7c6e07ba303664f 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 , Rimsha Azhar , Marcel Ramos , Ludwig Geistlinger , Levi Waldron Maintainer: Lucas Schiffer URL: https://github.com/waldronlab/HMP16SData VignetteBuilder: knitr BugReports: https://github.com/waldronlab/HMP16SData/issues git_url: https://git.bioconductor.org/packages/HMP16SData git_branch: RELEASE_3_9 git_last_commit: dacb5ae git_last_commit_date: 2019-05-21 Date/Publication: 2019-05-23 source.ver: src/contrib/HMP16SData_1.4.1.tar.gz vignettes: vignettes/HMP16SData/inst/doc/HMP16SData.html vignetteTitles: HMP16SData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HMP16SData/inst/doc/HMP16SData.R dependencyCount: 113 Package: hmyriB36 Version: 1.20.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.5.5), GGBase Suggests: GGtools, illuminaHumanv1.db License: Artistic-2.0 MD5sum: e08284e8555bcedcdbdb4b1aa677b748 NeedsCompilation: no Title: YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes Description: YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes biocViews: ExperimentData, Genome, SNPData, HapMap Author: Vincent Carey Maintainer: Vincent Carey git_url: https://git.bioconductor.org/packages/hmyriB36 git_branch: RELEASE_3_9 git_last_commit: f100098 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/hmyriB36_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 61 Package: HSMMSingleCell Version: 1.4.0 Depends: R (>= 2.10) License: Artistic-2.0 MD5sum: 8ee141b0de4637baf95d871cb0ff163b NeedsCompilation: no Title: Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM) Description: Skeletal myoblasts undergo a well-characterized sequence of morphological and transcriptional changes during differentiation. In this experiment, primary human skeletal muscle myoblasts (HSMM) were expanded under high mitogen conditions (GM) and then differentiated by switching to low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several hundred cells taken over a time-course of serum-induced differentiation. Between 49 and 77 cells were captured at each of four time points (0, 24, 48, 72 hours) following serum switch using the Fluidigm C1 microfluidic system. RNA from each cell was isolated and used to construct mRNA-Seq libraries, which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell. biocViews: ExperimentData, RNASeqData Author: Cole Trapnell Maintainer: Cole Trapnell git_url: https://git.bioconductor.org/packages/HSMMSingleCell git_branch: RELEASE_3_9 git_last_commit: 8f4e03a git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/HSMMSingleCell_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: HumanAffyData Version: 1.10.0 Depends: ExperimentHub, Biobase, R (>= 3.3) Suggests: BiocStyle License: Artistic-2.0 MD5sum: d013a2b88fb9a47ff7cd962099c6fd28 NeedsCompilation: no Title: GEO accession GSE64985 and ArrayExpress accession E-MTAB-62 as ExpressionSet objects Description: Re-analysis of human gene expression data generated on the Affymetrix HG_U133PlusV2 (EH176) and Affymetrix HG_U133A (EH177) platforms. The original data were normalized using robust multiarray averaging (RMA) to obtain an integrated gene expression atlas across diverse biological sample types and conditions. The entire compendia comprisee 9395 arrays for EH176 and 5372 arrays for EH177. biocViews: ExperimentData, GEO, ArrayExpress, Homo_sapiens_Data, MicroarrayData, ExpressionData Author: Brad Nelms Maintainer: Brad Nelms git_url: https://git.bioconductor.org/packages/HumanAffyData git_branch: RELEASE_3_9 git_last_commit: a228f0f git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/HumanAffyData_1.10.0.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 dependencyCount: 66 Package: humanStemCell Version: 0.24.0 Depends: Biobase (>= 2.5.5), hgu133plus2.db License: Artistic-2.0 MD5sum: c4dd3efd3d8f2024250bf8f0f0610e1b NeedsCompilation: no Title: Human Stem Cells time course experiment Description: Affymetrix time course experiment on human stem cells (two time points: undifferentiated and differentiated). biocViews: ExperimentData, Homo_sapiens_Data Author: R. Gentleman, N. Le Meur, M. Tewari Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/humanStemCell git_branch: RELEASE_3_9 git_last_commit: d4f8e14 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/humanStemCell_0.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 34 Package: IHWpaper Version: 1.12.0 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, pasilla, DESeq, locfdr, tidyr, ggbio, latex2exp License: Artistic-2.0 MD5sum: e697c090241b0d3437827f2f375a4fcf NeedsCompilation: yes Title: Reproduce figures in IHW paper Description: This package conveniently wraps all functions needed to reproduce the figures in the IHW paper (https://www.nature.com/articles/nmeth.3885) and the latest arXiv preprint available under http://arxiv.org/abs/1701.05179. Thus it is a companion package to the Bioconductor IHW package. biocViews: ReproducibleResearch, ExperimentData, RNASeqData, ExpressionData Author: Nikos Ignatiadis [aut, cre] Maintainer: Nikos Ignatiadis VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/IHWpaper git_branch: RELEASE_3_9 git_last_commit: 18edf06 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/IHWpaper_1.12.0.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/IHW_censoring_storey_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", "Stats paper: IHW-censoring & Storey 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/IHW_censoring_storey_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: 120 Package: Illumina450ProbeVariants.db Version: 1.20.0 Depends: R (>= 3.0.1) License: GPL-3 MD5sum: 248d5c2f16cab95dafd3af53acd1b05f NeedsCompilation: no Title: Annotation Package combining variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes Description: Includes details on variants for each probe on the 450k bead chip for each of the four populations (Asian, American, African and European) biocViews: Homo_sapiens_Data, CancerData, ChipOnChipData, SNPData Author: Lee Butcher Maintainer: Tiffany Morris git_url: https://git.bioconductor.org/packages/Illumina450ProbeVariants.db git_branch: RELEASE_3_9 git_last_commit: 7561fb0 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/Illumina450ProbeVariants.db_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: IlluminaDataTestFiles Version: 1.22.0 License: Artistic-2.0 MD5sum: 546621b97e6be804d7e9db2262d4469e NeedsCompilation: no Title: Illumina microarray files (IDAT) for testing Description: Example data for Illumina microarray output files, for testing purposes biocViews: MicroarrayData Author: Kasper Daniel Hansen, Mike L. Smith Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/IlluminaDataTestFiles git_branch: RELEASE_3_9 git_last_commit: 2b88bcf git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/IlluminaDataTestFiles_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: ITALICSData Version: 2.22.0 Depends: R (>= 2.0.0) License: GPL MD5sum: 20e86e82a58cd3beddddf7ebd31f649b NeedsCompilation: no Title: ITALICSData Description: Data needed to use the ITALICS package biocViews: ExperimentData, HapMap Author: Guillem Rigaill Maintainer: Guillem Rigaill URL: http://bioinfo.curie.fr git_url: https://git.bioconductor.org/packages/ITALICSData git_branch: RELEASE_3_9 git_last_commit: 1ddce0c git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ITALICSData_2.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: Iyer517 Version: 1.26.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 22360bdd418629479e66c15026f99c7b NeedsCompilation: no Title: exprSets for Iyer, Eisen et all 1999 Science paper Description: representation of public Iyer data from http://genome-www.stanford.edu/serum/clusters.html biocViews: ExperimentData Author: Vishy Iyer Maintainer: Vince Carey git_url: https://git.bioconductor.org/packages/Iyer517 git_branch: RELEASE_3_9 git_last_commit: 8c790cf git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/Iyer517_1.26.0.tar.gz vignettes: vignettes/Iyer517/inst/doc/Iyer517.pdf vignetteTitles: Iyer517 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Iyer517/inst/doc/Iyer517.R dependencyCount: 7 Package: JASPAR2014 Version: 1.20.0 Depends: R (>= 3.0.1), methods, Biostrings (>= 2.29.19) License: GPL-2 MD5sum: 4e907b35b06421d73433cc13987ddb9a NeedsCompilation: no Title: Data package for JASPAR Description: Data package for JASPAR 2014. To search this databases, please use the package TFBSTools. biocViews: ExperimentData, SequencingData Author: Ge Tan Maintainer: Ge Tan URL: http://jaspar.genereg.net/ git_url: https://git.bioconductor.org/packages/JASPAR2014 git_branch: RELEASE_3_9 git_last_commit: 843fe41 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/JASPAR2014_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 12 Package: JASPAR2016 Version: 1.12.0 Depends: R (>= 3.2.2), methods License: GPL-2 MD5sum: 010a850897534622a73f91dedb64dc4e NeedsCompilation: no Title: Data package for JASPAR 2016 Description: Data package for JASPAR 2016. To search this databases, please use the package TFBSTools (>= 1.8.1). biocViews: ExperimentData, MotifAnnotation, GeneRegulation Author: Ge Tan Maintainer: Ge Tan URL: http://jaspar.genereg.net/ git_url: https://git.bioconductor.org/packages/JASPAR2016 git_branch: RELEASE_3_9 git_last_commit: 98ff5b4 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/JASPAR2016_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 1 Package: JctSeqData Version: 1.14.0 Depends: R (>= 3.3) Suggests: knitr, BiocStyle, DESeq2, DEXSeq, edgeR, JunctionSeq License: file LICENSE MD5sum: 26cbe5468815dbc5bb9d0e86c90cb88d NeedsCompilation: no Title: Example Junction Count data for use with JunctionSeq Description: Junction count data from an example dataset taken from a subset of the RNA-seq reads from six samples. Data was subsampled and modified to provide edge cases for testing and to reduce file sizes. biocViews: Rattus_norvegicus_Data, ExperimentData, Genome, RNASeqData, RepositoryData, GEO Author: Stephen Hartley [aut, cre] (PhD) Maintainer: Stephen Hartley URL: http://hartleys.github.io/JunctionSeq/ VignetteBuilder: knitr BugReports: http://github.com/hartleys/JunctionSeq/issues git_url: https://git.bioconductor.org/packages/JctSeqData git_branch: RELEASE_3_9 git_last_commit: 39064c8 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/JctSeqData_1.14.0.tar.gz vignettes: vignettes/JctSeqData/inst/doc/JunctionSeqExampleData.pdf vignetteTitles: Example Walkthrough hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: KEGGandMetacoreDzPathwaysGEO Version: 1.4.0 Depends: R (>= 2.15.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: 7d61c7d151e5cb9b955199a4b184a761 NeedsCompilation: no Title: Disease Datasets from GEO Description: This is a collection of 18 data sets for which the phenotype is a disease with a corresponding pathway in either KEGG or metacore database.This collection of datasets were used as gold standard in comparing gene set analysis methods. biocViews: ExperimentData, GEO Author: Gaurav Bhatti Maintainer: Gaurav Bhatti git_url: https://git.bioconductor.org/packages/KEGGandMetacoreDzPathwaysGEO git_branch: RELEASE_3_9 git_last_commit: 9da26df git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/KEGGandMetacoreDzPathwaysGEO_1.4.0.tar.gz vignettes: vignettes/KEGGandMetacoreDzPathwaysGEO/inst/doc/KEGGandMetacoreDzPathwaysGEO.pdf vignetteTitles: KEGGandMetacoreDzPathwaysGEO Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/KEGGandMetacoreDzPathwaysGEO/inst/doc/KEGGandMetacoreDzPathwaysGEO.R dependencyCount: 7 Package: KEGGdzPathwaysGEO Version: 1.22.0 Depends: R (>= 2.13.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: 89a8755fa8639a60b631b1f72336e98f NeedsCompilation: no Title: KEGG Disease Datasets from GEO Description: This is a collection of 24 data sets for which the phenotype is a disease with a corresponding pathway in the KEGG database.This collection of datasets were used as gold standard in comparing gene set analysis methods by the PADOG package. biocViews: MicroarrayData, GEO, ExperimentData Author: Gaurav Bhatti, Adi L. Tarca Maintainer: Gaurav Bhatti git_url: https://git.bioconductor.org/packages/KEGGdzPathwaysGEO git_branch: RELEASE_3_9 git_last_commit: a161670 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/KEGGdzPathwaysGEO_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: kidpack Version: 1.26.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5) License: GPL-2 MD5sum: 380a3108979f90114e23c9756fb10bd0 NeedsCompilation: no Title: DKFZ kidney package Description: kidney microarray data biocViews: ExperimentData, CancerData, KidneyCancerData, MicroarrayData, ArrayExpress Author: Wolfgang Huber Maintainer: Wolfgang Huber URL: http://www.dkfz.de/mga git_url: https://git.bioconductor.org/packages/kidpack git_branch: RELEASE_3_9 git_last_commit: 786c887 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/kidpack_1.26.0.tar.gz vignettes: vignettes/kidpack/inst/doc/kidpack.pdf vignetteTitles: kidpack - overview over the DKFZ kidney data package hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/kidpack/inst/doc/kidpack.R dependencyCount: 7 Package: KOdata Version: 1.10.0 Depends: R (>= 3.3.0) License: MIT + file LICENSE MD5sum: 4decbccf4763a957a56256bf026fd955 NeedsCompilation: no Title: LINCS Knock-Out Data Package Description: Contains consensus genomic signatures (CGS) for experimental cell-line specific gene knock-outs as well as baseline gene expression data for a subset of experimental cell-lines. Intended for use with package KEGGlincs. biocViews: ExpressionData, CancerData, Homo_sapiens_Data Author: Shana White Maintainer: Shana White git_url: https://git.bioconductor.org/packages/KOdata git_branch: RELEASE_3_9 git_last_commit: 58c1fbc git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/KOdata_1.10.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: leeBamViews Version: 1.20.0 Depends: R (>= 2.15.0), Biobase, Rsamtools (>= 0.1.50), BSgenome Imports: GenomicRanges, GenomicAlignments, methods Suggests: GenomeGraphs, biomaRt, org.Sc.sgd.db, edgeR Enhances: multicore License: Artistic 2.0 MD5sum: 6e912f317ff209d059e12093b2816993 NeedsCompilation: no Title: leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009 Description: data from PMID 19096707; prototype for managing multiple NGS samples biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData, SNPData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/leeBamViews git_branch: RELEASE_3_9 git_last_commit: e25ae04 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/leeBamViews_1.20.0.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 dependencyCount: 39 Package: leukemiasEset Version: 1.20.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: d8ae541fe7fb33d22bff4cbf35d73a2c NeedsCompilation: no Title: Leukemia's microarray gene expression data (expressionSet). Description: Expressionset containing gene expresion data from 60 bone marrow samples of patients with one of the four main types of leukemia (ALL, AML, CLL, CML) or non-leukemia. biocViews: Tissue, Genome, Homo_sapiens_Data, CancerData, LeukemiaCancerData, MicroarrayData, ChipOnChipData, TissueMicroarrayData, GEO Author: Sara Aibar, Celia Fontanillo and Javier De Las Rivas. Bioinformatics and Functional Genomics Group. Cancer Research Center (CiC-IBMCC, CSIC/USAL). Salamanca. Spain. Maintainer: Sara Aibar git_url: https://git.bioconductor.org/packages/leukemiasEset git_branch: RELEASE_3_9 git_last_commit: 9b4e280 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/leukemiasEset_1.20.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: LiebermanAidenHiC2009 Version: 0.22.0 Depends: KernSmooth, IRanges License: LGPL MD5sum: f5bbf8ccf81d37918ff8ab7d55d8c5cc NeedsCompilation: no Title: Selected data from the HiC paper of E. Lieberman-Aiden et al. in Science (2009) Description: This package provides data that were presented in the article "Comprehensive mapping of long-range interactions reveals folding principles of the human genome", Science 2009 Oct 9;326(5950):289-93. PMID: 19815776 biocViews: ExperimentData, Genome, SequencingData, DNASeqData, ChIPSeqData, miRNAData, SmallRNAData, ChipOnChipData, GEO, NCI, ENCODE Author: Wolfgang Huber, Felix Klein Maintainer: Felix Klein git_url: https://git.bioconductor.org/packages/LiebermanAidenHiC2009 git_branch: RELEASE_3_9 git_last_commit: 1f8743b git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/LiebermanAidenHiC2009_0.22.0.tar.gz vignettes: vignettes/LiebermanAidenHiC2009/inst/doc/LiebermanAidenHiC2009.pdf vignetteTitles: Exploration of HiC data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/LiebermanAidenHiC2009/inst/doc/LiebermanAidenHiC2009.R dependencyCount: 10 Package: ListerEtAlBSseq Version: 1.16.0 Depends: R (>= 3.1.1), methylPipe Suggests: BSgenome.Hsapiens.UCSC.hg18 License: Artistic 2.0 MD5sum: 65a04e46b826417c971c461fa1599ba2 NeedsCompilation: no Title: BS-seq data of H1 and IMR90 cell line excerpted from Lister et al. 2009 Description: Base resolution bisulfite sequencing data of Human DNA methylomes biocViews: ExperimentData, Homo_sapiens_Data, SequencingData Author: Kamal Kishore Maintainer: Kamal Kishore git_url: https://git.bioconductor.org/packages/ListerEtAlBSseq git_branch: RELEASE_3_9 git_last_commit: bb169d0 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ListerEtAlBSseq_1.16.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 134 Package: lumiBarnes Version: 1.24.0 Depends: R (>= 2.0), Biobase (>= 2.5.5), lumi (>= 1.1.0) License: LGPL MD5sum: b611fcdaf9f3f878f2122a2a67fe946a NeedsCompilation: no Title: Barnes Benchmark Illumina Tissues Titration Data Description: The Barnes benchmark dataset can be used to evaluate the algorithms for Illumina microarrays. It measured a titration series of two human tissues, blood and placenta, and includes six samples with the titration ratio of blood and placenta as 100:0, 95:5, 75:25, 50:50, 25:75 and 0:100. The samples were hybridized on HumanRef-8 BeadChip (Illumina, Inc) in duplicate. The data is loaded as an LumiBatch Object (see documents in the lumi package). biocViews: ExperimentData, Tissue, MicroarrayData, ChipOnChipData Author: Pan Du Maintainer: Pan Du git_url: https://git.bioconductor.org/packages/lumiBarnes git_branch: RELEASE_3_9 git_last_commit: 6fd2b3a git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/lumiBarnes_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 145 Package: LungCancerACvsSCCGEO Version: 1.20.0 Depends: R (>= 2.15.0) License: GPL-2 MD5sum: 4a61ccf290a9409dc3126805139c4577 NeedsCompilation: no Title: A lung cancer dataset that can be used with maPredictDSC package for developing outcome prediction models from Affymetrix CEL files. Description: This package contains 30 Affymetrix CEL files for 7 Adenocarcinoma (AC) and 8 Squamous cell carcinoma (SCC) lung cancer samples taken at random from 3 GEO datasets (GSE10245, GSE18842 and GSE2109) and other 15 samples from a dataset produced by the organizers of the IMPROVER Diagnostic Signature Challenge available from GEO (GSE43580). biocViews: CancerData, LungCancerData, MicroarrayData, GEO Author: Adi Laurentiu Tarca Maintainer: Adi Laurentiu Tarca URL: http://bioinformaticsprb.med.wayne.edu/ git_url: https://git.bioconductor.org/packages/LungCancerACvsSCCGEO git_branch: RELEASE_3_9 git_last_commit: 4e49240 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/LungCancerACvsSCCGEO_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: LungCancerLines Version: 0.22.0 Imports: Rsamtools License: Artistic-2.0 MD5sum: 96f8ced18a07cd538b51bd1d9bf5f50a NeedsCompilation: no Title: Reads from Two Lung Cancer Cell Lines Description: Reads from an RNA-seq experiment between two lung cancer cell lines: H1993 (met) and H2073 (primary). The reads are stored as Fastq files and are meant for use with the TP53Genome object in the gmapR package. biocViews: ExperimentData, Genome, CancerData, LungCancerData, RNASeqData Author: Cory Barr, Michael Lawrence Maintainer: Cory Barr git_url: https://git.bioconductor.org/packages/LungCancerLines git_branch: RELEASE_3_9 git_last_commit: d8a5a56 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/LungCancerLines_0.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 26 Package: lungExpression Version: 0.22.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: ca0abb60a770427af34dbe8f5498effc NeedsCompilation: no Title: ExpressionSets for Parmigiani et al., 2004 Clinical Cancer Research paper Description: Data from three large lung cancer studies provided as ExpressionSets biocViews: ExperimentData, CancerData, LungCancerData Author: Robert Scharpf , Simens Zhong , Giovanni Parmigiani Maintainer: Robert Scharpf git_url: https://git.bioconductor.org/packages/lungExpression git_branch: RELEASE_3_9 git_last_commit: c6f17f9 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/lungExpression_0.