Package: ABAData Version: 1.0.0 Depends: R (>= 3.2) Suggests: BiocStyle, knitr License: GPL (>= 2) MD5sum: b89dc7f7c544357f65d64d2a742c1dc3 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 source.ver: src/contrib/ABAData_1.0.0.tar.gz vignettes: vignettes/ABAData/inst/doc/ hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE htmlDocs: vignettes/ABAData/inst/doc/ABAData.html htmlTitles: "ABAData: gene expression data to use with enrichment analysis package ABAEnrichment" Package: affycompData Version: 1.8.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp License: GPL (>= 2) MD5sum: 0803f43dd2f1f97ed9b20273b03db87a 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 source.ver: src/contrib/affycompData_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: affydata Version: 1.18.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Imports: methods Suggests: hgu95av2cdf, hgu133acdf License: GPL (>= 2) MD5sum: 695ae63e426353ed70108d4323fa26ad 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 source.ver: src/contrib/affydata_1.18.0.tar.gz vignettes: vignettes/affydata/inst/doc/affydata.pdf vignetteTitles: affydata primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Affyhgu133A2Expr Version: 1.6.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 0c109cf1142c2463c3b15870dc1879ea 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 source.ver: src/contrib/Affyhgu133A2Expr_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Affyhgu133aExpr Version: 1.8.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: a1eded062083fe4af27c2c2071906d57 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 source.ver: src/contrib/Affyhgu133aExpr_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Affyhgu133Plus2Expr Version: 1.4.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 3890ec7db5e1f4a053e93c8f0ca29e06 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 source.ver: src/contrib/Affyhgu133Plus2Expr_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: AffymetrixDataTestFiles Version: 0.8.0 Depends: R (>= 2.5.0) License: LGPL-2.1 MD5sum: b09403e51c1b881586d45ddecdf9b016 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 source.ver: src/contrib/AffymetrixDataTestFiles_0.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Affymoe4302Expr Version: 1.8.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 2012458540d50c8936c3e606dde4b34c 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 source.ver: src/contrib/Affymoe4302Expr_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: airway Version: 0.104.0 Depends: R (>= 2.10), SummarizedExperiment Suggests: knitr, GEOquery License: LGPL MD5sum: 8caadca4d72d67bca9621d9037cd073e 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 source.ver: src/contrib/airway_0.104.0.tar.gz vignettes: vignettes/airway/inst/doc/ hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE htmlDocs: vignettes/airway/inst/doc/airway.html htmlTitles: "Airway smooth muscle cells" Package: ALL Version: 1.12.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Suggests: rpart License: Artistic-2.0 MD5sum: ce5fc3a7270c1213ba0cbed8e02138af 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 source.ver: src/contrib/ALL_1.12.0.tar.gz vignettes: vignettes/ALL/inst/doc/ALLintro.pdf vignetteTitles: ALL data intro hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: SNAGEEdata Package: ALLMLL Version: 1.10.0 Depends: R (>= 2.10), affy (>= 1.23.4) License: GPL-2 MD5sum: 7a5240f4c7217b68eb53e8943bb77766 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 source.ver: src/contrib/ALLMLL_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: AmpAffyExample Version: 1.10.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Suggests: hgu133acdf License: LGPL (>= 2) MD5sum: 864b8a468db46622086efcb1696cbe75 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 source.ver: src/contrib/AmpAffyExample_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: antiProfilesData Version: 1.6.0 Depends: Biobase, Suggests: frma, GEOquery, GEOmetadb License: Artistic-2.0 MD5sum: 81c34af8c41ed80b05986b4c27ebf6d0 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 source.ver: src/contrib/antiProfilesData_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ARRmData Version: 1.6.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: 51a09b2e481a8e75c8db6624a4cf5182 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 source.ver: src/contrib/ARRmData_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: AshkenazimSonChr21 Version: 1.0.0 Suggests: knitr, VariantAnnotation License: Artistic-2.0 MD5sum: 99c0dcfb97a8b82477f22993ffc9bfbb 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 source.ver: src/contrib/AshkenazimSonChr21_1.0.0.tar.gz vignettes: vignettes/AshkenazimSonChr21/inst/doc/AshkenazimSonChr21.pdf vignetteTitles: RareVariantVis hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bcellViper Version: 1.6.0 Depends: R(>= 2.14.0), Biobase, methods License: GPL (>=2) MD5sum: 97f129db0f7ae46dc65c9cd8600bc585 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 source.ver: src/contrib/bcellViper_1.6.0.tar.gz vignettes: vignettes/bcellViper/inst/doc/bcellViper.pdf vignetteTitles: Using bcellViper hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: beadarrayExampleData Version: 1.8.0 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>= 2.0.0) License: GPL-2 MD5sum: 5dfd2a3f9b38fec99b028ccef2c64e1c 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 source.ver: src/contrib/beadarrayExampleData_1.8.0.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 Package: BeadArrayUseCases Version: 1.8.0 Imports: beadarray (>= 2.3.18), limma, GEOquery Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db License: GPL-2 MD5sum: 5b3d94bd63c4b4808c35a86b916f5ee8 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 source.ver: src/contrib/BeadArrayUseCases_1.8.0.tar.gz vignettes: vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.pdf vignetteTitles: BeadArrayUseCases.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: beta7 Version: 1.8.0 Depends: R (>= 2.4.0), marray License: LGPL MD5sum: e9e1e5468ac8e439231ffa008ed18202 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 source.ver: src/contrib/beta7_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bladderbatch Version: 1.8.0 Depends: Biobase License: Artistic-2.0 MD5sum: fbcbe1eef454146c2beaa437bfa47bcd 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 source.ver: src/contrib/bladderbatch_1.8.0.tar.gz vignettes: vignettes/bladderbatch/inst/doc/bladderbatch.pdf vignetteTitles: bladderbatchTutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: blimaTestingData Version: 0.104.0 Depends: R(>= 3.0.0) Suggests: blima, beadarray, illuminaHumanv4.db, BiocStyle License: GPL-3 MD5sum: b7b5147451fe0c3b70e37e7bc217c008 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 source.ver: src/contrib/blimaTestingData_0.104.0.tar.gz vignettes: vignettes/blimaTestingData/inst/doc/blimaTestingData.pdf vignetteTitles: blimaTestingData.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerMAINZ Version: 1.8.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: b7d2c7817a960c136c044500e103072a 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/ source.ver: src/contrib/breastCancerMAINZ_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerNKI Version: 1.8.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: d237d954a3f300f90a6c563832df709f 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/ source.ver: src/contrib/breastCancerNKI_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: seventyGeneData Package: breastCancerTRANSBIG Version: 1.8.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 7f4227aaa9e34e135397a90c8eb29a39 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/ source.ver: src/contrib/breastCancerTRANSBIG_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerUNT Version: 1.8.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 50d6f9d4819fd6fde79deff4fc861143 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/ source.ver: src/contrib/breastCancerUNT_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerUPP Version: 1.8.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 1796f0e82919b2db9a7d0fd346d475df 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/ source.ver: src/contrib/breastCancerUPP_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerVDX Version: 1.8.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: bad923153dead0f2db91d5a15dfa03a9 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/ source.ver: src/contrib/breastCancerVDX_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bronchialIL13 Version: 1.8.0 Depends: R(>= 2.10.0), affy (>= 1.23.4) License: GPL-2 MD5sum: 34756661cba689cb2f32391a768d7362 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 source.ver: src/contrib/bronchialIL13_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bsseqData Version: 0.8.0 Depends: R (>= 2.15), bsseq (>= 1.5.4) License: Artistic-2.0 MD5sum: 39800600a3c60b99ecdf8171be26d5cc 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 source.ver: src/contrib/bsseqData_0.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cancerdata Version: 1.8.0 Depends: R (>= 2.10.1), Biobase License: GPL (>= 2) MD5sum: 4d1954d9c82c073ceff61b6202fe8f53 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 source.ver: src/contrib/cancerdata_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CardinalWorkflows Version: 1.2.0 Depends: R (>= 2.10), Cardinal Suggests: BiocStyle License: Artistic-2.0 MD5sum: 273ce5a08aef51af8658bc320132afb2 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: Kyle D. Bemis Maintainer: Kyle D. Bemis source.ver: src/contrib/CardinalWorkflows_1.2.0.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 Package: CCl4 Version: 1.8.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), limma License: Artistic-2.0 MD5sum: 91c7ce7c268c645c840a6b7ad1866cf0 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 source.ver: src/contrib/CCl4_1.8.0.tar.gz vignettes: vignettes/CCl4/inst/doc/CCl4.pdf vignetteTitles: CCl4 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ccTutorial Version: 1.8.0 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: e56daf283e0f372d66d66d389a61d6ee 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 source.ver: src/contrib/ccTutorial_1.8.0.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 Package: ceu1kg Version: 0.8.0 Depends: R (>= 2.12.0), GGBase (>= 3.9.0), GGtools, Biobase Suggests: SNPlocs.Hsapiens.dbSNP.20101109 License: Artistic-2.0 MD5sum: fbefb915530e927a97faabb33268f587 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 source.ver: src/contrib/ceu1kg_0.8.0.tar.gz vignettes: vignettes/ceu1kg/inst/doc/ceu1kg.pdf vignetteTitles: ceu1kg overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ceu1kgv Version: 0.12.0 Depends: R (>= 3.0), GGBase Imports: Biobase License: Artistic-2.0 MD5sum: 1c12a40ee1628107a8e5dd1d69141ea8 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 source.ver: src/contrib/ceu1kgv_0.12.0.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 Package: ceuhm3 Version: 0.8.0 Depends: R (>= 2.12.0), GGBase, Biobase Imports: GGtools License: Artistic-2.0 MD5sum: f48b54007627915eecfb143c53d26313 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 source.ver: src/contrib/ceuhm3_0.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cgdv17 Version: 0.8.0 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: bf3279fe9f6ae212ffb40e569a1da505 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 source.ver: src/contrib/cgdv17_0.8.0.