Package: affycompData Version: 1.1.5 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp License: GPL (>= 2) MD5sum: 06bd899be5ee1fc0e3ccac09dbb65e9f NeedsCompilation: no Title: affycomp data Description: Data needed by the affycomp package. biocViews: OneChannel, Microarray, Preprocessing Author: Rafael A. Irizarry and Zhijin Wu with contributions from Simon Cawley Maintainer: Harris Jaffee source.ver: src/contrib/affycompData_1.1.5.tar.gz win.binary.ver: bin/windows/contrib/2.16/affycompData_1.1.5.zip mac.binary.ver: bin/macosx/contrib/2.16/affycompData_1.1.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: affydata Version: 1.11.18 Depends: R (>= 2.4.0), affy (>= 1.23.4) Imports: methods Suggests: hgu95av2cdf, hgu133acdf License: GPL (>= 2) MD5sum: af4551eb4c9f228bca08b63fe3be85f8 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, OneChannel, Microarray Author: Laurent Gautier Maintainer: Harris Jaffee source.ver: src/contrib/affydata_1.11.18.tar.gz win.binary.ver: bin/windows/contrib/2.16/affydata_1.11.18.zip mac.binary.ver: bin/macosx/contrib/2.16/affydata_1.11.18.tgz vignettes: vignettes/affydata/inst/doc/affydata.pdf vignetteTitles: affydata primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/affydata/inst/doc/affydata.R Package: AffymetrixDataTestFiles Version: 0.1.6 Depends: R (>= 2.5.0) License: LGPL-2.1 MD5sum: 24a24f8d20605482f98477e5ad85a057 NeedsCompilation: no Title: Affymetrix data files (CEL, CDF, CHP, EXP, 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. biocViews: Microarray, OneChannel, AnnotationData, ExperimentData Author: Henrik Bengtsson, James Bullard, Kasper Daniel Hansen Maintainer: Henrik Bengtsson source.ver: src/contrib/AffymetrixDataTestFiles_0.1.6.tar.gz win.binary.ver: bin/windows/contrib/2.16/AffymetrixDataTestFiles_0.1.6.zip mac.binary.ver: bin/macosx/contrib/2.16/AffymetrixDataTestFiles_0.1.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ALL Version: 1.4.14 Depends: R (>= 2.10), Biobase (>= 2.5.5) Suggests: rpart License: Artistic-2.0 MD5sum: 03308d3eb4835f6a105b8a2715efc1b3 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, Cancer, Leukemia Author: Xiaochun Li Maintainer: Robert Gentleman source.ver: src/contrib/ALL_1.4.14.tar.gz win.binary.ver: bin/windows/contrib/2.16/ALL_1.4.14.zip mac.binary.ver: bin/macosx/contrib/2.16/ALL_1.4.14.tgz vignettes: vignettes/ALL/inst/doc/ALLintro.pdf vignetteTitles: ALL data intro hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ALL/inst/doc/ALLintro.R suggestsMe: SNAGEEdata Package: ALLMLL Version: 1.2.14 Depends: R (>= 2.10), affy (>= 1.23.4) License: GPL-2 MD5sum: ac118f42d889797bfa35344990d5bdc3 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, Cancer, Leukemia Author: B. M. Bolstad source.ver: src/contrib/ALLMLL_1.2.14.tar.gz win.binary.ver: bin/windows/contrib/2.16/ALLMLL_1.2.14.zip mac.binary.ver: bin/macosx/contrib/2.16/ALLMLL_1.2.14.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: AmpAffyExample Version: 1.2.12 Depends: R (>= 2.4.0), affy (>= 1.23.4) Suggests: hgu133acdf License: LGPL (>= 2) MD5sum: 23e2ce500a0a60618dd619765794fc70 NeedsCompilation: no Title: Example of Amplified Data Description: Six arrays. Three from amplified RNA, three from the typical procedure. biocViews: ExperimentData Author: Rafael A. Irizarry Maintainer: Rafael A. Irizarry source.ver: src/contrib/AmpAffyExample_1.2.12.tar.gz win.binary.ver: bin/windows/contrib/2.16/AmpAffyExample_1.2.12.zip mac.binary.ver: bin/macosx/contrib/2.16/AmpAffyExample_1.2.12.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: antiProfilesData Version: 0.99.1 Depends: Biobase, Suggests: frma, GEOquery, GEOmetadb License: Artistic-2.0 MD5sum: f3306bd14309134de7e53403c399ee81 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, RNAExpressionData, Cancer, NormalTissue Author: Hector Corrada Bravo, Matthew McCall and Rafael A. Irizarry Maintainer: Hector Corrada Bravo source.ver: src/contrib/antiProfilesData_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/2.16/antiProfilesData_0.99.1.zip mac.binary.ver: bin/macosx/contrib/2.16/antiProfilesData_0.99.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ARRmData Version: 0.99.2 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: f2e118dd517b14c05028232ef8032fca 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, HighThroughputSequencingData, IlluminaChip Author: Jean-Philippe Fortin, Celia M.T. Greenwood, Aurelie Labbe Maintainer: Jean-Philippe Fortin source.ver: src/contrib/ARRmData_0.99.2.tar.gz win.binary.ver: bin/windows/contrib/2.16/ARRmData_0.99.2.zip mac.binary.ver: bin/macosx/contrib/2.16/ARRmData_0.99.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: beadarrayExampleData Version: 1.0.6 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>= 2.0.0) License: GPL-2 MD5sum: 77bb2909b0405d56a48d0b46d44f561f 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: Microarray, OneChannel, QualityControl, Preprocessing, ExperimentData Author: Mark Dunning Maintainer: Mark Dunning source.ver: src/contrib/beadarrayExampleData_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/2.16/beadarrayExampleData_1.0.6.zip mac.binary.ver: bin/macosx/contrib/2.16/beadarrayExampleData_1.0.6.tgz 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: 1.0.10 Imports: beadarray (>= 2.3.18), limma, GEOquery Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db License: GPL-2 MD5sum: 7fe03db6caa34e4eaf84f29af97760ac 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: DifferentialExpression, Microarray Author: Mark Dunning, Wei Shi, Andy Lynch, Mike Smith, Matt Ritchie Maintainer: Mike Smith source.ver: src/contrib/BeadArrayUseCases_1.0.10.tar.gz win.binary.ver: bin/windows/contrib/2.16/BeadArrayUseCases_1.0.10.zip mac.binary.ver: bin/macosx/contrib/2.16/BeadArrayUseCases_1.0.10.tgz vignettes: vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.pdf, vignettes/BeadArrayUseCases/inst/doc/BeadChipSimple_old.pdf vignetteTitles: BeadArrayUseCases.pdf, BeadChipSimple_old.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.R Package: beta7 Version: 1.0.5 Depends: R (>= 2.4.0), marray License: LGPL MD5sum: 2df3d9bc92bc4a93077b239df0fd3878 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 Author: Jean Yang Maintainer: Jean Yang source.ver: src/contrib/beta7_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.16/beta7_1.0.5.zip mac.binary.ver: bin/macosx/contrib/2.16/beta7_1.0.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bladderbatch Version: 1.0.5 Depends: Biobase License: Artistic-2.0 MD5sum: 9d1eec34e2962ba1cf538fa75797fa4d 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,Cancer,RNAExpressionData Author: Jeffrey T. Leek Maintainer: Jeffrey T. Leek source.ver: src/contrib/bladderbatch_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.16/bladderbatch_1.0.5.zip mac.binary.ver: bin/macosx/contrib/2.16/bladderbatch_1.0.5.tgz vignettes: vignettes/bladderbatch/inst/doc/bladderbatch.pdf vignetteTitles: bladderbatchTutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bladderbatch/inst/doc/bladderbatch.R Package: breastCancerMAINZ Version: 1.0.5 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: f49492f42bbdd8c0cb058d1270c0d9de 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, Cancer, GeneExpression, Microarray 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_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.16/breastCancerMAINZ_1.0.5.zip mac.binary.ver: bin/macosx/contrib/2.16/breastCancerMAINZ_1.0.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerNKI Version: 1.0.5 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 1f26a1604bba2988e50787e26adf612a 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, Cancer, GeneExpression, Microarray 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_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.16/breastCancerNKI_1.0.5.zip mac.binary.ver: bin/macosx/contrib/2.16/breastCancerNKI_1.0.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerTRANSBIG Version: 1.0.5 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 8156e3e6f2c9782f455eae4e1852b409 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, Cancer, GeneExpression, Microarray 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_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.16/breastCancerTRANSBIG_1.0.5.zip mac.binary.ver: bin/macosx/contrib/2.16/breastCancerTRANSBIG_1.0.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerUNT Version: 1.0.5 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 7cd0d37525473ba4cc2b4e25557f7510 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, Cancer, GeneExpression, Microarray 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_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.16/breastCancerUNT_1.0.5.zip mac.binary.ver: bin/macosx/contrib/2.16/breastCancerUNT_1.0.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerUPP Version: 1.0.5 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 0592f875629636c3064f14d2983810ec 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, Cancer, GeneExpression, Microarray 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_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.16/breastCancerUPP_1.0.5.zip mac.binary.ver: bin/macosx/contrib/2.16/breastCancerUPP_1.0.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerVDX Version: 1.0.5 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: bac5c1124cfcb0a7c91c571dabd03361 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, Cancer, GeneExpression, Microarray 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_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.16/breastCancerVDX_1.0.5.zip mac.binary.ver: bin/macosx/contrib/2.16/breastCancerVDX_1.0.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bronchialIL13 Version: 1.0.11 Depends: R(>= 2.10.0), affy (>= 1.23.4) License: GPL-2 MD5sum: 8aaeeb37fb78b4d67ee9a5f28e73b022 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, TimeCourse Author: Vince Carey Maintainer: Vince Carey URL: http://www.biostat.harvard.edu/~carey source.ver: src/contrib/bronchialIL13_1.0.11.tar.gz win.binary.ver: bin/windows/contrib/2.16/bronchialIL13_1.0.11.zip mac.binary.ver: bin/macosx/contrib/2.16/bronchialIL13_1.0.11.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bsseqData Version: 0.1.3 Depends: R (>= 2.15), bsseq License: Artistic-2.0 MD5sum: b8d7471c1020f1c7d14b8e0baee8b9f2 NeedsCompilation: no Title: Example whole genome bisulfite data for the bsseq package Description: Example whole genome bisulfite data for the bsseq package biocViews: DNAMethylation Author: Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen source.ver: src/contrib/bsseqData_0.1.3.tar.gz win.binary.ver: bin/windows/contrib/2.16/bsseqData_0.1.3.zip mac.binary.ver: bin/macosx/contrib/2.16/bsseqData_0.1.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cancerdata Version: 1.1.2 Depends: R (>= 2.10.1), Biobase License: GPL (>= 2) MD5sum: cd0159a4315245f97bf91f32e587ff08 NeedsCompilation: no Title: Development and validation of diagnostic tests from high-dimensional molecular data: Datasets Description: Dataset for the R package cancerclass biocViews: Cancer, Microarray, Classification, Visualization Author: Jan Budczies, Daniel Kosztyla Maintainer: Daniel Kosztyla source.ver: src/contrib/cancerdata_1.1.2.tar.gz win.binary.ver: bin/windows/contrib/2.16/cancerdata_1.1.2.zip mac.binary.ver: bin/macosx/contrib/2.16/cancerdata_1.1.