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: lydata Version: 1.10.0 License: MIT + file LICENSE MD5sum: ddb7b13ac19ac940d615d9cb7ff14770 NeedsCompilation: no Title: Example Dataset for crossmeta Package Description: Raw data downloaded from GEO for the compound LY294002. Raw data is from multiple platforms from Affymetrix and Illumina. This data is used to illustrate the cross-platform meta-analysis of microarray data using the crossmeta package. biocViews: ExperimentData, MicroarrayData Author: Alex Pickering Maintainer: Alex Pickering git_url: https://git.bioconductor.org/packages/lydata git_branch: RELEASE_3_9 git_last_commit: 7d2ec80 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/lydata_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: M3DExampleData Version: 1.10.0 Depends: R (>= 3.3) License: GPL (>=2) MD5sum: ddaac0734044e83b21ecf67eb3532eb7 NeedsCompilation: no Title: M3Drop Example Data Description: Example data for M3Drop package. biocViews: Mus_musculus_Data, RNASeqData, ExpressionData, GEO, Tissue, ExperimentData Author: Tallulah Andrews Maintainer: Tallulah Andrews git_url: https://git.bioconductor.org/packages/M3DExampleData git_branch: RELEASE_3_9 git_last_commit: 128091d git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/M3DExampleData_1.10.0.tar.gz hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: macrophage Version: 1.0.0 Suggests: knitr License: GPL (>= 2) MD5sum: 323708aa316444965821e5662ef2ee7d NeedsCompilation: no Title: Human macrophage immune response Description: This package provides the output of running Salmon on a set of 24 RNA-seq samples from Alasoo, et al. "Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response", published in Nature Genetics, January 2018. For details on version numbers and how the samples were processed see the package vignette. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/macrophage git_branch: RELEASE_3_9 git_last_commit: 1fb3e6d git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/macrophage_1.0.0.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 dependencyCount: 0 Package: mammaPrintData Version: 1.20.0 Depends: R (>= 2.13.0) Suggests: Biobase, gdata, limma License: Artistic-2.0 MD5sum: 12cc4c98823e833df14c94a612bddad9 NeedsCompilation: no Title: RGLists from the Glas and Buyse breast cancer studies Description: Gene expression data for the two breast cancer cohorts published by Glas and Buyse in 2006. This cohorts were used to implement and validate the mammaPrint breast cancer test. biocViews: ExperimentData, ExpressionData, CancerData, BreastCancerData, MicroarrayData, TwoChannelData Author: Luigi Marchionni Maintainer: Luigi Marchionni URL: http://luigimarchionni.org/breastTSP.html git_url: https://git.bioconductor.org/packages/mammaPrintData git_branch: RELEASE_3_9 git_last_commit: 2f40efb git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/mammaPrintData_1.20.0.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: 1.16.0 Depends: R (>= 3.2.0) Suggests: Biobase License: Artistic-2.0 MD5sum: 9a0bc0eb61a441595cbe17308a2c7d7c NeedsCompilation: no Title: Gene expression data for testing of the package mAPKL. Description: Gene expression data from a breast cancer study published by Turashvili et al. in 2007, provided as an eSet. biocViews: ExperimentData, ExpressionData, Cancer, Breast Author: Argiris Sakellariou Maintainer: Argiris Sakellariou git_url: https://git.bioconductor.org/packages/mAPKLData git_branch: RELEASE_3_9 git_last_commit: 82589c6 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/mAPKLData_1.16.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: maqcExpression4plex Version: 1.28.0 Suggests: oligo, pdInfoBuilder License: GPL MD5sum: fa9ecd1de4f0ee49935ea8620c3605e2 NeedsCompilation: no Title: Sample Expression Data - MAQC / HG18 - NimbleGen Description: Data from human (HG18) 4plex NimbleGen array. It has 24k genes with 3 60mer probes per gene. biocViews: ExperimentData, CancerData Author: NimbleGen Systems Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/maqcExpression4plex git_branch: RELEASE_3_9 git_last_commit: 73b4dc7 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/maqcExpression4plex_1.28.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: MAQCsubset Version: 1.22.0 Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), lumi, methods Suggests: genefilter, codelink License: Artistic-2.0 MD5sum: 97b078cd701d3c46e2ad4342570b7e51 NeedsCompilation: no Title: Experimental Data Package: MAQCsubset Description: Data Package automatically created on Sun Nov 19 15:59:29 2006. biocViews: ExperimentData, MicroarrayData, GEO Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/MAQCsubset git_branch: RELEASE_3_9 git_last_commit: 0c15933 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/MAQCsubset_1.22.0.tar.gz vignettes: vignettes/MAQCsubset/inst/doc/maqcNotes.pdf vignetteTitles: MAQC notes hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MAQCsubset/inst/doc/maqcNotes.R dependencyCount: 145 Package: MAQCsubsetAFX Version: 1.22.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: c361d50c4fa96fe0fb4a8fa47f5b1522 NeedsCompilation: no Title: MAQC data subset for the Affymetrix platform Description: MAQC data subset for the Affymetrix platform biocViews: ExperimentData, Genome, Homo_sapiens_Data, MicroarrayData Author: Laurent Gatto Maintainer: Laurent Gatto git_url: https://git.bioconductor.org/packages/MAQCsubsetAFX git_branch: RELEASE_3_9 git_last_commit: bfdd142 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/MAQCsubsetAFX_1.22.0.tar.gz vignettes: vignettes/MAQCsubsetAFX/inst/doc/MAQCsubsetAFX.pdf vignetteTitles: MAQCsubsetAFX: MAQC data subset for the Affymetrix platform hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MAQCsubsetAFX/inst/doc/MAQCsubsetAFX.R dependencyCount: 13 Package: MAQCsubsetILM Version: 1.22.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), lumi License: Artistic-2.0 MD5sum: 29ec94614e117e09ca659d61b071618b NeedsCompilation: no Title: MAQC data subset for the Illumina platform Description: MAQC data subset for the Illumina platform biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData Author: Laurent Gatto Maintainer: Laurent Gatto git_url: https://git.bioconductor.org/packages/MAQCsubsetILM git_branch: RELEASE_3_9 git_last_commit: 48cae95 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/MAQCsubsetILM_1.22.0.tar.gz vignettes: vignettes/MAQCsubsetILM/inst/doc/MAQCsubsetILM.pdf vignetteTitles: MAQCsubsetILM: MAQC data subset for the Illumina platform hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MAQCsubsetILM/inst/doc/MAQCsubsetILM.R dependencyCount: 145 Package: mCSEAdata Version: 1.4.0 Depends: R (>= 3.5) Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 2ababb1156ca58b2075b8a78841f2d7b NeedsCompilation: no Title: Data package for mCSEA package Description: Data objects necessary to some mCSEA package functions. There are also example data objects to illustrate mCSEA package functionality. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData, ExperimentData Author: Jordi Martorell Marugán Maintainer: Jordi Martorell Marugán VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mCSEAdata git_branch: RELEASE_3_9 git_last_commit: e92e0db git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/mCSEAdata_1.4.0.tar.gz vignettes: vignettes/mCSEAdata/inst/doc/mCSEAdata.pdf vignetteTitles: Data for mCSEA package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mCSEAdata/inst/doc/mCSEAdata.R dependencyCount: 0 Package: mcsurvdata Version: 1.2.0 Depends: R (>= 3.5), ExperimentHub Imports: AnnotationHub, Biobase Suggests: knitr License: GPL (>=2) MD5sum: 3e2204677f27ed5f9a47551a24963bdd NeedsCompilation: no Title: Meta cohort survival data Description: This package stores two merged expressionSet objects that contain the gene expression profile and clinical information of -a- six breast cancer cohorts and -b- four colorectal cancer cohorts. Breast cancer data are employed in the vignette of the hrunbiased package for survival analysis of gene signatures. biocViews: ExperimentData, Homo_sapiens_Data, GEO, MicroarrayData Author: Adria Caballe Mestres [aut, cre], Antoni Berenguer Llergo [aut], Camille Stephan-Otto Attolini [aut] Maintainer: Adria Caballe Mestres URL: https://github.com/adricaba/mcsurvdata VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mcsurvdata git_branch: RELEASE_3_9 git_last_commit: 4b4fbce git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/mcsurvdata_1.2.0.tar.gz vignettes: vignettes/mcsurvdata/inst/doc/mcsurvdata.html vignetteTitles: analysis vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mcsurvdata/inst/doc/mcsurvdata.R dependencyCount: 66 Package: MEDIPSData Version: 1.20.0 Depends: R (>= 2.15.0) License: GPL (>= 2) MD5sum: 1f78f8ed24c8c17f2ceb8847a7b05ec1 NeedsCompilation: no Title: Example data for MEDIPS and QSEA packages Description: Example data for MEDIPS and QSEA packages, consisting of chromosome 22 MeDIP and control/Input sample data. Additionally, the package contains MeDIP seq data from 3 NSCLC samples and adjacent normal tissue (chr 20-22). All data has been aligned to human genome hg19. biocViews: ExperimentData, Genome, SequencingData Author: Lukas Chavez Maintainer: Lukas Chavez git_url: https://git.bioconductor.org/packages/MEDIPSData git_branch: RELEASE_3_9 git_last_commit: 32c9b1a git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/MEDIPSData_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: MEEBOdata Version: 1.22.0 License: LGPL MD5sum: 95cc758068d87d1b741390a5e0b5a30c NeedsCompilation: no Title: MEEBO set and MEEBO controls. Description: R objects describing the MEEBO set. biocViews: ExperimentData Author: Agnes Paquet Maintainer: Agnes Paquet URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/ git_url: https://git.bioconductor.org/packages/MEEBOdata git_branch: RELEASE_3_9 git_last_commit: 035f12a git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/MEEBOdata_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: MetaGxBreast Version: 1.4.0 Depends: Biobase, stats, lattice, impute, AnnotationHub, ExperimentHub, SummarizedExperiment, R (>= 3.6.0) Suggests: testthat, xtable License: Artistic-2.0 MD5sum: ebc1b88b0cbc809a6ee615a618ae9e87 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 , Deena M.A. Gendoo , Benjamin Haibe-Kains Maintainer: Michael Zon git_url: https://git.bioconductor.org/packages/MetaGxBreast git_branch: RELEASE_3_9 git_last_commit: 485b0f6 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/MetaGxBreast_1.4.0.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: 86 Package: MetaGxOvarian Version: 1.4.0 Depends: Biobase, stats, lattice, impute, AnnotationHub, ExperimentHub, SummarizedExperiment, R (>= 3.6.0) Suggests: testthat, xtable License: Artistic-2.0 MD5sum: 19c08da41e05075e9498397490027658 NeedsCompilation: no Title: Transcriptomic Ovarian Cancer Datasets Description: A collection of Ovarian Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium. biocViews: ExpressionData, ExperimentHub, CancerData, Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData, ExperimentData Author: Michael Zon , Deena M.A. Gendoo , Benjamin Haibe-Kains Maintainer: Michael Zon git_url: https://git.bioconductor.org/packages/MetaGxOvarian git_branch: RELEASE_3_9 git_last_commit: e2b8840 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/MetaGxOvarian_1.4.0.tar.gz vignettes: vignettes/MetaGxOvarian/inst/doc/MetaGxOvarian.pdf vignetteTitles: MetaGxOvarian: a package for ovarian cancer gene expression analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MetaGxOvarian/inst/doc/MetaGxOvarian.R dependencyCount: 86 Package: MetaGxPancreas Version: 1.4.0 Depends: Biobase, stats, lattice, impute, AnnotationHub, ExperimentHub, R (>= 3.6.0) Imports: SummarizedExperiment Suggests: testthat, xtable License: Artistic-2.0 MD5sum: 8c87608964940fa1f28b5713c6588414 NeedsCompilation: no Title: Transcriptomic Pancreatic Cancer Datasets Description: A collection of pancreatic 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 , Vandana Sandhu , Benjamin Haibe-Kains Maintainer: Michael Zon git_url: https://git.bioconductor.org/packages/MetaGxPancreas git_branch: RELEASE_3_9 git_last_commit: 897273a git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/MetaGxPancreas_1.4.0.tar.gz vignettes: vignettes/MetaGxPancreas/inst/doc/MetaGxPancreas.pdf vignetteTitles: MetaGxPancreas: a package for pancreas cancer gene expression analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MetaGxPancreas/inst/doc/MetaGxPancreas.R dependencyCount: 86 Package: metaMSdata Version: 1.20.0 License: GPL (>= 2) MD5sum: 60703c7f827a3e2f1ca0abe3afa39d5b 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: Ron Wehrens git_url: https://git.bioconductor.org/packages/metaMSdata git_branch: RELEASE_3_9 git_last_commit: bf01f7e git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/metaMSdata_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: MethylAidData Version: 1.16.0 Depends: MethylAid, R (>= 3.2) Suggests: BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC License: GPL (>= 2) MD5sum: 2ceb994d8b7cc00b2a7ccf2e4af60579 NeedsCompilation: no Title: MethylAid-summarized data for 2800 Illumina 450k array samples and 2620 EPIC array samples Description: A data package containing summarized Illumina 450k array data on 2800 samples and summarized EPIC data for 2620 samples. The data can be use as a background data set in the interactive application. biocViews: ExperimentData, TechnologyData, MicroarrayData, MethylationArrayData Author: Davy Cats, Tyler J. Gorrie-Stone, Bastiaan T. Heijmans, John W. Holloway, BIOS Consortium, Maarten van Iterson, Faisal I. Rezwam, Leonard Schalkwyk Maintainer: M. van Iterson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MethylAidData git_branch: RELEASE_3_9 git_last_commit: 6a7f8ed git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/MethylAidData_1.16.0.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 dependencyCount: 145 Package: methyvimData Version: 1.6.0 Depends: R (>= 3.4.0), minfi Suggests: Biobase, BiocStyle, SummarizedExperiment, knitr, rmarkdown License: file LICENSE MD5sum: a4c9dd38473186f1632b57e21a3ef671 NeedsCompilation: no Title: Example experimental data for use with the methyvim package Description: Contains a reduced set of simulated data inspired by data produced by the Infinium EPIC BeadChip assays by Illumina. The example data set is made available to highlight many of the key procedures that are available within the core functions of the methyvim package. biocViews: Clustering, DNAMethylation, DifferentialMethylation, MethylationArray, MethylSeq Author: Nima Hejazi [aut, cre] Maintainer: Nima Hejazi VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/methyvimData git_branch: RELEASE_3_9 git_last_commit: 0922439 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/methyvimData_1.6.0.tar.gz vignettes: vignettes/methyvimData/inst/doc/data_methyvim.html vignetteTitles: Anatomy of the `methyvimData` package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/methyvimData/inst/doc/data_methyvim.R dependencyCount: 125 Package: microRNAome Version: 1.6.0 Depends: R (>= 3.4), SummarizedExperiment Suggests: BiocGenerics, RUnit License: GPL (>= 2) MD5sum: ac73eb0ae684ab92a99aaf4618878bcc NeedsCompilation: no Title: SummarizedExperiment for the microRNAome project Description: This package provides a SummarizedExperiment object of read counts for microRNAs across tissues, cell-types, and cancer cell-lines. The read count matrix was prepared and provided by the author of the study: Towards the human cellular microRNAome. biocViews: ExperimentData, CellCulture, CancerData, SequencingData, RNASeqData, miRNAData Author: Matthew N. McCall , Marc K. Halushka Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/microRNAome git_branch: RELEASE_3_9 git_last_commit: 7637625 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/microRNAome_1.6.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 32 Package: MIGSAdata Version: 1.8.0 Depends: R (>= 3.4) Suggests: BiocGenerics License: GPL (>= 2) MD5sum: c510924ea1ebf2892f33b16b3fd21473 NeedsCompilation: no Title: MIGSA vignette data Description: MIGSA vignette data. The MIGSAdata package provides several data objects needed by MIGSA package to correctly generate its vignette, and follow it step by step. biocViews: ExperimentData, RepositoryData, ReproducibleResearch, CancerData, BreastCancerData, MicroarrayData Author: Juan C. Rodriguez, Cristobal Fresno, Andrea S. Llera and Elmer A. Fernandez Maintainer: Juan C. Rodriguez URL: http://www.bdmg.com.ar/ git_url: https://git.bioconductor.org/packages/MIGSAdata git_branch: RELEASE_3_9 git_last_commit: ca5de98 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/MIGSAdata_1.8.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: minfiData Version: 0.30.0 Depends: R (>= 3.3.0), minfi (>= 1.21.2), IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 License: Artistic-2.0 MD5sum: 91b5668c839ed8fcca5ea36439c46473 NeedsCompilation: no Title: Example data for the Illumina Methylation 450k array Description: Data from 6 samples across 2 groups from 450k methylation arrays. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData Author: Kasper Daniel Hansen, Martin Aryee, Winston Timp Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/minfiData git_branch: RELEASE_3_9 git_last_commit: 01c2121 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/minfiData_0.30.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MethylAidData dependencyCount: 127 Package: minfiDataEPIC Version: 1.10.0 Depends: R (>= 3.3), minfi (>= 1.21.2), IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: Artistic-2.0 MD5sum: 3a7541b38950d9ca5cdff14c8b721e31 NeedsCompilation: no Title: Example data for the Illumina Methylation EPIC array Description: Data from 3 technical replicates of the cell line GM12878 from the EPIC methylation array. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData Author: Jean-Philippe Fortin, Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/minfiDataEPIC git_branch: RELEASE_3_9 git_last_commit: 47cf7ad git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/minfiDataEPIC_1.10.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MethylAidData dependencyCount: 127 Package: minionSummaryData Version: 1.14.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: b5009bbbc5b2a0fa5e71180dd18a6a7b NeedsCompilation: no Title: Summarised MinION sequencing data published by Ashton et al. 2015 Description: Summarised MinION sequencing data for Salmonella Typhi published by Ashton et al. in 2015. Three replicate runs are each provided as Fast5Summary objects. biocViews: ExperimentData, SequencingData Author: Mike Smith [aut, cre] Maintainer: Mike Smith VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/minionSummaryData git_branch: RELEASE_3_9 git_last_commit: 37a17f8 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/minionSummaryData_1.14.0.tar.gz vignettes: vignettes/minionSummaryData/inst/doc/creating-Styphi-Dataset.html vignetteTitles: Creating example MinION summary dataset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/minionSummaryData/inst/doc/creating-Styphi-Dataset.R dependencyCount: 0 Package: miRcompData Version: 1.14.0 Depends: R (>= 3.2), Imports: utils License: GPL-3 | file LICENSE MD5sum: 30e555c141406e16ec2a98a71fb9dfb3 NeedsCompilation: no Title: Data used in the miRcomp package Description: Raw amplification data from a large microRNA mixture / dilution study. These data are used by the miRcomp package to assess the performance of methods that estimate expression from the amplification curves. biocViews: ExperimentData, ExpressionData, qPCRData, Homo_sapiens_Data Author: Matthew N. McCall Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/miRcompData git_branch: RELEASE_3_9 git_last_commit: 1513ffe git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/miRcompData_1.14.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 1 Package: miRNATarget Version: 1.22.0 Depends: R (>= 2.10), Biobase License: GPL MD5sum: f53ec633f1b577134140f432f0af82db NeedsCompilation: no Title: gene target tabale of miRNA for human/mouse used for MiRaGE package Description: gene target tabale of miRNA for human/mouse used for MiRaGE package biocViews: ExperimentData, Homo_sapiens_Data Author: Y-h. Taguchi Maintainer: Y-h. Taguchi git_url: https://git.bioconductor.org/packages/miRNATarget git_branch: RELEASE_3_9 git_last_commit: c570dbc git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/miRNATarget_1.22.0.