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 Package: ChAMPdata Version: 1.8.0 Depends: R (>= 3.0.1) License: GPL-3 MD5sum: 2f0d45e03bd1f4e19a2d8d2ef726fd59 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: Tiffany Morris, Lee Butcher and Andrew Teschendorff Maintainer: Tiffany Morris source.ver: src/contrib/ChAMPdata_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: charmData Version: 1.6.0 Depends: R(>= 2.11.0), charm, pd.charm.hg18.example License: LGPL (>= 2) MD5sum: 28ee896778560ed67fa9b2ecb9a5f5b4 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 source.ver: src/contrib/charmData_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cheung2010 Version: 0.8.0 Depends: R (>= 2.13.0), Biobase, GGtools, GenomicRanges, hgfocus.db Imports: AnnotationDbi Suggests: SNPlocs.Hsapiens.dbSNP.20120608 Enhances: parallel License: Artistic-2.0 MD5sum: 675daae4b6632824f491d4bdb3cd03b9 NeedsCompilation: no Title: resources for genetics of gene expression based on Cheung et al 2010 Description: Data resources related to the PLoS Biology paper Polymorphic Cis- and Trans-Regulation of Human Gene Expression, including small-footprint smlSet support for 147 hgfocus arrays and corresponding HapMap genotypes at 1.3 million SNP; 0.0.22+ includes cheung_eset... from Leek et al RECOUNT myrna output biocViews: Homo_sapiens_Data, SequencingData, RNASeqData, SNPData, HapMap Author: Vince Carey Maintainer: Vince Carey source.ver: src/contrib/cheung2010_0.8.0.tar.gz vignettes: vignettes/cheung2010/inst/doc/cheungTrans.pdf vignetteTitles: cheungTrans: checking trans eQTL with hgfocus arrays hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ggtut Package: ChimpHumanBrainData Version: 1.8.0 Depends: affy,qvalue,limma,hexbin,statmod License: MIT MD5sum: a076bcb78a34ccdbbd1e68c85be300f7 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 source.ver: src/contrib/ChimpHumanBrainData_1.8.0.tar.gz vignettes: vignettes/ChimpHumanBrainData/inst/doc/DiffExpressVignette.pdf vignetteTitles: DiffExpressVignette.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: chipenrich.data Version: 1.6.0 Depends: R (>= 2.15.0) Imports: methods, GenomicRanges (>= 1.10.0), IRanges (>= 1.16.0), BiocGenerics (>= 0.2.0) License: GPL-3 MD5sum: ffa174f90ba033a0d3468fba25091065 NeedsCompilation: no Title: Gene set enrichment analysis for ChIP-seq data Description: Supporting data for the chipenrich package. Includes pre-defined gene sets, gene locus definitions, and mappability estimates. biocViews: ExperimentData, Genome, ChIPSeqData Author: Ryan P. Welch [aut, cre, cph], Chee Lee [aut, cre], Raymond G. Cavalcante [aut, cre], Laura J. Scott [ths], Maureen A. Sartor [ths] Maintainer: Ryan P. Welch , Chee Lee , Raymond G. Cavalcante source.ver: src/contrib/chipenrich.data_1.6.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: ChIPXpressData Version: 1.8.0 Depends: bigmemory License: GPL (>=2) MD5sum: fcb63371b6a64ac632f16e85e6027f62 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 source.ver: src/contrib/ChIPXpressData_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CLL Version: 1.10.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: LGPL MD5sum: d04c151ad3aaf36e094294da5dbc8219 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 source.ver: src/contrib/CLL_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cMap2data Version: 1.6.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 680aee09c5e74b707950a75000ec2704 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 source.ver: src/contrib/cMap2data_1.6.0.tar.gz vignettes: vignettes/cMap2data/inst/doc/cMap2data.pdf vignetteTitles: cMap2data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cnvGSAdata Version: 1.6.0 Depends: R (>= 2.10), cnvGSA License: LGPL MD5sum: e3ce03e17b8cfe68e58f1822653e7e4a 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 source.ver: src/contrib/cnvGSAdata_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: COHCAPanno Version: 1.6.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: ebbf4728fc95220dcf5e7e67d67d2bb9 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 source.ver: src/contrib/COHCAPanno_1.6.0.tar.gz vignettes: vignettes/COHCAPanno/inst/doc/COHCAPanno.pdf vignetteTitles: COHCAPanno Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: colonCA Version: 1.12.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: 305cf94252f2f31006369e620aa09415 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 source.ver: src/contrib/colonCA_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ConnectivityMap Version: 1.6.0 Depends: R (>= 2.15.1) Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 90bbf90374080bd55236fb3fdd74df1b 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 source.ver: src/contrib/ConnectivityMap_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: COPDSexualDimorphism.data Version: 1.6.0 License: LGPL-2.1 MD5sum: 311551eaa9a7145ee9f46efde970e594 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 source.ver: src/contrib/COPDSexualDimorphism.data_1.6.0.tar.gz vignettes: vignettes/COPDSexualDimorphism.data/inst/doc/lgrc_data.pdf vignetteTitles: SDCD Genes hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CopyhelpeR Version: 1.2.0 Depends: R(>= 2.10) Suggests: BiocStyle License: GPL-2 MD5sum: f679632dad2973439e290fcf13f7a1cd 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: Thomas Kuilman source.ver: src/contrib/CopyhelpeR_1.2.0.tar.gz vignettes: vignettes/CopyhelpeR/inst/doc/CopyhelpeR.pdf vignetteTitles: CopyhelpeR hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: CopyNumber450kData Version: 1.6.0 Depends: R (>= 2.13.0), minfi, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 License: Artistic-2.0 MD5sum: 9eb6f6f54b9e2c9a1da1bce3d83a8e98 NeedsCompilation: no Title: Example data for the Illumina Methylation 450k array Description: Data from 52 control samples from 450k methylation arrays biocViews: Tissue, Homo_sapiens_Data, MicroarrayData, MethylationArrayData, TissueMicroarrayData Author: Simon Papillon-Cavanagh, Jean-Philippe Fortin, Nicolas De Jay Maintainer: Simon Papillon-Cavanagh source.ver: src/contrib/CopyNumber450kData_1.6.0.tar.gz vignettes: vignettes/CopyNumber450kData/inst/doc/CopyNumber450kData.pdf vignetteTitles: CopyNumber450kData User's Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: COSMIC.67 Version: 1.6.0 Depends: R (>= 3.0.2) Imports: GenomicRanges, SummarizedExperiment, VariantAnnotation Suggests: testthat, BiocStyle, knitr License: GPL-3 MD5sum: 3707f297d626e1a0fd5f2b8a573606ab 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 source.ver: src/contrib/COSMIC.67_1.6.0.tar.gz vignettes: vignettes/COSMIC.67/inst/doc/COSMIC.67.pdf vignetteTitles: COSMIC.67 - PDF hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CRCL18 Version: 0.104.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 85c0a03558fb9707c9ab172da509ce65 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 source.ver: src/contrib/CRCL18_0.104.0.tar.gz vignettes: vignettes/CRCL18/inst/doc/CRCL18Vignette.pdf vignetteTitles: CRCL18 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: curatedBladderData Version: 1.6.0 Depends: R (>= 2.10.0), affy Suggests: BiocStyle, survival, xtable, sva, genefilter, logging License: Artistic-2.0 MD5sum: 1828824e9ff1a311b897992c1d056b72 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 source.ver: src/contrib/curatedBladderData_1.6.0.tar.gz vignettes: vignettes/curatedBladderData/inst/doc/curatedBladderData_vignette.pdf vignetteTitles: curatedBladderData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: curatedBreastData Version: 1.2.0 Depends: R (>= 3.0.0), ggplot2, impute, XML, Biobase, BiocStyle License: GPL (>= 2) MD5sum: a73bb3a36e20c2b10de16e036447b965 NeedsCompilation: no Title: Curated breast gene expression data with survival and treatment information Description: Curated breast cancer S4 ExpresionSet datasets that all 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: GeneExpression, Microarray, ExperimentData, ReproducibleResearch Author: Katie Planey Maintainer: Katie Planey source.ver: src/contrib/curatedBreastData_1.2.0.tar.gz vignettes: vignettes/curatedBreastData/inst/doc/curatedBreastData-manual.pdf vignetteTitles: Manual hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: curatedCRCData Version: 2.2.0 Depends: R (>= 2.10.0), nlme Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle License: Artistic-2.0 MD5sum: aeb1706629f47b4fd31e918d80a12cb8 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 source.ver: src/contrib/curatedCRCData_2.2.0.tar.gz vignettes: vignettes/curatedCRCData/inst/doc/curatedCRCData_vignette.pdf vignetteTitles: curatedCRCData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: curatedOvarianData Version: 1.8.0 Depends: R (>= 2.10.0), affy Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle License: Artistic-2.0 MD5sum: 33584b4cdff387865243d862356e14df 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 source.ver: src/contrib/curatedOvarianData_1.8.0.tar.gz vignettes: vignettes/curatedOvarianData/inst/doc/curatedOvarianData_vignette.pdf vignetteTitles: curatedOvarianData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: davidTiling Version: 1.10.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db License: LGPL MD5sum: 9978a57c3d1c9533d65a801d437b014d 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 source.ver: src/contrib/davidTiling_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: derfinderData Version: 0.104.0 Depends: R(>= 3.1.1) Suggests: devtools (>= 1.6), knitcitations (>= 1.0.1), knitr (>= 1.6), knitrBootstrap (>= 0.9.0), RefManageR, rmarkdown (>= 0.3.3), License: Artistic-2.0 MD5sum: 03c4306771f464bc4c7481f5d2756113 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/lcolladotor/derfinderData VignetteBuilder: knitr BugReports: https://github.com/lcolladotor/derfinderData/issues source.ver: src/contrib/derfinderData_0.104.0.tar.gz vignettes: vignettes/derfinderData/inst/doc/ hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE htmlDocs: vignettes/derfinderData/inst/doc/derfinderData.html htmlTitles: "Introduction to derfinderData" Package: DeSousa2013 Version: 1.6.0 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: ab0b17895a4c8095e4b9fb42a06db2f7 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 source.ver: src/contrib/DeSousa2013_1.6.0.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 Package: diggitdata Version: 1.2.0 Depends: R(>= 2.14.0), Biobase, methods Imports: viper License: GPL (>=2) MD5sum: fc94cdfa9a3e3e81cb83a540d0a22192 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 source.ver: src/contrib/diggitdata_1.2.0.tar.gz vignettes: vignettes/diggitdata/inst/doc/diggitdata.pdf vignetteTitles: Using bcellViper hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: DLBCL Version: 1.10.0 Depends: R(>= 2.11.0), Biobase License: GPL (>=2) MD5sum: 8d0db3dfb9a8599ad8e7ff0c1aaf7490 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/ source.ver: src/contrib/DLBCL_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: DmelSGI Version: 1.2.0 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: e5d791e9217ab1112c05b71a2e73e220 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 source.ver: src/contrib/DmelSGI_1.2.0.tar.gz vignettes: vignettes/DmelSGI/inst/doc/DmelSGI.pdf vignetteTitles: DmelSGI hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: DMRcatedata Version: 1.6.1 Depends: R (>= 3.2.2), GenomicRanges Suggests: knitr License: GPL-3 MD5sum: 91ea94e8a50e6cd6d486d1725dbecbf1 NeedsCompilation: no Title: Data Package for DMRcate package Description: This package contains 7 data objects supporting functionality and examples of the Bioconductor package DMRcate. biocViews: ExperimentData, SNPData Author: Tim Peters Maintainer: Tim Peters VignetteBuilder: knitr source.ver: src/contrib/DMRcatedata_1.6.1.tar.gz vignettes: vignettes/DMRcatedata/inst/doc/DMRcatedata.pdf vignetteTitles: The DMRcate package user's guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: DonaPLLP2013 Version: 1.8.0 Depends: EBImage, parallel License: Artistic-2.0 MD5sum: 393cf18ec042df1ee9f9a693f9b649ea 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 source.ver: src/contrib/DonaPLLP2013_1.8.0.