Package: affycompData Version: 1.1.6 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp License: GPL (>= 2) MD5sum: 8e735060e06340f2eaea6ea43bc7579f 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_1.1.6.tar.gz win.binary.ver: bin/windows/contrib/3.0/affycompData_1.1.6.zip mac.binary.ver: bin/macosx/contrib/3.0/affycompData_1.1.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: affydata Version: 1.11.20 Depends: R (>= 2.4.0), affy (>= 1.23.4) Imports: methods Suggests: hgu95av2cdf, hgu133acdf License: GPL (>= 2) MD5sum: 6093705b32c13d1dedd4512726bfa4a8 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_1.11.20.tar.gz win.binary.ver: bin/windows/contrib/3.0/affydata_1.11.20.zip mac.binary.ver: bin/macosx/contrib/3.0/affydata_1.11.20.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: 0.1.7 Depends: R (>= 2.5.0) License: LGPL-2.1 MD5sum: 629c361324d21a305dc22345e9a3d459 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_0.1.7.tar.gz win.binary.ver: bin/windows/contrib/3.0/AffymetrixDataTestFiles_0.1.7.zip mac.binary.ver: bin/macosx/contrib/3.0/AffymetrixDataTestFiles_0.1.7.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ALL Version: 1.4.16 Depends: R (>= 2.10), Biobase (>= 2.5.5) Suggests: rpart License: Artistic-2.0 MD5sum: 405a0bff7e44a72733a1e854736e998d 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_1.4.16.tar.gz win.binary.ver: bin/windows/contrib/3.0/ALL_1.4.16.zip mac.binary.ver: bin/macosx/contrib/3.0/ALL_1.4.16.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: 1.2.15 Depends: R (>= 2.10), affy (>= 1.23.4) License: GPL-2 MD5sum: c47fc227f473c98a9c033634d72ce80b 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_1.2.15.tar.gz win.binary.ver: bin/windows/contrib/3.0/ALLMLL_1.2.15.zip mac.binary.ver: bin/macosx/contrib/3.0/ALLMLL_1.2.15.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: AmpAffyExample Version: 1.2.13 Depends: R (>= 2.4.0), affy (>= 1.23.4) Suggests: hgu133acdf License: LGPL (>= 2) MD5sum: 94a09ed84fea5f526775e96a462671af 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_1.2.13.tar.gz win.binary.ver: bin/windows/contrib/3.0/AmpAffyExample_1.2.13.zip mac.binary.ver: bin/macosx/contrib/3.0/AmpAffyExample_1.2.13.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: antiProfilesData Version: 0.99.2 Depends: Biobase, Suggests: frma, GEOquery, GEOmetadb License: Artistic-2.0 MD5sum: 58b00c1d85ff20999562b2a757a6958a 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_0.99.2.tar.gz win.binary.ver: bin/windows/contrib/3.0/antiProfilesData_0.99.2.zip mac.binary.ver: bin/macosx/contrib/3.0/antiProfilesData_0.99.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ARRmData Version: 0.99.3 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: f0c3c0019acc325df59dd6e83be2cd4f 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_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/ARRmData_0.99.3.zip mac.binary.ver: bin/macosx/contrib/3.0/ARRmData_0.99.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: beadarrayExampleData Version: 1.0.8 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>= 2.0.0) License: GPL-2 MD5sum: 67a68faaeb05a699392a814102469dc4 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_1.0.8.tar.gz win.binary.ver: bin/windows/contrib/3.0/beadarrayExampleData_1.0.8.zip mac.binary.ver: bin/macosx/contrib/3.0/beadarrayExampleData_1.0.8.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: 1.0.12 Imports: beadarray (>= 2.3.18), limma, GEOquery Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db License: GPL-2 MD5sum: 7797334f28aa545c326fc4d4e5c5f379 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_1.0.12.tar.gz win.binary.ver: bin/windows/contrib/3.0/BeadArrayUseCases_1.0.12.zip mac.binary.ver: bin/macosx/contrib/3.0/BeadArrayUseCases_1.0.12.tgz vignettes: vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.pdf vignetteTitles: BeadArrayUseCases.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.R Package: beta7 Version: 1.0.6 Depends: R (>= 2.4.0), marray License: LGPL MD5sum: 04941a06a10cb794fe9c913adb36391a 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_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/3.0/beta7_1.0.6.zip mac.binary.ver: bin/macosx/contrib/3.0/beta7_1.0.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bladderbatch Version: 1.0.7 Depends: Biobase License: Artistic-2.0 MD5sum: 6849bd2cf35f28ce5cf8f515e164f0f8 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_1.0.7.tar.gz win.binary.ver: bin/windows/contrib/3.0/bladderbatch_1.0.7.zip mac.binary.ver: bin/macosx/contrib/3.0/bladderbatch_1.0.7.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: 1.0.6 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 9df026c48a3bc647a7dc593375e57620 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_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/3.0/breastCancerMAINZ_1.0.6.zip mac.binary.ver: bin/macosx/contrib/3.0/breastCancerMAINZ_1.0.