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 dependencyCount: 7 Package: mitoODEdata Version: 1.20.0 Depends: R (>= 2.14.0) License: LGPL MD5sum: c306352e4f966d2f508a2b18ab299207 NeedsCompilation: no Title: Experimental data associated to the paper "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay" (submitted). Description: This package contains the experimental data (assay annotation, siRNA annotation, time-lapse cell counts) associated to the paper "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay" (submitted). The data ultimately come from the Mitocheck assay reported in "Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes" (Neumann, Walter et al, Nature 2010). biocViews: ExperimentData, Genome Author: Gregoire Pau Maintainer: Gregoire Pau SystemRequirements: git_url: https://git.bioconductor.org/packages/mitoODEdata git_branch: RELEASE_3_9 git_last_commit: 186952e git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/mitoODEdata_1.20.0.tar.gz vignettes: vignettes/mitoODEdata/inst/doc/mitoODEdata-introduction.pdf vignetteTitles: Mitoode data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mitoODEdata/inst/doc/mitoODEdata-introduction.R dependencyCount: 0 Package: MMDiffBamSubset Version: 1.20.0 Suggests: MMDiff2 License: LGPL MD5sum: a4db104aef49d0178d476f3539d5f218 NeedsCompilation: no Title: Example ChIP-Seq data for the MMDiff package Description: Subset of BAM files, including WT_2.bam, Null_2.bam, Resc_2.bam, Input.bam from the "Cfp1" experiment (see Clouaire et al., Genes Dev. 2012). Data is available under ArrayExpress accession numbers E-ERAD-79. Additionally, corresponding subset of peaks called by MACS biocViews: ExperimentData, Genome, StemCell, Mus_musculus_Data, DNASeqData, ChIPSeqData, ArrayExpress Author: Gabriele Schweikert Maintainer: Gabriele Schweikert git_url: https://git.bioconductor.org/packages/MMDiffBamSubset git_branch: RELEASE_3_9 git_last_commit: 4f03097 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/MMDiffBamSubset_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: MOFAdata Version: 1.0.0 Depends: R (>= 3.5) Suggests: knitr, MultiAssayExperiment License: LGPL-3 MD5sum: d6487d6a88855eff8711a5af287bbb2d NeedsCompilation: yes Title: Data package for Multi-Omics Factor Analysis (MOFA) Description: A collection of datasets to accompany the R package MOFA and illustrate running and analysing MOFA models. biocViews: ReproducibleResearch Author: Ricard Argelaguet, Britta Velten, Damien Arnol, Florian Buettner, Wolfgang Huber, Oliver Stegle Maintainer: Britta Velten VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MOFAdata git_branch: RELEASE_3_9 git_last_commit: 2af9c04 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/MOFAdata_1.0.0.tar.gz vignettes: vignettes/MOFAdata/inst/doc/MOFAdata.html vignetteTitles: MOFAdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MOFAdata/inst/doc/MOFAdata.R dependencyCount: 0 Package: mosaicsExample Version: 1.22.0 Depends: R (>= 2.11.1) License: GPL (>= 2) MD5sum: c87a905df5b38287895aff9adb2c8406 NeedsCompilation: no Title: Example data for the mosaics package, which implements MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data for transcription factor binding and histone modification Description: Data for the mosaics package, consisting of (1) chromosome 22 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding and H3K4me3 modification in MCF7 cell line from ENCODE database (HG19) and (2) chromosome 21 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding, with mappability, GC content, and sequence ambiguity scores of human genome HG18. biocViews: ExperimentData, ChIPseqData, Homo_sapiens Author: Dongjun Chung, Pei Fen Kuan, Rene Welch, Sunduz Keles Maintainer: Dongjun Chung URL: http://groups.google.com/group/mosaics_user_group git_url: https://git.bioconductor.org/packages/mosaicsExample git_branch: RELEASE_3_9 git_last_commit: 9da2d2e git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/mosaicsExample_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: mouse4302barcodevecs Version: 1.22.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 8d80293e4fa8d95431c9e1ccba298433 NeedsCompilation: no Title: mouse4302 data for barcode Description: Data used by the barcode package for microarrays of type mouse4302. biocViews: Mus_musculus_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/mouse4302barcodevecs git_branch: RELEASE_3_9 git_last_commit: 922d5eb git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/mouse4302barcodevecs_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: msd16s Version: 1.4.0 Depends: R (>= 2.10), Biobase, metagenomeSeq, License: Artistic-2.0 MD5sum: c6671e141bf8abb9df5fa623a5702fcb NeedsCompilation: no Title: Healthy and moderate to severe diarrhea 16S expression data Description: Gut 16S sequencing expression data from 992 healthy and moderate-to-severe diarrhetic samples used in 'Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition'. biocViews: ExperimentData, SequencingData, MicrobiomeData Author: Joseph N. Paulson, Hector Corrada Bravo, Mihai Pop Maintainer: Joseph N. Paulson URL: http://www.cbcb.umd.edu/research/projects/GEMS-pathogen-discovery git_url: https://git.bioconductor.org/packages/msd16s git_branch: RELEASE_3_9 git_last_commit: cd06a54 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/msd16s_1.4.0.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 dependencyCount: 31 Package: msdata Version: 0.24.1 Depends: R (>= 2.10) Suggests: xcms, mzR, MSnbase License: GPL (>= 2) MD5sum: 4f8f93fad60efa8606923e77651616bf NeedsCompilation: no Title: Various Mass Spectrometry raw data example files Description: Ion Trap positive ionization mode data in mzData file format. Subset from 500-850 m/z and 1190-1310 seconds, incl. MS2 and MS3, intensity threshold 100.000. Extracts from FTICR Apex III, m/z 400-450. Subset of UPLC - Bruker micrOTOFq data, both mzData, mzML and mz5. LC-MSMS and MRM files from proteomics experiments. PSI mzIdentML example files for various search engines. biocViews: ExperimentData, MassSpectrometryData Author: Steffen Neumann , Laurent Gatto with contriutions from Johannes Rainer Maintainer: Steffen Neumann , Laurent Gatto git_url: https://git.bioconductor.org/packages/msdata git_branch: RELEASE_3_9 git_last_commit: 18411b8 git_last_commit_date: 2019-07-09 Date/Publication: 2019-07-11 source.ver: src/contrib/msdata_0.24.1.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics dependencyCount: 0 Package: MSMB Version: 1.2.0 Depends: R (>= 2.10) Suggests: knitr, BiocStyle License: LGPL MD5sum: 8898fad9df534a2d3de0af0c74a5dfc5 NeedsCompilation: no Title: Data sets for the book 'Modern Statistics for Biology' Description: Data sets for the book 'Modern Statistics for Modern Biology', S.P. Holmes and W. Huber. biocViews: ExperimentData, ReproducibleResearch Author: Wolfgang Huber, Andrzej Oles, Mike Smith Maintainer: Wolfgang Huber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MSMB git_branch: RELEASE_3_9 git_last_commit: 9af44b2 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/MSMB_1.2.0.tar.gz vignettes: vignettes/MSMB/inst/doc/MSMB.pdf vignetteTitles: Modern Statistics for Modern Biology hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MSMB/inst/doc/MSMB.R dependencyCount: 0 Package: msPurityData Version: 1.12.0 Suggests: knitr License: GPL (>= 2) MD5sum: ae6f756fe49c343dac284309d67b26ac NeedsCompilation: no Title: Fragmentation spectral libraries and data to test the msPurity package Description: Fragmentation spectral libraries and data to test the msPurity package biocViews: ExperimentData, MassSpectrometryData Author: Thomas N. Lawson Maintainer: Thomas N. Lawson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/msPurityData git_branch: RELEASE_3_9 git_last_commit: 309d70c git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/msPurityData_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: msqc1 Version: 1.12.0 Depends: R (>= 3.6), lattice, stats, utils Suggests: BiocStyle, knitr, testthat, specL License: GPL MD5sum: ceb2ef3c5998e786e3bc8233b0d2724f NeedsCompilation: no Title: Sigma mix MSQC1 data Description: The data set contains an eight technical replicate data set and a three replicate dilution series of the MS Qual/Quant QC Mix standard sample (Sigma-Aldrich, Buchs, Switzerland) measured on five different mass spec platforms at the Functional Genomics Center Zurich. biocViews: ExperimentData, MassSpectrometryData, ReproducibleResearch Author: Tobias Kockmann [aut], Christian Trachsel [aut], Christian Panse [aut, cre] () Maintainer: Christian Panse URL: https://panoramaweb.org/labkey/MSQC1.url, http://fgcz-bfabric.uzh.ch/bfabric/project.html?projectId=1959 VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/msqc1 git_branch: RELEASE_3_9 git_last_commit: 64f83cc git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/msqc1_1.12.0.tar.gz vignettes: vignettes/msqc1/inst/doc/poster.pdf, vignettes/msqc1/inst/doc/chromatography.html, vignettes/msqc1/inst/doc/msqc1.html vignetteTitles: ASMS 2016 poster (in portrait) abstract ID number: 282492, LC Observations - Retention Time Stability, Introducing msqc1 - A Mass Spec Data set for Targeted Proteomics Performance Evaluation hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/msqc1/inst/doc/chromatography.R, vignettes/msqc1/inst/doc/msqc1.R, vignettes/msqc1/inst/doc/poster.R dependencyCount: 6 Package: MSstatsBioData Version: 1.6.0 Depends: R (>= 3.4) Suggests: BiocStyle, knitr, MSstats License: Artistic-2.0 MD5sum: a0a04b89a7eaee9c85a630483b296a0c NeedsCompilation: no Title: Datasets of published biological studies with DDA or SRM experiments Description: Provides the peak intensity data for detecting differentially abundant proteins in seven published biological investigations. biocViews: ExperimentData, MassSpectrometryData, Proteome Author: Meena Choi Maintainer: Meena Choi VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MSstatsBioData git_branch: RELEASE_3_9 git_last_commit: af03be3 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/MSstatsBioData_1.6.0.tar.gz vignettes: vignettes/MSstatsBioData/inst/doc/MSstatsBioData.html vignetteTitles: MSstatsBioData: Datasets of published biological studies with DDA or SRM experiments hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MSstatsBioData/inst/doc/MSstatsBioData.R dependencyCount: 0 Package: mtbls2 Version: 1.14.0 Depends: R (>= 2.10) Suggests: xcms (>= 3.0.0), CAMERA, Risa (>= 1.0.0), knitr, Heatplus, pcaMethods, sp License: CC0 MD5sum: c6b95b76c7aa21672c277100dbf75f19 NeedsCompilation: no Title: MetaboLights MTBLS2: Comparative LC/MS-based profiling of silver nitrate-treated Arabidopsis thaliana leaves of wild-type and cyp79B2 cyp79B3 double knockout plants. Böttcher et al. (2004) Description: Indole-3-acetaldoxime (IAOx) represents an early intermediate of the biosynthesis of a variety of indolic secondary metabolites including the phytoanticipin indol-3-ylmethyl glucosinolate and the phytoalexin camalexin (3-thiazol-2'-yl-indole). Arabidopsis thaliana cyp79B2 cyp79B3 double knockout plants are completely impaired in the conversion of tryptophan to indole-3-acetaldoxime and do not accumulate IAOx-derived metabolites any longer. Consequently, comparative analysis of wild-type and cyp79B2 cyp79B3 plant lines has the potential to explore the complete range of IAOx-derived indolic secondary metabolites. biocViews: MassSpectrometryData, RepositoryData Author: Steffen Neumann Maintainer: Steffen Neumann URL: http://www.ebi.ac.uk/metabolights/MTBLS2, https://github.com/sneumann/mtbls2 VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mtbls2 git_branch: RELEASE_3_9 git_last_commit: 1091a2b git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/mtbls2_1.14.0.tar.gz vignettes: vignettes/mtbls2/inst/doc/MTBLS2-xcms3.html, vignettes/mtbls2/inst/doc/MTBLS2.html vignetteTitles: MTBLS2 Processing and Analysis with xcms3,, CAMERA and export to MetaboLights, MTBLS2 Processing and Analysis with xcms,, CAMERA and export to MetaboLights hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mtbls2/inst/doc/MTBLS2-xcms3.R, vignettes/mtbls2/inst/doc/MTBLS2.R dependencyCount: 0 Package: MTseekerData Version: 1.2.0 Depends: R (>= 3.5) Imports: utils, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, VariantAnnotation, Homo.sapiens, MTseeker Suggests: gmapR, xml2, rtracklayer License: Artistic-2.0 MD5sum: f36216a2c91f9d02efbca8071367edc1 NeedsCompilation: no Title: Supporting Data for the MTseeker Package Description: Provides examples for the MTseeker package vignette. biocViews: ExperimentData, Genome Author: Tim Triche, Jr; Noor Sohail; Ben Johnson Maintainer: Tim Triche, Jr. git_url: https://git.bioconductor.org/packages/MTseekerData git_branch: RELEASE_3_9 git_last_commit: 6fba809 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/MTseekerData_1.2.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 113 Package: MUGAExampleData Version: 1.4.0 Depends: R (>= 2.10.0) License: GPL-3 MD5sum: 307ef40b4459572843bf422be2dc998b NeedsCompilation: no Title: Example {M}ouse {U}niversal {G}enotyping {A}rray data for genome reconstruction and quantitative trait locus mapping. Description: This package contains example data for the MUGA array that is used by the R package DOQTL. biocViews: ExperimentData, Mus_musculus_Data Author: Daniel Gatti Maintainer: Daniel Gatti git_url: https://git.bioconductor.org/packages/MUGAExampleData git_branch: RELEASE_3_9 git_last_commit: e1c7554 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/MUGAExampleData_1.4.0.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: Mulder2012 Version: 0.24.0 Depends: R (>= 2.14), org.Hs.eg.db, KEGG.db Imports: igraph, HTSanalyzeR, PANR, RedeR, pvclust, MASS Suggests: snow License: Artistic-2.0 MD5sum: cf1ccb7133defdc49f889dfe9efabbf4 NeedsCompilation: no Title: Predicting functional networks and modules of chromatin factors controlling adult stem cell fate from RNA interference screens Description: This package provides functions to reproduce results and figures in Mulder K. et. al. published in Nature Cell Biology 2012 and Wang X. et. al. published in PLoS Computational Biology 2012. biocViews: StemCell, CancerData Author: Xin Wang , Florian Markowetz Maintainer: Xin Wang git_url: https://git.bioconductor.org/packages/Mulder2012 git_branch: RELEASE_3_9 git_last_commit: 26fa5cf git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/Mulder2012_0.24.0.tar.gz vignettes: vignettes/Mulder2012/inst/doc/Mulder2012-Vignette.pdf vignetteTitles: Main vignette:Posterior association network and enriched functional gene modules inferred from rich phenotypes of gene perturbations hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Mulder2012/inst/doc/Mulder2012-Vignette.R dependencyCount: 111 Package: mvoutData Version: 1.20.0 Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4), lumi License: Artistic-2.0 MD5sum: dee1616c6e51610b038b7df786676238 NeedsCompilation: no Title: affy and illumina raw data for assessing outlier detector performance Description: affy and illumina raw data for assessing outlier detector performance biocViews: ExperimentData, MicroarrayData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/mvoutData git_branch: RELEASE_3_9 git_last_commit: 6b10138 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/mvoutData_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 145 Package: nanotubes Version: 1.0.0 Depends: R (>= 3.6) Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, rtracklayer, CAGEfightR License: GPL-3 MD5sum: 6f54f293086643f47c81eea20f55f165 NeedsCompilation: no Title: Mouse nanotube CAGE data Description: Cap Analysis of Gene Expression (CAGE) data from "Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo" by Bornholdt et al. supplied as CAGE Transcription Start Sites (CTSSs). biocViews: ExperimentData, SequencingData, ExpressionData Author: Malte Thodberg Maintainer: Malte Thodberg URL: https://github.com/MalteThodberg/nanotubes VignetteBuilder: knitr BugReports: https://github.com/MalteThodberg/nanotubes/issues git_url: https://git.bioconductor.org/packages/nanotubes git_branch: RELEASE_3_9 git_last_commit: ac67a11 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/nanotubes_1.0.0.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 dependencyCount: 0 Package: NCIgraphData Version: 1.20.0 Depends: R (>= 2.10.0) Suggests: Rgraphviz License: GPL-3 MD5sum: b69030f40d2818cbd1c004d33403a653 NeedsCompilation: no Title: Data for the NCIgraph software package Description: Provides pathways from the NCI Pathways Database as R graph objects biocViews: NCI Author: Laurent Jacob Maintainer: Laurent Jacob git_url: https://git.bioconductor.org/packages/NCIgraphData git_branch: RELEASE_3_9 git_last_commit: 3a55f8a git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/NCIgraphData_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: NestLink Version: 1.0.0 Depends: R (>= 3.6), AnnotationHub (>= 2.15.3), ExperimentHub (>= 0.99.6), Biostrings (>= 2.51.1), gplots (>= 3.0.0), protViz (>= 0.4.0), ShortRead (>= 1.41.0) Imports: grDevices, graphics, stats, utils Suggests: BiocStyle (>= 2.2.0), DT, ggplot2, knitr, rmarkdown, testthat, specL, lattice, scales License: GPL MD5sum: f71e0add07a81dd57fb97103af33762f 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] (), Lucy Poveda [ctb] (), Hans-Anton Keserue [ctb], Christian Panse [aut, cre] (), Bernd Roschitzki [aut] (), Markus Seeger [aut] () Maintainer: Christian Panse VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/NestLink git_branch: RELEASE_3_9 git_last_commit: 4b44f10 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/NestLink_1.0.0.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: 99 Package: Neve2006 Version: 0.22.0 Depends: R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0), hgu133a.db, annotate License: Artistic-2.0 MD5sum: 1649911c89a1d20393bd58b3376e622d NeedsCompilation: no Title: expression and CGH data on breast cancer cell lines Description: Experimental organization of combined expression and CGH data biocViews: ExperimentData, CancerData, BreastCancerData Author: M. Neve et al. in Gray Lab at LBL Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/Neve2006 git_branch: RELEASE_3_9 git_last_commit: 192094d git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/Neve2006_0.22.0.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: 39 Package: NGScopyData Version: 1.4.0 License: GPL (>=2) MD5sum: a1ad1b18cdab0cb0f60674d0482e3e6b NeedsCompilation: no Title: Subset of BAM files of human tumor and pooled normal sequencing data (Zhao et al. 2014) for the NGScopy package Description: Subset of BAM files of human lung tumor and pooled normal samples by targeted panel sequencing. [Zhao et al 2014. Targeted Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using the University of North Carolina (UNC) Sequencing Assay Captures Most Previously Described Genetic Aberrations in NSCLC. In preparation.] Each sample is a 10 percent random subsample drawn from the original sequencing data. The pooled normal sample has been rescaled accroding to the total number of normal samples in the "pool". Here provided is the subsampled data on chr6 (hg19). biocViews: ExperimentData, CancerData, LungCancerData, SequencingData Author: Xiaobei Zhao [aut, cre, cph] Maintainer: Xiaobei Zhao URL: http://www.bioconductor.org/packages/release/data/experiment/html/NGScopyData.html git_url: https://git.bioconductor.org/packages/NGScopyData git_branch: RELEASE_3_9 git_last_commit: ebba550 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/NGScopyData_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: oct4 Version: 1.0.0 Suggests: knitr License: GPL (>= 2) MD5sum: 4258694f3a51f0723ee90a5cdc241d03 NeedsCompilation: no Title: Conditional knockdown of OCT4 in mouse ESCs Description: This package provides the output of running Salmon on a set of 12 RNA-seq samples from King & Klose, "The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells", published in eLIFE, March 2017. For details on version numbers and how the samples were processed see the package vignette. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/oct4 git_branch: RELEASE_3_9 git_last_commit: dd9cd72 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/oct4_1.0.0.tar.gz vignettes: vignettes/oct4/inst/doc/oct4.html vignetteTitles: Salmon quantifications for condition OCT4 knockdown in mouse ESCs hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/oct4/inst/doc/oct4.R dependencyCount: 0 Package: OMICsPCAdata Version: 1.2.0 Depends: R (>= 3.5.0), MultiAssayExperiment Suggests: knitr, kableExtra, rmarkdown License: GPL-3 MD5sum: 8edbe12b716d34eb42783e0b327582bf NeedsCompilation: no Title: Supporting data for package OMICsPCA Description: Supporting data for package OMICsPCA biocViews: RepositoryData, TechnologyData, ChIPSeqData, SequencingData, ExpressionData, ENCODE Author: Author: Subhadeep Das Maintainer: Subhadeep Das VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/OMICsPCAdata git_branch: RELEASE_3_9 git_last_commit: c9a2281 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/OMICsPCAdata_1.2.0.