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 Package: DREAM4 Version: 1.6.0 Depends: R (>= 2.15.1), SummarizedExperiment Suggests: RUnit, networkBMA License: GPL MD5sum: 7ad2b44629cd44f68e6fa78d18440c44 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 source.ver: src/contrib/DREAM4_1.6.0.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 Package: dressCheck Version: 0.8.0 Depends: R (>= 2.10.1), methods, Biobase (>= 2.5.5) Suggests: survival, chron License: Artistic-2.0 MD5sum: e3421e2483802ffb0da8ed74a3a224ac 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 source.ver: src/contrib/dressCheck_0.8.0.tar.gz vignettes: vignettes/dressCheck/inst/doc/short.pdf vignetteTitles: short review of dressCheck contents hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: DrugVsDiseasedata Version: 1.6.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: ef5dfc462334fa72cba3bdb2ab37e53e 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 source.ver: src/contrib/DrugVsDiseasedata_1.6.0.tar.gz vignettes: vignettes/DrugVsDiseasedata/inst/doc/DrugVsDiseasedata.pdf vignetteTitles: DrugVsDiseasedata hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: dsQTL Version: 0.8.0 Depends: R (>= 2.15.0), utils, Biobase, SummarizedExperiment, GGBase (>= 3.31.1) Suggests: GGtools, rtracklayer License: Artistic-2.0 MD5sum: aa39750a5a61375c22cf16e6c7dc901f 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 source.ver: src/contrib/dsQTL_0.8.0.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 Package: DvDdata Version: 1.6.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 7d7551c554ccba27785f01e04fae54bb 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 source.ver: src/contrib/DvDdata_1.6.0.tar.gz vignettes: vignettes/DvDdata/inst/doc/DvDdata.pdf vignetteTitles: DvDdata hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: dyebiasexamples Version: 1.8.0 Depends: R (>= 1.4.1), marray, GEOquery Suggests: dyebias, convert, Biobase License: GPL-3 MD5sum: 89e903c0af0be53a8142df2196e0182d 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 source.ver: src/contrib/dyebiasexamples_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Package: EatonEtAlChIPseq Version: 0.8.0 Depends: GenomicRanges (>= 1.5.42), ShortRead, rtracklayer License: Artistic 2.0 MD5sum: 4c5f018baa4b3180378351200cadd536 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 source.ver: src/contrib/EatonEtAlChIPseq_0.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ecoliLeucine Version: 1.10.0 Depends: R (>= 1.9.0), affy (>= 1.23.4), ecolicdf License: GPL (>= 2) MD5sum: ddbcd81598360b297da7272d53db2e42 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 source.ver: src/contrib/ecoliLeucine_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ELMER.data Version: 1.0.0 Depends: R (>= 3.2.0) Imports: GenomicRanges Suggests: BiocStyle, knitr License: GPL-3 MD5sum: 7466cf8d042327c86bdb6dae71294f1a NeedsCompilation: no Title: Data for the ELMER package Description: Supporting data for the ELMER package. It includes Union.TSS, Union.enhancer, Probe.motif, human.TF and motif.relavent.TFs. biocViews: AssayDomainData Author: Lijing Yao Maintainer: Lijing Yao VignetteBuilder: knitr source.ver: src/contrib/ELMER.data_1.0.0.tar.gz vignettes: vignettes/ELMER.data/inst/doc/vignettes.pdf vignetteTitles: ELMER.data: Supporting data for the ELMER package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: encoDnaseI Version: 0.8.0 Depends: R (>= 2.15.0), methods, Biobase (>= 2.5.5), lattice, GGtools, GGBase Suggests: GGdata License: Artistic-2.0 MD5sum: d280a27064296546fa7010a4a328445a NeedsCompilation: no Title: data provided by UCSC for Cd4 raw measures of DnaseI hypersensitivity Description: data provided by UCSC for Cd4 raw measures of DnaseI hypersensitivity biocViews: ExperimentData, Genome, Homo_sapiens_Data, SNPData, ENCODE Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/encoDnaseI_0.8.0.tar.gz vignettes: vignettes/encoDnaseI/inst/doc/dnaseUse.pdf vignetteTitles: ENCODE/hg18 track demo: DNaseI hypersensitivity hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: estrogen Version: 1.16.0 Depends: R (>= 1.9.0), affy (>= 1.4) Suggests: Biobase (>= 1.13.16), affy, vsn, hgu95av2.db, genefilter License: LGPL MD5sum: a324e41d7515e1bd72739ec94cbd20fb NeedsCompilation: no Title: 2x2 factorial design exercise for the Bioconductor short course 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: R. Gentleman source.ver: src/contrib/estrogen_1.16.0.tar.gz vignettes: vignettes/estrogen/inst/doc/estrogen.pdf vignetteTitles: estrogen hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: faahKO Version: 1.10.0 Depends: xcms License: LGPL MD5sum: bb133761213cc7ff01b0046ca824c554 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 source.ver: src/contrib/faahKO_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fabiaData Version: 1.8.0 Depends: R (>= 2.10.0), Biobase Imports: utils Suggests: fabia License: LGPL (>= 2.1) MD5sum: 7de4695ea59d3306b6916e3bc93b5342 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 source.ver: src/contrib/fabiaData_1.8.0.tar.gz vignettes: vignettes/fabiaData/inst/doc/fabiaData.pdf vignetteTitles: fabiaData: Manual for the R Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: facopy.annot Version: 0.104.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 14facfe29586401758c27fa19a8348ff 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 source.ver: src/contrib/facopy.annot_0.104.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: facsDorit Version: 1.12.0 Depends: R (>= 1.9.1), prada (>= 1.0.5) License: GPL-2 MD5sum: d1ab5f45b8d5e02845b786afca3d8703 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 source.ver: src/contrib/facsDorit_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: FANTOM3and4CAGE Version: 1.6.0 Depends: R (>= 2.15.0) License: GPL-3 MD5sum: 429992928f7229b29737f00c521eecaa 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 source.ver: src/contrib/FANTOM3and4CAGE_1.6.0.tar.gz vignettes: vignettes/FANTOM3and4CAGE/inst/doc/FANTOM3and4CAGE.pdf vignetteTitles: FANTOM3and4CAGE hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ffpeExampleData Version: 1.8.0 Depends: R (>= 2.10.0), lumi Suggests: genefilter, affy License: GPL (>2) MD5sum: 244d68012f9572e888c1760bb5bd76b8 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 source.ver: src/contrib/ffpeExampleData_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fibroEset Version: 1.12.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: 38e03ff65cb28db5b5236db374925561 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 source.ver: src/contrib/fibroEset_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fission Version: 0.104.0 Depends: R (>= 2.10), SummarizedExperiment Suggests: knitr License: LGPL MD5sum: c0b55f353f557487d788f796f59f20ce 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 source.ver: src/contrib/fission_0.104.0.tar.gz vignettes: vignettes/fission/inst/doc/ hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE htmlDocs: vignettes/fission/inst/doc/fission.html htmlTitles: "Fission yeast time course" Package: Fletcher2013a Version: 1.6.0 Depends: R (>= 2.15), limma Imports: Biobase ,VennDiagram, gplots,grid License: GPL (>= 2) MD5sum: 27c888cb5e10e1173172aae53988436c 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 source.ver: src/contrib/Fletcher2013a_1.6.0.tar.gz vignettes: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.pdf vignetteTitles: Main vignette:Fletcher2013a hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: Fletcher2013b Package: Fletcher2013b Version: 1.6.0 Depends: R (>= 2.15), Fletcher2013a, RTN (>= 1.1.2), RedeR (>= 1.8.1), igraph Imports: RColorBrewer License: GPL (>= 2) MD5sum: e5622b085fc0d700df5d7d7c5db048a8 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 source.ver: src/contrib/Fletcher2013b_1.6.0.tar.gz vignettes: vignettes/Fletcher2013b/inst/doc/Fletcher2013b.pdf vignetteTitles: Main vignette:Fletcher2013b hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: flowFitExampleData Version: 1.6.0 Depends: R (>= 2.12.2), flowCore Imports: methods License: Artistic-2.0 MD5sum: 1ca8e6b7398db91ec246c94e0f598336 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 source.ver: src/contrib/flowFitExampleData_1.6.0.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 Package: FlowSorted.Blood.450k Version: 1.8.0 Depends: R (>= 2.13.0), minfi (>= 1.8.0) License: Artistic-2.0 MD5sum: 3ccca7649a7659f5f46447a2e18b1464 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: Homo_sapiens_Data, MicroarrayData, MethylationArrayData Author: Andrew E Jaffe Maintainer: Andrew E Jaffe source.ver: src/contrib/FlowSorted.Blood.450k_1.8.0.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 Package: FlowSorted.DLPFC.450k Version: 1.6.0 Depends: R (>= 2.13.0), minfi License: Artistic-2.0 MD5sum: ad66a7e5513649fa6980936d98ac1ad5 NeedsCompilation: no Title: Illumina HumanMethylation data on sorted frontal cortex cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays. biocViews: Homo_sapiens_Data, MicroarrayData Author: Andrew E Jaffe, Zachary A. Kaminsky Maintainer: Andrew E Jaffe source.ver: src/contrib/FlowSorted.DLPFC.450k_1.6.0.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 Package: flowWorkspaceData Version: 2.6.1 License: GPL-2 MD5sum: 289de64833257269090e08b121641232 NeedsCompilation: no Title: A data package containing two flowJo xml workspaces and associated fcs files for testing the flowWorkspace and openCyto 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 source.ver: src/contrib/flowWorkspaceData_2.6.1.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: frmaExampleData Version: 1.6.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: ea7c6e6e48a8baef7e0815f2fcf8f75a 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 source.ver: src/contrib/frmaExampleData_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: FunciSNP.data Version: 1.6.0 Depends: R (>= 2.14.0), IRanges Imports: rtracklayer License: GPL-3 MD5sum: d069dfc323301c2c593bf69ef8b5e6f7 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/ source.ver: src/contrib/FunciSNP.data_1.6.0.tar.gz vignettes: vignettes/FunciSNP.data/inst/doc/FunciSNP.data.pdf vignetteTitles: FunciSNP Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: gageData Version: 2.8.0 Depends: R (>= 2.10) Suggests: gage, pathview, genefilter License: GPL (>=2.0) MD5sum: b04d219020dc8c8b1850cb2b12df1547 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 source.ver: src/contrib/gageData_2.8.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: gaschYHS Version: 1.8.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: b3e0a6a940558636eeaf06c86fe8cc96 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 source.ver: src/contrib/gaschYHS_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gatingMLData Version: 2.10.0 Depends: R (>= 1.9.0) Suggests: flowUtils License: GPL MD5sum: e8130b91ad6412e710786cd32f9561df 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 source.ver: src/contrib/gatingMLData_2.