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CCl4 Version: 1.0.14 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), limma License: Artistic-2.0 MD5sum: 2e43c722d848cbac80dfc06acda002e9 NeedsCompilation: no Title: Carbon Tetrachloride (CCl4) treated hepatocytes Description: NChannelSet for rat hepatocytes treated with Carbon Tetrachloride (CCl4) data from LGC company. biocViews: ExperimentData Author: Audrey Kauffmann, Wolfgang Huber Maintainer: Audrey Kauffmann source.ver: src/contrib/CCl4_1.0.14.tar.gz win.binary.ver: bin/windows/contrib/2.16/CCl4_1.0.14.zip mac.binary.ver: bin/macosx/contrib/2.16/CCl4_1.0.14.tgz vignettes: vignettes/CCl4/inst/doc/CCl4.pdf vignetteTitles: CCl4 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CCl4/inst/doc/CCl4.R Package: ccTutorial Version: 1.0.23 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: 525526ad6447da882505d29e4cafac1f 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, ChIPchipData Author: Joern Toedling, Wolfgang Huber Maintainer: Joern Toedling source.ver: src/contrib/ccTutorial_1.0.23.tar.gz win.binary.ver: bin/windows/contrib/2.16/ccTutorial_1.0.23.zip mac.binary.ver: bin/macosx/contrib/2.16/ccTutorial_1.0.23.tgz vignettes: vignettes/ccTutorial/inst/doc/ccTutorial.pdf, vignettes/ccTutorial/inst/doc/ccTutorialSupplement.pdf vignetteTitles: A tutorial on how to analyze ChIP-chip readouts using Bioconductor, Supplement to A tutorial on how to analyze ChIP-chip readouts using Bioconductor hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ccTutorial/inst/doc/ccTutorial.R, vignettes/ccTutorial/inst/doc/ccTutorialSupplement.R Package: ceu1kg Version: 0.0.32 Depends: R (>= 2.12.0), GGBase (>= 3.9.0), GGtools, Biobase Suggests: SNPlocs.Hsapiens.dbSNP.20101109 License: Artistic-2.0 MD5sum: 6fef2de2dd00139698bb64878f975dc9 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: Genetics, SNP Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/ceu1kg_0.0.32.tar.gz win.binary.ver: bin/windows/contrib/2.16/ceu1kg_0.0.32.zip mac.binary.ver: bin/macosx/contrib/2.16/ceu1kg_0.0.32.tgz vignettes: vignettes/ceu1kg/inst/doc/ceu1kg.pdf vignetteTitles: ceu1kg overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ceu1kg/inst/doc/ceu1kg.R Package: ceuhm3 Version: 0.0.15 Depends: R (>= 2.12.0), GGBase, Biobase Imports: GGtools License: Artistic-2.0 MD5sum: 04fbb1a3e70de3299ef240308d48f012 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: Genetics, GeneExpression, GeneticVariability, SNP Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/ceuhm3_0.0.15.tar.gz win.binary.ver: bin/windows/contrib/2.16/ceuhm3_0.0.15.zip mac.binary.ver: bin/macosx/contrib/2.16/ceuhm3_0.0.15.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cgdv17 Version: 0.0.20 Depends: R (>= 2.15), VariantAnnotation, org.Hs.eg.db, methods, GGtools, TxDb.Hsapiens.UCSC.hg19.knownGene, parallel Imports: Biobase, IRanges License: Artistic 2.0 MD5sum: c654e468c39b0471bdd9535610a84ff6 NeedsCompilation: no Title: Complete Genomics Diversity Panel, chr17 on 46 individuals Description: Complete Genomics Diversity Panel, chr17 on 46 individuals biocViews: genetics Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/cgdv17_0.0.20.tar.gz win.binary.ver: bin/windows/contrib/2.16/cgdv17_0.0.20.zip mac.binary.ver: bin/macosx/contrib/2.16/cgdv17_0.0.20.tgz vignettes: vignettes/cgdv17/inst/doc/cgdv.pdf vignetteTitles: cgdv17: extract from Complete Genomics diversity panel hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cgdv17/inst/doc/cgdv.R Package: charmData Version: 0.99.8 Depends: R(>= 2.11.0), charm, pd.charm.hg18.example License: LGPL (>= 2) MD5sum: d7401a5ea2efbbdddfa7686bb588b39e NeedsCompilation: no Title: An example dataset for use with the charm package Description: An example dataset for use with the charm package biocViews: ExperimentData Author: Martin Aryee Maintainer: Martin Aryee source.ver: src/contrib/charmData_0.99.8.tar.gz win.binary.ver: bin/windows/contrib/2.16/charmData_0.99.8.zip mac.binary.ver: bin/macosx/contrib/2.16/charmData_0.99.8.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cheung2010 Version: 0.0.27 Depends: R (>= 2.13.0), Biobase, GGtools, GenomicRanges, hgfocus.db Imports: AnnotationDbi Suggests: SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, Enhances: parallel License: Artistic 2.0 MD5sum: 700c061d65c4a143e0d72f846830d27a 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: GeneticVariability, RNAseqData Author: Vince Carey Maintainer: Vince Carey source.ver: src/contrib/cheung2010_0.0.27.tar.gz win.binary.ver: bin/windows/contrib/2.16/cheung2010_0.0.27.zip mac.binary.ver: bin/macosx/contrib/2.16/cheung2010_0.0.27.tgz vignettes: vignettes/cheung2010/inst/doc/arr2hap.pdf, vignettes/cheung2010/inst/doc/cheungTrans.pdf vignetteTitles: arr2hap.pdf, cheungTrans: checking trans eQTL with hgfocus arrays hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cheung2010/inst/doc/cheungTrans.R dependsOnMe: ggtut Package: ChIPXpressData Version: 1.0.0 Depends: bigmemory License: GPL (>=2) MD5sum: dd7ccb0728e34674497659a43254ee61 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: AffymetrixChIP, Homo_sapiens, Mus_musculus Author: George Wu Maintainer: George Wu source.ver: src/contrib/ChIPXpressData_1.0.0.tar.gz mac.binary.ver: bin/macosx/contrib/2.16/ChIPXpressData_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CLL Version: 1.2.14 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: LGPL MD5sum: e6103f62f16af727b0505904b6684912 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, Cancer, Leukemia Author: Elizabeth Whalen Maintainer: Robert Gentleman source.ver: src/contrib/CLL_1.2.14.tar.gz win.binary.ver: bin/windows/contrib/2.16/CLL_1.2.14.zip mac.binary.ver: bin/macosx/contrib/2.16/CLL_1.2.14.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cMap2data Version: 0.99.2 Depends: R (>= 2.10) License: GPL-3 MD5sum: 8fd5643ac28cd474bc86e2a7b90e2b02 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: GeneExpression, Homo_sapiens, Microarray Author: C. Pacini Maintainer: J. Saez-Rodriguez source.ver: src/contrib/cMap2data_0.99.2.tar.gz win.binary.ver: bin/windows/contrib/2.16/cMap2data_0.99.2.zip mac.binary.ver: bin/macosx/contrib/2.16/cMap2data_0.99.2.tgz vignettes: vignettes/cMap2data/inst/doc/cMap2data.pdf vignetteTitles: cMap2data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cMap2data/inst/doc/cMap2data.R Package: cnvGSAdata Version: 0.99.4 Depends: R (>= 2.10), cnvGSA License: LGPL MD5sum: f4847ac5a63340bb0911670c6826fd6e 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 Author: Robert Ziman Maintainer: Robert Ziman source.ver: src/contrib/cnvGSAdata_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/2.16/cnvGSAdata_0.99.4.zip mac.binary.ver: bin/macosx/contrib/2.16/cnvGSAdata_0.99.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: colonCA Version: 1.4.11 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: 523197fd3e3c9701cfc54581539853d1 NeedsCompilation: no Title: exprSet for Alon et al. (1999) colon cancer data Description: exprSet for Alon et al. (1999) colon cancer data biocViews: ExperimentData, Cancer, Colon Author: Sylvia Merk Maintainer: W Sylvia Merk source.ver: src/contrib/colonCA_1.4.11.tar.gz win.binary.ver: bin/windows/contrib/2.16/colonCA_1.4.11.zip mac.binary.ver: bin/macosx/contrib/2.16/colonCA_1.4.11.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ConnectivityMap Version: 0.99.10 Depends: R (>= 2.15.1) Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: b75fff26cb1148229d9af5da9c0e9215 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: Microarray, GeneExpression, ExperimentData Author: Paul Shannon Maintainer: Paul Shannon source.ver: src/contrib/ConnectivityMap_0.99.10.tar.gz win.binary.ver: bin/windows/contrib/2.16/ConnectivityMap_0.99.10.zip mac.binary.ver: bin/macosx/contrib/2.16/ConnectivityMap_0.99.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: curatedOvarianData Version: 1.0.3 Depends: R (>= 2.10.0), affy Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, futile.logger, sva, xtable License: Artistic-2.0 MD5sum: 60949aef223811452b1dc19bd3e939e3 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, Cancer, Ovarian, RNAExpressionData 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_1.0.3.tar.gz win.binary.ver: bin/windows/contrib/2.16/curatedOvarianData_1.0.3.zip mac.binary.ver: bin/macosx/contrib/2.16/curatedOvarianData_1.0.3.tgz vignettes: vignettes/curatedOvarianData/inst/doc/curatedOvarianData_vignette.pdf vignetteTitles: curatedOvarianData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: davidTiling Version: 1.2.17 Depends: R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db License: LGPL MD5sum: 196c79191b25674153402364e8e5df32 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, Yeast Author: Wolfgang Huber , Joern Toedling Maintainer: Wolfgang Huber URL: http://www.ebi.ac.uk/huber source.ver: src/contrib/davidTiling_1.2.17.tar.gz win.binary.ver: bin/windows/contrib/2.16/davidTiling_1.2.17.zip mac.binary.ver: bin/macosx/contrib/2.16/davidTiling_1.2.17.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: DLBCL Version: 1.3.6 Depends: R(>= 2.11.0), Biobase License: GPL (>=2) MD5sum: 99567ede19af0e000b2d4b34bf1a97be 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, Cancer Author: Marcus Dittrich and Daniela Beisser Maintainer: Marcus Dittrich URL: http://bionet.bioapps.biozentrum.uni-wuerzburg.de/ source.ver: src/contrib/DLBCL_1.3.6.tar.gz win.binary.ver: bin/windows/contrib/2.16/DLBCL_1.3.6.zip mac.binary.ver: bin/macosx/contrib/2.16/DLBCL_1.3.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: DREAM4 Version: 0.99.17 Depends: R (>= 2.15.1), GenomicRanges Imports: BiocGenerics Suggests: RUnit, networkBMA License: GPL MD5sum: 873fcc56bdd06a41023e67cb3c4dff6f 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: RNAExpressionData, NetworkInference Author: Paul Shannon Maintainer: Paul Shannon source.ver: src/contrib/DREAM4_0.99.17.tar.gz win.binary.ver: bin/windows/contrib/2.16/DREAM4_0.99.17.zip mac.binary.ver: bin/macosx/contrib/2.16/DREAM4_0.99.17.tgz vignettes: vignettes/DREAM4/inst/doc/DREAM4_InSilico_Description.pdf, vignettes/DREAM4/inst/doc/DREAM4.pdf vignetteTitles: DREAM4_InSilico_Description.pdf, DREAM4 Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DREAM4/inst/doc/DREAM4.R Package: dressCheck Version: 0.1.7 Depends: R (>= 2.10.1), methods, Biobase (>= 2.5.5) Suggests: survival, chron License: Artistic-2.0 MD5sum: 0af6c56edb0b44b4887293b2e22b957a 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: Statistics, ExperimentData Author: Vincent Carey Maintainer: Vincent Carey source.ver: src/contrib/dressCheck_0.1.7.tar.gz win.binary.ver: bin/windows/contrib/2.16/dressCheck_0.1.7.zip mac.binary.ver: bin/macosx/contrib/2.16/dressCheck_0.1.7.tgz vignettes: vignettes/dressCheck/inst/doc/short.pdf vignetteTitles: short review of dressCheck contents hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/dressCheck/inst/doc/short.R Package: DrugVsDiseasedata Version: 0.99.4 Depends: R (>= 2.10) License: GPL-3 MD5sum: 6ed41b0cb0106c154ff09e94a31e4308 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: GeneExpression, Homo_sapiens, Microarray Author: C. Pacini Maintainer: J. Saez-Rodriguez source.ver: src/contrib/DrugVsDiseasedata_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/2.16/DrugVsDiseasedata_0.99.4.zip mac.binary.ver: bin/macosx/contrib/2.16/DrugVsDiseasedata_0.99.4.tgz