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: 58 Package: OnassisJavaLibs Version: 1.6.0 Depends: R (>= 3.4) Imports: rJava Suggests: BiocStyle, rmarkdown, knitr License: GPL-2 MD5sum: ec733ed33c8932261fc34adaad85d038 NeedsCompilation: no Title: OnassisJavaLibs, java libraries to run conceptmapper and semantic similarity Description: A package that contains java libraries to call conceptmapper and compute semnatic similarity from R biocViews: ExperimentData Author: Eugenia Galeota Maintainer: Eugenia Galeota SystemRequirements: Java (>= 1.8) VignetteBuilder: rmarkdown, knitr git_url: https://git.bioconductor.org/packages/OnassisJavaLibs git_branch: RELEASE_3_9 git_last_commit: 2a340de git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/OnassisJavaLibs_1.6.0.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: parathyroidSE Version: 1.22.0 Depends: SummarizedExperiment, R (>= 2.10) Suggests: Rsamtools, GenomicAlignments, GEOquery, SRAdb, GenomicFeatures, BiocStyle License: LGPL MD5sum: f0afc965e91000f48da3b5bb7b141b1f NeedsCompilation: no Title: RangedSummarizedExperiment for RNA-Seq of primary cultures of parathyroid tumors by Haglund et al., J Clin Endocrinol Metab 2012. Description: This package provides RangedSummarizedExperiment objects of read counts in genes and exonic parts for paired-end RNA-Seq data from experiments on primary cultures of parathyroid tumors. The data were presented in the article "Evidence of a Functional Estrogen Receptor in Parathyroid Adenomas" by Haglund F, Ma R, Huss M, Sulaiman L, Lu M, Nilsson IL, Hoog A, Juhlin CC, Hartman J, Larsson C, J Clin Endocrinol Metab. jc.2012-2484, Epub 2012 Sep 28, PMID: 23024189. The sequencing was performed on tumor cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control). One control sample was omitted by the paper authors due to low quality. The package vignette describes the creation of the object from raw sequencing data provided by NCBI Gene Expression Omnibus under accession number GSE37211. The gene and exon features are the GRCh37 Ensembl annotations. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love git_url: https://git.bioconductor.org/packages/parathyroidSE git_branch: RELEASE_3_9 git_last_commit: d220706 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/parathyroidSE_1.22.0.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 dependencyCount: 32 Package: pasilla Version: 1.12.0 Depends: R (>= 3.3.0) Suggests: DEXSeq, rmarkdown, BiocStyle, knitr License: LGPL MD5sum: 0bd04b62ac21a38cb820a74c4bd42534 NeedsCompilation: no Title: Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011. Description: This package provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in the article "Conservation of an RNA regulatory map between Drosophila and mammals" by Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR, Genome Res. 2011 Feb;21(2):193-202, Epub 2010 Oct 4, PMID: 20921232. The experiment studied the effect of RNAi knockdown of Pasilla, the Drosophila melanogaster ortholog of mammalian NOVA1 and NOVA2, on the transcriptome. The package vignette describes how the data provided here were derived from the RNA-Seq read sequence data that are provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. biocViews: ExperimentData, Genome, Drosophila_melanogaster_Data, RNASeqData Author: Wolfgang Huber, Alejandro Reyes Maintainer: Alejandro Reyes VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/pasilla git_branch: RELEASE_3_9 git_last_commit: 62b9dfa git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/pasilla_1.12.0.tar.gz vignettes: vignettes/pasilla/inst/doc/create_objects.html vignetteTitles: "Data preprocessing and creation of the data objects pasillaGenes and pasillaExons" hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pasilla/inst/doc/create_objects.R suggestsMe: IHWpaper, pasillaBamSubset dependencyCount: 0 Package: pasillaBamSubset Version: 0.22.0 Suggests: pasilla License: LGPL MD5sum: a941d288f2aa572abce323159e473271 NeedsCompilation: no Title: Subset of BAM files from "Pasilla" experiment Description: Subset of BAM files untreated1.bam (single-end reads) and untreated3.bam (paired-end reads) from "Pasilla" experiment (Pasilla knock-down by Brooks et al., Genome Research 2011). See the vignette in the pasilla data package for how BAM files untreated1.bam and untreated3.bam were obtained from the RNA-Seq read sequence data that is provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. Also contains the DNA sequence for fly chromosome 4 to which the reads can be mapped. biocViews: ExperimentData, Genome, DNASeqData, RNASeqData Author: Hervé Pagès Maintainer: Hervé Pagès git_url: https://git.bioconductor.org/packages/pasillaBamSubset git_branch: RELEASE_3_9 git_last_commit: b452fe9 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/pasillaBamSubset_0.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: PasillaTranscriptExpr Version: 1.12.0 Depends: R (>= 3.3.0) Suggests: rtracklayer, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: faceed94f7269a49ff908400b7aab192 NeedsCompilation: no Title: Data package with transcript expression obtained with kallisto from pasilla knock-down RNA-Seq data from Brooks et al. Description: Provides kallisto workflow and transcript expression of RNA-Seq data from Brooks et al. biocViews: Drosophila_melanogaster_Data, Genome, RNASeqData, ExperimentData, SequencingData, ExpressionData, GEO Author: Malgorzata Nowicka [aut, cre] Maintainer: Malgorzata Nowicka VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/PasillaTranscriptExpr git_branch: RELEASE_3_9 git_last_commit: 613b91a git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/PasillaTranscriptExpr_1.12.0.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 dependencyCount: 0 Package: PathNetData Version: 1.20.0 Depends: R (>= 1.14.0) License: GPL-3 MD5sum: 2001039db08246bf7daef431935a2ef6 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: Jason B. Smith git_url: https://git.bioconductor.org/packages/PathNetData git_branch: RELEASE_3_9 git_last_commit: 3470f07 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/PathNetData_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: pathprintGEOData Version: 1.14.0 Depends: R (>= 3.4) Suggests: pathprint, SummarizedExperiment License: GPL MD5sum: a7237e62dda8f356c41d35e50fef33e8 NeedsCompilation: no Title: Pathway fingerprint vectors representing a subsection of arrays from the GEO data repository Description: Pathway Fingerprint vectors that have been pre-calculated for ~390,000 publicly available arrays from the GEO corpus, spanning 6 species and 31 platforms. All data are accompanied by their associated metadata. biocViews: ExperimentData, ExpressionData, MicroarrayData, GEO, Homo_sapiens_Data, Mus_musculus_Data, Drosophila_melanogaster_Data, Rattus_norvegicus_Data, Caenorhabditis_elegans_Data, Danio_rerio_Data,Genome, SequencingData, OneChannelData, TwoChannelData,PathwayInteractionDatabase Author: Gabriel Altschuler, Sokratis Kariotis Maintainer: Sokratis Kariotis git_url: https://git.bioconductor.org/packages/pathprintGEOData git_branch: RELEASE_3_9 git_last_commit: 9819263 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/pathprintGEOData_1.14.0.tar.gz vignettes: vignettes/pathprintGEOData/inst/doc/usingPathprintGEOData.pdf vignetteTitles: pathprintGEOData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pathprintGEOData/inst/doc/usingPathprintGEOData.R dependencyCount: 0 Package: pcaGoPromoter.Hs.hg19 Version: 1.20.0 License: GPL (>= 2) MD5sum: 74341bab4a5971398732071dad1898b0 NeedsCompilation: no Title: pcaGoPromoter.Hs.hg19 is a data package used by pcaGoPromoter Description: Contains the data for transciption factors analysis of organism Homo Sapiens with package pcaGoPromoter biocViews: Homo_sapiens_Data Author: Morten Hansen Maintainer: Morten Hansen git_url: https://git.bioconductor.org/packages/pcaGoPromoter.Hs.hg19 git_branch: RELEASE_3_9 git_last_commit: ec1cadf git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/pcaGoPromoter.Hs.hg19_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: pcaGoPromoter.Mm.mm9 Version: 1.20.0 License: GPL (>= 2) MD5sum: cdcf550e2a810757e4f0fdd661c0e1a9 NeedsCompilation: no Title: pcaGoPromoter.Mm.mm9 is a data package used by pcaGoPromoter Description: Contains the data for transciption factors analysis of organism Mus musculus with package pcaGoPromoter biocViews: Mus_musculus_Data Author: Morten Hansen, Maintainer: Morten Hansen git_url: https://git.bioconductor.org/packages/pcaGoPromoter.Mm.mm9 git_branch: RELEASE_3_9 git_last_commit: 4dbb1a1 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/pcaGoPromoter.Mm.mm9_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: pcaGoPromoter.Rn.rn4 Version: 1.20.0 License: GPL (>= 2) MD5sum: 0ed2f9e355f461739739ac1d67bbce29 NeedsCompilation: no Title: pcaGoPromoter.Rn.rn4 is a data package used by pcaGoPromoter Description: Contains the data for transciption factors analysis of organism Rattus norvegicus with package pcaGoPromoter biocViews: Rattus_norvegicus_Data Author: Morten Hansen Maintainer: Morten Hansen, git_url: https://git.bioconductor.org/packages/pcaGoPromoter.Rn.rn4 git_branch: RELEASE_3_9 git_last_commit: d0337dd git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/pcaGoPromoter.Rn.rn4_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: PCHiCdata Version: 1.12.0 Depends: R (>= 3.2), Chicago Suggests: testthat, BiocStyle, knitr License: Artistic-2.0 MD5sum: 18936bf2c0bf4b12b969b6bf8141773a NeedsCompilation: no Title: Promoter Capture Hi-C data Description: Subsets of Promoter Capture Hi-C data conveniently packaged for Chicago users. Data includes interactions detected for chromosomes 20 and 21 in GM12878 cells and for chromosomes 18 and 19 in mESC. biocViews: ExperimentData, SequencingData, Homo_sapiens_Data, Mus_musculus_Data, StemCell Author: Paula Freire-Pritchett, Jonathan Cairns, Steven Wingett, Mikhail Spivakov Maintainer: Paula Freire-Pritchett VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/PCHiCdata git_branch: RELEASE_3_9 git_last_commit: b270578 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/PCHiCdata_1.12.0.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 dependencyCount: 74 Package: pcxnData Version: 2.6.0 Depends: R (>= 3.4) Suggests: pcxn License: MIT + file LICENSE MD5sum: 49ae7b9155cd6680c186180c03869e7f NeedsCompilation: no Title: Correlation coefficients and p values between pre-defined pathway/gene sets Description: PCxN database contains correlation coefficients and p values between pre-defined gene sets within MSigDB H hallmark gene sets, MSigDB C2 CP (Canonical pathways), MSigDB C5 GO BP gene sets and Pathprint respectively, as well as adjusted pathway correlations to account for the shared genes between pathway pairs. biocViews: ExperimentData, ExpressionData, MicroarrayData, GEO, Homo_sapiens_Data, OneChannelData, PathwayInteractionDatabase Author: Sokratis Kariotis, Yered Pita-Juarez, Wenbin Wei, Winston Hide Maintainer: Sokratis Kariotis git_url: https://git.bioconductor.org/packages/pcxnData git_branch: RELEASE_3_9 git_last_commit: 14da2e9 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/pcxnData_2.6.0.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 dependencyCount: 0 Package: pd.atdschip.tiling Version: 0.22.0 Depends: R (>= 2.14.0), methods, RSQLite (>= 0.10.0), oligoClasses (>= 1.15.58), oligo (>= 1.17.3), DBI Imports: Biostrings (>= 2.21.11), IRanges (>= 1.11.31), S4Vectors License: Artistic-2.0 MD5sum: 00f43b23dba09ecca0ff49cf28c013e9 NeedsCompilation: no Title: Platform Design Info for Affymetrix Atdschip_tiling Description: Platform Design Info for Affymetrix Atdschip_tiling biocViews: Arabidopsis_thaliana_Data, MicroarrayData, SNPData Author: Kristof De Beuf Maintainer: Kristof De Beuf git_url: https://git.bioconductor.org/packages/pd.atdschip.tiling git_branch: RELEASE_3_9 git_last_commit: 505a183 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/pd.atdschip.tiling_0.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 63 Package: pepDat Version: 1.4.0 Depends: R(>= 3.0.0) Imports: GenomicRanges Suggests: knitr License: Artistic-2.0 MD5sum: c72c91f64f3099c7ac03fe30244a4a9d NeedsCompilation: no Title: Peptide microarray data package Description: Provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV. biocViews: MicroarrayData Author: Renan Sauteraud, Raphael Gottardo Maintainer: Renan Sauteraud VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/pepDat git_branch: RELEASE_3_9 git_last_commit: 8acc21f git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/pepDat_1.4.0.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 dependencyCount: 16 Package: PepsNMRData Version: 1.2.0 Depends: R (>= 3.5) Suggests: knitr, markdown, rmarkdown, BiocStyle License: GPL-2 | file LICENSE MD5sum: 4426ad09c50010889fece7df54bf184d NeedsCompilation: no Title: Datasets for the PepsNMR package Description: This package contains all the datasets used in the PepsNMR package. biocViews: ExperimentData, OrganismData, Homo_sapiens_Data Author: Manon Martin [aut, cre], Bernadette Govaerts [aut, ths], Pascal de Tullio [dtc] Maintainer: Manon Martin BugReports: https://github.com/ManonMartin/PepsNMRData/issues git_url: https://git.bioconductor.org/packages/PepsNMRData git_branch: RELEASE_3_9 git_last_commit: 1de55b8 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/PepsNMRData_1.2.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 0 Package: plasFIA Version: 1.12.0 Depends: proFIA License: LGPL MD5sum: 047cd501ce813df543a0e502d20cbbc5 NeedsCompilation: no Title: FIA-HRMS plasma dataset Description: Positive Ionization FIA-HRMS data of human plasma spiked with a pool of 40 compounds acquired in FIA-HRMS mode on an orbitrap fusion. plasFIA also include the result of the processing by the proFIA package with adapted parameters for an Orbitrap Fusion. biocViews: ExperimentData, MassSpectrometryData Author: Alexis Delabriere, Etienne Thevenot, Ulli Hohenester and Christophe Junot. Maintainer: Alexis Delabriere git_url: https://git.bioconductor.org/packages/plasFIA git_branch: RELEASE_3_9 git_last_commit: 21dd928 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/plasFIA_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 94 Package: ppiData Version: 0.22.0 Depends: graph Imports: AnnotationDbi Suggests: org.Sc.sgd.db, ppiStats License: Artistic-2.0 MD5sum: 93d6dce530ee9a0d3ed886ae0e53b909 NeedsCompilation: no Title: A package that contains the bait to prey directed graphs for protein-protein interactions. Description: This package contains the directed graphs for protein interaction data as derived from Y2H and APMS as well as the code used to obtain the y2h data from IntAct Repository. biocViews: ExperimentData Author: Tony Chiang Maintainer: Bioconductor Package Maintainer git_url: https://git.bioconductor.org/packages/ppiData git_branch: RELEASE_3_9 git_last_commit: 907852b git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ppiData_0.22.0.tar.gz vignettes: vignettes/ppiData/inst/doc/ppiData.pdf vignetteTitles: Using the package ppiStats hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ppiData/inst/doc/ppiData.R dependencyCount: 33 Package: prebsdata Version: 1.20.0 Depends: R (>= 2.14.0) License: Artistic-2.0 MD5sum: fd5ede83923d6157b6303b81d058678f NeedsCompilation: no Title: Data for 'prebs' package Description: This package contains data required to run examples in 'prebs' package. The data files include: 1) Small sample bam files for demonstration purposes 2) Probe sequence mappings for Custom CDF (taken from http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp) 3) Probe sequence mappings for manufacturer's CDF (manually created using bowtie) biocViews: ExperimentData, SequencingData, RNASeqData Author: Karolis Uziela and Antti Honkela Maintainer: Karolis Uziela git_url: https://git.bioconductor.org/packages/prebsdata git_branch: RELEASE_3_9 git_last_commit: e57aac7 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/prebsdata_1.20.0.tar.gz vignettes: vignettes/prebsdata/inst/doc/prebsdata.pdf vignetteTitles: prebsdata User Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: PREDAsampledata Version: 0.24.0 Depends: R (>= 2.10.0), methods, PREDA, Biobase, affy, annotate Suggests: hgu133plus2.db, hgu133plus2cdf License: Artistic-2.0 MD5sum: b8ad6ccaa9332b95fe1c17172c39e4d7 NeedsCompilation: no Title: expression and copy number data on clear cell renal carcinoma samples Description: Sample data for PREDA package. (annotations objects synchronized with GeneAnnot custom CDFs version 2.2.0) biocViews: ExperimentData, Tissue, CancerData, KidneyCancerData, MicroarrayData, TissueMicroarrayData, ArrayExpress Author: I. Cifola et al. in Cristina Battaglia Lab, University of Milan Maintainer: Francesco Ferrari git_url: https://git.bioconductor.org/packages/PREDAsampledata git_branch: RELEASE_3_9 git_last_commit: 90dcff3 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/PREDAsampledata_0.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 53 Package: ProData Version: 1.22.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL MD5sum: 1f8da0ea4c4c1ec424901ab1e4246b48 NeedsCompilation: no Title: SELDI-TOF data of Breast cancer samples Description: A data package of SELDI-TOF protein mass spectrometry data of 167 breast cancer and normal samples. biocViews: ExperimentData, CancerData, BreastCancerData, MassSpectrometryData, NCI Author: Xiaochun Li Maintainer: Xiaochun Li git_url: https://git.bioconductor.org/packages/ProData git_branch: RELEASE_3_9 git_last_commit: 9df6912 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/ProData_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: pRolocdata Version: 1.22.0 Depends: R (>= 2.15), MSnbase Imports: Biobase, utils Suggests: pRoloc (>= 1.13.8), testthat License: GPL-2 MD5sum: 1234945e2ea61bb519cdfa9d1e712b63 NeedsCompilation: no Title: Data accompanying the pRoloc package Description: Mass-spectrometry based spatial proteomics data sets and protein complex separation data. Also contains the time course expression experiment from Mulvey et al. 2015. biocViews: ExperimentData, Homo_sapiens_Data, MassSpectrometryData, Arabidopsis_thaliana_Data, Drosophila_melanogaster_Data, Mus_musculus_Data, StemCell, Proteome Author: Laurent Gatto, Olive M. Crook and Lisa M. Breckels Maintainer: Laurent Gatto URL: https://github.com/lgatto/pRolocdata BugReports: https://github.com/lgatto/pRolocdata/issues git_url: https://git.bioconductor.org/packages/pRolocdata git_branch: RELEASE_3_9 git_last_commit: 16ac667 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/pRolocdata_1.22.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics dependencyCount: 79 Package: prostateCancerCamcap Version: 1.12.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 2f595f639b4adeb9a7a9c7ac8326840e NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Ross-Adams (2015) Prostate Cancer dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerCamcap git_branch: RELEASE_3_9 git_last_commit: 81b13a4 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/prostateCancerCamcap_1.12.0.tar.gz vignettes: vignettes/prostateCancerCamcap/inst/doc/prostateCancerCamcap.pdf vignetteTitles: prostateCancerCamcap hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/prostateCancerCamcap/inst/doc/prostateCancerCamcap.R dependencyCount: 7 Package: prostateCancerGrasso Version: 1.12.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 6bf3e5b205d0f15bd2ffb93d87029a16 NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Grasso (2012) Prostate Cancer dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerGrasso git_branch: RELEASE_3_9 git_last_commit: 6d03630 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/prostateCancerGrasso_1.12.0.tar.gz vignettes: vignettes/prostateCancerGrasso/inst/doc/prostateCancerGrasso.pdf vignetteTitles: prostateCancerGrasso hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/prostateCancerGrasso/inst/doc/prostateCancerGrasso.R dependencyCount: 7 Package: prostateCancerStockholm Version: 1.12.0 Depends: Biobase , R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: b800030dbb59abf7e492e57b6d063b89 NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Stockholm dataset biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerStockholm git_branch: RELEASE_3_9 git_last_commit: c8cf7ec git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/prostateCancerStockholm_1.12.0.tar.gz vignettes: vignettes/prostateCancerStockholm/inst/doc/prostateCancerStockholm.pdf vignetteTitles: prostateCancerStockholm hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/prostateCancerStockholm/inst/doc/prostateCancerStockholm.R dependencyCount: 7 Package: prostateCancerTaylor Version: 1.12.