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerNKI Version: 1.0.6 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 06e4f96af8f258a09b494a6f6049e529 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_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/3.0/breastCancerNKI_1.0.6.zip mac.binary.ver: bin/macosx/contrib/3.0/breastCancerNKI_1.0.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: seventyGeneData Package: breastCancerTRANSBIG Version: 1.0.6 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: f31a6688aa535e16742290f37a5bd595 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_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/3.0/breastCancerTRANSBIG_1.0.6.zip mac.binary.ver: bin/macosx/contrib/3.0/breastCancerTRANSBIG_1.0.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerUNT Version: 1.0.6 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 2280f3812f478694195b0051e592b595 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_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/3.0/breastCancerUNT_1.0.6.zip mac.binary.ver: bin/macosx/contrib/3.0/breastCancerUNT_1.0.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerUPP Version: 1.0.6 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 93779ee5a8c1ff1eb601589701a1ee86 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_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/3.0/breastCancerUPP_1.0.6.zip mac.binary.ver: bin/macosx/contrib/3.0/breastCancerUPP_1.0.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerVDX Version: 1.0.6 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: fb5ae58b3df6a5fea41171f9e0e27a96 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_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/3.0/breastCancerVDX_1.0.6.zip mac.binary.ver: bin/macosx/contrib/3.0/breastCancerVDX_1.0.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bronchialIL13 Version: 1.0.12 Depends: R(>= 2.10.0), affy (>= 1.23.4) License: GPL-2 MD5sum: 646408993037cddf4de5b8761799caed 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_1.0.12.tar.gz win.binary.ver: bin/windows/contrib/3.0/bronchialIL13_1.0.12.zip mac.binary.ver: bin/macosx/contrib/3.0/bronchialIL13_1.0.12.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bsseqData Version: 0.1.5 Depends: R (>= 2.15), bsseq (>= 0.9.6) License: Artistic-2.0 MD5sum: b94251c4031b4c239c45bced28451277 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_0.1.5.tar.gz win.binary.ver: bin/windows/contrib/3.0/bsseqData_0.1.5.zip mac.binary.ver: bin/macosx/contrib/3.0/bsseqData_0.1.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cancerdata Version: 1.1.3 Depends: R (>= 2.10.1), Biobase License: GPL (>= 2) MD5sum: b6f3a4b3ee045967f6e1d82fcc348ee0 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_1.1.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/cancerdata_1.1.3.zip mac.binary.ver: bin/macosx/contrib/3.0/cancerdata_1.1.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CCl4 Version: 1.0.16 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), limma License: Artistic-2.0 MD5sum: a24ed1dea401e543b4b6ee91a47a5f53 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_1.0.16.tar.gz win.binary.ver: bin/windows/contrib/3.0/CCl4_1.0.16.zip mac.binary.ver: bin/macosx/contrib/3.0/CCl4_1.0.16.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: 1.0.26 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: 7ae43ef2794b0b21306c7fdd46ce5fe3 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_1.0.26.tar.gz win.binary.ver: bin/windows/contrib/3.0/ccTutorial_1.0.26.zip mac.binary.ver: bin/macosx/contrib/3.0/ccTutorial_1.0.26.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: 0.0.34 Depends: R (>= 2.12.0), GGBase (>= 3.9.0), GGtools, Biobase Suggests: SNPlocs.Hsapiens.dbSNP.20101109 License: Artistic-2.0 MD5sum: 3cb28ab019decc41a02cc0be71518742 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_0.0.34.tar.gz win.binary.ver: bin/windows/contrib/3.0/ceu1kg_0.0.34.zip mac.binary.ver: bin/macosx/contrib/3.0/ceu1kg_0.0.34.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: ceu1kgv Version: 0.5.3 Depends: GGBase Imports: Biobase License: Artistic-2.0 MD5sum: 896e45fbad30df46367fb2c7e7a2b1f0 NeedsCompilation: no Title: expression + genotype on 79 unrelated CEU individuals Description: expression + genotype on 79 unrelated CEU individuals Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/ceu1kgv_0.5.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/ceu1kgv_0.5.3.zip mac.binary.ver: bin/macosx/contrib/3.0/ceu1kgv_0.5.3.tgz vignettes: vignettes/ceu1kgv/inst/doc/ceu1kgv.pdf vignetteTitles: ceu1kgv -- genotype plus expression for HapMap CEU hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ceu1kgv/inst/doc/ceu1kgv.R Package: ceuhm3 Version: 0.0.16 Depends: R (>= 2.12.0), GGBase, Biobase Imports: GGtools License: Artistic-2.0 MD5sum: 4e9441fe8b2537ae7d1940e9e566b136 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_0.0.16.tar.gz win.binary.ver: bin/windows/contrib/3.0/ceuhm3_0.0.16.zip mac.binary.ver: bin/macosx/contrib/3.0/ceuhm3_0.0.16.