vignettes: vignettes/DrugVsDiseasedata/inst/doc/DrugVsDiseasedata.pdf vignetteTitles: DrugVsDiseasedata hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DrugVsDiseasedata/inst/doc/DrugVsDiseasedata.R Package: dsQTL Version: 0.0.23 Depends: R (>= 2.15.0), utils, GenomicRanges, Biobase, GGBase License: Artistic-2.0 MD5sum: 8ae9f9f2c7d7a86e4517d205972795c2 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: genetics, HighThroughputSequencingData, ExperimentData Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/dsQTL_0.0.23.tar.gz win.binary.ver: bin/windows/contrib/2.16/dsQTL_0.0.23.zip mac.binary.ver: bin/macosx/contrib/2.16/dsQTL_0.0.23.tgz vignettes: vignettes/dsQTL/inst/doc/dsq.pdf vignetteTitles: dsQTL,, data excerpt from Degner et al. 2012 Nature letter hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/dsQTL/inst/doc/dsq.R Package: DvDdata Version: 0.99.1 Depends: R (>= 2.10) License: GPL-3 MD5sum: 6db2469ff296497bda64348a338c92f3 NeedsCompilation: no Title: Drug versus Disease Data Description: Data package which provides default drug and disease expression profiles for the DvD package. Author: C. Pacini Maintainer: J. Saez-Rodriguez source.ver: src/contrib/DvDdata_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/2.16/DvDdata_0.99.1.zip mac.binary.ver: bin/macosx/contrib/2.16/DvDdata_0.99.1.tgz vignettes: vignettes/DvDdata/inst/doc/DvDdata.pdf vignetteTitles: DvDdata hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DvDdata/inst/doc/DvDdata.R Package: dyebiasexamples Version: 1.0.10 Depends: R (>= 1.4.1), marray, GEOquery Suggests: dyebias, convert, Biobase License: GPL-3 MD5sum: b2b7ef628b71612cf0dac8d646b47df6 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: Microarray, TwoChannel, ExperimentData Author: Philip Lijnzaad and Thanasis Margaritis Maintainer: Philip Lijnzaad URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad source.ver: src/contrib/dyebiasexamples_1.0.10.tar.gz win.binary.ver: bin/windows/contrib/2.16/dyebiasexamples_1.0.10.zip mac.binary.ver: bin/macosx/contrib/2.16/dyebiasexamples_1.0.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Package: EatonEtAlChIPseq Version: 0.0.9 Depends: GenomicRanges (>= 1.5.42), ShortRead, rtracklayer License: Artistic 2.0 MD5sum: 32b0d36e64608224dd02305db448a524 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, Yeast, ChIPseqData Author: Patrick Aboyoun Maintainer: Patrick Aboyoun source.ver: src/contrib/EatonEtAlChIPseq_0.0.9.tar.gz win.binary.ver: bin/windows/contrib/2.16/EatonEtAlChIPseq_0.0.9.zip mac.binary.ver: bin/macosx/contrib/2.16/EatonEtAlChIPseq_0.0.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ecoliLeucine Version: 1.2.10 Depends: R (>= 1.9.0), affy (>= 1.23.4), ecolicdf License: GPL (>= 2) MD5sum: 23ac942642e3357056b0a9ba97049370 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, EColiData Author: Laurent Gautier Maintainer: Laurent Gautier source.ver: src/contrib/ecoliLeucine_1.2.10.tar.gz win.binary.ver: bin/windows/contrib/2.16/ecoliLeucine_1.2.10.zip mac.binary.ver: bin/macosx/contrib/2.16/ecoliLeucine_1.2.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: encoDnaseI Version: 0.1.16 Depends: R (>= 2.15.0), methods, Biobase (>= 2.5.5), lattice, GGtools, GGBase Suggests: GGdata License: Artistic-2.0 MD5sum: 1ce71886be5e8ec073eb3c5e485478fb 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 Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/encoDnaseI_0.1.16.tar.gz win.binary.ver: bin/windows/contrib/2.16/encoDnaseI_0.1.16.zip mac.binary.ver: bin/macosx/contrib/2.16/encoDnaseI_0.1.16.tgz vignettes: vignettes/encoDnaseI/inst/doc/dnaseUse.pdf vignetteTitles: ENCODE/hg18 track demo: DNaseI hypersensitivity hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/encoDnaseI/inst/doc/dnaseUse.R Package: estrogen Version: 1.8.10 Depends: R (>= 1.9.0), affy (>= 1.4) Suggests: Biobase (>= 1.13.16), affy, vsn, hgu95av2.db, genefilter License: LGPL MD5sum: 023b8e3b29a016865f2214a97e9ae2d7 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 Author: Wolfgang Huber, Robert Gentleman Maintainer: R. Gentleman source.ver: src/contrib/estrogen_1.8.10.tar.gz win.binary.ver: bin/windows/contrib/2.16/estrogen_1.8.10.zip mac.binary.ver: bin/macosx/contrib/2.16/estrogen_1.8.10.tgz vignettes: vignettes/estrogen/inst/doc/estrogen.pdf vignetteTitles: estrogen hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/estrogen/inst/doc/estrogen.R Package: faahKO Version: 1.2.15 Depends: xcms License: LGPL MD5sum: 5558c3250765ac3c4540d2b3c9567b65 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_1.2.15.tar.gz win.binary.ver: bin/windows/contrib/2.16/faahKO_1.2.15.zip mac.binary.ver: bin/macosx/contrib/2.16/faahKO_1.2.15.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fabiaData Version: 1.0.2 Depends: R (>= 2.10.0), Biobase Imports: utils Suggests: fabia License: LGPL (>= 2.1) MD5sum: 6737b2d95b667dc1171bba4293aaedfb 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: Bioinformatics, Statistics, Microarray, DifferentialExpression, MultipleComparisons, Clustering, Visualization Author: Sepp Hochreiter Maintainer: Sepp Hochreiter URL: http://www.bioinf.jku.at/software/fabia/fabia.html source.ver: src/contrib/fabiaData_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.16/fabiaData_1.0.2.zip mac.binary.ver: bin/macosx/contrib/2.16/fabiaData_1.0.2.tgz vignettes: vignettes/fabiaData/inst/doc/fabiaData.pdf vignetteTitles: fabiaData: Manual for the R Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/fabiaData/inst/doc/fabiaData.R Package: facsDorit Version: 1.4.7 Depends: R (>= 1.9.1), prada (>= 1.0.5) License: GPL-2 MD5sum: 52e5d173c83dabecc6e90f57aad7668f 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 Author: Florian Hahne Maintainer: Florian Hahne URL: http://www.dkfz.de/mga source.ver: src/contrib/facsDorit_1.4.7.tar.gz win.binary.ver: bin/windows/contrib/2.16/facsDorit_1.4.7.zip mac.binary.ver: bin/macosx/contrib/2.16/facsDorit_1.4.7.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: FANTOM3and4CAGE Version: 0.99.1 Depends: R (>= 2.15.0) License: GPL-3 MD5sum: c4d160a22a1683fb5a6d412121f1db09 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, TimeCourse, Transcription, HighThroughputSequencing Author: Vanja Haberle, Department of Biology, University of Bergen, Norway Maintainer: Vanja Haberle source.ver: src/contrib/FANTOM3and4CAGE_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/2.16/FANTOM3and4CAGE_0.99.1.zip mac.binary.ver: bin/macosx/contrib/2.16/FANTOM3and4CAGE_0.99.1.tgz vignettes: vignettes/FANTOM3and4CAGE/inst/doc/FANTOM3and4CAGE.pdf vignetteTitles: FANTOM3and4CAGE hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FANTOM3and4CAGE/inst/doc/FANTOM3and4CAGE.R Package: ffpeExampleData Version: 1.0.3 Depends: R (>= 2.10.0), lumi Suggests: genefilter, affy License: GPL (>2) MD5sum: c4be991ead957d8a8c185b3cb4410f8d 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: Microarray, GeneExpression Author: Levi Waldron Maintainer: Levi Waldron source.ver: src/contrib/ffpeExampleData_1.0.3.tar.gz win.binary.ver: bin/windows/contrib/2.16/ffpeExampleData_1.0.3.zip mac.binary.ver: bin/macosx/contrib/2.16/ffpeExampleData_1.0.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fibroEset Version: 1.4.9 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: b3e96c7411a17aa45da7a0525e2a1792 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 Author: Sylvia Merk Maintainer: Sylvia Merk source.ver: src/contrib/fibroEset_1.4.9.tar.gz win.binary.ver: bin/windows/contrib/2.16/fibroEset_1.4.9.zip mac.binary.ver: bin/macosx/contrib/2.16/fibroEset_1.4.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: flowWorkspaceData Version: 1.99.9 License: GPL-2 MD5sum: d30c3dab56ea7065ee26752fe2250c15 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 Author: Greg Finak Maintainer: Mike Jiang source.ver: src/contrib/flowWorkspaceData_1.99.9.tar.gz win.binary.ver: bin/windows/contrib/2.16/flowWorkspaceData_1.99.9.zip mac.binary.ver: bin/macosx/contrib/2.16/flowWorkspaceData_1.99.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: frmaExampleData Version: 0.99.5 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 36a6a436af2039c25ec176e0720cd292 NeedsCompilation: no Title: Frma Example Data Description: Data files used by the examples in frma and frmaTools packages biocViews: Microarray, AffymetrixChip, Homo_sapiens Author: Matthew N. McCall Maintainer: Matthew N. McCall source.ver: src/contrib/frmaExampleData_0.99.5.tar.gz win.binary.ver: bin/windows/contrib/2.16/frmaExampleData_0.99.5.zip mac.binary.ver: bin/macosx/contrib/2.16/frmaExampleData_0.99.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: FunciSNP.data Version: 0.99.2 Depends: R (>= 2.14.0) Imports: rtracklayer License: GPL-3 MD5sum: 2ea1394e00ed614af76326fde361e713 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: Infrastructure, DataRepresentation, DataImport, SequenceMatching, Annotation 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_0.99.2.tar.gz win.binary.ver: bin/windows/contrib/2.16/FunciSNP.data_0.99.2.zip mac.binary.ver: bin/macosx/contrib/2.16/FunciSNP.data_0.99.2.tgz vignettes: vignettes/FunciSNP.data/inst/doc/FunciSNP.data.pdf vignetteTitles: FunciSNP Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FunciSNP.data/inst/doc/FunciSNP.data.R Package: gageData Version: 2.0.2 Depends: R (>= 2.10) Suggests: gage, pathview, genefilter License: GPL (>=2.0) MD5sum: 9abec8bb3a62ed115ee42adc22aab3f0 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, Cancer Author: Weijun Luo Maintainer: Weijun Luo source.ver: src/contrib/gageData_2.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.16/gageData_2.0.2.zip mac.binary.ver: bin/macosx/contrib/2.16/gageData_2.0.2.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: gaschYHS Version: 1.0.11 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 965d2bcf3feb7c316dacfdc9b4f49ae9 NeedsCompilation: no Title: ExpressionSet for response of yeast to heat shock and other environmental stresses Description: Data from PMID 11102521 biocViews: ExperimentData, Yeast 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_1.0.11.tar.gz win.binary.ver: bin/windows/contrib/2.16/gaschYHS_1.0.11.zip mac.binary.ver: bin/macosx/contrib/2.16/gaschYHS_1.0.11.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gatingMLData Version: 1.0.7 Depends: R (>= 1.9.0) Suggests: flowUtils License: GPL MD5sum: 5ad1ef143a154e12d8c23a20aab903eb NeedsCompilation: no Title: Data and XML files for GatingML Test suite Description: Test data & XML files for Testing compliance with the GatingML 1.5 standards in package flowUtils. biocViews: ExperimentData Author: Nishant Gopalakrishnan Maintainer: Nishant Gopalakrishnan source.ver: src/contrib/gatingMLData_1.0.7.tar.gz win.binary.ver: bin/windows/contrib/2.16/gatingMLData_1.0.7.zip mac.binary.ver: bin/macosx/contrib/2.16/gatingMLData_1.0.7.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gcspikelite Version: 1.0.9 Depends: R (>= 2.5.0) License: LGPL MD5sum: c2564532e04a622115f9f1a05a2b6b00 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_1.0.9.tar.gz win.binary.ver: bin/windows/contrib/2.16/gcspikelite_1.0.9.zip mac.binary.ver: bin/macosx/contrib/2.16/gcspikelite_1.0.