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery, org.Hs.eg.db License: Artistic-2.0 MD5sum: b95fe8d4d6ecd8bfbaeba23a0d53c829 NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Taylor et al (2010) dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerTaylor git_branch: RELEASE_3_9 git_last_commit: 855bf33 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/prostateCancerTaylor_1.12.0.tar.gz vignettes: vignettes/prostateCancerTaylor/inst/doc/prostateCancerTaylor.pdf vignetteTitles: prostateCancerTaylor hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/prostateCancerTaylor/inst/doc/prostateCancerTaylor.R dependencyCount: 7 Package: prostateCancerVarambally Version: 1.12.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 47ad7ca82845afe9830f4cb1ad3f27c5 NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Varambally dataset biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerVarambally git_branch: RELEASE_3_9 git_last_commit: fa5b435 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/prostateCancerVarambally_1.12.0.tar.gz vignettes: vignettes/prostateCancerVarambally/inst/doc/prostateCancerVarambally.pdf vignetteTitles: prostateCancerVarambally hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/prostateCancerVarambally/inst/doc/prostateCancerVarambally.R dependencyCount: 7 Package: PtH2O2lipids Version: 1.10.0 Depends: R (>= 3.3), xcms, CAMERA, LOBSTAHS, methods, utils Suggests: gplots, RColorBrewer, cluster, vegan, clustsig License: MIT + file LICENSE MD5sum: ed9ec8732208f082981ca3ef9c8a1367 NeedsCompilation: no Title: P. tricornutum HPLC-ESI-MS Lipid Data from van Creveld et al. (2015) Description: Annotated HPLC-ESI-MS lipid data in positive ionization mode from an experiment in which cultures of the marine diatom Phaeodactylum tricornutum were treated with various concentrations of hydrogen peroxide (H2O2) to induce oxidative stress. The experiment is described in Graff van Creveld, et al., 2015, "Early perturbation in mitochondria redox homeostasis in response to environmental stress predicts cell fate in diatoms," ISME Journal 9:385-395. PtH2O2lipids consists of two objects: A CAMERA xsAnnotate object (ptH2O2lipids$xsAnnotate) and LOBSTAHS LOBSet object (ptH2O2lipids$xsAnnotate$LOBSet). The LOBSet includes putative compound assignments from the default LOBSTAHS database. Isomer annotation is recorded in three other LOBSet slots. biocViews: ReproducibleResearch, CellCulture, MassSpectrometryData, Phaeodactylum_tricornutum_data Author: Shiri Graff van Creveld [aut], Shilo Rosenwasser [aut], Daniella Schatz [aut], Ilan Koren [aut], Assaf Vardi [aut], James Collins [cre] Maintainer: James Collins URL: http://dx.doi.org/10.1038/ismej.2014.136, https://github.com/vanmooylipidomics/PtH2O2lipids, http://www.whoi.edu/page.do?pid=133616&tid=282&cid=192529 BugReports: https://github.com/vanmooylipidomics/PtH2O2lipids/issues/new git_url: https://git.bioconductor.org/packages/PtH2O2lipids git_branch: RELEASE_3_9 git_last_commit: c8ee721 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/PtH2O2lipids_1.10.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE dependencyCount: 117 Package: pumadata Version: 2.20.0 Depends: R (>= 3.2.0), affy (>= 1.46.0), Biobase (>= 2.5.5),puma ,oligo(>= 1.32.0) License: LGPL MD5sum: bc4a7df5441823c28dfaa3c291750d5a 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: Richard Pearson URL: http://umber.sbs.man.ac.uk/resources/puma git_url: https://git.bioconductor.org/packages/pumadata git_branch: RELEASE_3_9 git_last_commit: 43fc0e8 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/pumadata_2.20.0.tar.gz vignettes: vignettes/pumadata/inst/doc/pumadata.pdf vignetteTitles: pumadata User Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pumadata/inst/doc/pumadata.R dependencyCount: 66 Package: PWMEnrich.Dmelanogaster.background Version: 4.18.0 Depends: methods, PWMEnrich License: GPL-3 MD5sum: ccbaca13154018cdc8ab613a92b77d67 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: Robert Stojnic git_url: https://git.bioconductor.org/packages/PWMEnrich.Dmelanogaster.background git_branch: RELEASE_3_9 git_last_commit: cdec337 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/PWMEnrich.Dmelanogaster.background_4.18.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 19 Package: PWMEnrich.Hsapiens.background Version: 4.18.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: ddb7753fa5b296989688aa37ebb52a66 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: Robert Stojnic git_url: https://git.bioconductor.org/packages/PWMEnrich.Hsapiens.background git_branch: RELEASE_3_9 git_last_commit: c7feff4 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/PWMEnrich.Hsapiens.background_4.18.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 19 Package: PWMEnrich.Mmusculus.background Version: 4.18.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: d9cab0ba0958913a7cfaac48f615513a 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: Robert Stojnic git_url: https://git.bioconductor.org/packages/PWMEnrich.Mmusculus.background git_branch: RELEASE_3_9 git_last_commit: b8c9b92 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/PWMEnrich.Mmusculus.background_4.18.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 19 Package: QDNAseq.hg19 Version: 1.14.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: 18bb6347a3912c344deca9f2646087b4 NeedsCompilation: no Title: QDNAseq bin annotation for hg19 Description: This package provides QDNAseq bin annotations for the human genome build hg19. biocViews: ExperimentData, OrganismData, Homo_sapiens_Data Author: Daoud Sie [aut, cre] Maintainer: Daoud Sie URL: https://github.com/tgac-vumc/QDNAseq.hg19 BugReports: https://github.com/tgac-vumc/QDNAseq.hg19/issues git_url: https://git.bioconductor.org/packages/QDNAseq.hg19 git_branch: RELEASE_3_9 git_last_commit: e7801f1 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/QDNAseq.hg19_1.14.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 41 Package: QDNAseq.mm10 Version: 1.14.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: 6f2c864b3e8cba93980603dd0c5b215e NeedsCompilation: no Title: Bin annotation mm10 Description: This package provides QDNAseq bin annotations for the mouse genome build mm10. biocViews: ExperimentData, OrganismData, Mus_musculus_Data Author: Daoud Sie [aut, cre] Maintainer: Daoud Sie URL: https://github.com/tgac-vumc/QDNAseq.mm10 BugReports: https://github.com/tgac-vumc/QDNAseq.mm10/issues git_url: https://git.bioconductor.org/packages/QDNAseq.mm10 git_branch: RELEASE_3_9 git_last_commit: ad421db git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/QDNAseq.mm10_1.14.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 41 Package: qPLEXdata Version: 1.2.0 Depends: R (>= 3.5), qPLEXanalyzer Imports: utils, knitr, MSnbase, dplyr License: GPL-2 MD5sum: e60329bb0a7c25957e0504beb98dd1f8 NeedsCompilation: no Title: Data accompanying qPLEXanalyzer package Description: qPLEX-RIME and Full proteome TMT mass spectrometry datasets. biocViews: ExperimentData, MassSpectrometryData, Proteome Author: Kamal Kishore Developer [aut, cre] Maintainer: Kamal Kishore Developer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/qPLEXdata git_branch: RELEASE_3_9 git_last_commit: c3fe91f git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/qPLEXdata_1.2.0.tar.gz vignettes: vignettes/qPLEXdata/inst/doc/qPLEXdata.pdf vignetteTitles: qPLEXdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/qPLEXdata/inst/doc/qPLEXdata.R dependencyCount: 102 Package: QUBICdata Version: 1.12.0 Depends: R (>= 3.1) Suggests: knitr, rmarkdown License: Unlimited | file LICENSE MD5sum: db90386771c4b586cb2e466881e897d6 NeedsCompilation: no Title: Data employed in the vignette of the QUBIC package Description: The data employed in the vignette of the QUBIC package. These data belong to Many Microbe Microarrays Database and STRING v10. biocViews: Escherichia_coli_Data, OrganismData, ExperimentData Author: Yu Zhang [aut, cre], Qin Ma [aut] Maintainer: Yu Zhang URL: http://github.com/zy26/QUBICdata VignetteBuilder: knitr BugReports: http://github.com/zy26/QUBICdata/issues git_url: https://git.bioconductor.org/packages/QUBICdata git_branch: RELEASE_3_9 git_last_commit: 5db46a0 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/QUBICdata_1.12.0.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 dependencyCount: 0 Package: rcellminerData Version: 2.6.0 Depends: R (>= 3.1.1), Biobase Suggests: knitr, testthat, BiocStyle, rcellminer License: LGPL-3 + file LICENSE MD5sum: d45f5a4a645566548f7b472e787b710a NeedsCompilation: no Title: rcellminerData: Molecular Profiles and Drug Response for the NCI-60 Cell Lines Description: The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data. biocViews: CancerData, CopyNumberVariationData, ExpressionData, SNPData, NCI, MicroarrayData, miRNAData Author: Augustin Luna, Vinodh Rajapakse, Fabricio Sousa Maintainer: Augustin Luna , Vinodh Rajapakse , Fathi Elloumi VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/rcellminerData git_branch: RELEASE_3_9 git_last_commit: 0e25f63 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/rcellminerData_2.6.0.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 dependencyCount: 7 Package: RcisTarget.hg19.motifDBs.cisbpOnly.500bp Version: 1.4.0 Depends: R (>= 3.3) Imports: data.table License: GPL-3 MD5sum: 2558d0f1567d5e36b21cc109a030d844 NeedsCompilation: no Title: RcisTarget motif databases for human (hg19) - Subset of 4.6k motifs Description: RcisTarget databases: Gene-based motif rankings and annotation to transcription factors. This package contains a subset of 4.6k motifs (cisbp motifs), scored only within 500bp upstream and the TSS. See RcisTarget tutorial to download the full databases, containing 20k motifs and search space up to 10kbp around the TSS. biocViews: Homo_sapiens_Data Author: Sara Aibar, Gert Hulselmans, Stein Aerts. Laboratory of Computational Biology, KU Leuven Center for Human Genetics. Leuven, Belgium. Maintainer: Sara Aibar URL: http://scenic.aertslab.org git_url: https://git.bioconductor.org/packages/RcisTarget.hg19.motifDBs.cisbpOnly.500bp git_branch: RELEASE_3_9 git_last_commit: 863d18b git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.4.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 2 Package: RegParallel Version: 1.2.0 Depends: doParallel, foreach, parallel, iterators, data.table, stringr, survival, arm, MASS, stats, utils, methods Suggests: RUnit, BiocGenerics, knitr, DESeq2, airway, magrittr, Biobase, GEOquery, biomaRt, survminer License: GPL-3 MD5sum: cebd94e58b4216cd3c14e4586d8761e1 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, Bayesian logistic regression, and negative binomial regression. biocViews: DiseaseModel Author: Kevin Blighe Maintainer: Kevin Blighe URL: https://github.com/kevinblighe/RegParallel VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RegParallel git_branch: RELEASE_3_9 git_last_commit: bcf64e7 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RegParallel_1.2.0.tar.gz vignettes: vignettes/RegParallel/inst/doc/RegParallel.html vignetteTitles: Standard regression functions in R enabled for parallel processing over large data-frames hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RegParallel/inst/doc/RegParallel.R dependencyCount: 32 Package: restfulSEData Version: 1.6.0 Depends: R (>= 3.4), SummarizedExperiment, ExperimentHub Imports: utils, methods Suggests: knitr License: Artistic-2.0 MD5sum: b057b9fc07de16899fa3ef2879d06f33 NeedsCompilation: no Title: Example metadata for the "restfulSE" R package Description: Metadata RangedSummarizedExperiment shell for use with restfulSE. biocViews: ExperimentData, Mus_musculus_Data, Homo_sapiens_Data, ExpressionData, SequencingData Author: Vincent Carey [aut], Shweta Gopaulakrishnan [cre, aut] Maintainer: Bioconductor Package Maintainer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/restfulSEData git_branch: RELEASE_3_9 git_last_commit: a7cadc5 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/restfulSEData_1.6.0.tar.gz vignettes: vignettes/restfulSEData/inst/doc/restfulSEData.pdf vignetteTitles: restfulSEData -- SummarizedExperiment shells for remote assay data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/restfulSEData/inst/doc/restfulSEData.R dependencyCount: 85 Package: RforProteomics Version: 1.22.0 Depends: MSnbase (>= 2.5.3) Imports: R.utils, shiny, biocViews, BiocManager Suggests: AnnotationDbi, rpx, DT, knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, isobar, MALDIquant (>= 1.12), MALDIquantForeign, readBrukerFlexData, rTANDEM, synapter, synapterdata, IPPD, Rdisop, OrgMassSpecR, SummarizedExperiment, BRAIN, rols, hpar, GO.db, org.Hs.eg.db, e1071, biomaRt, RColorBrewer, ggplot2, reshape2, xtable, lattice, mzID, pRoloc, pRolocdata, MSGFplus, MSGFgui, MSnID, msmsTests, msmsEDA, DEP, corrplot, beanplot, Heatplus, gplots, VennDiagram, protViz, genefilter, plotly, gridExtra, dplyr, lubridate Enhances: cleaver License: Artistic-2.0 MD5sum: b3512efa8224bd8069e638bae018384b NeedsCompilation: no Title: Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication Description: This package contains code to illustrate the 'Using R and Bioconductor for proteomics data analysis' and 'Visualisation of proteomics data using R and Bioconductor' manuscripts. The vignettes describe the code and data needed to reproduce the examples and figures described in the paper and functionality for proteomics visualisation. It also contain various function to discover R software for mass spectrometry and proteomics. biocViews: ExperimentData, MassSpectrometryData, ReproducibleResearch Author: Laurent Gatto [aut, cre], Thomas Lin Pedersen [ctb], Sebastian Gibb [ctb], Vlad Petyuk [ctb] Maintainer: Laurent Gatto URL: http://lgatto.github.com/RforProteomics/ VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RforProteomics git_branch: RELEASE_3_9 git_last_commit: 44f65d0 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RforProteomics_1.22.0.tar.gz vignettes: vignettes/RforProteomics/inst/doc/RforProteomics.html, vignettes/RforProteomics/inst/doc/RProtVis.html vignetteTitles: Using R for proteomics data analysis, Visualisation of proteomics data using R and Bioconductor hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RforProteomics/inst/doc/RforProteomics.R, vignettes/RforProteomics/inst/doc/RProtVis.R dependencyCount: 98 Package: RGMQLlib Version: 1.4.0 Depends: R(>= 3.4.2) Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: da01b2fe647643af1df9d3563c61f446 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, Marco Masseroli Maintainer: Simone Pallotta URL: http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/ VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RGMQLlib git_branch: RELEASE_3_9 git_last_commit: 15a2b14 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RGMQLlib_1.4.0.tar.gz vignettes: vignettes/RGMQLlib/inst/doc/RGMQLlib.pdf vignetteTitles: RGMQLlib: scala Libraries to support GMQL hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: rheumaticConditionWOLLBOLD Version: 1.22.0 Depends: R (>= 2.10.0) Suggests: genefilter, Biobase, hgu133plus2.db License: Artistic-2.0 MD5sum: b5d1fcb87c69694aaf7e3ceb24b15452 NeedsCompilation: no Title: Normalized gene expression dataset published by Wollbold et al. [2009] (WOLLBOLD). Description: Normalized gene expression data from rheumatic diseases from study published by Wollbold et al. in 2009, provided as an eSet. biocViews: ExperimentData, Tissue, MicroarrayData, MultiChannelData, ChipOnChipData, TissueMicroarrayData, GEO, ArrayExpress Author: Alejandro Quiroz-Zarate, John Quackenbush Maintainer: Alejandro Quiroz-Zarate URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/rheumaticConditionWOLLBOLD git_branch: RELEASE_3_9 git_last_commit: 2135e96 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/rheumaticConditionWOLLBOLD_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: RIPSeekerData Version: 1.20.0 Depends: RIPSeeker License: GPL-2 MD5sum: 5393a250ac8618929a6240d902c738d1 NeedsCompilation: no Title: test data for RIPSeeker Description: The RIP-seq data in BAM format are the test data for the package RIPSeeker. The data correspond to two RIP-seq experiments, namely PRC2 and CCNT1. Raw data from NCBI Gene Expression Omnibus under accession numbers GSE17064 for PRC2 and in-house for CCNT1. biocViews: ExperimentData, Genome, StemCell, SequencingData, RIPSeqData, GEO Author: Yue Li Maintainer: Alejandro Reyes git_url: https://git.bioconductor.org/packages/RIPSeekerData git_branch: RELEASE_3_9 git_last_commit: b125ca2 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RIPSeekerData_1.20.0.tar.gz vignettes: vignettes/RIPSeekerData/inst/doc/RIPSeekerData.pdf vignetteTitles: RIP-seq datasets for testing RIPSeeker package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RIPSeekerData/inst/doc/RIPSeekerData.R dependencyCount: 39 Package: RITANdata Version: 1.8.0 Depends: R (>= 3.4) License: file LICENSE MD5sum: 1e056a9bac392cc82d544af54324449e NeedsCompilation: no Title: This package contains the annotation and network data sets Description: Data such as is contained in these two R data files in this package are required for the RITAN package. Users may use their own or additional resources in conjunction with RITANdata. See the RITAN vignettes for more information. biocViews: AnnotationData, Homo_sapiens Author: Michael Zimmermann Maintainer: Michael Zimmermann VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RITANdata git_branch: RELEASE_3_9 git_last_commit: d91b2a4 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RITANdata_1.8.0.tar.gz vignettes: vignettes/RITANdata/inst/doc/RITANdata.html vignetteTitles: Vignette Title hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/RITANdata/inst/doc/RITANdata.R dependencyCount: 0 Package: RMassBankData Version: 1.22.0 Suggests: RMassBank License: Artistic-2.0 MD5sum: fc66ede0eb4d7ad10d96b38d2c1a212a NeedsCompilation: no Title: Test dataset for RMassBank Description: Example spectra, example compound list(s) and an example annotation list for a narcotics dataset; required to test RMassBank. The package is described in the man page for RMassBankData. Includes new XCMS test data. biocViews: ExperimentData, MassSpectrometryData Author: Michael Stravs, Emma Schymanski, Steffen Neumann Maintainer: Michael Stravs, Emma Schymanski git_url: https://git.bioconductor.org/packages/RMassBankData git_branch: RELEASE_3_9 git_last_commit: 4454ba9 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RMassBankData_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: RNAinteractMAPK Version: 1.22.0 Depends: R (>= 2.12.0), methods, fields, sparseLDA, RNAinteract Imports: grid, gdata, MASS, genefilter Suggests: qvalue, lattice License: Artistic-2.0 MD5sum: d8ae6fcd34f94ad097f1948ccdefcc5e NeedsCompilation: no Title: Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi Description: This package includes all data used in the paper -Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi- by Horn, Sandmann, Fischer et al.., Nat. Methods, 2011. The package vignette shows the R code to reproduce all figures in the paper. biocViews: ExperimentData, MicrotitrePlateAssayData, Drosophila_melanogaster_Data, CellCulture Author: Bernd Fischer Maintainer: Bernd Fischer git_url: https://git.bioconductor.org/packages/RNAinteractMAPK git_branch: RELEASE_3_9 git_last_commit: eaf7b3f git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RNAinteractMAPK_1.22.0.tar.gz vignettes: vignettes/RNAinteractMAPK/inst/doc/RNAinteractMAPK.pdf vignetteTitles: RNAinteractMAPK hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RNAinteractMAPK/inst/doc/RNAinteractMAPK.R suggestsMe: DmelSGI dependencyCount: 114 Package: RNAseqData.HNRNPC.bam.chr14 Version: 0.22.0 Suggests: GenomicAlignments, BiocManager License: LGPL MD5sum: 355b2ea49c593b0f4d0284d7c47f8686 NeedsCompilation: no Title: Aligned reads from RNAseq experiment: Transcription profiling by high throughput sequencing of HNRNPC knockdown and control HeLa cells Description: The package contains 8 BAM files, 1 per sequencing run. Each BAM file was obtained by (1) aligning the reads (paired-end) to the full hg19 genome with TopHat2, and then (2) subsetting to keep only alignments on chr14. See accession number E-MTAB-1147 in the ArrayExpress database for details about the experiment, including links to the published study (by Zarnack et al., 2012) and to the FASTQ files. biocViews: ExperimentData, Genome, Homo_sapiens_Data, SequencingData, GEO, NCI, RNASeqData, ArrayExpress Author: Hervé Pagès Maintainer: Hervé Pagès URL: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1147/ git_url: https://git.bioconductor.org/packages/RNAseqData.HNRNPC.bam.chr14 git_branch: RELEASE_3_9 git_last_commit: 3d6d343 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RNAseqData.HNRNPC.bam.chr14_0.