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gcspikelite Version: 1.8.0 Depends: R (>= 2.5.0) License: LGPL MD5sum: cf5ca1abb006307cfb24f2e3cc7c4b37 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 source.ver: src/contrib/gcspikelite_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: geneLenDataBase Version: 1.6.0 Depends: R (>= 2.11.0) Imports: utils, rtracklayer, GenomicFeatures (>= 1.3.15) License: LGPL (>= 2) MD5sum: 3038e8243c534c06da3108feb952e849 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: Nadia Davidson source.ver: src/contrib/geneLenDataBase_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: genomationData Version: 1.2.0 Suggests: knitr License: GPL-3 MD5sum: 3f3aac34eda98ab42dcd2d211e9490c8 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 source.ver: src/contrib/genomationData_1.2.0.tar.gz vignettes: vignettes/genomationData/inst/doc/genomationData-knitr.pdf vignetteTitles: genomationData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: geuvPack Version: 1.2.0 Depends: R (>= 2.10), SummarizedExperiment License: Artistic-2.0 MD5sum: ccf716395a5288a826920d157b547169 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 source.ver: src/contrib/geuvPack_1.2.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: geuvStore Version: 1.2.0 Depends: BatchJobs, GenomicRanges Imports: methods, gQTLBase Suggests: Homo.sapiens, knitr (>= 1.7), rmarkdown License: Artistic-2.0 MD5sum: 609d64c7a18a6f8f0f9d3b362df6222f NeedsCompilation: no Title: demonstrate storage discipline for eQTL enumerations 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 source.ver: src/contrib/geuvStore_1.2.0.tar.gz vignettes: vignettes/geuvStore/inst/doc/geuvStore.pdf vignetteTitles: geuvStore.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GGdata Version: 1.8.0 Depends: R (>= 2.12.0), methods, Biobase (>= 2.5.5), GGBase, snpStats, illuminaHumanv1.db, AnnotationDbi Enhances: GGtools License: LGPL MD5sum: b61993048584040a01ef63af345c0b26 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 source.ver: src/contrib/GGdata_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ggtut suggestsMe: encoDnaseI Package: ggtut Version: 0.7.0 Depends: R (>= 2.14.0), GGtools (>= 3.11.32), ff, GenomicRanges, snpStats, GGdata, GenomicFeatures, ChIPpeakAnno, Rsamtools(>= 1.5.35), cheung2010, SNPlocs.Hsapiens.dbSNP.20120608, hmyriB36 Suggests: rtracklayer, GenomicFeatures, ChIPpeakAnno, TxDb.Hsapiens.UCSC.hg18.knownGene License: Artistic-2.0 MD5sum: ab00ad0aa06b2b06b1b1b57e28bd8fed NeedsCompilation: no Title: support for tutorial on genetics of gene expression ISMB 2011 Description: various resources for genetics of expression with R/bioc biocViews: SequencingData, MicroarrayData, SNPData Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/ggtut_0.7.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: golubEsets Version: 1.12.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: LGPL MD5sum: 0587f14c33a2c018c27a05b3c3bda1b2 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 source.ver: src/contrib/golubEsets_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: grndata Version: 1.2.0 Depends: R (>= 2.10) Suggests: RUnit, BiocGenerics, knitr License: GPL-3 MD5sum: c672271ad7a037521efa64e13bce675b 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 source.ver: src/contrib/grndata_1.2.0.tar.gz vignettes: vignettes/grndata/inst/doc/ hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE htmlDocs: vignettes/grndata/inst/doc/grndata.html htmlTitles: "GRNdata" Package: GSBenchMark Version: 0.104.0 Depends: R (>= 2.13.1) License: GPL-2 MD5sum: b1d00d2d77f77c269250878f680e4624 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 source.ver: src/contrib/GSBenchMark_0.104.0.tar.gz vignettes: vignettes/GSBenchMark/inst/doc/GSBenchMark.pdf vignetteTitles: Working with the GSBenchMark package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gskb Version: 1.2.0 Depends: R (>= 3.2.0) License: Artistic-2.0 MD5sum: 9440ed3b4d696a1d042a375d8787ab0b 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://bioinformatics.sdstate.edu/gskb/db/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://bioinformatics.sdstate.edu/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 source.ver: src/contrib/gskb_1.2.0.tar.gz vignettes: vignettes/gskb/inst/doc/gskb.pdf vignetteTitles: gskb: mouse data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: GSVAdata Version: 1.6.0 Depends: R (>= 2.10), Biobase, GSEABase, hgu95a.db License: GPL (>= 2) MD5sum: a5c126f30d4d19e17f4c03f23823b5be 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 source.ver: src/contrib/GSVAdata_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GWASdata Version: 1.8.0 Depends: GWASTools License: Artistic-2.0 MD5sum: b6238f3ab8f80eece55464dda9e27c09 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 source.ver: src/contrib/GWASdata_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: h5vcData Version: 1.104.0 Suggests: h5vc License: GPL (>= 3) MD5sum: 493091be88f386ef4f958569b9b1f83a 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 source.ver: src/contrib/h5vcData_1.104.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap100khind Version: 1.12.0 Suggests: oligo License: GPL MD5sum: 1a8b1bb83541ffa0802059e425180239 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 source.ver: src/contrib/hapmap100khind_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap100kxba Version: 1.12.0 Suggests: oligo License: GPL MD5sum: 773a13f8cb96bad5caf19bc8d3c005bf 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 source.ver: src/contrib/hapmap100kxba_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap500knsp Version: 1.12.0 Suggests: oligo License: GPL MD5sum: 7de6a2a18ed8ab4a1f5e91f0268b86d0 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 source.ver: src/contrib/hapmap500knsp_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap500ksty Version: 1.12.0 Suggests: oligo License: GPL MD5sum: 2f5e3f0f7acb9955d45a1daba458a3ed 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 source.ver: src/contrib/hapmap500ksty_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmapsnp5 Version: 1.12.0 Suggests: oligo License: GPL MD5sum: faae11da5190d525b65a0c4d1fd1c7fa 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 source.ver: src/contrib/hapmapsnp5_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmapsnp6 Version: 1.12.0 Depends: R (>= 2.15) Suggests: oligo, oligoClasses License: GPL MD5sum: d6598bf3c85752a7ab52b8246c944fab 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 source.ver: src/contrib/hapmapsnp6_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: harbChIP Version: 1.8.0 Depends: R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5), Biostrings Imports: methods, stats License: Artistic-2.0 MD5sum: 39dea080556e27b50901d5289199f084 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 source.ver: src/contrib/harbChIP_1.8.0.tar.gz vignettes: vignettes/harbChIP/inst/doc/yeastUpstream.pdf vignetteTitles: upstream sequence management for yeast hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: HD2013SGI Version: 1.10.0 Depends: R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots, limma, vcd, LSD,EBImage Suggests: BiocStyle License: Artistic-2.0 MD5sum: 53f1a366ef919397709cf1219a81098b 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 source.ver: src/contrib/HD2013SGI_1.10.0.tar.gz vignettes: vignettes/HD2013SGI/inst/doc/HD2013SGI.pdf vignetteTitles: HD2013SGI hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: healthyFlowData Version: 1.8.0 Depends: R (>= 2.15.0), flowCore Imports: methods License: Artistic-2.0 MD5sum: 7ec12ceb074efbd9ee75bd0f63cd7305 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 source.ver: src/contrib/healthyFlowData_1.8.0.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 Package: HEEBOdata Version: 1.8.0 License: LGPL MD5sum: 13d117237b932f82e7c60ff6bfc3f14d 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/ source.ver: src/contrib/HEEBOdata_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu133abarcodevecs Version: 1.8.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: a536fe2086bd236518c3b42a84f375b0 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 source.ver: src/contrib/hgu133abarcodevecs_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu133plus2barcodevecs Version: 1.8.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 234b21c4085095a579d937ea4881e3fc 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 source.ver: src/contrib/hgu133plus2barcodevecs_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu2beta7 Version: 1.10.0 Depends: R (>= 2.0.0) License: Artistic-2.0 MD5sum: 4ebf2ea2cf9e3424fdca69c4c5b55868 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 source.ver: src/contrib/hgu2beta7_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: HiCDataHumanIMR90 Version: 0.104.0 Depends: R (>= 2.10) Suggests: HiTC License: GPL-3 MD5sum: 588d331ad4ee7c1eb0b63c88cd02ce27 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 source.ver: src/contrib/HiCDataHumanIMR90_0.104.0.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 Package: HiCDataLymphoblast Version: 1.6.0 Suggests: GOTHiC, ShortRead License: GPL-3 MD5sum: 15e6d72d70847beecff7ffa8f12586a3 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 source.ver: src/contrib/HiCDataLymphoblast_1.6.0.tar.gz vignettes: vignettes/HiCDataLymphoblast/inst/doc/package_vignettes.pdf vignetteTitles: package_vignettes.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Hiiragi2013 Version: 1.6.0 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: 2d8518d7537100078d22cd2ce95b790b 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 source.ver: src/contrib/Hiiragi2013_1.6.0.tar.gz vignettes: vignettes/Hiiragi2013/inst/doc/Hiiragi2013.pdf vignetteTitles: Hiiragi2013 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: HIVcDNAvantWout03 Version: 1.10.0 License: GPL (>= 2) MD5sum: a1b6b6b3c70972ea10aea0b92fa1cef1 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 source.ver: src/contrib/HIVcDNAvantWout03_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hmyriB36 Version: 1.6.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.5.5), GGBase Suggests: GGtools, illuminaHumanv1.db License: Artistic-2.0 MD5sum: 006e81d6bbb12f3e2a3e474d47493416 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 source.ver: src/contrib/hmyriB36_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ggtut suggestsMe: ind1KG Package: HSMMSingleCell Version: 0.104.0 Depends: R (>= 2.10) License: Artistic-2.0 MD5sum: bd4664db11f7654318b695b3562189b0 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 source.ver: src/contrib/HSMMSingleCell_0.104.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: humanStemCell Version: 0.10.0 Depends: Biobase (>= 2.5.5), hgu133plus2.db License: Artistic-2.0 MD5sum: d6f7f4cec23f17888c92dac3ea1b5406 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 source.ver: src/contrib/humanStemCell_0.