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: geneLenDataBase Version: 0.99.11 Depends: R (>= 2.11.0) Imports: utils, rtracklayer, GenomicFeatures (>= 1.3.15) License: LGPL (>= 2) MD5sum: 6b7a6f4bd3e073b2e1364dd8881cc919 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: HighThroughputSequencingData, ExperimentData, Transcription, RNAseq Author: Matthew Young Maintainer: Matthew Young , Nadia Davidson source.ver: src/contrib/geneLenDataBase_0.99.11.tar.gz win.binary.ver: bin/windows/contrib/2.16/geneLenDataBase_0.99.11.zip mac.binary.ver: bin/macosx/contrib/2.16/geneLenDataBase_0.99.11.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GGdata Version: 1.0.21 Depends: R (>= 2.12.0), methods, Biobase (>= 2.5.5), GGBase, snpStats, illuminaHumanv1.db, AnnotationDbi Enhances: GGtools License: LGPL MD5sum: 3817167fd420b4b6f1ea24408a2a9b63 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 Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/GGdata_1.0.21.tar.gz win.binary.ver: bin/windows/contrib/2.16/GGdata_1.0.21.zip mac.binary.ver: bin/macosx/contrib/2.16/GGdata_1.0.21.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ggtut suggestsMe: encoDnaseI Package: ggtut Version: 0.0.44 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: 6b9945c61d7f1cf2bf08a841f0a0819c NeedsCompilation: no Title: support for tutorial on genetics of gene expression ISMB 2011 Description: various resources for genetics of expression with R/bioc Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/ggtut_0.0.44.tar.gz win.binary.ver: bin/windows/contrib/2.16/ggtut_0.0.44.zip mac.binary.ver: bin/macosx/contrib/2.16/ggtut_0.0.44.tgz vignettes: vignettes/ggtut/inst/doc/careyGGtutslides.pdf, vignettes/ggtut/inst/doc/extras.pdf, vignettes/ggtut/inst/doc/tut11.pdf, vignettes/ggtut/inst/doc/tut12.pdf vignetteTitles: careyGGtutslides.pdf, extras.pdf, tut11.pdf, tut12.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: golubEsets Version: 1.4.13 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: LGPL MD5sum: 712f67e73561a3e8fd725e704a06ad4d 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, Cancer, Leukemia Author: Todd Golub Maintainer: Vince Carey source.ver: src/contrib/golubEsets_1.4.13.tar.gz win.binary.ver: bin/windows/contrib/2.16/golubEsets_1.4.13.zip mac.binary.ver: bin/macosx/contrib/2.16/golubEsets_1.4.13.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GSVAdata Version: 0.99.10 Depends: R (>= 2.10), Biobase, GSEABase, hgu95a.db License: GPL (>= 2) MD5sum: 13e99fc5abf4cdb7cb5dd447e29c8f50 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, RNAExpressionData, Cancer, Leukemia Author: Robert Castelo Maintainer: Robert Castelo source.ver: src/contrib/GSVAdata_0.99.10.tar.gz win.binary.ver: bin/windows/contrib/2.16/GSVAdata_0.99.10.zip mac.binary.ver: bin/macosx/contrib/2.16/GSVAdata_0.99.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GWASdata Version: 1.0.9 Depends: GWASTools License: Artistic-2.0 MD5sum: a898dc6cbc5addce1f4fdacc78143b80 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, SNP, Microarray Author: Stephanie Gogarten Maintainer: Stephanie Gogarten source.ver: src/contrib/GWASdata_1.0.9.tar.gz win.binary.ver: bin/windows/contrib/2.16/GWASdata_1.0.9.zip mac.binary.ver: bin/macosx/contrib/2.16/GWASdata_1.0.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap100khind Version: 1.4.2 Suggests: oligo License: GPL MD5sum: 58d49fe9977fc53e6c2424dc54b59be4 NeedsCompilation: no Title: Sample data - Hapmap 100K HIND Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap Author: Hapmap Consortium Maintainer: Benilton Carvalho source.ver: src/contrib/hapmap100khind_1.4.2.tar.gz win.binary.ver: bin/windows/contrib/2.16/hapmap100khind_1.4.2.zip mac.binary.ver: bin/macosx/contrib/2.16/hapmap100khind_1.4.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap100kxba Version: 1.4.2 Suggests: oligo License: GPL MD5sum: 9f964492258eef6c32bc06225eb8063b NeedsCompilation: no Title: Sample data - Hapmap 100K XBA Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap Author: Hapmap Consortium Maintainer: Benilton Carvalho source.ver: src/contrib/hapmap100kxba_1.4.2.tar.gz win.binary.ver: bin/windows/contrib/2.16/hapmap100kxba_1.4.2.zip mac.binary.ver: bin/macosx/contrib/2.16/hapmap100kxba_1.4.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap500knsp Version: 1.4.2 Suggests: oligo License: GPL MD5sum: c23de7f014e1e93e9cacd5418744fa5d NeedsCompilation: no Title: Sample data - Hapmap 500K NSP Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap Author: Hapmap Consortium Maintainer: Benilton Carvalho source.ver: src/contrib/hapmap500knsp_1.4.2.tar.gz win.binary.ver: bin/windows/contrib/2.16/hapmap500knsp_1.4.2.zip mac.binary.ver: bin/macosx/contrib/2.16/hapmap500knsp_1.4.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap500ksty Version: 1.4.2 Suggests: oligo License: GPL MD5sum: ec50f3835d419bf61e8485ab94054555 NeedsCompilation: no Title: Sample data - Hapmap 500K STY Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap Author: Hapmap Consortium Maintainer: Benilton Carvalho source.ver: src/contrib/hapmap500ksty_1.4.2.tar.gz win.binary.ver: bin/windows/contrib/2.16/hapmap500ksty_1.4.2.zip mac.binary.ver: bin/macosx/contrib/2.16/hapmap500ksty_1.4.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmapsnp5 Version: 1.4.2 Suggests: oligo License: GPL MD5sum: c9bdb584b930b7b486b96cf0b71d35ec NeedsCompilation: no Title: Sample data - Hapmap SNP 5.0 Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap Author: Hapmap Consortium Maintainer: Benilton Carvalho source.ver: src/contrib/hapmapsnp5_1.4.2.tar.gz win.binary.ver: bin/windows/contrib/2.16/hapmapsnp5_1.4.2.zip mac.binary.ver: bin/macosx/contrib/2.16/hapmapsnp5_1.4.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmapsnp6 Version: 1.4.2 Depends: R (>= 2.15) Suggests: oligo, oligoClasses License: GPL MD5sum: aecef7ba327a0c692ae01e9abedbdf11 NeedsCompilation: no Title: Sample data - Hapmap SNP 6.0 Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap Author: Hapmap Consortium Maintainer: Benilton Carvalho source.ver: src/contrib/hapmapsnp6_1.4.2.tar.gz win.binary.ver: bin/windows/contrib/2.16/hapmapsnp6_1.4.2.zip mac.binary.ver: bin/macosx/contrib/2.16/hapmapsnp6_1.4.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: harbChIP Version: 1.0.10 Depends: R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5), Biostrings Imports: methods, stats License: Artistic-2.0 MD5sum: d3ca4fc194edd864b47e1eae8573abcf NeedsCompilation: no Title: Experimental Data Package: harbChIP Description: data from a yeast ChIP-chip experiment biocViews: ExperimentData, Yeast, ChIPchip Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/harbChIP_1.0.10.tar.gz win.binary.ver: bin/windows/contrib/2.16/harbChIP_1.0.10.zip mac.binary.ver: bin/macosx/contrib/2.16/harbChIP_1.0.10.tgz vignettes: vignettes/harbChIP/inst/doc/yeastUpstream.pdf vignetteTitles: upstream sequence management for yeast hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/harbChIP/inst/doc/yeastUpstream.R Package: HD2013SGI Version: 1.00.1 Depends: RColorBrewer, gplots, geneplotter, splots, limma, vcd, LSD,EBImage License: Artistic-2.0 MD5sum: 70a9a51836407752c7e95d1702dfed25 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,CellBasedAssays,NetworkAnalysis,QualityControl,CellBiology,Cancer,Colon Author: Bernd Fischer Maintainer: Bernd Fischer SystemRequirements: GNU make source.ver: src/contrib/HD2013SGI_1.00.1.tar.gz win.binary.ver: bin/windows/contrib/2.16/HD2013SGI_1.00.1.zip mac.binary.ver: bin/macosx/contrib/2.16/HD2013SGI_1.00.1.tgz vignettes: vignettes/HD2013SGI/inst/doc/HD2013SGI.pdf vignetteTitles: HD2013SGI hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HD2013SGI/inst/doc/HD2013SGI.R Package: HEEBOdata Version: 1.0.5 License: LGPL MD5sum: bb55c079c64eca34180c07809d11f7f9 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_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.16/HEEBOdata_1.0.5.zip mac.binary.ver: bin/macosx/contrib/2.16/HEEBOdata_1.0.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu133abarcodevecs Version: 1.0.6 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: b5099068dfe693402bf809ad3d84519a NeedsCompilation: no Title: hgu133a data for barcode Description: Data used by the barcode package for microarrays of type hgu133a. biocViews: AnnotationData, AffymetrixChip, hgu133a, Homo_sapiens Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall source.ver: src/contrib/hgu133abarcodevecs_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/2.16/hgu133abarcodevecs_1.0.6.zip mac.binary.ver: bin/macosx/contrib/2.16/hgu133abarcodevecs_1.0.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu133plus2barcodevecs Version: 1.0.6 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 1db90591ba23bd44a1c1b372daabcafe NeedsCompilation: no Title: hgu133plus2 data for barcode Description: Data used by the barcode package for microarrays of type hgu133plus2. biocViews: AnnotationData, AffymetrixChip, hgu133plus2, Homo_sapiens Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall source.ver: src/contrib/hgu133plus2barcodevecs_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/2.16/hgu133plus2barcodevecs_1.0.6.zip mac.binary.ver: bin/macosx/contrib/2.16/hgu133plus2barcodevecs_1.0.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu2beta7 Version: 1.2.8 Depends: R (>= 2.0.0) License: Artistic-2.0 MD5sum: e22217ea1507c581749505eab3d3254c 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: AnnotationData Author: Chenwei Lin Maintainer: Bioconductor Package Maintainer source.ver: src/contrib/hgu2beta7_1.2.8.tar.gz win.binary.ver: bin/windows/contrib/2.16/hgu2beta7_1.2.8.zip mac.binary.ver: bin/macosx/contrib/2.16/hgu2beta7_1.2.8.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: HIVcDNAvantWout03 Version: 1.2.8 License: GPL (>= 2) MD5sum: c6005d22731916c9fdad230453faf8c2 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, HIV 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_1.2.8.tar.gz win.binary.ver: bin/windows/contrib/2.16/HIVcDNAvantWout03_1.2.8.zip mac.binary.ver: bin/macosx/contrib/2.16/HIVcDNAvantWout03_1.2.8.tgz vignettes: vignettes/HIVcDNAvantWout03/inst/doc/hivData.pdf vignetteTitles: hivData.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hmyriB36 Version: 0.99.17 Depends: R (>= 2.13.0), methods, Biobase (>= 2.5.5), GGBase Suggests: GGtools, illuminaHumanv1.db License: Artistic-2.0 MD5sum: b8dbc414014d018f2d6664e04b8dc034 NeedsCompilation: no Title: YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes Description: YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes biocViews: Statistics, ExperimentData Author: Vincent Carey Maintainer: Vincent Carey source.ver: src/contrib/hmyriB36_0.99.17.tar.gz win.binary.ver: bin/windows/contrib/2.16/hmyriB36_0.99.17.zip mac.binary.ver: bin/macosx/contrib/2.16/hmyriB36_0.99.17.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ggtut suggestsMe: ind1KG Package: humanStemCell Version: 0.2.8 Depends: Biobase (>= 2.5.5), hgu133plus2.db License: Artistic-2.0 MD5sum: 98a316eb83af3194398855a012867cd7 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, StemCells Author: R. Gentleman, N. Le Meur, M. Tewari Maintainer: R. Gentleman source.ver: src/contrib/humanStemCell_0.2.8.tar.gz win.binary.ver: bin/windows/contrib/2.16/humanStemCell_0.2.8.zip mac.binary.ver: bin/macosx/contrib/2.16/humanStemCell_0.2.8.