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: RNASeqRData Version: 1.2.0 Depends: R (>= 3.5.0) Suggests: png, grid License: Artistic-2.0 MD5sum: 48362fed1dbde122a713bc0c238b85ce NeedsCompilation: no Title: RNASeqRData: sample data for RNASeqR software package demonstration Description: RNASeqRData is a helper experiment package for vignette demonstration purpose in RNASeqR software package. biocViews: ExperimentData, Saccharomyces_cerevisiae_Data Author: Kuan-Hao Chao Maintainer: Kuan-Hao Chao git_url: https://git.bioconductor.org/packages/RNASeqRData git_branch: RELEASE_3_9 git_last_commit: 6bc6aad git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RNASeqRData_1.2.0.tar.gz vignettes: vignettes/RNASeqRData/inst/doc/RNASeqRData.html vignetteTitles: RNASeqRData.html hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: RnaSeqSampleSizeData Version: 1.16.0 Depends: edgeR,R (>= 2.10) Suggests: BiocStyle, knitr License: GPL (>= 2) MD5sum: b5807095357790233a3b0901e093d4e2 NeedsCompilation: no Title: RnaSeqSampleSizeData Description: RnaSeqSampleSizeData package provides the read counts and dispersion distribution from real RNA-seq experiments. It can be used by RnaSeqSampleSize package to estimate sample size and power for RNA-seq experiment design. biocViews: ExperimentData, CancerData, RNASeqData Author: Shilin Zhao, Chung-I Li, Yan Guo, Quanhu Sheng, Yu Shyr Maintainer: Shilin Zhao VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RnaSeqSampleSizeData git_branch: RELEASE_3_9 git_last_commit: b07ddb5 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RnaSeqSampleSizeData_1.16.0.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 dependencyCount: 11 Package: RnBeads.hg19 Version: 1.16.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 49124fe698070ac641edccd84738a403 NeedsCompilation: no Title: RnBeads.hg19 Description: Automatically generated RnBeads annotation package for the assembly hg19. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.hg19 git_branch: RELEASE_3_9 git_last_commit: e9d1d50 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RnBeads.hg19_1.16.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 16 Package: RnBeads.hg38 Version: 1.16.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 1f69ca76421c139e33d51cd6257d61ec NeedsCompilation: no Title: RnBeads.hg38 Description: Automatically generated RnBeads annotation package for the assembly hg38. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.hg38 git_branch: RELEASE_3_9 git_last_commit: 06c5c71 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RnBeads.hg38_1.16.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 16 Package: RnBeads.mm10 Version: 1.16.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: bc59c0c33a16831ea8b9b55e17a9b3dc NeedsCompilation: no Title: RnBeads.mm10 Description: Automatically generated RnBeads annotation package for the assembly mm10. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.mm10 git_branch: RELEASE_3_9 git_last_commit: 54898a6 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RnBeads.mm10_1.16.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 16 Package: RnBeads.mm9 Version: 1.16.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: bf09e958b0bbf362715e29f29f1f9089 NeedsCompilation: no Title: RnBeads.mm9 Description: Automatically generated RnBeads annotation package for the assembly mm9. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.mm9 git_branch: RELEASE_3_9 git_last_commit: 1cd37b8 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RnBeads.mm9_1.16.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 16 Package: RnBeads.rn5 Version: 1.16.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 1fa4dc52e604abd00c95bf29702eb9f2 NeedsCompilation: no Title: RnBeads.rn5 Description: Automatically generated RnBeads annotation package for the assembly rn5. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.rn5 git_branch: RELEASE_3_9 git_last_commit: 2cc1f6e git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RnBeads.rn5_1.16.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 16 Package: RRBSdata Version: 1.4.0 Depends: R (>= 3.1.0), BiSeq (>= 1.9.2) License: LGPL-3 MD5sum: 53ac77ef644a80ac96da8a6b8ff1ae80 NeedsCompilation: no Title: An RRBS data set with 12 samples and 10,000 simulated DMRs Description: RRBS data set comprising 12 samples with simulated differentially methylated regions (DMRs). biocViews: ExperimentData, CancerData, SequencingData, CpGIslandData Author: Katja Hebestreit, Hans-Ulrich Klein Maintainer: Katja Hebestreit git_url: https://git.bioconductor.org/packages/RRBSdata git_branch: RELEASE_3_9 git_last_commit: 1725258 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RRBSdata_1.4.0.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: 74 Package: rRDPData Version: 1.4.0 Depends: rRDP License: GPL-2 MD5sum: c86d4a780bd0a4c15addf5654bda6fc9 NeedsCompilation: no Title: Database for the Default RDP Classifier Description: Database used by the default RDP Classifier biocViews: SequencingData, MicrobiomeData Author: Michael Hahsler, Anurag Nagar Maintainer: Michael Hahsler SystemRequirements: Java git_url: https://git.bioconductor.org/packages/rRDPData git_branch: RELEASE_3_9 git_last_commit: e08e8e2 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/rRDPData_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 13 Package: RTCGA.clinical Version: 20151101.14.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 7d65d00fe077a509138e6234d9195cd3 NeedsCompilation: no Title: Clinical datasets from The Cancer Genome Atlas Project Description: Package provides clinical datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Clinical data format is explained here https://wiki.nci.nih.gov/display/TCGA/Clinical+Data+Overview. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.clinical git_branch: RELEASE_3_9 git_last_commit: 60183e6 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RTCGA.clinical_20151101.14.0.tar.gz vignettes: vignettes/RTCGA.clinical/inst/doc/downloading_clinical_datasets.html vignetteTitles: Using RTCGA to download clinical data as included in RTCGA.clinical hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.clinical/inst/doc/downloading_clinical_datasets.R dependencyCount: 92 Package: RTCGA.CNV Version: 1.12.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 45de80778e2b1ff9334485bf4b86d268 NeedsCompilation: no Title: CNV (Copy-number variation) datasets from The Cancer Genome Atlas Project Description: Package provides CNV (based on Merge snp) datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Retrieving +Data+Using+the+Data+Matrix. Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Przemyslaw Biecek Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.CNV git_branch: RELEASE_3_9 git_last_commit: 34011b6 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RTCGA.CNV_1.12.0.tar.gz vignettes: vignettes/RTCGA.CNV/inst/doc/downloading_cnv_datasets.html, vignettes/RTCGA.CNV/inst/doc/frequency_of_cnv_for_mdm3.html vignetteTitles: Using RTCGA to download CNV data as included in RTCGA.CNV, Using RTCGA to estimate ratio of MDM2 duplications hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.CNV/inst/doc/downloading_cnv_datasets.R, vignettes/RTCGA.CNV/inst/doc/frequency_of_cnv_for_mdm3.R dependencyCount: 92 Package: RTCGA.methylation Version: 1.12.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 39f7bae6e164ffe53315ddbf7ed3b168 NeedsCompilation: no Title: Methylation datasets from The Cancer Genome Atlas Project Description: Package provides methylation (humanmethylation27) datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/DNA+methylation Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Marcin Kosinski [aut, cre], Witold Chodor [aut] Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.methylation git_branch: RELEASE_3_9 git_last_commit: a6fce73 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RTCGA.methylation_1.12.0.tar.gz vignettes: vignettes/RTCGA.methylation/inst/doc/downloading_methylation_datasets.html vignetteTitles: Using RTCGA to download methylation data as included in RTCGA.methylation hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.methylation/inst/doc/downloading_methylation_datasets.R dependencyCount: 92 Package: RTCGA.miRNASeq Version: 1.12.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 8b0c9b1c5fb35170ec999dc1875194a9 NeedsCompilation: no Title: miRNASeq datasets from The Cancer Genome Atlas Project Description: Package provides miRNASeq datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/miRNASeq#miRNASeq-DataOverview Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.miRNASeq git_branch: RELEASE_3_9 git_last_commit: 5b3935f git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RTCGA.miRNASeq_1.12.0.tar.gz vignettes: vignettes/RTCGA.miRNASeq/inst/doc/downloading_miRNASeq_datasets.html vignetteTitles: Using RTCGA to download miRNASeq data as included in RTCGA.miRNASeq hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.miRNASeq/inst/doc/downloading_miRNASeq_datasets.R dependencyCount: 92 Package: RTCGA.mRNA Version: 1.12.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 87f5ceb10640bc62bf465e6d0137fd0e NeedsCompilation: no Title: mRNA datasets from The Cancer Genome Atlas Project Description: Package provides mRNA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Gene+expression+data Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.mRNA git_branch: RELEASE_3_9 git_last_commit: 6096167 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RTCGA.mRNA_1.12.0.tar.gz vignettes: vignettes/RTCGA.mRNA/inst/doc/downloading_mRNA_datasets.html vignetteTitles: Using RTCGA to download mRNA data as included in RTCGA.mRNA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.mRNA/inst/doc/downloading_mRNA_datasets.R dependencyCount: 92 Package: RTCGA.mutations Version: 20151101.14.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: cf3d79748430e6c9afc08dc1d28aa8a9 NeedsCompilation: no Title: Mutations datasets from The Cancer Genome Atlas Project Description: Package provides mutations datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Mutations data format is explained here https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+(MAF)+Specification. There is extra one column with patients' barcodes. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.mutations git_branch: RELEASE_3_9 git_last_commit: 8d81a06 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RTCGA.mutations_20151101.14.0.tar.gz vignettes: vignettes/RTCGA.mutations/inst/doc/downloading_mutations_datasets.html vignetteTitles: Using RTCGA to download mutations data as included in RTCGA.mutations hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.mutations/inst/doc/downloading_mutations_datasets.R dependencyCount: 92 Package: RTCGA.PANCAN12 Version: 1.12.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: d245828f779b7cf0ca7cf3263d700b15 NeedsCompilation: no Title: PanCan 12 from Genome Cancer Browser Description: Package provides clinical, expression, cnv and mutation data from Genome Cancer Browser. biocViews: AnnotationData Author: Przemyslaw Biecek Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.PANCAN12 git_branch: RELEASE_3_9 git_last_commit: b4dc746 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RTCGA.PANCAN12_1.12.0.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 dependencyCount: 92 Package: RTCGA.rnaseq Version: 20151101.14.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 2a388fc3928cbbd967a5a7a742574a16 NeedsCompilation: no Title: Rna-seq datasets from The Cancer Genome Atlas Project Description: Package provides rna-seq datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Rna-seq data format is explained here https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2. Data source is illumina hiseq Level 3 RSEM normalized expression data. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.rnaseq git_branch: RELEASE_3_9 git_last_commit: 3365f5f git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RTCGA.rnaseq_20151101.14.0.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 dependencyCount: 92 Package: RTCGA.RPPA Version: 1.12.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 0e74a091c00ddaabd10c8ccab0e38248 NeedsCompilation: no Title: RPPA datasets from The Cancer Genome Atlas Project Description: Package provides RPPA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Protein+Array +Data+Format+Specification?src=search biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.RPPA git_branch: RELEASE_3_9 git_last_commit: adfc3dd git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RTCGA.RPPA_1.12.0.tar.gz vignettes: vignettes/RTCGA.RPPA/inst/doc/downloading_RPPA_datasets.html vignetteTitles: Using RTCGA to download RPPA data as included in RTCGA.RPPA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.RPPA/inst/doc/downloading_RPPA_datasets.R dependencyCount: 92 Package: RUVnormalizeData Version: 1.4.0 Depends: R (>= 2.10.0), Biobase License: GPL-3 MD5sum: cf46437c54508c46e43c5679bdedf2b0 NeedsCompilation: no Title: Gender data for the RUVnormalize package Description: Microarray gene expression data from the study of Vawter et al., 2004. biocViews: MicroarrayData Author: Laurent Jacob Maintainer: Laurent Jacob git_url: https://git.bioconductor.org/packages/RUVnormalizeData git_branch: RELEASE_3_9 git_last_commit: 1a8dd93 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/RUVnormalizeData_1.4.0.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 dependencyCount: 7 Package: sampleClassifierData Version: 1.8.0 Depends: R (>= 3.4), SummarizedExperiment Suggests: BiocStyle License: Artistic-2.0 MD5sum: 6fcc9c1340d095ffb07ab865540dbe72 NeedsCompilation: no Title: Pre-processed data for use with the sampleClassifier package Description: This package contains two microarray and two RNA-seq datasets that have been preprocessed for use with the sampleClassifier package. The RNA-seq data are derived from Fagerberg et al. (2014) and the Illumina Body Map 2.0 data. The microarray data are derived from Roth et al. (2006) and Ge et al. (2005). biocViews: ExperimentData, ExpressionData, MicroarrayData, SequencingData, RNASeqData, ArrayExpress Author: Khadija El Amrani Maintainer: Khadija El Amrani git_url: https://git.bioconductor.org/packages/sampleClassifierData git_branch: RELEASE_3_9 git_last_commit: d02d670 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/sampleClassifierData_1.8.0.tar.gz vignettes: vignettes/sampleClassifierData/inst/doc/sampleClassifierData.pdf vignetteTitles: sampleClassifierData Introduction hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/sampleClassifierData/inst/doc/sampleClassifierData.R dependencyCount: 32 Package: SCLCBam Version: 1.16.0 Depends: R(>= 2.10) Suggests: BiocStyle License: GPL-2 MD5sum: e3a0df322f55197c0f2edf05cb00e655 NeedsCompilation: no Title: Sequence data from chromosome 4 of a small-cell lung tumor Description: Whole-exome sequencing data from a murine small-cell lung tumor; only contains data of chromosome 4. biocViews: SequencingData, LungCancerData Author: Thomas Kuilman Maintainer: Oscar Krijgsman git_url: https://git.bioconductor.org/packages/SCLCBam git_branch: RELEASE_3_9 git_last_commit: 9903b74 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/SCLCBam_1.16.0.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: scRNAseq Version: 1.10.0 Depends: R (>= 3.3), SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown License: CC0 MD5sum: e9aded444d5781911c8678274f7abbbe NeedsCompilation: no Title: A Collection of Public Single-Cell RNA-Seq Datasets Description: Gene-level read counts of three public scRNA-seq datasets. See vignette for details. biocViews: ExperimentData, ExpressionData, SequencingData, RNASeqData Author: Davide Risso [aut, cre, cph], Michael Cole [aut] Maintainer: Davide Risso VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/scRNAseq git_branch: RELEASE_3_9 git_last_commit: 9461d1f git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/scRNAseq_1.10.0.tar.gz vignettes: vignettes/scRNAseq/inst/doc/scRNAseq.html vignetteTitles: scRNAseq hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scRNAseq/inst/doc/scRNAseq.R dependencyCount: 32 Package: seq2pathway.data Version: 1.16.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: a41f1f988fee568e2437562bfca8703c 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: Xinan Holly Yang git_url: https://git.bioconductor.org/packages/seq2pathway.data git_branch: RELEASE_3_9 git_last_commit: e116492 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/seq2pathway.data_1.16.0.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 dependencyCount: 0 Package: seqc Version: 1.18.0 Depends: R (>= 2.10) Imports: utils, Biobase License: GPL-3 MD5sum: 8ed0537e3d25d12ed357d0e570e30049 NeedsCompilation: no Title: RNA-seq data generated from SEQC (MAQC-III) study Description: The SEQC/MAQC-III Consortium has produced benchmark RNA-seq data for the assessment of RNA sequencing technologies and data analysis methods (Nat Biotechnol, 2014). Billions of sequence reads have been generated from ten different sequencing sites. This package contains the summarized read count data for ~2000 sequencing libraries. It also includes all the exon-exon junctions discovered from the study. TaqMan RT-PCR data for ~1000 genes and ERCC spike-in sequence data are included in this package as well. biocViews: ExperimentData, RNASeqData, qPCRData, SequencingData Author: Yang Liao and Wei Shi with contributions from Gordon K Smyth and Steve Lianoglou. Maintainer: Yang Liao and Wei Shi URL: http://bioconductor.org/packages/release/data/experiment/html/seqc.html git_url: https://git.bioconductor.org/packages/seqc git_branch: RELEASE_3_9 git_last_commit: ed11949 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/seqc_1.18.0.tar.gz vignettes: vignettes/seqc/inst/doc/seqc.pdf vignetteTitles: SEQC Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/seqc/inst/doc/seqc.R dependencyCount: 7 Package: seqCNA.annot Version: 1.20.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 4a10eacbb147f709e82af786f2566def NeedsCompilation: no Title: Annotation for the copy number analysis of deep sequencing cancer data with seqCNA Description: Provides annotation on GC content, mappability and genomic features for various genomes biocViews: Genome, CopyNumberVariationData Author: David Mosen-Ansorena Maintainer: David Mosen-Ansorena git_url: https://git.bioconductor.org/packages/seqCNA.annot git_branch: RELEASE_3_9 git_last_commit: 17d7022 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/seqCNA.annot_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: serumStimulation Version: 1.20.0 Depends: R (>= 2.10) License: GPL (>= 2) MD5sum: 7fabd88ad4038ffd70bb9b8b27738947 NeedsCompilation: no Title: serumStimulation is a data package which is used by examples in package pcaGoPromoter Description: Contains 13 micro array data results from a serum stimulation experiment biocViews: ExperimentData, MicroarrayData Author: Morten Hansen Maintainer: Morten Hansen, git_url: https://git.bioconductor.org/packages/serumStimulation git_branch: RELEASE_3_9 git_last_commit: 4fbbf08 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/serumStimulation_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: sesameData Version: 1.2.0 Depends: R (>= 3.5), ExperimentHub, AnnotationHub Imports: utils, curl Suggests: GenomicRanges, BiocGenerics, sesame, testthat, knitr License: Artistic-2.0 MD5sum: 1be0375bcd00351ee53e3ea7b812bfab NeedsCompilation: no Title: Supporting Data for SeSAMe Package Description: Provides supporting annotation and test data for SeSAMe package. biocViews: ExperimentData, MicroarrayData, Genome Author: Wanding Zhou [aut, cre], Hui Shen [aut], Timothy Triche [ctb] Maintainer: Wanding Zhou VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/sesameData git_branch: RELEASE_3_9 git_last_commit: 70056dc git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/sesameData_1.2.0.