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Illumina450ProbeVariants.db Version: 1.6.0 Depends: R (>= 3.0.1) License: GPL-3 MD5sum: f2f8233d6b2124a143808d6a6b642af0 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)License: GPL-3 biocViews: Homo_sapiens_Data, CancerData, ChipOnChipData, SNPData Author: Lee Butcher Maintainer: Tiffany Morris source.ver: src/contrib/Illumina450ProbeVariants.db_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: IlluminaDataTestFiles Version: 1.8.0 License: Artistic-2.0 MD5sum: d07c7e98489279cbedfb0c22c920a3a2 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 source.ver: src/contrib/IlluminaDataTestFiles_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ind1KG Version: 0.8.0 Depends: R (>= 2.10.1), chopsticks Suggests: Rsamtools, rtracklayer, GenomicFeatures, org.Hs.eg.db, SNPlocs.Hsapiens.dbSNP.20090506, TxDb.Hsapiens.UCSC.hg18.knownGene, lumiHumanIDMapping, GGBase, GGtools, hmyriB36 License: Artistic-2.0 MD5sum: 5a85e3e37cc19b70b524f0c59966ba23 NeedsCompilation: no Title: Data from 1000 Genomes, NA19240 (female) chr6 excerpt Description: Elements of samtools/bioc workflow for dealing with personal sequence focusing on identification and interpretation of rare variants biocViews: Genome, MicroarrayData, SNPData Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/ind1KG_0.8.0.tar.gz vignettes: vignettes/ind1KG/inst/doc/ind1KG.pdf, vignettes/ind1KG/inst/doc/nov09rv.pdf vignetteTitles: ind1KG -- 1000 genomes data demo, Notes for eSet developers hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: iontreeData Version: 1.6.0 License: GPL-2 MD5sum: 6300dbaf52da4fa938b934e5e7b90f1c NeedsCompilation: no Title: Data provided to show the usage of functions in iontree package Description: Raw MS2, MS3 scans from direct infusion mass spectrometry (DIMS) and a demo ion tree database 'mzDB' derived from the DIMS data are included. The demo database is used to show the functionalities provided by the 'iontree' package, not for the purpose of compound identification by any means. biocViews: ExperimentData, MassSpectrometryData Author: Mingshu Cao Maintainer: Mingshu Cao source.ver: src/contrib/iontreeData_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ITALICSData Version: 2.8.0 Depends: R (>= 2.0.0) License: GPL MD5sum: 0db8b4016d461e65268fee82c0fd2965 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 source.ver: src/contrib/ITALICSData_2.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Iyer517 Version: 1.12.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 99c3d3ac70bf4db386315819b50a1f75 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 source.ver: src/contrib/Iyer517_1.12.0.tar.gz vignettes: vignettes/Iyer517/inst/doc/Iyer517.pdf vignetteTitles: Iyer517 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: JASPAR2014 Version: 1.6.0 Depends: R (>= 3.0.1), methods, Biostrings (>= 2.29.19) License: GPL-2 MD5sum: 52b3b252276f71edf044c98adb5ec200 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/ source.ver: src/contrib/JASPAR2014_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: KEGGandMetacoreDzPathwaysGEO Version: 0.104.0 Depends: R (>= 2.15.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: f6d9017de411639a4d90fe8bfda90700 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 source.ver: src/contrib/KEGGandMetacoreDzPathwaysGEO_0.104.0.tar.gz vignettes: vignettes/KEGGandMetacoreDzPathwaysGEO/inst/doc/KEGGandMetacoreDzPathwaysGEO.pdf vignetteTitles: KEGGandMetacoreDzPathwaysGEO Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: KEGGdzPathwaysGEO Version: 1.8.0 Depends: R (>= 2.13.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: fb0a563988f4a789642781324516b255 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 source.ver: src/contrib/KEGGdzPathwaysGEO_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: kidpack Version: 1.12.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5) License: GPL-2 MD5sum: f35e00423e97fe0d11957ce71f7ee327 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 source.ver: src/contrib/kidpack_1.12.0.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 Package: leeBamViews Version: 1.6.0 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: 62827b1cc76605bf9b626960f84cec70 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 source.ver: src/contrib/leeBamViews_1.6.0.tar.gz vignettes: vignettes/leeBamViews/inst/doc/leeViews.pdf vignetteTitles: managing multiple NGS samples with bamViews hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: leukemiasEset Version: 1.6.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 19de867b8d19d94241cb90a10076df0c 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 source.ver: src/contrib/leukemiasEset_1.6.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: LiebermanAidenHiC2009 Version: 0.8.0 Depends: KernSmooth, IRanges License: LGPL MD5sum: 51496473d9ca7e57e668f066e24cb485 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 source.ver: src/contrib/LiebermanAidenHiC2009_0.8.0.tar.gz vignettes: vignettes/LiebermanAidenHiC2009/inst/doc/LiebermanAidenHiC2009.pdf vignetteTitles: Exploration of HiC data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ListerEtAlBSseq Version: 1.2.0 Depends: R (>= 3.1.1), methylPipe Suggests: BSgenome.Hsapiens.UCSC.hg18 License: Artistic 2.0 MD5sum: 4c8cc0a6884d775eceefb60b4148f95e 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 source.ver: src/contrib/ListerEtAlBSseq_1.2.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: lumiBarnes Version: 1.10.0 Depends: R (>= 2.0), Biobase (>= 2.5.5), lumi (>= 1.1.0) License: LGPL MD5sum: 2c7192225dfb09e8ea571a438984bfd5 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 source.ver: src/contrib/lumiBarnes_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: LungCancerACvsSCCGEO Version: 1.6.0 Depends: R (>= 2.15.0) License: GPL-2 MD5sum: 6de5f285ce3d86481e755d34951cd3c4 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/ source.ver: src/contrib/LungCancerACvsSCCGEO_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: LungCancerLines Version: 0.8.0 Imports: Rsamtools License: Artistic-2.0 MD5sum: 10c51ff70445ab33625c8617c943d457 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 source.ver: src/contrib/LungCancerLines_0.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: lungExpression Version: 0.8.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: e9e452c0efa58ded2288344754b2569a 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 source.ver: src/contrib/lungExpression_0.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mammaPrintData Version: 1.6.0 Depends: R (>= 2.13.0) Suggests: Biobase, gdata, limma License: Artistic-2.0 MD5sum: cf743eef3aaf1cd5282cff8e2e7951c7 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 biocViews: ExperimentData, ExpressionData, CancerData, BreastCancerData, MicroarrayData, TwoChannelData Author: Luigi Marchionni Maintainer: Luigi Marchionni URL: http://luigimarchionni.org/breastTSP.html source.ver: src/contrib/mammaPrintData_1.6.0.tar.gz vignettes: vignettes/mammaPrintData/inst/doc/mammaPrintData.pdf vignetteTitles: Working with the mammaPrintData package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mAPKLData Version: 1.2.0 Depends: R (>= 3.2.0) Suggests: Biobase License: Artistic-2.0 MD5sum: 0a1585f812bf301ab328e6768fa59b1e 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 source.ver: src/contrib/mAPKLData_1.2.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: maqcExpression4plex Version: 1.14.0 Suggests: oligo, pdInfoBuilder License: GPL MD5sum: fcf094cde2d64ddd97ad80242114c1e1 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 source.ver: src/contrib/maqcExpression4plex_1.14.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MAQCsubset Version: 1.8.0 Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), lumi, methods Suggests: genefilter, codelink License: Artistic-2.0 MD5sum: 5bcbe2e6ee0e5ba7ff691343d320f2bc 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 source.ver: src/contrib/MAQCsubset_1.8.0.tar.gz vignettes: vignettes/MAQCsubset/inst/doc/maqcNotes.pdf vignetteTitles: MAQC notes hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MAQCsubsetAFX Version: 1.8.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: bba4402bd6cff25f01255d3e702c5d43 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 source.ver: src/contrib/MAQCsubsetAFX_1.8.0.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 Package: MAQCsubsetILM Version: 1.8.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), lumi License: Artistic-2.0 MD5sum: 7ddc03f7d29318a2bf5953ab8e083cf8 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 source.ver: src/contrib/MAQCsubsetILM_1.8.0.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 Package: MEALData Version: 1.0.0 Depends: R (>= 3.2.0) License: Artistic-2.0 MD5sum: 780915b844103accad62cc6577e0cb42 NeedsCompilation: no Title: Example data of MEAL package Description: The package contains methylation, expression and SNPs data obtained from GSE53261. It is used in MEAL case example to show MEAL functionalities. biocViews: Homo_sapiens_Data, MicroarrayData Author: Ruiz Carlos [aut, cre], Hernndez Carles [aut], Gonzalez JR [aut] Maintainer: Ruiz Carlos source.ver: src/contrib/MEALData_1.0.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MEDIPSData Version: 1.6.0 Depends: R (>= 2.15.0) License: GPL (>= 2) MD5sum: 2380029e941aa6a04ae49972311f0b87 NeedsCompilation: no Title: Example data for the MEDIPS package. Description: Data for the MEDIPS package, consisting of chromosome 22 MeDIP and control/Input sample data from DNA methylation analysis of human embryonic stem cells and mapped to the human genome hg19 using bowtie. biocViews: ExperimentData, Genome, SequencingData Author: Lukas Chavez Maintainer: Lukas Chavez source.ver: src/contrib/MEDIPSData_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MEEBOdata Version: 1.8.0 License: LGPL MD5sum: 9d64b79c2665d5bb824e94618cf9e544 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/ source.ver: src/contrib/MEEBOdata_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: metaMSdata Version: 1.6.0 License: GPL (>= 2) MD5sum: 570fcee7f471b45a4f787998e1ff9f27 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 source.ver: src/contrib/metaMSdata_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MethylAidData Version: 1.2.0 Depends: MethylAid, R (>= 3.2) Suggests: BiocParallel, BiocStyle, knitr License: GPL (>= 2) MD5sum: 473606cccc31098ee7ce291d9d21c0cc NeedsCompilation: no Title: MethylAid-summarized data on 2800 Illumina 450k array samples Description: A data package containing summarized Illumina 450k array data on 2800 samples. The data can be use as a background data set in the interactive application. biocViews: ExperimentData Author: Maarten van Iterson, Elmar. Tobi, Roderick Slieker, Wouter den Hollander, Rene Luijk and Bas Heijmans Maintainer: M. van Iterson URL: http://shiny.bioexp.nl/MethylAid VignetteBuilder: knitr source.ver: src/contrib/MethylAidData_1.2.0.tar.gz vignettes: vignettes/MethylAidData/inst/doc/MethylAidData.pdf vignetteTitles: hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: minfiData Version: 0.12.0 Depends: R (>= 2.13.0), minfi, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 License: Artistic-2.0 MD5sum: 8b48c10da188ced9f19d47e0f7cfadc5 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 Author: Kasper Daniel Hansen, Martin Aryee, Winston Timp Maintainer: Kasper Daniel Hansen source.ver: src/contrib/minfiData_0.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: minionSummaryData Version: 1.0.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: ef7b46d617401ad9b602ac97dc652fcd 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 source.ver: src/contrib/minionSummaryData_1.0.0.tar.gz vignettes: vignettes/minionSummaryData/inst/doc/ hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE htmlDocs: vignettes/minionSummaryData/inst/doc/creating-Styphi-Dataset.html htmlTitles: "Creating example MinION summary dataset" Package: miRcompData Version: 1.0.0 Depends: R (>= 3.2), Imports: utils License: GPL-3 | file LICENSE MD5sum: b2d2bedd651cae9c3e092b0475cf79e4 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 source.ver: src/contrib/miRcompData_1.0.