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ind1KG Version: 0.1.15 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: ceefecac2e883548345584e894b278ed 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: Genetics, HighThroughputSequencing Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/ind1KG_0.1.15.tar.gz win.binary.ver: bin/windows/contrib/2.16/ind1KG_0.1.15.zip mac.binary.ver: bin/macosx/contrib/2.16/ind1KG_0.1.15.tgz 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 Rfiles: vignettes/ind1KG/inst/doc/ind1KG.R, vignettes/ind1KG/inst/doc/nov09rv.R Package: iontreeData Version: 0.99.8 License: GPL-2 MD5sum: 80ae8ad965d409ffb0b53395e2fb3316 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, Metabolomics Author: Mingshu Cao Maintainer: Mingshu Cao source.ver: src/contrib/iontreeData_0.99.8.tar.gz win.binary.ver: bin/windows/contrib/2.16/iontreeData_0.99.8.zip mac.binary.ver: bin/macosx/contrib/2.16/iontreeData_0.99.8.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ITALICSData Version: 2.0.7 Depends: R (>= 2.0.0) License: GPL MD5sum: 95a9f78fc676df33f0281791d57bc1f7 NeedsCompilation: no Title: ITALICSData Description: Data needed to use the ITALICS package biocViews: ExperimentData Author: Guillem Rigaill Maintainer: Guillem Rigaill URL: http://bioinfo.curie.fr source.ver: src/contrib/ITALICSData_2.0.7.tar.gz win.binary.ver: bin/windows/contrib/2.16/ITALICSData_2.0.7.zip mac.binary.ver: bin/macosx/contrib/2.16/ITALICSData_2.0.7.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Iyer517 Version: 1.4.12 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 52d4456ccbb290872e7fb098fd2e5bc0 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_1.4.12.tar.gz win.binary.ver: bin/windows/contrib/2.16/Iyer517_1.4.12.zip mac.binary.ver: bin/macosx/contrib/2.16/Iyer517_1.4.12.tgz vignettes: vignettes/Iyer517/inst/doc/Iyer517.pdf vignetteTitles: Iyer517 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Iyer517/inst/doc/Iyer517.R Package: KEGGdzPathwaysGEO Version: 1.1.2 Depends: R (>= 2.13.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: 1cc6e4d2bfcf1aab94661532ae01ce88 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. Author: Gaurav Bhatti, Adi L. Tarca Maintainer: Gaurav Bhatti source.ver: src/contrib/KEGGdzPathwaysGEO_1.1.2.tar.gz win.binary.ver: bin/windows/contrib/2.16/KEGGdzPathwaysGEO_1.1.2.zip mac.binary.ver: bin/macosx/contrib/2.16/KEGGdzPathwaysGEO_1.1.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: kidpack Version: 1.5.12 Depends: R (>= 2.6.0), Biobase (>= 2.5.5) License: GPL-2 MD5sum: ef4f8783f412fc1844ca1f3b4d9ccc74 NeedsCompilation: no Title: DKFZ kidney package Description: kidney microarray data biocViews: ExperimentData, Cancer, Kidney Author: Wolfgang Huber Maintainer: Wolfgang Huber URL: http://www.dkfz.de/mga source.ver: src/contrib/kidpack_1.5.12.tar.gz win.binary.ver: bin/windows/contrib/2.16/kidpack_1.5.12.zip mac.binary.ver: bin/macosx/contrib/2.16/kidpack_1.5.12.tgz vignettes: vignettes/kidpack/inst/doc/kidpack.pdf vignetteTitles: kidpack - overview over the DKFZ kidney data package hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/kidpack/inst/doc/kidpack.R Package: leeBamViews Version: 0.99.22 Depends: R (>= 2.15.0), Biobase, Rsamtools (>= 0.1.50), BSgenome Imports: GenomicRanges, methods Suggests: GenomeGraphs, biomaRt, org.Sc.sgd.db, edgeR Enhances: multicore License: Artistic 2.0 MD5sum: 05f56e6cd0bfe0f12742c2de3dced627 NeedsCompilation: no Title: leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009 Description: data from PMID 19096707; prototype for managing multiple NGS samples biocViews: HighThroughputSequencing, RNAseq, CellBiology, Genetics, DifferentialExpression, RNAseqData Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/leeBamViews_0.99.22.tar.gz win.binary.ver: bin/windows/contrib/2.16/leeBamViews_0.99.22.zip mac.binary.ver: bin/macosx/contrib/2.16/leeBamViews_0.99.22.tgz vignettes: vignettes/leeBamViews/inst/doc/leeViews.pdf vignetteTitles: managing multiple NGS samples with bamViews hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/leeBamViews/inst/doc/leeViews.R Package: leukemiasEset Version: 0.99.3 Depends: R (>= 2.10.1), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 72d1f94d10a51affd881eabc24309ad4 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: Bioinformatics,Classification,Microarray,GeneExpression,Leukemia,Cancer 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_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/2.16/leukemiasEset_0.99.3.zip mac.binary.ver: bin/macosx/contrib/2.16/leukemiasEset_0.99.3.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: LiebermanAidenHiC2009 Version: 0.1.14 Depends: KernSmooth, IRanges License: LGPL MD5sum: 56118e5f6dc364b0c329698190f18734 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 Author: Wolfgang Huber, Felix Klein Maintainer: Felix Klein source.ver: src/contrib/LiebermanAidenHiC2009_0.1.14.tar.gz win.binary.ver: bin/windows/contrib/2.16/LiebermanAidenHiC2009_0.1.14.zip mac.binary.ver: bin/macosx/contrib/2.16/LiebermanAidenHiC2009_0.1.14.tgz vignettes: vignettes/LiebermanAidenHiC2009/inst/doc/LiebermanAidenHiC2009.pdf vignetteTitles: Exploration of HiC data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: lumiBarnes Version: 1.3.10 Depends: R (>= 2.0), Biobase (>= 2.5.5), lumi (>= 1.1.0) License: LGPL MD5sum: c7c8a1781504e93995f1b3dd91e07aed 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, OneChannel, RNAExpressionData, NormalTissue Author: Pan Du Maintainer: Pan Du source.ver: src/contrib/lumiBarnes_1.3.10.tar.gz win.binary.ver: bin/windows/contrib/2.16/lumiBarnes_1.3.10.zip mac.binary.ver: bin/macosx/contrib/2.16/lumiBarnes_1.3.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: LungCancerLines Version: 0.0.8 Imports: Rsamtools License: Artistic-2.0 MD5sum: b21f7bf69103664c0336f19faab38855 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. Author: Cory Barr, Michael Lawrence Maintainer: Cory Barr source.ver: src/contrib/LungCancerLines_0.0.8.tar.gz win.binary.ver: bin/windows/contrib/2.16/LungCancerLines_0.0.8.zip mac.binary.ver: bin/macosx/contrib/2.16/LungCancerLines_0.0.8.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: lungExpression Version: 0.0.15 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 9340d9e4b1106bff98029e0ea32d29e2 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, Cancer, Lung Author: Robert Scharpf , Simens Zhong , Giovanni Parmigiani Maintainer: Robert Scharpf source.ver: src/contrib/lungExpression_0.0.15.tar.gz win.binary.ver: bin/windows/contrib/2.16/lungExpression_0.0.15.zip mac.binary.ver: bin/macosx/contrib/2.16/lungExpression_0.0.15.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: maqcExpression4plex Version: 1.6.2 Suggests: oligo, pdInfoBuilder License: GPL MD5sum: cd3a0c23be2bf5ab4263c7a2b60ff7fc 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 Author: NimbleGen Systems Maintainer: Benilton Carvalho source.ver: src/contrib/maqcExpression4plex_1.6.2.tar.gz win.binary.ver: bin/windows/contrib/2.16/maqcExpression4plex_1.6.2.zip mac.binary.ver: bin/macosx/contrib/2.16/maqcExpression4plex_1.6.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MAQCsubset Version: 1.0.27 Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), lumi, methods Suggests: genefilter, codelink License: Artistic-2.0 MD5sum: f9f93b5ecce408c977b08797c4ae9763 NeedsCompilation: no Title: Experimental Data Package: MAQCsubset Description: Data Package automatically created on Sun Nov 19 15:59:29 2006. biocViews: ExperimentData Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/MAQCsubset_1.0.27.tar.gz win.binary.ver: bin/windows/contrib/2.16/MAQCsubset_1.0.27.zip mac.binary.ver: bin/macosx/contrib/2.16/MAQCsubset_1.0.27.tgz vignettes: vignettes/MAQCsubset/inst/doc/maqcNotes.pdf vignetteTitles: MAQC notes hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MAQCsubset/inst/doc/maqcNotes.R Package: MAQCsubsetAFX Version: 1.0.11 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: c226a4358387a34b91f20af1810c5c34 NeedsCompilation: no Title: MAQC data subset for the Affymetrix platform Description: MAQC data subset for the Affymetrix platform biocViews: Microarray, ExperimentData Author: Laurent Gatto Maintainer: Laurent Gatto source.ver: src/contrib/MAQCsubsetAFX_1.0.11.tar.gz win.binary.ver: bin/windows/contrib/2.16/MAQCsubsetAFX_1.0.11.zip mac.binary.ver: bin/macosx/contrib/2.16/MAQCsubsetAFX_1.0.11.tgz vignettes: vignettes/MAQCsubsetAFX/inst/doc/MAQCsubsetAFX.pdf vignetteTitles: MAQCsubsetAFX: MAQC data subset for the Affymetrix platform hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MAQCsubsetAFX/inst/doc/MAQCsubsetAFX.R Package: MAQCsubsetILM Version: 1.0.10 Depends: R (>= 2.10), Biobase (>= 2.5.5), lumi License: Artistic-2.0 MD5sum: 8c6198266f85f2e900e8d78ea1ab9c59 NeedsCompilation: no Title: MAQC data subset for the Illumina platform Description: MAQC data subset for the Illumina platform biocViews: Microarray, ExperimentData Author: Laurent Gatto Maintainer: Laurent Gatto source.ver: src/contrib/MAQCsubsetILM_1.0.10.tar.gz win.binary.ver: bin/windows/contrib/2.16/MAQCsubsetILM_1.0.10.zip mac.binary.ver: bin/macosx/contrib/2.16/MAQCsubsetILM_1.0.10.tgz vignettes: vignettes/MAQCsubsetILM/inst/doc/MAQCsubsetILM.pdf vignetteTitles: MAQCsubsetILM: MAQC data subset for the Illumina platform hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MAQCsubsetILM/inst/doc/MAQCsubsetILM.R Package: MEDIPSData Version: 0.99.4 Depends: R (>= 2.15.0) License: GPL (>= 2) MD5sum: a9b3acc4ba95f7d5287efe294a1a01a2 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, ChIPseq, DNAMethylation, DifferentialExpression, HighThroughputSequencing, Methylseq, Preprocessing, QualityControl, Sequencing, Software, Visualization Author: Lukas Chavez Maintainer: Lukas Chavez source.ver: src/contrib/MEDIPSData_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/2.16/MEDIPSData_0.99.4.zip mac.binary.ver: bin/macosx/contrib/2.16/MEDIPSData_0.99.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MEEBOdata Version: 1.0.5 License: LGPL MD5sum: 1eae708f3e3664040cddbcee370710c0 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_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.16/MEEBOdata_1.0.5.zip mac.binary.ver: bin/macosx/contrib/2.16/MEEBOdata_1.0.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: minfiData Version: 0.3.4 Depends: R (>= 2.13.0), minfi, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kannotation.ilmn.v1.2 License: Artistic-2.0 MD5sum: 3a6edb0e12264f2d34466882588ee61e NeedsCompilation: no Title: Example data for the Illumina Methylation 450k array Description: Data from 6 samples across 2 groups from 450k methylation arrays biocViews: DNAMethylation Author: Kasper Daniel Hansen, Martin Aryee, Winston Timp Maintainer: Kasper Daniel Hansen source.ver: src/contrib/minfiData_0.3.4.tar.gz win.binary.ver: bin/windows/contrib/2.16/minfiData_0.3.4.zip mac.binary.ver: bin/macosx/contrib/2.16/minfiData_0.3.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: miRNATarget Version: 0.99.3 Depends: R (>= 2.10), Biobase License: GPL MD5sum: 2155e1c9f01afd0e801fb93bcf9e3adf 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, Author: Y-h. Taguchi Maintainer: Y-h. Taguchi source.ver: src/contrib/miRNATarget_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/2.16/miRNATarget_0.99.3.zip mac.binary.ver: bin/macosx/contrib/2.16/miRNATarget_0.99.3.tgz vignettes: vignettes/miRNATarget/inst/doc/miRNATarget.pdf vignetteTitles: miRNATargetTutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/miRNATarget/inst/doc/miRNATarget.R Package: MMDiffBamSubset Version: 0.99.3 Suggests: MMDiff License: LGPL MD5sum: f5c537700f91ed4cb84b07fde35d57fb 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, ChIPseqData Author: Gabriele Schweikert Maintainer: Gabriele Schweikert source.ver: src/contrib/MMDiffBamSubset_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/2.16/MMDiffBamSubset_0.99.3.zip mac.binary.ver: bin/macosx/contrib/2.16/MMDiffBamSubset_0.99.