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 dependencyCount: 66 Package: seventyGeneData Version: 1.20.0 Depends: R (>= 2.13.0) Suggests: Biobase, gdata, limma, breastCancerNKI License: Artistic-2.0 MD5sum: 8a2c6bc5c05bb81a31f58667cde3018d NeedsCompilation: no Title: ExpressionSets from the van't Veer and Van de Vijver breast cancer studies Description: Gene expression data for the two breast cancer cohorts published by van't Veer and Van de Vijver in 2002 biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData Author: Luigi Marchionni Maintainer: Luigi Marchionni URL: http://luigimarchionni.org/breastTSP.html git_url: https://git.bioconductor.org/packages/seventyGeneData git_branch: RELEASE_3_9 git_last_commit: 896f589 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/seventyGeneData_1.20.0.tar.gz vignettes: vignettes/seventyGeneData/inst/doc/seventyGeneData.pdf vignetteTitles: Working with the seventyGeneData package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/seventyGeneData/inst/doc/seventyGeneData.R dependencyCount: 0 Package: shinyMethylData Version: 1.4.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: f646ba21155e7392c9b00814e56e6967 NeedsCompilation: no Title: Example dataset of input data for shinyMethyl Description: Extracted data from 369 TCGA Head and Neck Cancer DNA methylation samples. The extracted data serve as an example dataset for the package shinyMethyl. Original samples are from 450k methylation arrays, and were obtained from The Cancer Genome Atlas (TCGA). 310 samples are from tumor, 50 are matched normals and 9 are technical replicates of a control cell line. biocViews: Genome, CancerData Author: Jean-Philippe Fortin [cre, aut], Kasper Daniel Hansen [aut] Maintainer: Jean-Philippe Fortin git_url: https://git.bioconductor.org/packages/shinyMethylData git_branch: RELEASE_3_9 git_last_commit: 4086d7e git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/shinyMethylData_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: simpIntLists Version: 1.20.0 License: GPL (>= 2) MD5sum: 27879fea1d9ddd0404829b7de8eaae77 NeedsCompilation: no Title: The package contains BioGRID interactions for various organisms in a simple format Description: The package contains BioGRID interactions for arabidopsis(thale cress), c.elegans, fruit fly, human, mouse, yeast( budding yeast ) and S.pombe (fission yeast) . Entrez ids, official names and unique ids can be used to find proteins. The format of interactions are lists. For each gene/protein, there is an entry in the list with "name" containing name of the gene/protein and "interactors" containing the list of genes/proteins interacting with it. biocViews: ExperimentData, Arabidopsis_thaliana_Data Author: Kircicegi Korkmaz, Volkan Atalay, Rengul Cetin-Atalay Maintainer: Kircicegi Korkmaz git_url: https://git.bioconductor.org/packages/simpIntLists git_branch: RELEASE_3_9 git_last_commit: 8f02722 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/simpIntLists_1.20.0.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 dependencyCount: 0 Package: Single.mTEC.Transcriptomes Version: 1.12.0 Depends: R (>= 3.5.0) Suggests: DESeq2, GenomicRanges, GenomicFeatures, genefilter, statmod, gdata, RColorBrewer, ggplot2, gplots, cluster, clue, grid, gridExtra, ggbio, Gviz, geneplotter, matrixStats, pheatmap, BiocStyle, knitr License: LGPL MD5sum: 8d1e883b5ca8e20ba358a4988827fb6c NeedsCompilation: no Title: Single Cell Transcriptome Data and Analysis of Mouse mTEC cells Description: This data package contains the code used to analyse the single-cell RNA-seq and the bulk ATAC-seq data from the manuscript titled: Single-cell transcriptome analysis reveals coordinated ectopic-gene expression patterns in medullary thymic epithelial cells. This paper was published in Nature Immunology 16,933-941(2015). The data objects provided in this package has been pre-processed: the raw data files can be downloaded from ArrayExpress under the accession identifiers E-MTAB-3346 and E-MTAB-3624. The vignette of this data package provides a documented and reproducible workflow that includes the code that was used to generate each statistic and figure from the manuscript. biocViews: ExperimentData Author: Alejandro Reyes Maintainer: Alejandro Reyes VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/Single.mTEC.Transcriptomes git_branch: RELEASE_3_9 git_last_commit: 21064d4 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/Single.mTEC.Transcriptomes_1.12.0.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: SNAData Version: 1.30.0 Depends: R (>= 2.4.0), graph Suggests: Rgraphviz License: LGPL MD5sum: aebebfd31a60cb7878138c1aadea000d NeedsCompilation: no Title: Social Networks Analysis Data Examples Description: Data from Wasserman & Faust (1999) "Social Network Analysis" biocViews: ExperimentData Author: Denise Scholtens Maintainer: Denise Scholtens git_url: https://git.bioconductor.org/packages/SNAData git_branch: RELEASE_3_9 git_last_commit: ee8f6eb git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/SNAData_1.30.0.tar.gz vignettes: vignettes/SNAData/inst/doc/SNAData.pdf vignetteTitles: SNAData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SNAData/inst/doc/SNAData.R dependencyCount: 8 Package: SNAGEEdata Version: 1.20.0 Depends: R (>= 2.6.0) Suggests: ALL, hgu95av2.db, SNAGEE License: Artistic-2.0 MD5sum: 6f95756e911a82831c37171ed8192d7a NeedsCompilation: no Title: SNAGEE data Description: SNAGEE data - gene list and correlation matrix biocViews: MicroarrayData Author: David Venet Maintainer: David Venet URL: http://fleming.ulb.ac.be/SNAGEE git_url: https://git.bioconductor.org/packages/SNAGEEdata git_branch: RELEASE_3_9 git_last_commit: 5341a91 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/SNAGEEdata_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: SNPhoodData Version: 1.14.0 Depends: R (>= 3.2) Suggests: BiocStyle,knitr,rmarkdown License: LGPL (>= 3) MD5sum: 932f101b78576f7a6407704d3031fdbf NeedsCompilation: no Title: Additional and more complex example data for the SNPhood package Description: This companion package for SNPhood provides some example datasets of a larger size than allowed for the SNPhood package. They include full and real-world examples for performing analyses with the SNPhood package. biocViews: ExperimentData Author: Christian Arnold, Judith Zaugg Maintainer: Christian Arnold VignetteBuilder: knitr BugReports: christian.arnold@embl.de git_url: https://git.bioconductor.org/packages/SNPhoodData git_branch: RELEASE_3_9 git_last_commit: 78a0557 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/SNPhoodData_1.14.0.tar.gz vignettes: vignettes/SNPhoodData/inst/doc/SNPhoodData.html vignetteTitles: The *SNPhoodData* package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: SomatiCAData Version: 1.22.0 Depends: R (>= 2.14) License: Artistic-2.0 MD5sum: 59d6519327a11557942dceb5765787bb NeedsCompilation: no Title: An example cancer whole genome sequencing data for the SomatiCA package Description: An example cancer whole genome sequencing data for the SomatiCA package biocViews: ExperimentData, Genome, CancerData, SequencingData Author: Mengjie Chen Maintainer: Mengjie Chen git_url: https://git.bioconductor.org/packages/SomatiCAData git_branch: RELEASE_3_9 git_last_commit: bb7beb1 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/SomatiCAData_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: SomaticCancerAlterations Version: 1.20.0 Depends: R (>= 3.0.0) Imports: GenomicRanges, exomeCopy, stringr, IRanges, S4Vectors Suggests: testthat, ggbio, ggplot2, knitr License: GPL-3 MD5sum: aaf2b8c5ef006b545d1c383fefa35dca NeedsCompilation: no Title: Somatic Cancer Alterations Description: Collection of somatic cancer alteration datasets biocViews: ExperimentData, Genome, CancerData, Project1000genomes, NCI Author: Julian Gehring (EMBL Heidelberg) Maintainer: Julian Gehring VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/SomaticCancerAlterations git_branch: RELEASE_3_9 git_last_commit: b4005ea git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/SomaticCancerAlterations_1.20.0.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 dependencyCount: 32 Package: SpikeIn Version: 1.26.0 Depends: R (>= 1.6), affy (>= 1.23.4) License: Artistic-2.0 MD5sum: 3c7f3d87c555ee68feafd95a518caf1d NeedsCompilation: no Title: Affymetrix Spike-In Experiment Data Description: Contains the HGU133 and HGU95 spikein experiment data. biocViews: ExperimentData, MicroarrayData Author: Rafael Irizarry Maintainer: Rafael A. Irizarry git_url: https://git.bioconductor.org/packages/SpikeIn git_branch: RELEASE_3_9 git_last_commit: e2a8dd5 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/SpikeIn_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 13 Package: SpikeInSubset Version: 1.24.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5), affy (>= 1.23.4) License: LGPL MD5sum: 5b7cc17fe60a8c139f555c9ddd25eada NeedsCompilation: no Title: Part of Affymetrix's Spike-In Experiment Data Description: Includes probe-level and expression data for the HGU133 and HGU95 spike-in experiments biocViews: ExperimentData, MicroarrayData Author: Rafael Irizarry and Zhijin Wu Maintainer: Rafael A. Irizarry git_url: https://git.bioconductor.org/packages/SpikeInSubset git_branch: RELEASE_3_9 git_last_commit: 957e773 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/SpikeInSubset_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 13 Package: stemHypoxia Version: 1.20.0 Depends: R (>= 2.14.1) License: GPL (>=2) MD5sum: a70572433e20a5cc9cdbac997ab05728 NeedsCompilation: no Title: Differentiation of Human Embryonic Stem Cells under Hypoxia gene expression dataset by Prado-Lopez et al. (2010) Description: Expression profiling using microarray technology to prove if 'Hypoxia Promotes Efficient Differentiation of Human Embryonic Stem Cells to Functional Endothelium' by Prado-Lopez et al. (2010) Stem Cells 28:407-418. Full data available at Gene Expression Omnibus series GSE37761. biocViews: ExperimentData, Tissue, StemCell, Homo_sapiens_Data, CancerData, MicroarrayData, TissueMicroarrayData, GEO Author: Cristobal Fresno and Elmer A. Fernandez Maintainer: Cristobal Fresno URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37761, http://onlinelibrary.wiley.com/doi/10.1002/stem.295/abstract git_url: https://git.bioconductor.org/packages/stemHypoxia git_branch: RELEASE_3_9 git_last_commit: b6867f0 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/stemHypoxia_1.20.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: stjudem Version: 1.24.0 Depends: R (>= 2.10), utils License: LGPL (>= 2) MD5sum: 35358ac2317e7d083d373b6db1d0cbd9 NeedsCompilation: no Title: Microarray Data from Yeoh et al. in MACAT format Description: This is a microarray data set on acute lymphoblastic leukemia, published in 2002 (Yeoh et al.Cancer Cell 2002). The experiments were conducted in the St.Jude Children's Research Hospital, Memphis, Tenessee, USA. The raw data was preprocessed by variance stabilizing normalization (Huber et al.) on probe and subsequent summarization of probe expression values into probe set expression values using median polish. biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData, ChipOnChipData Author: Benjamin Georgi, Matthias Heinig, Sebastian Schmeier, Joern Toedling Maintainer: Joern Toedling git_url: https://git.bioconductor.org/packages/stjudem git_branch: RELEASE_3_9 git_last_commit: 65ab209 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/stjudem_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 1 Package: SVM2CRMdata Version: 1.16.0 Depends: R(>= 3.2.0) License: LGPL (>= 2) MD5sum: 205df5b059ee9465b8d95c0ed1f6d4dc NeedsCompilation: no Title: An example dataset for use with the SVM2CRM package Description: An example dataset for use with the SVM2CRM package. biocViews: ExperimentData, ChIPSeq, HistoneModification, Preprocessing, DataImport Author: Guidantonio Malagoli Tagliazucchi Maintainer: Guidantonio Malagoli Tagliazucchi git_url: https://git.bioconductor.org/packages/SVM2CRMdata git_branch: RELEASE_3_9 git_last_commit: 2a184f0 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/SVM2CRMdata_1.16.0.tar.gz vignettes: vignettes/SVM2CRMdata/inst/doc/SVM2CRMdata.pdf vignetteTitles: The \Rpackage{SVM2CRMdata} Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SVM2CRMdata/inst/doc/SVM2CRMdata.R dependencyCount: 0 Package: synapterdata Version: 1.22.0 Depends: R (>= 2.10), synapter (>= 1.99.2) Imports: utils License: GPL-2 MD5sum: 65584fbc942c508d5dd722f1eebc73d7 NeedsCompilation: no Title: Data accompanying the synapter package Description: Data independant acquisition of UPS1 protein mix in an E. coli background obtained on a Waters Synapt G2 instrument. biocViews: ExperimentData, MassSpectrometryData Author: Laurent Gatto, Sebastian Gibb and Pavel V. Shliaha Maintainer: Laurent Gatto git_url: https://git.bioconductor.org/packages/synapterdata git_branch: RELEASE_3_9 git_last_commit: 740fc32 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/synapterdata_1.22.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics dependencyCount: 101 Package: systemPipeRdata Version: 1.12.0 Depends: methods Imports: BiocGenerics Suggests: RUnit, BiocStyle, knitr, rmarkdown, systemPipeR License: Artistic-2.0 MD5sum: c8d11c0e23f871eea5f073d749b26be0 NeedsCompilation: no Title: systemPipeRdata: NGS 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 Author: Thomas Girke Maintainer: Thomas Girke URL: https://github.com/tgirke/systemPipeRdata VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/systemPipeRdata git_branch: RELEASE_3_9 git_last_commit: 47e924d git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/systemPipeRdata_1.12.0.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: ChIP-Seq Workflow Template, systemPipeRdata: NGS workflow templates and sample data, RIBO-Seq Workflow Template, RNA-Seq Workflow Template, VAR-Seq Workflow Template hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/systemPipeRdata/inst/doc/systemPipeChIPseq.R, vignettes/systemPipeRdata/inst/doc/systemPipeRdata.R, vignettes/systemPipeRdata/inst/doc/systemPipeRIBOseq.R, vignettes/systemPipeRdata/inst/doc/systemPipeRNAseq.R, vignettes/systemPipeRdata/inst/doc/systemPipeVARseq.R dependencyCount: 6 Package: TabulaMurisData Version: 1.2.0 Depends: R (>= 3.5) Imports: ExperimentHub, utils Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran, scater, iSEE, testthat License: MIT + file LICENSE MD5sum: ba5ccbb99aed729f12a3805313f53cd3 NeedsCompilation: no Title: 10x And SmartSeq2 Data From The Tabula Muris Consortium Description: Access to processed 10x (droplet) and SmartSeq2 (on FACS-sorted cells) single-cell RNA-seq data from the Tabula Muris consortium (http://tabula-muris.ds.czbiohub.org/). biocViews: SingleCellData, ExperimentData, RNASeqData Author: Charlotte Soneson [aut, cre] () Maintainer: Charlotte Soneson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TabulaMurisData git_branch: RELEASE_3_9 git_last_commit: d4f5ddf git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/TabulaMurisData_1.2.0.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: 66 Package: TargetScoreData Version: 1.20.0 Suggests: TargetScore, gplots License: GPL-2 MD5sum: efd1b3db6b4f1ed8c3ac1ddb159a811e NeedsCompilation: no Title: TargetScoreData Description: Precompiled and processed miRNA-overexpression fold-changes from 84 Gene Expression Omnibus (GEO) series corresponding to 6 platforms, 77 human cells or tissues, and 113 distinct miRNAs. Accompanied with the data, we also included in this package the sequence feature scores from TargetScanHuman 6.1 including the context+ score and the probabilities of conserved targeting for each miRNA-mRNA interaction. Thus, the user can use these static sequence-based scores together with user-supplied tissue/cell-specific fold-change due to miRNA overexpression to predict miRNA targets using the package TargetScore (download separately) biocViews: ExperimentData, RNASeqData, miRNAData Author: Yue Li Maintainer: Yue Li git_url: https://git.bioconductor.org/packages/TargetScoreData git_branch: RELEASE_3_9 git_last_commit: a8d7dcb git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/TargetScoreData_1.20.0.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 dependencyCount: 0 Package: TargetSearchData Version: 1.22.0 License: GPL (>= 2) MD5sum: 5930865598f2ac84a58a11111f3ba7ac NeedsCompilation: no Title: Example GC-MS data for TargetSearch Package Description: This package provides example GC-MS data for TargetSearch Package. biocViews: ExperimentData, Escherichia_coli_Data Author: Alvaro Cuadros-Inostroza, Henning Redestig, Matt Hannah Maintainer: Alvaro Cuadros-Inostroza git_url: https://git.bioconductor.org/packages/TargetSearchData git_branch: RELEASE_3_9 git_last_commit: 2b3687f git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/TargetSearchData_1.22.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: TBX20BamSubset Version: 1.20.0 Depends: Rsamtools (>= 1.9.8) Imports: xtable License: LGPL MD5sum: bb066042b00d5950e90ce73215301c43 NeedsCompilation: no Title: Subset of BAM files from the "TBX20" experiment Description: Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. A subset of the RNA-Seq data. biocViews: ExperimentData, SequencingData, RNASeqData Author: D. Bindreither Maintainer: D. Bindreither git_url: https://git.bioconductor.org/packages/TBX20BamSubset git_branch: RELEASE_3_9 git_last_commit: 973cffe git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/TBX20BamSubset_1.20.0.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 dependencyCount: 27 Package: TCGAbiolinksGUI.data Version: 1.4.0 Depends: R (>= 3.5.0) Suggests: BiocStyle, knitr, readr, readxl, dplyr, caret, randomForest, doMC, e1071, DT License: GPL-3 MD5sum: 919f2748bfd2dab5e1b95969a4a212ae NeedsCompilation: no Title: Data for the TCGAbiolinksGUI package Description: Supporting data for the TCGAbiolinksGUI package. It includes the following objects: glioma.gcimp.model, glioma.idhwt.model glioma.idhmut.model,glioma.idh.mode, probes2rm, maf.tumor,GDCdisease. biocViews: AssayDomainData, TechnologyData, OrganismData Author: Tiago Chedraoui Silva Maintainer: Tiago Chedraoui Silva URL: https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data VignetteBuilder: knitr BugReports: https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data/issues git_url: https://git.bioconductor.org/packages/TCGAbiolinksGUI.data git_branch: RELEASE_3_9 git_last_commit: 34f5b51 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/TCGAbiolinksGUI.data_1.4.0.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 dependencyCount: 0 Package: TCGAcrcmiRNA Version: 1.4.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 9fb98232249dc4c36f0b455b4bcbfb36 NeedsCompilation: no Title: TCGA CRC 450 miRNA dataset Description: colorectal cancer miRNA profile provided by TCGA biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/TCGAcrcmiRNA git_branch: RELEASE_3_9 git_last_commit: b12f3ba git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/TCGAcrcmiRNA_1.4.0.tar.gz vignettes: vignettes/TCGAcrcmiRNA/inst/doc/TcgaCrcVignette.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TCGAcrcmiRNA/inst/doc/TcgaCrcVignette.R dependencyCount: 7 Package: TCGAcrcmRNA Version: 1.4.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 210ae0298467a9daaf342873ee1a9504 NeedsCompilation: no Title: TCGA CRC 450 mRNA dataset Description: colorectal cancer mRNA profile provided by TCGA biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/TCGAcrcmRNA git_branch: RELEASE_3_9 git_last_commit: 4ebfd8c git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/TCGAcrcmRNA_1.4.0.tar.gz vignettes: vignettes/TCGAcrcmRNA/inst/doc/TcgaCrcVignette.