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Package: miRNATarget Version: 1.8.0 Depends: R (>= 2.10), Biobase License: GPL MD5sum: 859cf57eb60295319e1a2168f88af5cb 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 source.ver: src/contrib/miRNATarget_1.8.0.tar.gz vignettes: vignettes/miRNATarget/inst/doc/miRNATarget.pdf vignetteTitles: miRNATargetTutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mitoODEdata Version: 1.6.0 Depends: R (>= 2.14.0) License: LGPL MD5sum: 868eb27f4e97a8f94bc2ff8bf3756be3 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: source.ver: src/contrib/mitoODEdata_1.6.0.tar.gz vignettes: vignettes/mitoODEdata/inst/doc/mitoODEdata-introduction.pdf vignetteTitles: Mitoode data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: MMDiffBamSubset Version: 1.6.0 Suggests: MMDiff License: LGPL MD5sum: 34a8501e3f26a8f4312e3d2b58e32415 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 source.ver: src/contrib/MMDiffBamSubset_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mosaicsExample Version: 1.6.0 Depends: R (>= 2.11.1) License: GPL (>= 2) MD5sum: 5721038f6cd991ee9083238f892abc13 NeedsCompilation: no Title: Example data for the mosaics package, which implements MOSAiCS, a statistical framework to analyze one-sample or two-sample ChIP-seq data Description: Data for the mosaics package, consisting of 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, Genome, Homo_sapiens_Data, ChIPSeqData Author: Dongjun Chung, Pei Fen Kuan, Sunduz Keles Maintainer: Dongjun Chung URL: http://groups.google.com/group/mosaics_user_group source.ver: src/contrib/mosaicsExample_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mouse4302barcodevecs Version: 1.8.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 37d52e52b4517a4f5e18d0d448370bf1 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 source.ver: src/contrib/mouse4302barcodevecs_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MSBdata Version: 0.8.0 License: LGPL MD5sum: d0f1b38635b6bb1e9e434077f7bfcd49 NeedsCompilation: no Title: Data sets for the book 'Modern Statistics for Biology' Description: Data sets for the book 'Modern Statistics for Biology' biocViews: ExperimentData, ReproducibleResearch Author: Wolfgang Huber and Andrzej Oles Maintainer: Wolfgang Huber source.ver: src/contrib/MSBdata_0.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: msd16s Version: 0.104.0 Depends: R (>= 2.10), Biobase, metagenomeSeq, License: Artistic-2.0 MD5sum: 083514dc551ecd79f9a4f4a5dfcbb531 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 source.ver: src/contrib/msd16s_0.104.0.tar.gz vignettes: vignettes/msd16s/inst/doc/msd16s.pdf vignetteTitles: msd16s hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: msdata Version: 0.8.0 Suggests: xcms License: GPL (>= 2) MD5sum: bb08f4f1bf33715e0ff0e099c2f46c7c 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. PSI mzIdentML example files for various search engines. biocViews: ExperimentData, MassSpectrometryData Author: Steffen Neumann Maintainer: Steffen Neumann source.ver: src/contrib/msdata_0.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics Package: mtbls2 Version: 1.0.0 Depends: R (>= 2.10) Suggests: xcms (>= 1.43.3), CAMERA, Risa (>= 1.0.0), knitr, Heatplus, pcaMethods, sp License: CC0 MD5sum: f3a7240eab5385a4769181df9474b99c 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 source.ver: src/contrib/mtbls2_1.0.0.tar.gz vignettes: vignettes/mtbls2/inst/doc/ hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE htmlDocs: vignettes/mtbls2/inst/doc/MTBLS2.html htmlTitles: "MTBLS2" Package: MUGAExampleData Version: 0.104.0 Depends: R (>= 2.10.0) License: GPL-3 MD5sum: d9967fb62ba8a03124c064e97dff1d08 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 source.ver: src/contrib/MUGAExampleData_0.104.0.tar.gz vignettes: vignettes/MUGAExampleData/inst/doc/MUGAExampleData.pdf vignetteTitles: User Manual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Mulder2012 Version: 0.10.0 Depends: R (>= 2.14), org.Hs.eg.db, KEGG.db Imports: igraph, HTSanalyzeR, PANR, RedeR, pvclust, MASS Suggests: snow License: Artistic-2.0 MD5sum: fc720a0e293b44a6d142f9f2397ceb88 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 source.ver: src/contrib/Mulder2012_0.10.0.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 Package: mvoutData Version: 1.6.0 Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4), lumi License: Artistic-2.0 MD5sum: 8ab7bedb57f891824d8b0635b20c483b 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 source.ver: src/contrib/mvoutData_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: NCIgraphData Version: 1.6.0 Depends: R (>= 2.10.0) Suggests: Rgraphviz License: GPL-3 MD5sum: 3e4bcd19efcf7e6939bf486f5a27504e 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 source.ver: src/contrib/NCIgraphData_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Neve2006 Version: 0.8.0 Depends: R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0), hgu133a.db, annotate License: Artistic-2.0 MD5sum: e2555ec12028b094201b89a382c1c851 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 source.ver: src/contrib/Neve2006_0.8.0.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 Package: NGScopyData Version: 0.104.0 License: GPL (>=2) MD5sum: 9ef185b71f8701ec0baca68a1b5d7016 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 source.ver: src/contrib/NGScopyData_0.104.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: parathyroidSE Version: 1.8.0 Depends: SummarizedExperiment, R (>= 2.10) Suggests: Rsamtools, GenomicAlignments, GEOquery, SRAdb, GenomicFeatures, BiocStyle License: LGPL MD5sum: 31261ffb4b275464124cd7494a6162c1 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 source.ver: src/contrib/parathyroidSE_1.8.0.tar.gz vignettes: vignettes/parathyroidSE/inst/doc/parathyroidSE.pdf vignetteTitles: parathyroidGenesSE hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pasilla Version: 0.10.0 Suggests: locfit, edgeR, xtable, DEXSeq, DESeq License: LGPL MD5sum: c50392a223b780a564bf6d3aa2d0bdaf 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 is 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 source.ver: src/contrib/pasilla_0.10.0.tar.gz vignettes: vignettes/pasilla/inst/doc/create_objects.pdf vignetteTitles: Data preprocessing and creation of the data objects pasillaGenes and pasillaExons hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: pasillaBamSubset Package: pasillaBamSubset Version: 0.8.0 Suggests: pasilla License: LGPL MD5sum: b2e16ed4882e76d83006b60e0a850774 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: H. Pages Maintainer: H. Pages source.ver: src/contrib/pasillaBamSubset_0.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: PathNetData Version: 1.6.0 Depends: R (>= 1.14.0) License: GPL-3 MD5sum: 6df78c91693137e4487e582cb5b7988b 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 source.ver: src/contrib/PathNetData_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Hs.hg19 Version: 1.6.0 License: GPL (>= 2) MD5sum: 780eb77209a22813dd0915512226f3fe 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, source.ver: src/contrib/pcaGoPromoter.Hs.hg19_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Mm.mm9 Version: 1.6.0 License: GPL (>= 2) MD5sum: 251db17180125b74d8b5a2139ae9612b 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, source.ver: src/contrib/pcaGoPromoter.Mm.mm9_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Rn.rn4 Version: 1.6.0 License: GPL (>= 2) MD5sum: a10d5cff0570df8b84f8bff2558fc169 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, source.ver: src/contrib/pcaGoPromoter.Rn.rn4_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pd.atdschip.tiling Version: 0.8.0 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: 7080994fcfd04d24e59bf6785f00f4ea 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 source.ver: src/contrib/pd.atdschip.tiling_0.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pepDat Version: 0.104.0 Depends: R(>= 3.0.0) Imports: GenomicRanges Suggests: knitr License: Artistic-2.0 MD5sum: 2fb0bf956dcda5fe9faf660a6997bb73 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 source.ver: src/contrib/pepDat_0.104.0.tar.gz vignettes: vignettes/pepDat/inst/doc/pepDat.pdf vignetteTitles: The pepDat users guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ppiData Version: 0.8.0 Depends: graph Imports: AnnotationDbi Suggests: org.Sc.sgd.db, ppiStats License: Artistic-2.0 MD5sum: 170ae2be8287170a0607916b73ee3e75 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 source.ver: src/contrib/ppiData_0.8.0.tar.gz vignettes: vignettes/ppiData/inst/doc/ppiData.pdf vignetteTitles: Using the package ppiStats hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: prebsdata Version: 1.6.0 Depends: R (>= 2.14.0) License: Artistic-2.0 MD5sum: 68ba81e376f3b92a4e56c17f648a5127 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 source.ver: src/contrib/prebsdata_1.6.0.tar.gz vignettes: vignettes/prebsdata/inst/doc/prebsdata.pdf vignetteTitles: prebsdata User Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: PREDAsampledata Version: 0.10.0 Depends: R (>= 2.9.0), methods, PREDA, Biobase, affy, annotate, gahgu133plus2.db, gahgu133plus2cdf Suggests: hgu133plus2.db, hgu133plus2cdf License: Artistic-2.0 MD5sum: 53e457a4c936077a49102db81252023d 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 source.ver: src/contrib/PREDAsampledata_0.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ProData Version: 1.8.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL MD5sum: ad79f039917b51e89f42751ad7dc02d7 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 source.ver: src/contrib/ProData_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pRolocdata Version: 1.8.0 Depends: R (>= 2.15), MSnbase Imports: Biobase Suggests: pRoloc License: GPL-2 MD5sum: 680838ceb48032b0e147e1dbe7f9b8fe NeedsCompilation: no Title: Data accompanying the pRoloc package Description: Mass-spectrometry based spatial proteomics data sets from Dunkley et al. (2006), Foster et al. (2006), Tan et al. (2009), Hall et al. (2009), Trotter et al. (2010), Ferro et al. (2010), Nikolovski et al. (2012, 2014), Breckels et al. (2013), Groen et al. (2014) and Christoforou 2015, and protein complex separation data from Kristensen et al. (2012), Havugimana et al. (2012), Kirkwood et al. (2013) and Fabre et al. (2015). biocViews: ExperimentData, Homo_sapiens_Data, MassSpectrometryData, Arabidopsis_thaliana_Data, Drosophila_melanogaster_Data, Mus_musculus_Data, StemCell Author: Laurent Gatto and Lisa M. Breckels Maintainer: Laurent Gatto URL: https://github.com/lgatto/pRolocdata BugReports: https://github.com/lgatto/pRolocdata/issues source.ver: src/contrib/pRolocdata_1.8.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics Package: pumadata Version: 2.6.0 Depends: R (>= 3.2.0), affy (>= 1.46.0), Biobase (>= 2.5.5),puma ,oligo(>= 1.32.0) License: LGPL MD5sum: 50499cb27e91ebec6af5dff10780e2bf 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 source.ver: src/contrib/pumadata_2.6.0.tar.gz vignettes: vignettes/pumadata/inst/doc/pumadata.pdf vignetteTitles: pumadata User Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: PWMEnrich.Dmelanogaster.background Version: 4.4.0 Depends: methods, PWMEnrich License: GPL-3 MD5sum: 38a6b7c256aad1e99a4947a22ecf74a1 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 source.ver: src/contrib/PWMEnrich.Dmelanogaster.background_4.4.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: PWMEnrich.Hsapiens.background Version: 4.4.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: 150b10d5a245d0eb98b67ec9ba700ca5 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 source.ver: src/contrib/PWMEnrich.Hsapiens.background_4.4.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: PWMEnrich.Mmusculus.background Version: 4.4.