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mosaicsExample Version: 0.99.8 Depends: R (>= 2.11.1) License: GPL (>= 2) MD5sum: a149480188ff8db68eefca85d69c8ae2 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, ChIPseqData, Homo_sapiens 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_0.99.8.tar.gz win.binary.ver: bin/windows/contrib/2.16/mosaicsExample_0.99.8.zip mac.binary.ver: bin/macosx/contrib/2.16/mosaicsExample_0.99.8.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mouse4302barcodevecs Version: 1.0.6 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 5edb8e93a70410346c907b50bfd8ad1c NeedsCompilation: no Title: mouse4302 data for barcode Description: Data used by the barcode package for microarrays of type mouse4302. biocViews: AnnotationData, AffymetrixChip, mouse4302, Mus_musculus Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall source.ver: src/contrib/mouse4302barcodevecs_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/2.16/mouse4302barcodevecs_1.0.6.zip mac.binary.ver: bin/macosx/contrib/2.16/mouse4302barcodevecs_1.0.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: msdata Version: 0.1.13 Suggests: xcms License: GPL (>= 2) MD5sum: 2bed858e0c9064e84966dc3c3fb0594a 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 and mzML. biocViews: ExperimentData, MassSpectrometryData Author: Steffen Neumann Maintainer: Steffen Neumann source.ver: src/contrib/msdata_0.1.13.tar.gz win.binary.ver: bin/windows/contrib/2.16/msdata_0.1.13.zip mac.binary.ver: bin/macosx/contrib/2.16/msdata_0.1.13.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics Package: Mulder2012 Version: 0.2.3 Depends: R (>= 2.14), org.Hs.eg.db, KEGG.db Imports: igraph, HTSanalyzeR, PANR, RedeR, pvclust, MASS Suggests: snow License: Artistic-2.0 MD5sum: a7fcef007695416742b9c328659f87ae 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: Bioinformatics Author: Xin Wang , Florian Markowetz Maintainer: Xin Wang source.ver: src/contrib/Mulder2012_0.2.3.tar.gz win.binary.ver: bin/windows/contrib/2.16/Mulder2012_0.2.3.zip mac.binary.ver: bin/macosx/contrib/2.16/Mulder2012_0.2.3.tgz vignettes: vignettes/Mulder2012/inst/doc/Arora2010_PAN.pdf, vignettes/Mulder2012/inst/doc/Arora2010_sigMod.pdf, vignettes/Mulder2012/inst/doc/Mulder2012_enrich.pdf, vignettes/Mulder2012/inst/doc/Mulder2012_PAN.pdf, vignettes/Mulder2012/inst/doc/Mulder2012_sigMod.pdf, vignettes/Mulder2012/inst/doc/Mulder2012-Vignette.pdf vignetteTitles: Arora2010_PAN.pdf, Arora2010_sigMod.pdf, Mulder2012_enrich.pdf, Mulder2012_PAN.pdf, Mulder2012_sigMod.pdf, Main vignette:Posterior association network and enriched functional gene modules inferred from rich phenotypes of gene perturbations hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Mulder2012/inst/doc/Mulder2012-Vignette.R Package: mvoutData Version: 0.99.10 Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4), lumi License: Artistic-2.0 MD5sum: 4ff75bcd6ba3b072ddc3ce0e10aedd2f 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 Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/mvoutData_0.99.10.tar.gz win.binary.ver: bin/windows/contrib/2.16/mvoutData_0.99.10.zip mac.binary.ver: bin/macosx/contrib/2.16/mvoutData_0.99.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: NCIgraphData Version: 0.99.6 Depends: R (>= 2.10.0) Suggests: Rgraphviz License: GPL-3 MD5sum: 8636470d7da934e7407940f765be7927 NeedsCompilation: no Title: Data for the NCIgraph software package Description: Provides pathways from the NCI Pathways Database as R graph objects biocViews: Bioinformatics, GraphsAndNetworks Author: Laurent Jacob Maintainer: Laurent Jacob source.ver: src/contrib/NCIgraphData_0.99.6.tar.gz win.binary.ver: bin/windows/contrib/2.16/NCIgraphData_0.99.6.zip mac.binary.ver: bin/macosx/contrib/2.16/NCIgraphData_0.99.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Neve2006 Version: 0.1.16 Depends: R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0), hgu133a.db, annotate License: Artistic-2.0 MD5sum: 0ba2c514b6cf2488639adffbe868115c NeedsCompilation: no Title: expression and CGH data on breast cancer cell lines Description: Experimental organization of combined expression and CGH data biocViews: ExperimentData, Cancer, Breast Author: M. Neve et al. in Gray Lab at LBL Maintainer: VJ Carey source.ver: src/contrib/Neve2006_0.1.16.tar.gz win.binary.ver: bin/windows/contrib/2.16/Neve2006_0.1.16.zip mac.binary.ver: bin/macosx/contrib/2.16/Neve2006_0.1.16.tgz vignettes: vignettes/Neve2006/inst/doc/neve06notes.pdf vignetteTitles: Neve 2006: combined CGH and expression data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Neve2006/inst/doc/neve06notes.R Package: parathyroid Version: 0.99.6 Depends: DEXSeq, DESeq, R (>= 2.10) Suggests: GEOquery, SRAdb License: LGPL MD5sum: ae41e0fcc47c38243ba28401374de076 NeedsCompilation: no Title: RNA-Seq data of primary cultures of parathyroid tumors by Haglund et al., J Clin Endocrinol Metab 2012. Description: This package provides a CountDataSet and ExonCountSet of read counts 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 objects from raw sequencing data provided by NCBI Gene Expression Omnibus under accession number GSE37211. The gene and exon features are the GRCh37 Ensembl annotations, release 66. biocViews: ExperimentData, RNAseqData Author: Michael Love Maintainer: Michael Love source.ver: src/contrib/parathyroid_0.99.6.tar.gz win.binary.ver: bin/windows/contrib/2.16/parathyroid_0.99.6.zip mac.binary.ver: bin/macosx/contrib/2.16/parathyroid_0.99.6.tgz vignettes: vignettes/parathyroid/inst/doc/create_objects.pdf vignetteTitles: parathyroidExons and parathyroidGenes hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/parathyroid/inst/doc/create_objects.R Package: parathyroidSE Version: 0.99.5 Depends: GenomicRanges, R (>= 2.10) Suggests: Rsamtools, GEOquery, SRAdb License: LGPL MD5sum: db03ee6c8d2e3eab8ceaa014d022539a NeedsCompilation: no Title: SummarizedExperiment for RNA-Seq of primary cultures of parathyroid tumors by Haglund et al., J Clin Endocrinol Metab 2012. Description: This package provides SummarizedExperiment 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, release 69. biocViews: ExperimentData, RNAseqData Author: Michael Love Maintainer: Michael Love source.ver: src/contrib/parathyroidSE_0.99.5.tar.gz win.binary.ver: bin/windows/contrib/2.16/parathyroidSE_0.99.5.zip mac.binary.ver: bin/macosx/contrib/2.16/parathyroidSE_0.99.5.tgz vignettes: vignettes/parathyroidSE/inst/doc/parathyroidSE.pdf vignetteTitles: parathyroidGenesSE hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/parathyroidSE/inst/doc/parathyroidSE.R Package: pasilla Version: 0.2.16 Depends: DEXSeq, DESeq Suggests: locfit, edgeR, xtable License: LGPL MD5sum: 2f6182bd0a48710573098a968acb5a81 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, RNAseqData Author: Wolfgang Huber, Alejandro Reyes Maintainer: Alejandro Reyes source.ver: src/contrib/pasilla_0.2.16.tar.gz win.binary.ver: bin/windows/contrib/2.16/pasilla_0.2.16.zip mac.binary.ver: bin/macosx/contrib/2.16/pasilla_0.2.16.tgz 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 Rfiles: vignettes/pasilla/inst/doc/create_objects.R suggestsMe: pasillaBamSubset Package: pasillaBamSubset Version: 0.0.7 Suggests: pasilla License: LGPL MD5sum: fb6fb4efc7af686082d9d25315f5722d 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, RNAseqData Author: H. Pages Maintainer: H. Pages source.ver: src/contrib/pasillaBamSubset_0.0.7.tar.gz win.binary.ver: bin/windows/contrib/2.16/pasillaBamSubset_0.0.7.zip mac.binary.ver: bin/macosx/contrib/2.16/pasillaBamSubset_0.0.7.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: PathNetData Version: 0.99.2 Depends: R (>= 1.14.0) License: GPL-3 MD5sum: b925c19ab129d2c1af055d677e2d5337 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 Author: Bhaskar Dutta , Anders Wallqvist , and Jaques Reifman Maintainer: Jason B. Smith source.ver: src/contrib/PathNetData_0.99.2.tar.gz win.binary.ver: bin/windows/contrib/2.16/PathNetData_0.99.2.zip mac.binary.ver: bin/macosx/contrib/2.16/PathNetData_0.99.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Hs.hg19 Version: 0.99.4 License: GPL (>= 2) MD5sum: 84b900434bf4086fe27b2b43a9f737c4 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: AnnotationData, Homo_sapiens Author: Morten Hansen, Maintainer: Morten Hansen, source.ver: src/contrib/pcaGoPromoter.Hs.hg19_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/2.16/pcaGoPromoter.Hs.hg19_0.99.4.zip mac.binary.ver: bin/macosx/contrib/2.16/pcaGoPromoter.Hs.hg19_0.99.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Mm.mm9 Version: 0.99.4 License: GPL (>= 2) MD5sum: 2bf6fdc3e0d757cdbd5bcff097a0ccb2 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: AnnotationData, Mus_musculus Author: Morten Hansen, Maintainer: Morten Hansen, source.ver: src/contrib/pcaGoPromoter.Mm.mm9_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/2.16/pcaGoPromoter.Mm.mm9_0.99.4.zip mac.binary.ver: bin/macosx/contrib/2.16/pcaGoPromoter.Mm.mm9_0.99.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Rn.rn4 Version: 0.99.4 License: GPL (>= 2) MD5sum: 6d70db5ae0c9028799c8fffc36c0e89f 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: AnnotationData, Rattus_norvegicus Author: Morten Hansen, Maintainer: Morten Hansen, source.ver: src/contrib/pcaGoPromoter.Rn.rn4_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/2.16/pcaGoPromoter.Rn.rn4_0.99.4.zip mac.binary.ver: bin/macosx/contrib/2.16/pcaGoPromoter.Rn.rn4_0.99.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pd.atdschip.tiling Version: 0.0.5 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) License: Artistic-2.0 MD5sum: 1207e2973d97067e72311f1983291265 NeedsCompilation: no Title: Platform Design Info for Affymetrix Atdschip_tiling Description: Platform Design Info for Affymetrix Atdschip_tiling biocViews: AnnotationData Author: Kristof De Beuf Maintainer: Kristof De Beuf source.ver: src/contrib/pd.atdschip.tiling_0.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.16/pd.atdschip.tiling_0.0.5.zip mac.binary.ver: bin/macosx/contrib/2.16/pd.atdschip.tiling_0.0.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ppiData Version: 0.1.22 Depends: graph Imports: AnnotationDbi Suggests: org.Sc.sgd.db, ppiStats License: Artistic-2.0 MD5sum: 6f5935507435df4ae6b50e7bcce87360 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_0.1.22.tar.gz win.binary.ver: bin/windows/contrib/2.16/ppiData_0.1.22.zip mac.binary.ver: bin/macosx/contrib/2.16/ppiData_0.1.22.tgz vignettes: vignettes/ppiData/inst/doc/ppiData.pdf vignetteTitles: Using the package ppiStats hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ppiData/inst/doc/ppiData.R Package: prebsdata Version: 0.99.4 Depends: R (>= 2.14.0) License: Artistic-2.0 MD5sum: fa05bb2d60fe3777691be8d5cb949d06 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, RNAseqData Author: Karolis Uziela and Antti Honkela Maintainer: Karolis Uziela source.ver: src/contrib/prebsdata_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/2.16/prebsdata_0.99.4.zip mac.binary.ver: bin/macosx/contrib/2.16/prebsdata_0.99.4.tgz vignettes: vignettes/prebsdata/inst/doc/prebsdata.pdf vignetteTitles: prebsdata User Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/prebsdata/inst/doc/prebsdata.R Package: PREDAsampledata Version: 0.2.7 Depends: R (>= 2.9.0), methods, PREDA, Biobase, affy, annotate, gahgu133plus2.db, gahgu133plus2cdf Suggests: hgu133plus2.db, hgu133plus2cdf License: Artistic-2.0 MD5sum: 1c0be7e6bb81a37dc24341cdc7c1c9c5 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, Cancer Author: I. Cifola et al. in Cristina Battaglia Lab, University of Milan Maintainer: Francesco Ferrari source.ver: src/contrib/PREDAsampledata_0.2.7.tar.gz win.binary.ver: bin/windows/contrib/2.16/PREDAsampledata_0.2.7.zip mac.binary.ver: bin/macosx/contrib/2.16/PREDAsampledata_0.2.7.