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TCGAcrcmRNA/inst/doc/TcgaCrcVignette.R dependencyCount: 7 Package: TCGAMethylation450k Version: 1.20.0 License: GPL-2 MD5sum: 84b02ffc29f555bdb04e40476fd86fff NeedsCompilation: no Title: The Cancer Genome Atlas Illumina 450k methylation example data Description: The Cancer Genome Atlas (TCGA) is applying genomics technologies to over 20 different types of cancer. This package contains a small set of 450k array data in idat format. biocViews: Genome, CancerData, MethylationArrayData Author: Sean Davis Maintainer: Sean Davis git_url: https://git.bioconductor.org/packages/TCGAMethylation450k git_branch: RELEASE_3_9 git_last_commit: ff52acb git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/TCGAMethylation450k_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: tcgaWGBSData.hg19 Version: 1.2.0 Depends: R (>= 3.5.0), ExperimentHub Imports: bsseq, knitr License: GPL-2 MD5sum: 0016ac6074b918439dac0a52151c4ffa NeedsCompilation: no Title: Data Description: Data package for WGBS Data in TCGA. Data is stored as SummarizedExperiment Format. See vignette on how to extract the data and perform differential methylation analysis. biocViews: Genome, SequencingData, ExperimentData, Homo_sapiens_Data, CancerData Author: Divy Kangeyan Maintainer: Divy Kangeyan VignetteBuilder: knitr BugReports: https://github.com/aryeelab/tcgaWGBSData.hg19/issues git_url: https://git.bioconductor.org/packages/tcgaWGBSData.hg19 git_branch: RELEASE_3_9 git_last_commit: ee5bed2 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/tcgaWGBSData.hg19_1.2.0.tar.gz vignettes: vignettes/tcgaWGBSData.hg19/inst/doc/tcgaWGBSData.hg19.html vignetteTitles: Vignette Title hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tcgaWGBSData.hg19/inst/doc/tcgaWGBSData.hg19.R dependencyCount: 119 Package: TCGAWorkflowData Version: 1.8.0 Depends: R (>= 3.4.0) Imports: SummarizedExperiment Suggests: knitr, rmarkdown, pander, testthat License: GPL-3 MD5sum: 90d52109bd55f983c51da4ae7bc8a63c NeedsCompilation: no Title: Data for TCGA Workflow Description: This experimental data package contains 11 data sets necessary to follow the "TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages". biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData, CancerData Author: Tiago Chedraoui Silva Maintainer: Tiago Chedraoui Silva URL: https://f1000research.com/articles/5-1542/v2 VignetteBuilder: knitr BugReports: https://github.com/BioinformaticsFMRP/TCGAWorkflow/issues git_url: https://git.bioconductor.org/packages/TCGAWorkflowData git_branch: RELEASE_3_9 git_last_commit: c334e91 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/TCGAWorkflowData_1.8.0.tar.gz vignettes: vignettes/TCGAWorkflowData/inst/doc/TCGAWorkflowData.html vignetteTitles: 'Example data for TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages' hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TCGAWorkflowData/inst/doc/TCGAWorkflowData.R dependencyCount: 32 Package: TENxBrainData Version: 1.4.0 Depends: SingleCellExperiment, HDF5Array Imports: AnnotationHub (>= 2.9.22), ExperimentHub Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel, data.table License: CC BY 4.0 MD5sum: 7e6d88a566de22896659fada4fd8192b NeedsCompilation: no Title: Data from the 10X 1.3 Million Brain Cell Study Description: Single-cell RNA-seq data for 1.3 million brain cells from E18 mice, generated by 10X Genomics. biocViews: SequencingData, RNASeqData, ExpressionData, SingleCellData Author: Aaron Lun [aut], Martin Morgan [aut], Bioconductor Package Maintainer [cre] Maintainer: Bioconductor Package Maintainer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TENxBrainData git_branch: RELEASE_3_9 git_last_commit: c689f01 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/TENxBrainData_1.4.0.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 dependencyCount: 89 Package: TENxPBMCData Version: 1.2.0 Depends: SingleCellExperiment, HDF5Array Imports: AnnotationHub, ExperimentHub Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel License: CC BY 4.0 MD5sum: ffe941067700fd429028dda58bf5fc3e 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, SingleCellData Author: Kasper D. Hansen [aut], Davide Risso [aut], Stephanie Hicks [aut, cre] Maintainer: Stephanie Hicks VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TENxPBMCData git_branch: RELEASE_3_9 git_last_commit: b35686f git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/TENxPBMCData_1.2.0.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 dependencyCount: 89 Package: TimerQuant Version: 1.14.0 Depends: shiny Imports: ggplot2, grid, gridExtra, deSolve, dplyr, locfit Suggests: BiocStyle, reshape2, knitr, shinyBS License: Artistic-2.0 MD5sum: 3e09837187e65aa1b4f59165a35c7df4 NeedsCompilation: no Title: Timer Quantification Description: Supplementary Data package for tandem timer methods paper by Barry et al. (2015) including TimerQuant shiny applications. biocViews: ExperimentData, Danio_rerio_Data, HighThroughputImagingData, Tissue Author: Joseph Barry Maintainer: Joseph Barry VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TimerQuant git_branch: RELEASE_3_9 git_last_commit: 5ac49b3 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/TimerQuant_1.14.0.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: 63 Package: tinesath1cdf Version: 1.22.0 License: Artistic-2.0 MD5sum: c75413e9dc533ceb727d576dfbbdac49 NeedsCompilation: no Title: tinesath1cdf Description: A package containing an environment represeting the newcdf/tinesATH1.cdf.cdf file. biocViews: Arabidopsis_thaliana_Data, ChipOnChipData Author: Tine Casneuf Maintainer: Tine Casneuf git_url: https://git.bioconductor.org/packages/tinesath1cdf git_branch: RELEASE_3_9 git_last_commit: 10568f1 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/tinesath1cdf_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: XhybCasneuf dependencyCount: 0 Package: tinesath1probe Version: 1.22.0 Depends: R (>= 1.6), AnnotationDbi (>= 1.11.9) License: LGPL MD5sum: 6fe2994d1ed55ca9ef93b47721ea464c NeedsCompilation: no Title: Probe sequence data for microarrays of type tinesath1 Description: This package was automatically created by package matchprobes version 1.4.0. The probe sequence data was obtained from http://www.affymetrix.com. biocViews: Arabidopsis_thaliana_Data, SequencingData, MicroarrayData Author: The Bioconductor Project www.bioconductor.org Maintainer: Tine Casneuf git_url: https://git.bioconductor.org/packages/tinesath1probe git_branch: RELEASE_3_9 git_last_commit: 3ae4818 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/tinesath1probe_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 32 Package: tissueTreg Version: 1.4.0 Depends: R (>= 3.5) Suggests: BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq, SummarizedExperiment License: GPL (>= 2) MD5sum: 3aecd23a2936c42a2abc0f292bfc4615 NeedsCompilation: no Title: TWGBS and RNA-seq data from tissue T regulatory cells from mice Description: The package provides ready to use epigenomes (obtained from TWGBS) and transcriptomes (RNA-seq) from various tissues as obtained in the study (Delacher and Imbusch 2017, PMID: 28783152). Regulatory T cells (Treg cells) perform two distinct functions: they maintain self-tolerance, and they support organ homeostasis by differentiating into specialized tissue Treg cells. The underlying dataset characterises the epigenetic and transcriptomic modifications for specialized tissue Treg cells. biocViews: ExperimentData, Tissue, Mus_musculus_Data, SequencingData, RNASeqData Author: Charles Imbusch [aut, cre], Michael Delacher [aut], Markus Feuerer [aut], Benedikt Brors [aut] Maintainer: Charles Imbusch URL: https://github.com/cimbusch/tissueTreg VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tissueTreg git_branch: RELEASE_3_9 git_last_commit: e16363e git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/tissueTreg_1.4.0.tar.gz vignettes: vignettes/tissueTreg/inst/doc/tissueTreg.html vignetteTitles: tissueTreg hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tissueTreg/inst/doc/tissueTreg.R dependencyCount: 0 Package: tofsimsData Version: 1.12.0 Depends: R (>= 3.2.0) Suggests: knitr, rmarkdown, tools License: GPL-3 MD5sum: 5d746a53346a01cbf016e711cc70bdd9 NeedsCompilation: no Title: Import, process and analysis of ToF-SIMS imaging data Description: This packages contains data to be used with the 'tofsims' package. biocViews: ExperimentData, MassSpectrometry, ImagingMassSpectrometry, DataImport Author: Lorenz Gerber, Viet Mai Hoang Maintainer: Lorenz Gerber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tofsimsData git_branch: RELEASE_3_9 git_last_commit: 2a4e8af git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/tofsimsData_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: topdownrdata Version: 1.6.0 Depends: topdownr License: GPL (>= 3) MD5sum: 4d7e386274b91c3c71ab578ee607b393 NeedsCompilation: no Title: Example Files for the topdownr R Package Description: Example data for the topdownr package generated on a Thermo Orbitrap Fusion Lumos MS device. biocViews: ExperimentData, MassSpectrometryData Author: Sebastian Gibb [aut, cre], Pavel Shliaha [aut], Ole Nørregaard Jensen [aut] Maintainer: Sebastian Gibb URL: https://github.com/sgibb/topdownrdata/ BugReports: https://github.com/sgibb/topdownrdata/issues/ git_url: https://git.bioconductor.org/packages/topdownrdata git_branch: RELEASE_3_9 git_last_commit: 612b14c git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/topdownrdata_1.6.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 82 Package: tweeDEseqCountData Version: 1.22.0 Depends: Biobase, R (>= 2.10) License: GPL (>=2) MD5sum: 7da122e4ba4097fa0742d460abc0b6b1 NeedsCompilation: no Title: RNA-seq count data employed in the vignette of the tweeDEseq package Description: RNA-seq count data from Pickrell et al. (2010) employed to illustrate the use of the Poisson-Tweedie family of distributions with the tweeDEseq package. biocViews: Genome, Homo_sapiens_Data, RNASeqData Author: Juan R Gonzalez and Mikel Esnaola (with contributions from Robert Castelo ) Maintainer: Juan R Gonzalez URL: http://www.creal.cat/jrgonzalez/software.htm git_url: https://git.bioconductor.org/packages/tweeDEseqCountData git_branch: RELEASE_3_9 git_last_commit: c66b372 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/tweeDEseqCountData_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: tximportData Version: 1.12.0 Suggests: knitr License: GPL (>= 2) MD5sum: 8ac5ace87e64a47a3b4c68acfd5ae976 NeedsCompilation: no Title: tximportData Description: This package provides the output of running various transcript abundance quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project. The quantifiers were Cufflinks, RSEM, kallisto, Salmon and Sailfish. For details on version numbers, sample information, and details on calls, see the package vignette. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tximportData git_branch: RELEASE_3_9 git_last_commit: 4452317 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/tximportData_1.12.0.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 dependencyCount: 0 Package: VariantToolsData Version: 1.8.0 Depends: R (>= 2.10), VariantAnnotation (>= 1.7.35) Imports: BiocGenerics, GenomicRanges Suggests: VariantTools (>= 1.3.4), gmapR (>= 1.3.3), BiocStyle License: Artistic-2.0 MD5sum: dd2739d2dc782b7ff7778010799037f9 NeedsCompilation: no Title: Data for the VariantTools tutorial Description: Data from the sequencing of a 50/50 mixture of HapMap trio samples NA12878 (CEU) and NA19240 (YRI), subset to the TP53 region. biocViews: ExperimentData, SequencingData, HapMap, SNPData Author: Michael Lawrence Maintainer: Michael Lawrence git_url: https://git.bioconductor.org/packages/VariantToolsData git_branch: RELEASE_3_9 git_last_commit: 1de3c34 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/VariantToolsData_1.8.0.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: 75 Package: vulcandata Version: 1.6.0 Imports: utils License: LGPL-3 MD5sum: f4b88fcd71e15eaa28291dfa423b90b5 NeedsCompilation: no Title: VirtUaL ChIP-Seq data Analysis using Networks, dummy dataset Description: This package provides a dummy regulatory network and ChIP-Seq dataset for running examples in the vulcan package biocViews: ExperimentData, Homo_sapiens_Data, CancerData, ChIPSeqData Author: Federico M. Giorgi, Andrew N. Holding, Florian Markowetz Maintainer: Federico M. Giorgi git_url: https://git.bioconductor.org/packages/vulcandata git_branch: RELEASE_3_9 git_last_commit: e351d43 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/vulcandata_1.6.0.tar.gz vignettes: vignettes/vulcandata/inst/doc/vulcandata.pdf vignetteTitles: Vulcan: VirtUaL ChIP-Seq Analysis through Networks,, dummy datasets hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/vulcandata/inst/doc/vulcandata.R dependencyCount: 1 Package: waveTilingData Version: 1.20.0 Depends: R (>= 2.14.0) License: GPL (>= 2) MD5sum: b6a9a41570c55fa3057b879f72817f6d NeedsCompilation: no Title: waveTiling Example Data Description: Experiment and Annotation Data files used by the examples / vignette in the waveTiling package biocViews: ExperimentData, Arabidopsis_thaliana_Data, MicroarrayData Author: Kristof De Beuf Maintainer: Kristof De Beuf git_url: https://git.bioconductor.org/packages/waveTilingData git_branch: RELEASE_3_9 git_last_commit: e49a02a git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/waveTilingData_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: WES.1KG.WUGSC Version: 1.16.0 License: GPL-2 MD5sum: 6d660e6f8bddd1aa81e578e887a8712b NeedsCompilation: no Title: Whole Exome Sequencing (WES) of chromosome 22 401st to 500th exon from the 1000 Genomes (1KG) Project by the Washington University Genome Sequencing Center (WUGSC). Description: The assembled .bam files of whole exome sequencing data from the 1000 Genomes Project. 46 samples sequenced by the Washington University Genome Sequencing Center are included. biocViews: ExperimentData, Project1000genomes, SequencingData, DNASeqData, Homo_sapiens_Data Author: Yuchao Jiang, Nancy R. Zhang Maintainer: Yuchao Jiang git_url: https://git.bioconductor.org/packages/WES.1KG.WUGSC git_branch: RELEASE_3_9 git_last_commit: f9998da git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/WES.1KG.WUGSC_1.16.0.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 dependencyCount: 0 Package: XhybCasneuf Version: 1.22.0 Depends: R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf , RColorBrewer , methods, grid License: Artistic-2.0 MD5sum: 0d53ee29e521d6b33cb3dc9073970b58 NeedsCompilation: no Title: EBI/PSB cross-hybridisation study package Description: Cross-hybridisation study on the ATH1 Affymetrix GeneChip biocViews: ExperimentData, Tissue, MicroarrayData, TissueMicroarrayData Author: Tineke Casneuf Maintainer: Tineke Casneuf git_url: https://git.bioconductor.org/packages/XhybCasneuf git_branch: RELEASE_3_9 git_last_commit: b95aa64 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/XhybCasneuf_1.22.0.tar.gz vignettes: vignettes/XhybCasneuf/inst/doc/Xhyb.pdf vignetteTitles: Xhyb hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/XhybCasneuf/inst/doc/Xhyb.R dependencyCount: 42 Package: yeastCC Version: 1.24.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 55504ef44f97f3cf418c6817f9884538 NeedsCompilation: no Title: Spellman et al. (1998) and Pramila/Breeden (2006) yeast cell cycle microarray data Description: ExpressionSet for Spellman et al. (1998) yeast cell cycle microarray experiment biocViews: ExperimentData, CellCulture, Saccharomyces_cerevisiae_Data, CancerData, MicroarrayData, OneChannelData, GEO Author: Sandrine Dudoit Maintainer: Sandrine Dudoit git_url: https://git.bioconductor.org/packages/yeastCC git_branch: RELEASE_3_9 git_last_commit: 4a022cc git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/yeastCC_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 7 Package: yeastExpData Version: 0.30.0 Depends: R (>= 2.4), graph (>= 1.9.26) Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db License: GPL MD5sum: 92da053cb8de00d3e1bbf897491b8177 NeedsCompilation: no Title: Yeast Experimental Data Description: A collection of different sets of experimental data from yeast. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data Author: R. Gentleman Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/yeastExpData git_branch: RELEASE_3_9 git_last_commit: 833bc23 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/yeastExpData_0.30.0.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 dependencyCount: 8 Package: yeastGSData Version: 0.22.0 License: Artistic-2.0 MD5sum: 76b11f991c186a0141182b94668dfb70 NeedsCompilation: no Title: Yeast Gold Standard Data Description: A collection of so-called gold (and other) standard data sets biocViews: ExperimentData, Saccharomyces_cerevisiae_Data Author: R. Gentleman Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/yeastGSData git_branch: RELEASE_3_9 git_last_commit: 2cd2165 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/yeastGSData_0.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: yeastNagalakshmi Version: 1.20.0 License: Artistic-2.0 MD5sum: 756b38f28259e1a99dec46e80bd64646 NeedsCompilation: no Title: Yeast genome RNA sequencing data based on Nagalakshmi et. al. Description: The yeast genome data was retrieved from the sequence read archive, aligned with bwa, and converted to BAM format with samtools. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, SequencingData, BiocViews, ChIPSeqData Author: Martin Morgan Maintainer: Bioconductor Package Maintainer git_url: https://git.bioconductor.org/packages/yeastNagalakshmi git_branch: RELEASE_3_9 git_last_commit: 7611cea git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/yeastNagalakshmi_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 0 Package: yeastRNASeq Version: 0.22.0 Depends: R (>= 2.4) Suggests: Biobase, ShortRead, IRanges License: GPL MD5sum: d49325eb63e76bea71a4e26d08e877ac NeedsCompilation: no Title: Yeast RNA-Seq Experimental Data from Lee et al. 2008 Description: A selection of RNA-Seq data from a yeast transcriptome experiment. biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData Author: James H. Bullard and Kasper D. Hansen Maintainer: J. Bullard git_url: https://git.bioconductor.org/packages/yeastRNASeq git_branch: RELEASE_3_9 git_last_commit: 00cff77 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/yeastRNASeq_0.22.0.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 dependencyCount: 0 Package: yri1kgv Version: 0.26.0 Depends: GGBase Imports: Biobase License: Artistic-2.0 MD5sum: 323d8f0ad9c359b2acf16f7802c5efdd NeedsCompilation: no Title: expression + genotype on 79 unrelated YRI individuals Description: expression + genotype on 79 unrelated YRI individuals biocViews: ArrayExpress Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/yri1kgv git_branch: RELEASE_3_9 git_last_commit: e057d5c git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/yri1kgv_0.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependencyCount: 61 Package: yriMulti Version: 0.14.0 Depends: Homo.sapiens, geuvPack, MultiAssayExperiment (>= 1.3.14) Imports: GenomicFiles (>= 1.13.6), VariantAnnotation (>= 1.23.1), gQTLBase, SummarizedExperiment, GenomicRanges, dsQTL, GenomeInfoDb Suggests: erma, BiocStyle, knitr, rmarkdown, gQTLstats (>= 1.9.2), doParallel, geuvPack, knitcitations, bibtex License: Artistic-2.0 MD5sum: 7701a6d945562afbfed3d9c4f620ef89 NeedsCompilation: no Title: support for expression, methylation, DHS, VCF for YRI Description: expression, methylation, DHS for YRI Author: VJ Carey Maintainer: VJ Carey VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/yriMulti git_branch: RELEASE_3_9 git_last_commit: 4de2345 git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/yriMulti_0.14.0.tar.gz vignettes: vignettes/yriMulti/inst/doc/yriMulti.pdf vignetteTitles: yriMulti -- HapMap YRI population,, multiassay interfaces hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/yriMulti/inst/doc/yriMulti.R dependencyCount: 120 Package: zebrafishRNASeq Version: 1.4.0 Depends: R (>= 2.10) Suggests: BiocStyle, knitr License: GPL MD5sum: de296bfd0e03bcb980519bb70371b65b NeedsCompilation: no Title: Zebrafish RNA-Seq Experimental Data from Ferreira et al. (2014) Description: Gene-level read counts from RNA-Seq for gallein-treated and control zebrafish. biocViews: ExperimentData, Danio_rerio_Data, RNASeqData Author: Davide Risso Maintainer: Davide Risso VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/zebrafishRNASeq git_branch: RELEASE_3_9 git_last_commit: e4dcbad git_last_commit_date: 2019-05-02 Date/Publication: 2019-05-07 source.ver: src/contrib/zebrafishRNASeq_1.4.0.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 dependencyCount: 0 Package: PGPC Version: 1.12.0 Depends: R (>= 3.0), EBImage, imageHTS, SearchTrees, limma, RColorBrewer, gplots, splots, ggplot2, geneplotter, ChemmineR, reshape2, plyr Suggests: BiocStyle, knitr License: Artistic-2.0 NeedsCompilation: no Title: Experimental data and analysis of the chemical-genetic interaction screen in isogenic HCT116 cell lines Description: This package contains the experimental data and a vignette guiding through the analysis of a chemical-genenetic interaction screen in isogenic HCT116 cell lines. The code can be executed to generate all results and figures for the manuscript "A chemical-genetic interaction map of small molecules using high-throughput imaging in cancer cells" accepted for publicaton at Molecular Systems Biology. Data availability: Complementary views on this dataset are available through different repositories. The image data files are available from the BioStudies database at the European Bioinformatics Institute (EMBL-EBI) under the accession S-BSMS-PGPC1 (http://wwwdev.ebi.ac.uk/biostudies/studies/S-BSMS-PGPC1) An interactive front-end for exploration of the images is provided by the IDR database http://dx.doi.org/10.17867/10000101. The authors are hosting an interactive webpage to browse images and interaction profiles at http://dedomena.embl.de/PGPC. biocViews: CancerData, ColonCancerData, ExperimentData Author: Felix Klein Maintainer: Felix Klein VignetteBuilder: knitr PackageStatus: Deprecated git_url: https://git.bioconductor.org/packages/PGPC git_branch: RELEASE_3_9 git_last_commit: a529c75 git_last_commit_date: 2019-05-02 Date/Publication: 2019-10-17