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: a3cc540ce9885ffbef1079e3f0db26cc 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 source.ver: src/contrib/PWMEnrich.Mmusculus.background_4.4.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: QDNAseq.hg19 Version: 1.0.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: a748e5f35ebeeed853895d3636be89de 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 source.ver: src/contrib/QDNAseq.hg19_1.0.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: QDNAseq.mm10 Version: 1.0.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: b16301e1d1babc4b724b944eea9da267 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 source.ver: src/contrib/QDNAseq.mm10_1.0.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: rcellminerData Version: 1.2.2 Depends: R (>= 3.1.1), Biobase Suggests: knitr, testthat, BiocStyle, rcellminer License: LGPL-3 MD5sum: 498f3261132aff243aea7301bc092aff 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 VignetteBuilder: knitr source.ver: src/contrib/rcellminerData_1.2.2.tar.gz vignettes: vignettes/rcellminerData/inst/doc/ hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE htmlDocs: vignettes/rcellminerData/inst/doc/rcellminerDataUsage.html htmlTitles: "Accessing CellMiner Data" Package: RforProteomics Version: 1.8.0 Depends: MSnbase Imports: R.utils, Biobase, rpx, biocViews, BiocInstaller, interactiveDisplay, shiny Suggests: knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, isobar, MALDIquant (>= 1.12), MALDIquantForeign, readBrukerFlexData, rTANDEM, synapter, synapterdata, IPPD, Rdisop, OrgMassSpecR, BRAIN, rols, hpar, GO.db, org.Hs.eg.db, biomaRt, RColorBrewer, ggplot2, reshape2, xtable, lattice, mzID, pRoloc, pRolocdata, MSGFplus, MSGFgui, MSnID, msmsTests, msmsEDA, corrplot, Heatplus, gplots, VennDiagram Enhances: cleaver License: Artistic-2.0 MD5sum: 4613d751cd864afdc2ff57d5cec62a8c 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' paper. Two vignettes describe the code and data needed to reproduce the examples and figures descibed in the paper and functionality for proteomics visualisation. 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 source.ver: src/contrib/RforProteomics_1.8.0.tar.gz vignettes: vignettes/RforProteomics/inst/doc/Bioc2013poster.pdf, vignettes/RforProteomics/inst/doc/HUPO2014poster.pdf, vignettes/RforProteomics/inst/doc/RforProteomics.pdf vignetteTitles: RforProteomics Bioc2013 poster, A current perspective on using R and Bioconductor for proteomics data analysis, Using R for proteomics data analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RforProteomics/inst/doc/RforProteomics.R htmlDocs: vignettes/RforProteomics/inst/doc/RProtVis.html htmlTitles: "Visualisation of proteomics data using R and Bioconductor" Package: rheumaticConditionWOLLBOLD Version: 1.8.0 Depends: R (>= 2.10.0) Suggests: genefilter, Biobase, hgu133plus2.db License: Artistic-2.0 MD5sum: dfaad689315ecba1eccf773f03f8a18e 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/ source.ver: src/contrib/rheumaticConditionWOLLBOLD_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RIPSeekerData Version: 1.6.0 Depends: RIPSeeker License: GPL-2 MD5sum: dc9b016063189c0bf39bf3b97def6644 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 source.ver: src/contrib/RIPSeekerData_1.6.0.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 Package: RMassBankData Version: 1.8.0 Suggests: RMassBank License: Artistic-2.0 MD5sum: 7543e00a08b973e8ea6b0b2e3a6181a1 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 source.ver: src/contrib/RMassBankData_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RNAinteractMAPK Version: 1.8.0 Depends: R (>= 2.12.0), methods, fields, sparseLDA, RNAinteract Imports: grid, gdata, MASS, genefilter Suggests: qvalue, lattice License: Artistic-2.0 MD5sum: 6cf050ad5d41ad853a610077ecf8eb02 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 source.ver: src/contrib/RNAinteractMAPK_1.8.0.tar.gz vignettes: vignettes/RNAinteractMAPK/inst/doc/RNAinteractMAPK.pdf vignetteTitles: RNAinteractMAPK hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: DmelSGI Package: RNAseqData.HNRNPC.bam.chr14 Version: 0.8.0 Suggests: GenomicAlignments, BiocInstaller License: LGPL MD5sum: 8f8e21eb9b624b10e00e9d77ce534e32 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: H. Pages Maintainer: H. Pages URL: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1147/ source.ver: src/contrib/RNAseqData.HNRNPC.bam.chr14_0.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RnaSeqSampleSizeData Version: 1.2.0 Depends: edgeR,R (>= 2.10) Suggests: BiocStyle, knitr License: GPL (>= 2) MD5sum: 1fd0cc38f3d5b848d792465eb82bf0d3 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 source.ver: src/contrib/RnaSeqSampleSizeData_1.2.0.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 Package: RnaSeqTutorial Version: 0.8.0 Depends: R (>= 3.0.2), methods, easyRNASeq Suggests: Rsamtools, ShortRead, BSgenome.Dmelanogaster.UCSC.dm3, GenomicAlignments, biomaRt, genomeIntervals License: Artistic-2.0 MD5sum: 774f1f8b94e0d4aa6062fe99ee62d56b NeedsCompilation: no Title: RNA-Seq Tutorial (EBI Cambridge UK, October 2011) Description: A selection of RNA-Seq data to get familiar with the related Bioconductor core packages and the easyRNASeq package. biocViews: ExperimentData, Drosophila_melanogaster_Data, RNASeqData Author: Nicolas Delhomme, Ismael Padioleau Maintainer: Nicolas Delhomme source.ver: src/contrib/RnaSeqTutorial_0.8.0.tar.gz vignettes: vignettes/RnaSeqTutorial/inst/doc/RnaSeqTutorial.pdf vignetteTitles: RNA-Seq Tutorial hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: RnBeads.hg19 Version: 1.2.1 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: f5358cfc0702c1fce8782e1b0128b0f1 NeedsCompilation: no Title: RnBeads.hg19 Description: Automatically generated RnBeads annotation package for the assembly hg19. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator source.ver: src/contrib/RnBeads.hg19_1.2.1.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: RnBeads.hg38 Version: 1.2.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 657af31efc6454ea056cf462988fa452 NeedsCompilation: no Title: RnBeads.hg38 Description: Automatically generated RnBeads annotation package for the assembly hg38. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator source.ver: src/contrib/RnBeads.hg38_1.2.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: RnBeads.mm10 Version: 1.2.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: ba0854796ad789cf5f98b20c57cbc334 NeedsCompilation: no Title: RnBeads.mm10 Description: Automatically generated RnBeads annotation package for the assembly mm10. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator source.ver: src/contrib/RnBeads.mm10_1.2.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: RnBeads.mm9 Version: 1.2.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 523d3ea39b4af40d58270eb2ad9dd23f NeedsCompilation: no Title: RnBeads.mm9 Description: Automatically generated RnBeads annotation package for the assembly mm9. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator source.ver: src/contrib/RnBeads.mm9_1.2.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: RnBeads.rn5 Version: 1.2.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 43613ca055c432b8a7361e805f89794d NeedsCompilation: no Title: RnBeads.rn5 Description: Automatically generated RnBeads annotation package for the assembly rn5. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator source.ver: src/contrib/RnBeads.rn5_1.2.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: RRBSdata Version: 0.104.0 Depends: R (>= 3.1.0), BiSeq (>= 1.9.2) License: LGPL-3 MD5sum: b454dd4ff9df57117842e9046624c727 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 source.ver: src/contrib/RRBSdata_0.104.0.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 Package: rRDPData Version: 0.104.0 Depends: rRDP License: GPL-2 MD5sum: 615c95ec7fd96f03b3149380326bbc96 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 source.ver: src/contrib/rRDPData_0.104.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RTCGA.clinical Version: 1.0.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 334178ef110212e15298d4a094827849 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. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/mi2-warsaw/RTCGA.data/issues source.ver: src/contrib/RTCGA.clinical_1.0.0.tar.gz vignettes: vignettes/RTCGA.clinical/inst/doc/ hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE htmlDocs: vignettes/RTCGA.clinical/inst/doc/downloading_clinical_datasets.html htmlTitles: "Using RTCGA package to download clinical data that are included in RTCGA.clinical package" Package: RTCGA.mutations Version: 1.0.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 849b542e124e87a6a98ea4b17b3b275b 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. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/mi2-warsaw/RTCGA.data/issues source.ver: src/contrib/RTCGA.mutations_1.0.0.tar.gz vignettes: vignettes/RTCGA.mutations/inst/doc/ hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE htmlDocs: vignettes/RTCGA.mutations/inst/doc/downloading_mutations_datasets.html htmlTitles: "Using RTCGA package to download mutations data that are included in RTCGA.mutations package" Package: RTCGA.rnaseq Version: 1.0.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 0cbc1f1cd96a1d1509424d055ada1424 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. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/mi2-warsaw/RTCGA.data/issues source.ver: src/contrib/RTCGA.rnaseq_1.0.0.tar.gz vignettes: vignettes/RTCGA.rnaseq/inst/doc/ hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE htmlDocs: vignettes/RTCGA.rnaseq/inst/doc/downloading_rnaseq_datasets.html htmlTitles: "Using RTCGA package to download rna-seq data that are included in RTCGA.rnaseq package" Package: RUVnormalizeData Version: 0.104.0 Depends: R (>= 2.10.0), Biobase License: GPL-3 MD5sum: 194dea37a1bde60e4b9f33b1946c298c 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 source.ver: src/contrib/RUVnormalizeData_0.104.0.tar.gz vignettes: vignettes/RUVnormalizeData/inst/doc/RUVnormalizeData.pdf vignetteTitles: RUVnormalizeData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SCLCBam Version: 1.2.0 Depends: R(>= 2.10) Suggests: BiocStyle License: GPL-2 MD5sum: e627eb5e7a45328ef1d75c6baa8ab553 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: Thomas Kuilman source.ver: src/contrib/SCLCBam_1.2.0.tar.gz vignettes: vignettes/SCLCBam/inst/doc/SCLCBam.pdf vignetteTitles: SCLCBam hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: seq2pathway.data Version: 1.2.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 7d6a5bb905b54ae755eab844458b0ea3 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 source.ver: src/contrib/seq2pathway.data_1.2.0.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 Package: seqc Version: 1.4.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 88dd90c7cfa4b59d99a3a97bb4a63a70 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 Steve Lianoglou Maintainer: Yang Liao and Wei Shi URL: http://bioconductor.org/packages/release/data/experiment/html/seqc.html source.ver: src/contrib/seqc_1.4.0.tar.gz vignettes: vignettes/seqc/inst/doc/seqc.pdf vignetteTitles: SEQC Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: seqCNA.annot Version: 1.6.