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ProData Version: 1.0.8 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL MD5sum: 5c745a321c3cfcfad7197d651c4d70f2 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, Cancer, Breast Author: Xiaochun Li Maintainer: Xiaochun Li source.ver: src/contrib/ProData_1.0.8.tar.gz win.binary.ver: bin/windows/contrib/2.16/ProData_1.0.8.zip mac.binary.ver: bin/macosx/contrib/2.16/ProData_1.0.8.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pRolocdata Version: 1.0.2 Depends: R (>= 2.15), MSnbase Suggests: pRoloc License: GPL-2 MD5sum: 76257c2634ef0e6de4627b7ddd27ee23 NeedsCompilation: no Title: Data accompanying the pRoloc package Description: Mass-spectrometry based organelle 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) and Breckels et al. (2013). biocViews: ExperimentData, MassSpectrometry, Proteomics Author: Laurent Gatto and Lisa M. Breckels Maintainer: Laurent Gatto source.ver: src/contrib/pRolocdata_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.16/pRolocdata_1.0.2.zip mac.binary.ver: bin/macosx/contrib/2.16/pRolocdata_1.0.2.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: pumadata Version: 1.99.5 Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), puma License: LGPL MD5sum: 0e2eb0c95cc9d9dc93e166a70b2a9933 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 Author: Richard Pearson Maintainer: Richard Pearson URL: http://umber.sbs.man.ac.uk/resources/puma source.ver: src/contrib/pumadata_1.99.5.tar.gz win.binary.ver: bin/windows/contrib/2.16/pumadata_1.99.5.zip mac.binary.ver: bin/macosx/contrib/2.16/pumadata_1.99.5.tgz vignettes: vignettes/pumadata/inst/doc/pumadata.pdf vignetteTitles: pumadata User Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pumadata/inst/doc/pumadata.R Package: PWMEnrich.Dmelanogaster.background Version: 2.1.0 Depends: methods, PWMEnrich License: GPL-3 MD5sum: 48de7f07baeff9c6c01ce3abe962f972 NeedsCompilation: no Title: D. melanogaster background for PWMEnrich Description: PWMEnrich pre-compiled background objects for Drosophila melanogaster and MotifDb D. melanogaster motifs. biocViews: AnnotationData, Drosophila_melanogaster Author: Robert Stojnic Maintainer: Robert Stojnic source.ver: src/contrib/PWMEnrich.Dmelanogaster.background_2.1.0.tar.gz win.binary.ver: bin/windows/contrib/2.16/PWMEnrich.Dmelanogaster.background_2.1.0.zip mac.binary.ver: bin/macosx/contrib/2.16/PWMEnrich.Dmelanogaster.background_2.1.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: RforProteomics Version: 1.0.13 Imports: R.utils, Biobase Suggests: mzR, MSnbase, xcms, msdata, isobar, MALDIquant, MALDIquantForeign, readBrukerFlexData, rTANDEM, synapter, synapterdata, IPPD, Rdisop, OrgMassSpecR, BRAIN, rols, hpar, GO.db, org.Hs.eg.db, biomaRt, RColorBrewer, ggplot2, reshape2, knitr, biocViews, xtable Enhances: cleaver License: Artistic-2.0 MD5sum: 229b8740d3d6533e9f2aab1fe4f48672 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' manuscript. The vignette describes the code and data needed to reproduce the examples and figures descibed in the paper as well as functions to download the PXD000001 data files. biocViews: ExperimentData, MassSpectrometry, Proteomics, MassSpectrometryData Author: Laurent Gatto [aut, cre], Sebastian Gibb [ctb] Maintainer: Laurent Gatto URL: http://lgatto.github.com/RforProteomics/ source.ver: src/contrib/RforProteomics_1.0.13.tar.gz win.binary.ver: bin/windows/contrib/2.16/RforProteomics_1.0.13.zip mac.binary.ver: bin/macosx/contrib/2.16/RforProteomics_1.0.13.tgz vignettes: vignettes/RforProteomics/inst/doc/Bioc2013_poster.pdf, vignettes/RforProteomics/inst/doc/RforProteomics.pdf vignetteTitles: RforProteomics Bioc2013 poster, R for Proteomics hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RforProteomics/inst/doc/Bioc2013_poster.R, vignettes/RforProteomics/inst/doc/RforProteomics.R Package: rheumaticConditionWOLLBOLD Version: 1.0.3 Depends: R (>= 2.10.0) Suggests: genefilter, Biobase, hgu133plus2.db License: Artistic-2.0 MD5sum: 1c8d6d1d9dbd4381f3e54341c3b5fbdf 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, Rheumatic diseases,Arthritis, Osteoarthritis, GeneExpression, Microarray Author: Alejandro Quiroz-Zarate, John Quackenbush Maintainer: Alejandro Quiroz-Zarate URL: http://compbio.dfci.harvard.edu/ source.ver: src/contrib/rheumaticConditionWOLLBOLD_1.0.3.tar.gz win.binary.ver: bin/windows/contrib/2.16/rheumaticConditionWOLLBOLD_1.0.3.zip mac.binary.ver: bin/macosx/contrib/2.16/rheumaticConditionWOLLBOLD_1.0.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RIPSeekerData Version: 0.99.1 Depends: RIPSeeker License: GPL-2 MD5sum: 9032d0f3e23e10164c29c6714ccac54d NeedsCompilation: no 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, RIPseqData Author: Yue Li Maintainer: Alejandro Reyes source.ver: src/contrib/RIPSeekerData_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/2.16/RIPSeekerData_0.99.1.zip mac.binary.ver: bin/macosx/contrib/2.16/RIPSeekerData_0.99.1.tgz vignettes: vignettes/RIPSeekerData/inst/doc/RIPSeekerData.pdf vignetteTitles: RIP-seq datasets for testing RIPSeeker package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RIPSeekerData/inst/doc/RIPSeekerData.R Package: RMassBankData Version: 0.99.2 Suggests: RMassBank License: Artistic-2.0 MD5sum: 76b7f33ded2e6071a73f83ad255cf8bb NeedsCompilation: no Title: Test dataset for RMassBank Description: Example spectra, a example compound list and an example annotation list for a narcotics dataset; required to test RMassBank. The package is described in the man page for RMassBankData. biocViews: ExperimentData, MassSpectrometryData Author: Michael Stravs Maintainer: Michael Stravs source.ver: src/contrib/RMassBankData_0.99.2.tar.gz win.binary.ver: bin/windows/contrib/2.16/RMassBankData_0.99.2.zip mac.binary.ver: bin/macosx/contrib/2.16/RMassBankData_0.99.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RNAinteractMAPK Version: 1.0.11 Depends: R (>= 2.12.0), methods, fields, sparseLDA, RNAinteract Imports: grid, gdata, MASS, genefilter Suggests: qvalue, lattice License: Artistic-2.0 MD5sum: 792cfadcd0d789a25c738e51dbcdc39a 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 Author: Bernd Fischer Maintainer: Bernd Fischer source.ver: src/contrib/RNAinteractMAPK_1.0.11.tar.gz win.binary.ver: bin/windows/contrib/2.16/RNAinteractMAPK_1.0.11.zip mac.binary.ver: bin/macosx/contrib/2.16/RNAinteractMAPK_1.0.11.tgz vignettes: vignettes/RNAinteractMAPK/inst/doc/RNAinteractMAPK.pdf vignetteTitles: RNAinteractMAPK hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RNAinteractMAPK/inst/doc/RNAinteractMAPK.R Package: RNAseqData.HeLa.bam.chr14 Version: 0.1.4 Depends: RNAseqData.HNRNPC.bam.chr14 Imports: RNAseqData.HNRNPC.bam.chr14 License: LGPL MD5sum: 25818bce46e73abdf2547be89d367632 NeedsCompilation: no Title: DEPRECATED (was renamed RNAseqData.HNRNPC.bam.chr14) Description: This package was renamed RNAseqData.HNRNPC.bam.chr14. RNAseqData.HeLa.bam.chr14 is still available but is DEPRECATED. Please use the RNAseqData.HNRNPC.bam.chr14 package instead. biocViews: ExperimentData, RNAseqData, Homo_sapiens Author: H. Pages Maintainer: H. Pages source.ver: src/contrib/RNAseqData.HeLa.bam.chr14_0.1.4.tar.gz win.binary.ver: bin/windows/contrib/2.16/RNAseqData.HeLa.bam.chr14_0.1.4.zip mac.binary.ver: bin/macosx/contrib/2.16/RNAseqData.HeLa.bam.chr14_0.1.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RNAseqData.HNRNPC.bam.chr14 Version: 0.1.3 Suggests: Rsamtools, BiocInstaller License: LGPL MD5sum: 369686c4b3b75ff6b5fb9f57d451fd1a 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, RNAseqData, Homo_sapiens 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_0.1.3.tar.gz win.binary.ver: bin/windows/contrib/2.16/RNAseqData.HNRNPC.bam.chr14_0.1.3.zip mac.binary.ver: bin/macosx/contrib/2.16/RNAseqData.HNRNPC.bam.chr14_0.1.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: RNAseqData.HeLa.bam.chr14 importsMe: RNAseqData.HeLa.bam.chr14 Package: RNASeqDataSubset Version: 0.99.1 Depends: Rsamtools (>= 1.9.8) Imports: xtable License: LGPL MD5sum: 35bf9fa7b2f23b48d6e4f267f0cbde7f 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, RNAseqData Author: D. Bindreither Maintainer: D. Bindreither source.ver: src/contrib/RNASeqDataSubset_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/2.16/RNASeqDataSubset_0.99.1.zip vignettes: vignettes/RNASeqDataSubset/inst/doc/RNASeqDataSubset.pdf vignetteTitles: TBX20 RNA-Seq data subset hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RNASeqDataSubset/inst/doc/RNASeqDataSubset.R Package: RnaSeqTutorial Version: 0.0.12 Depends: R (>= 2.15.0), methods, easyRNASeq Suggests: Rsamtools, ShortRead, BSgenome.Dmelanogaster.UCSC.dm3, GenomicRanges, biomaRt, genomeIntervals License: Artistic-2.0 MD5sum: 805df85c3baf7091c08055be0b972144 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, RNAseqData Author: Nicolas Delhomme, Ismael Padioleau Maintainer: Nicolas Delhomme source.ver: src/contrib/RnaSeqTutorial_0.0.12.tar.gz win.binary.ver: bin/windows/contrib/2.16/RnaSeqTutorial_0.0.12.zip mac.binary.ver: bin/macosx/contrib/2.16/RnaSeqTutorial_0.0.12.tgz vignettes: vignettes/RnaSeqTutorial/inst/doc/RnaSeqTutorial.pdf vignetteTitles: RNA-Seq Tutorial hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RnaSeqTutorial/inst/doc/RnaSeqTutorial.R Package: serumStimulation Version: 0.99.4 Depends: R (>= 2.10) License: GPL (>= 2) MD5sum: 9013b307d5723b0dd4a0c13ddb213329 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 Author: Morten Hansen, Maintainer: Morten Hansen, source.ver: src/contrib/serumStimulation_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/2.16/serumStimulation_0.99.4.zip mac.binary.ver: bin/macosx/contrib/2.16/serumStimulation_0.99.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: simpIntLists Version: 0.99.4 License: GPL (>= 2) MD5sum: 458e8cda1b22f3dc798f114f85b29a64 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 Author: Kircicegi Korkmaz, Volkan Atalay, Rengul Cetin-Atalay Maintainer: Kircicegi Korkmaz source.ver: src/contrib/simpIntLists_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/2.16/simpIntLists_0.99.4.zip mac.binary.ver: bin/macosx/contrib/2.16/simpIntLists_0.99.4.tgz vignettes: vignettes/simpIntLists/inst/doc/simpIntLists.pdf vignetteTitles: simpIntLists hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/simpIntLists/inst/doc/simpIntLists.R Package: SNAData Version: 1.8.6 Depends: R (>= 2.4.0), graph Suggests: Rgraphviz License: LGPL MD5sum: 577ac57c499c1bf8a6dcdd00df008dac 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_1.8.6.tar.gz win.binary.ver: bin/windows/contrib/2.16/SNAData_1.8.6.zip mac.binary.ver: bin/macosx/contrib/2.16/SNAData_1.8.6.tgz vignettes: vignettes/SNAData/inst/doc/SNAData.pdf vignetteTitles: SNAData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SNAData/inst/doc/SNAData.R Package: SNAGEEdata Version: 0.99.1 Depends: R (>= 2.6.0) Suggests: ALL, hgu95av2.db, SNAGEE License: Artistic-2.0 MD5sum: 65227796015c68c494785ca4e0e86084 NeedsCompilation: no Title: SNAGEE data Description: SNAGEE data - gene list and correlation matrix biocViews: Microarray, OneChannel, TwoChannel, QualityControl Author: David Venet Maintainer: David Venet URL: http://fleming.ulb.ac.be/SNAGEE source.ver: src/contrib/SNAGEEdata_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/2.16/SNAGEEdata_0.99.1.zip mac.binary.ver: bin/macosx/contrib/2.16/SNAGEEdata_0.99.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SomatiCAData Version: 1.1.0 Depends: R (>= 2.14) License: Artistic-2.0 MD5sum: 7150f3d30d1f92cf86d65e3cff94db9a 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: Sequencing, ExperimentData Author: Mengjie Chen Maintainer: Mengjie Chen source.ver: src/contrib/SomatiCAData_1.1.0.tar.gz win.binary.ver: bin/windows/contrib/2.16/SomatiCAData_1.1.0.zip mac.binary.ver: bin/macosx/contrib/2.16/SomatiCAData_1.1.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SpikeIn Version: 1.4.10 Depends: R (>= 1.6), affy (>= 1.23.4) License: Artistic-2.0 MD5sum: 6ad3a3d770e097a93edcc446cac36745 NeedsCompilation: no Title: Affymetrix Spike-In Experiment Data Description: Contains the HGU133 and HGU95 spikein experiment data. biocViews: ExperimentData Author: Rafael Irizarry Maintainer: Rafael A. Irizarry source.ver: src/contrib/SpikeIn_1.4.10.tar.gz win.binary.ver: bin/windows/contrib/2.16/SpikeIn_1.4.10.zip mac.binary.ver: bin/macosx/contrib/2.16/SpikeIn_1.4.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SpikeInSubset Version: 1.2.13 Depends: R (>= 2.4.0), Biobase (>= 2.5.5), affy (>= 1.23.4) License: LGPL MD5sum: 4da1b26d44b98c28c35f24d2216dbbd0 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 Author: Rafael Irizarry and Zhijin Wu Maintainer: Rafael A. Irizarry source.ver: src/contrib/SpikeInSubset_1.2.13.tar.gz win.binary.ver: bin/windows/contrib/2.16/SpikeInSubset_1.2.13.zip mac.binary.ver: bin/macosx/contrib/2.16/SpikeInSubset_1.2.13.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: stemHypoxia Version: 0.99.3 Depends: R (>= 2.14.1) License: GPL (>=2) MD5sum: ed94359540545f15a9bb8ab556753a15 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, Cancer, GeneExpression, Microarray 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_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/2.16/stemHypoxia_0.99.3.zip mac.binary.ver: bin/macosx/contrib/2.16/stemHypoxia_0.99.3.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: stjudem Version: 1.2.9 Depends: R (>= 2.10), utils License: LGPL (>= 2) MD5sum: 61dd3e8c459a85159812e365e4223580 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 Author: Benjamin Georgi, Matthias Heinig, Sebastian Schmeier, Joern Toedling Maintainer: Joern Toedling source.ver: src/contrib/stjudem_1.2.9.tar.gz win.binary.ver: bin/windows/contrib/2.16/stjudem_1.2.9.zip mac.binary.ver: bin/macosx/contrib/2.16/stjudem_1.2.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: synapterdata Version: 1.0.0 Depends: R (>= 2.10), synapter (>= 0.99.6) License: GPL-2 MD5sum: f2cd39a0a975f4af61930cfeaaeb8182 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, MassSpectrometry, MassSpectrometryData, Proteomics Author: Laurent Gatto and Pavel V. Shliaha Maintainer: Laurent Gatto source.ver: src/contrib/synapterdata_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.16/synapterdata_1.0.0.zip mac.binary.ver: bin/macosx/contrib/2.16/synapterdata_1.0.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics Package: TargetSearchData Version: 1.0.9 Depends: TargetSearch License: GPL (>= 2) MD5sum: b377943c30b5cd43e37a74dfe4bda6da NeedsCompilation: no Title: Example GC-MS data for TargetSearch Package Description: This package provides example GC-MS data for TargetSearch Package. biocViews: ExperimentData Author: Alvaro Cuadros-Inostroza, Henning Redestig, Matt Hannah Maintainer: Alvaro Cuadros-Inostroza Henning Redestig , Matt Hannah source.ver: src/contrib/TargetSearchData_1.0.9.tar.gz win.binary.ver: bin/windows/contrib/2.16/TargetSearchData_1.0.9.zip mac.binary.ver: bin/macosx/contrib/2.16/TargetSearchData_1.0.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: TBX20BamSubset Version: 0.99.2 Depends: Rsamtools (>= 1.9.8) Imports: xtable License: LGPL MD5sum: d31adfb7ca3274e4c688719ebdb4e6a6 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, RNAseqData Author: D. Bindreither Maintainer: D. Bindreither source.ver: src/contrib/TBX20BamSubset_0.99.2.tar.gz win.binary.ver: bin/windows/contrib/2.16/TBX20BamSubset_0.99.2.zip mac.binary.ver: bin/macosx/contrib/2.16/TBX20BamSubset_0.99.2.tgz vignettes: vignettes/TBX20BamSubset/inst/doc/TBX20BamSubset.pdf vignetteTitles: TBX20 RNA-Seq data subset hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TBX20BamSubset/inst/doc/TBX20BamSubset.R Package: TCGAMethylation450k Version: 0.99.4 License: GPL-2 MD5sum: 82fca4c74226b66417aa59ce42fd4a89 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. Author: Sean Davis Maintainer: Sean Davis source.ver: src/contrib/TCGAMethylation450k_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/2.16/TCGAMethylation450k_0.99.4.zip mac.binary.ver: bin/macosx/contrib/2.16/TCGAMethylation450k_0.99.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: tinesath1cdf Version: 1.0.9 License: Artistic-2.0 MD5sum: 26ab25c51866b5adb05c02101904fced NeedsCompilation: no Title: tinesath1cdf Description: A package containing an environment represeting the newcdf/tinesATH1.cdf.cdf file. biocViews: AnnotationData, AffymetrixChip, ath1121501, Arabidopsis_thaliana Author: Tine Casneuf Maintainer: Tine Casneuf source.ver: src/contrib/tinesath1cdf_1.0.9.tar.gz win.binary.ver: bin/windows/contrib/2.16/tinesath1cdf_1.0.9.zip mac.binary.ver: bin/macosx/contrib/2.16/tinesath1cdf_1.0.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: XhybCasneuf Package: tinesath1probe Version: 1.0.9 Depends: R (>= 1.6), AnnotationDbi (>= 1.11.9) License: LGPL MD5sum: 2ef967cb45feecef2c464323ca3c9886 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: AnnotationData, AffymetrixChip, tinesath1, Arabidopsis_thaliana Author: The Bioconductor Project www.bioconductor.org Maintainer: Tine Casneuf source.ver: src/contrib/tinesath1probe_1.0.9.tar.gz win.binary.ver: bin/windows/contrib/2.16/tinesath1probe_1.0.9.zip mac.binary.ver: bin/macosx/contrib/2.16/tinesath1probe_1.0.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: tweeDEseqCountData Version: 1.0.9 Depends: Biobase, R (>= 2.10) License: GPL (>=2) MD5sum: fbacf2b5b969db791fc6f50e7fdc1d1a 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: HighThroughputSequencingData, 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_1.0.9.tar.gz win.binary.ver: bin/windows/contrib/2.16/tweeDEseqCountData_1.0.9.zip mac.binary.ver: bin/macosx/contrib/2.16/tweeDEseqCountData_1.0.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: waveTilingData Version: 0.99.2 Depends: R (>= 2.14.0) License: GPL (>= 2) MD5sum: 810a2febfe885d185fa7c5c8dae8cc50 NeedsCompilation: no Title: waveTiling Example Data Description: Experiment and Annotation Data files used by the examples / vignette in the waveTiling package biocViews: Microarray, AnnotationData, ExperimentData Author: Kristof De Beuf Maintainer: Kristof De Beuf source.ver: src/contrib/waveTilingData_0.99.2.tar.gz win.binary.ver: bin/windows/contrib/2.16/waveTilingData_0.99.2.zip mac.binary.ver: bin/macosx/contrib/2.16/waveTilingData_0.99.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: XhybCasneuf Version: 1.0.11 Depends: R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf , RColorBrewer , methods, grid License: Artistic-2.0 MD5sum: 40b83a5f52b1118bd5129563a7d581da NeedsCompilation: no Title: EBI/PSB cross-hybridisation study package Description: Cross-hybridisation study on the ATH1 Affymetrix GeneChip biocViews: ExperimentData Author: Tineke Casneuf Maintainer: Tineke Casneuf source.ver: src/contrib/XhybCasneuf_1.0.11.tar.gz win.binary.ver: bin/windows/contrib/2.16/XhybCasneuf_1.0.11.zip mac.binary.ver: bin/macosx/contrib/2.16/XhybCasneuf_1.0.11.tgz vignettes: vignettes/XhybCasneuf/inst/doc/Xhyb.pdf vignetteTitles: Xhyb hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/XhybCasneuf/inst/doc/Xhyb.R Package: yeastCC Version: 1.2.18 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 74e41a9e3542162ff82c03d7bbdf1ac1 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, Yeast Author: Sandrine Dudoit Maintainer: Sandrine Dudoit source.ver: src/contrib/yeastCC_1.2.18.tar.gz win.binary.ver: bin/windows/contrib/2.16/yeastCC_1.2.18.zip mac.binary.ver: bin/macosx/contrib/2.16/yeastCC_1.2.18.tgz vignettes: vignettes/yeastCC/inst/doc/Spellmanetal.pdf vignetteTitles: Spellmanetal.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastExpData Version: 0.9.22 Depends: R (>= 2.4), graph (>= 1.9.26) Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db License: GPL MD5sum: 3f310c6873752bdbed01e333c73d4718 NeedsCompilation: no Title: Yeast Experimental Data Description: A collection of different sets of experimental data from yeast. biocViews: ExperimentData, Yeast Author: R. Gentleman Maintainer: R. Gentleman source.ver: src/contrib/yeastExpData_0.9.22.tar.gz win.binary.ver: bin/windows/contrib/2.16/yeastExpData_0.9.22.zip mac.binary.ver: bin/macosx/contrib/2.16/yeastExpData_0.9.22.tgz vignettes: vignettes/yeastExpData/inst/doc/yeastExample.pdf vignetteTitles: Yeast PPI Example hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/yeastExpData/inst/doc/yeastExample.R Package: yeastGSData Version: 0.1.10 License: Artistic-2.0 MD5sum: 3256eadccabd583bf4fed64b8d6604b0 NeedsCompilation: no Title: Yeast Gold Standard Data Description: A collection of so-called gold (and other) standard data sets biocViews: ExperimentData, Yeast Author: R. Gentleman Maintainer: R. Gentleman source.ver: src/contrib/yeastGSData_0.1.10.tar.gz win.binary.ver: bin/windows/contrib/2.16/yeastGSData_0.1.10.zip mac.binary.ver: bin/macosx/contrib/2.16/yeastGSData_0.1.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastNagalakshmi Version: 0.99.6 License: Artistic-2.0 MD5sum: e8ebf3daa53e737609d5620528f00edc 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, Yeast, ChIPseqData Author: Martin Morgan Maintainer: Bioconductor Package Maintainer source.ver: src/contrib/yeastNagalakshmi_0.99.6.tar.gz win.binary.ver: bin/windows/contrib/2.16/yeastNagalakshmi_0.99.6.zip mac.binary.ver: bin/macosx/contrib/2.16/yeastNagalakshmi_0.99.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastRNASeq Version: 0.0.8 Depends: R (>= 2.4) Suggests: Biobase, ShortRead, IRanges License: GPL MD5sum: 214b3f9f29ad7e03ab619923674e5713 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, Yeast, RNAseqData Author: James H. Bullard and Kasper D. Hansen Maintainer: J. Bullard source.ver: src/contrib/yeastRNASeq_0.0.8.tar.gz win.binary.ver: bin/windows/contrib/2.16/yeastRNASeq_0.0.8.zip mac.binary.ver: bin/macosx/contrib/2.16/yeastRNASeq_0.0.8.tgz vignettes: vignettes/yeastRNASeq/inst/doc/yeastRNASeq.pdf vignetteTitles: An overview of yeastRNASeq hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/yeastRNASeq/inst/doc/yeastRNASeq.R