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: aa95c4fc837ede400c759f047ed8f264 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 source.ver: src/contrib/seqCNA.annot_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: serumStimulation Version: 1.6.0 Depends: R (>= 2.10) License: GPL (>= 2) MD5sum: d438744e00a9fa6ac9b7b9b7a4092858 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, source.ver: src/contrib/serumStimulation_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: seventyGeneData Version: 1.6.0 Depends: R (>= 2.13.0) Suggests: Biobase, gdata, limma, breastCancerNKI License: Artistic-2.0 MD5sum: 9ebdef8ab3a262b5e43e34c76296b764 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 source.ver: src/contrib/seventyGeneData_1.6.0.tar.gz vignettes: vignettes/seventyGeneData/inst/doc/seventyGeneData.pdf vignetteTitles: Working with the seventyGeneData package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: shinyMethylData Version: 0.104.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: d2852bc80fc53140fd5b55f0538300bc 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 source.ver: src/contrib/shinyMethylData_0.104.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: simpIntLists Version: 1.6.0 License: GPL (>= 2) MD5sum: a97719d4c56b18e521dd4c054914a1a2 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 source.ver: src/contrib/simpIntLists_1.6.0.tar.gz vignettes: vignettes/simpIntLists/inst/doc/simpIntLists.pdf vignetteTitles: simpIntLists hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SNAData Version: 1.16.0 Depends: R (>= 2.4.0), graph Suggests: Rgraphviz License: LGPL MD5sum: 84746e880760b6968b6e3e206d92d894 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 source.ver: src/contrib/SNAData_1.16.0.tar.gz vignettes: vignettes/SNAData/inst/doc/SNAData.pdf vignetteTitles: SNAData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SNAGEEdata Version: 1.6.0 Depends: R (>= 2.6.0) Suggests: ALL, hgu95av2.db, SNAGEE License: Artistic-2.0 MD5sum: 9ee9bdbe7288a610bf7d407d21779ab1 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 source.ver: src/contrib/SNAGEEdata_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SNPhoodData Version: 1.0.0 Depends: R (>= 3.2) Suggests: BiocStyle,knitr,rmarkdown License: LGPL (>= 3) MD5sum: 7c3efcd6a62bee5a704c2465c22b77e9 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 source.ver: src/contrib/SNPhoodData_1.0.0.tar.gz vignettes: vignettes/SNPhoodData/inst/doc/ hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE htmlDocs: vignettes/SNPhoodData/inst/doc/SNPhoodData.html htmlTitles: "The SNPhoodData package" Package: SomatiCAData Version: 1.8.0 Depends: R (>= 2.14) License: Artistic-2.0 MD5sum: de01e4729afaac8e421418ced448fe53 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 source.ver: src/contrib/SomatiCAData_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SomaticCancerAlterations Version: 1.6.1 Depends: R (>= 3.0.0) Imports: GenomicRanges, exomeCopy, stringr, IRanges Suggests: testthat, ggbio, ggplot2, knitr License: GPL-3 MD5sum: d28a587de486892f110132c82d30d931 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 source.ver: src/contrib/SomaticCancerAlterations_1.6.1.tar.gz vignettes: vignettes/SomaticCancerAlterations/inst/doc/ hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE htmlDocs: vignettes/SomaticCancerAlterations/inst/doc/SomaticCancerAlterations-html.html htmlTitles: "SomaticCancerAlterations - HTML" Package: SpikeIn Version: 1.12.0 Depends: R (>= 1.6), affy (>= 1.23.4) License: Artistic-2.0 MD5sum: f6ec6e24d8b6b30cdc3de58fae6d5bdd 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 source.ver: src/contrib/SpikeIn_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SpikeInSubset Version: 1.10.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5), affy (>= 1.23.4) License: LGPL MD5sum: 07153ca5e9fae1f0df44dfe3b8411087 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 source.ver: src/contrib/SpikeInSubset_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: stemHypoxia Version: 1.6.0 Depends: R (>= 2.14.1) License: GPL (>=2) MD5sum: 8bb0b673dd6946dbea39f24b0259cf36 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 source.ver: src/contrib/stemHypoxia_1.6.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: stjudem Version: 1.10.0 Depends: R (>= 2.10), utils License: LGPL (>= 2) MD5sum: 85286ed83f6eb7c8f48944f0383fdd8f 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 source.ver: src/contrib/stjudem_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SVM2CRMdata Version: 1.2.0 Depends: R(>= 3.2.0) License: LGPL (>= 2) MD5sum: 325b16702f00556234ba89bc93ad4718 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 source.ver: src/contrib/SVM2CRMdata_1.2.0.tar.gz vignettes: vignettes/SVM2CRMdata/inst/doc/SVM2CRMdata.pdf vignetteTitles: Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: synapterdata Version: 1.8.0 Depends: R (>= 2.10), synapter (>= 0.99.6) License: GPL-2 MD5sum: 2211d7a2adc45af1c0b087f1282fc111 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 source.ver: src/contrib/synapterdata_1.8.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics Package: systemPipeRdata Version: 1.0.1 Depends: methods Imports: BiocGenerics Suggests: RUnit, BiocStyle, knitr, rmarkdown, systemPipeR License: Artistic-2.0 MD5sum: 123ad8d6d0dd0636c8967d58989af4be 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, 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 Author: Thomas Girke Maintainer: Thomas Girke URL: https://github.com/tgirke/systemPipeRdata VignetteBuilder: knitr source.ver: src/contrib/systemPipeRdata_1.0.1.tar.gz vignettes: vignettes/systemPipeRdata/inst/doc/ hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE htmlDocs: vignettes/systemPipeRdata/inst/doc/systemPipeRdata.html htmlTitles: "Overview Vignette" Package: TargetScoreData Version: 1.6.0 Suggests: TargetScore, gplots License: GPL-2 MD5sum: d6467e0271c010d34671ce8189f9afd4 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 source.ver: src/contrib/TargetScoreData_1.6.0.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 Package: TargetSearchData Version: 1.8.0 Depends: TargetSearch License: GPL (>= 2) MD5sum: e36472cc13cfcd02ba12c29804a8202e 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 Henning Redestig , Matt Hannah source.ver: src/contrib/TargetSearchData_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: TBX20BamSubset Version: 1.6.0 Depends: Rsamtools (>= 1.9.8) Imports: xtable License: LGPL MD5sum: 1325b05141917f3d4e89b2b6de78da18 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 source.ver: src/contrib/TBX20BamSubset_1.6.0.tar.gz vignettes: vignettes/TBX20BamSubset/inst/doc/TBX20BamSubset.pdf vignetteTitles: TBX20 RNA-Seq data subset hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: TCGAcrcmiRNA Version: 0.104.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 9fe6d623f414b53f633c1df45200c794 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 source.ver: src/contrib/TCGAcrcmiRNA_0.104.0.tar.gz vignettes: vignettes/TCGAcrcmiRNA/inst/doc/TcgaCrcVignette.pdf vignetteTitles: TCGAcrcmiRNA hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: TCGAcrcmRNA Version: 0.104.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: b44888141c23e93f04eaee261e33de23 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 source.ver: src/contrib/TCGAcrcmRNA_0.104.0.tar.gz vignettes: vignettes/TCGAcrcmRNA/inst/doc/TcgaCrcVignette.pdf vignetteTitles: TCGAcrcmRNA hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: TCGAMethylation450k Version: 1.6.0 License: GPL-2 MD5sum: 875bb1793dd0823d3cb8dbbb2103009c 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 source.ver: src/contrib/TCGAMethylation450k_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: TimerQuant Version: 1.0.0 Depends: shiny Imports: ggplot2, grid, gridExtra, deSolve, dplyr, locfit Suggests: BiocStyle, reshape2, knitr, shinyBS License: Artistic-2.0 MD5sum: de93480402b07dd880bfa6a08ffbb781 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 source.ver: src/contrib/TimerQuant_1.0.0.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 Package: tinesath1cdf Version: 1.8.0 License: Artistic-2.0 MD5sum: fe327331633d402cee644dfd4e3217c5 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 source.ver: src/contrib/tinesath1cdf_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: XhybCasneuf Package: tinesath1probe Version: 1.8.0 Depends: R (>= 1.6), AnnotationDbi (>= 1.11.9) License: LGPL MD5sum: 47e0c0a1053d6cb3cda61d11df7522ea 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 source.ver: src/contrib/tinesath1probe_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: tweeDEseqCountData Version: 1.8.0 Depends: Biobase, R (>= 2.10) License: GPL (>=2) MD5sum: 6f2cadbce4917985963a3d2fe136729e 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 source.ver: src/contrib/tweeDEseqCountData_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: waveTilingData Version: 1.6.0 Depends: R (>= 2.14.0) License: GPL (>= 2) MD5sum: 5e0656e43754e3a7466c0ba8d5b68355 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 source.ver: src/contrib/waveTilingData_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: WES.1KG.WUGSC Version: 1.2.0 License: GPL-2 MD5sum: 4191ff66eaf0c36c2687c31e39d8b64b 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 source.ver: src/contrib/WES.1KG.WUGSC_1.2.0.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 Package: XhybCasneuf Version: 1.8.0 Depends: R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf , RColorBrewer , methods, grid License: Artistic-2.0 MD5sum: 6065c2269a4baf29ffc4ac0068b15e08 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 source.ver: src/contrib/XhybCasneuf_1.8.0.tar.gz vignettes: vignettes/XhybCasneuf/inst/doc/Xhyb.pdf vignetteTitles: Xhyb hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastCC Version: 1.10.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: a7327d81262628c5f14f555502a6b8ec 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 source.ver: src/contrib/yeastCC_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastExpData Version: 0.16.0 Depends: R (>= 2.4), graph (>= 1.9.26) Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db License: GPL MD5sum: 5e41bff54d8514654ddbbebe13fd0104 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 source.ver: src/contrib/yeastExpData_0.16.0.tar.gz vignettes: vignettes/yeastExpData/inst/doc/yeastExample.pdf vignetteTitles: Yeast PPI Example hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastGSData Version: 0.8.0 License: Artistic-2.0 MD5sum: 9ec0fbff434933983ccc0fb73c898898 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 source.ver: src/contrib/yeastGSData_0.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastNagalakshmi Version: 1.6.0 License: Artistic-2.0 MD5sum: 5a5d9ae3ade804dfe94a7370a5df4ef1 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 source.ver: src/contrib/yeastNagalakshmi_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastRNASeq Version: 0.8.0 Depends: R (>= 2.4) Suggests: Biobase, ShortRead, IRanges License: GPL MD5sum: e06797c488ed8bc883ebb45a8e067e1a 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 source.ver: src/contrib/yeastRNASeq_0.8.0.tar.gz vignettes: vignettes/yeastRNASeq/inst/doc/yeastRNASeq.pdf vignetteTitles: An overview of yeastRNASeq hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yri1kgv Version: 0.12.0 Depends: GGBase Imports: Biobase License: Artistic-2.0 MD5sum: 16d91c717a4a6d65e2d4323642661efe 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 source.ver: src/contrib/yri1kgv_0.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: zebrafishRNASeq Version: 0.104.0 Depends: R (>= 2.10) Suggests: BiocStyle, knitr License: GPL MD5sum: 54a281cd515ae13b550ef07908551feb 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 source.ver: src/contrib/zebrafishRNASeq_0.104.0.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