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cgdv17 Version: 0.0.21 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: 5ef0f3937fd7531179fb496a2fb15319 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_0.0.21.tar.gz win.binary.ver: bin/windows/contrib/3.0/cgdv17_0.0.21.zip mac.binary.ver: bin/macosx/contrib/3.0/cgdv17_0.0.21.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: ChAMPdata Version: 0.99.6 Depends: R (>= 3.0.1) License: GPL-3 MD5sum: 39eefeb83cf50c8505c63ba6471ac0c3 NeedsCompilation: no Title: Data Packages for ChAMP package Description: More about what it does (maybe more than one line) biocViews: ExpressionData, IlluminaChip Author: Andrew Teschendorff and Lee Butcher Maintainer: Tiffany Morris source.ver: src/contrib/ChAMPdata_0.99.6.tar.gz win.binary.ver: bin/windows/contrib/3.0/ChAMPdata_0.99.6.zip mac.binary.ver: bin/macosx/contrib/3.0/ChAMPdata_0.99.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: charmData Version: 0.99.9 Depends: R(>= 2.11.0), charm, pd.charm.hg18.example License: LGPL (>= 2) MD5sum: be2df97e81c3d9b0827a7d884b6a20af 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_0.99.9.tar.gz win.binary.ver: bin/windows/contrib/3.0/charmData_0.99.9.zip mac.binary.ver: bin/macosx/contrib/3.0/charmData_0.99.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cheung2010 Version: 0.0.29 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: 9c1a8864144b7b7966df51b7efb09836 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_0.0.29.tar.gz win.binary.ver: bin/windows/contrib/3.0/cheung2010_0.0.29.zip mac.binary.ver: bin/macosx/contrib/3.0/cheung2010_0.0.29.tgz vignettes: vignettes/cheung2010/inst/doc/cheungTrans.pdf vignetteTitles: 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: chipenrich.data Version: 0.99.4 Depends: R (>= 2.15.0) Imports: methods, GenomicRanges (>= 1.10.0), IRanges (>= 1.16.0), BiocGenerics (>= 0.2.0) License: GPL-3 MD5sum: 0b74e66bf25a7d890c1f1a6781459c06 NeedsCompilation: no Title: Gene set enrichment analysis for ChIP-seq data Description: Supporting data for the chipenrich package. Includes pre-defined gene sets, gene locus definitions, and mappability estimates. biocViews: ExperimentData Author: Ryan P. Welch [aut, cre, cph], Chee Lee [aut], Laura J. Scott [ths], Maureen A. Sartor [ths] Maintainer: Ryan P. Welch source.ver: src/contrib/chipenrich.data_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/3.0/chipenrich.data_0.99.4.zip mac.binary.ver: bin/macosx/contrib/3.0/chipenrich.data_0.99.4.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: ChIPXpressData Version: 1.0.1 Depends: bigmemory License: GPL (>=2) MD5sum: 4cbf009e318514b0096ac41dceb3e32e 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_1.0.1.tar.gz mac.binary.ver: bin/macosx/contrib/3.0/ChIPXpressData_1.0.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CLL Version: 1.2.15 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: LGPL MD5sum: f490b89426cba1e93dea0caebeee04c8 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_1.2.15.tar.gz win.binary.ver: bin/windows/contrib/3.0/CLL_1.2.15.zip mac.binary.ver: bin/macosx/contrib/3.0/CLL_1.2.15.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cMap2data Version: 0.99.4 Depends: R (>= 2.10) License: GPL-3 MD5sum: e022f1dad956411575ca11a36d1c06f6 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_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/3.0/cMap2data_0.99.4.zip mac.binary.ver: bin/macosx/contrib/3.0/cMap2data_0.99.4.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: 0.99.5 Depends: R (>= 2.10), cnvGSA License: LGPL MD5sum: 514a4b532d287a0661a7ba961e7fa8d0 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_0.99.5.tar.gz win.binary.ver: bin/windows/contrib/3.0/cnvGSAdata_0.99.5.zip mac.binary.ver: bin/macosx/contrib/3.0/cnvGSAdata_0.99.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: colonCA Version: 1.4.12 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: f846272be2b4c27812131418af5d3fe8 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_1.4.12.tar.gz win.binary.ver: bin/windows/contrib/3.0/colonCA_1.4.12.zip mac.binary.ver: bin/macosx/contrib/3.0/colonCA_1.4.12.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ConnectivityMap Version: 0.99.11 Depends: R (>= 2.15.1) Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 74786f55fd4859b146e3b5fcc344c3e1 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_0.99.11.tar.gz win.binary.ver: bin/windows/contrib/3.0/ConnectivityMap_0.99.11.zip mac.binary.ver: bin/macosx/contrib/3.0/ConnectivityMap_0.99.11.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: curatedBladderData Version: 0.99.2 Depends: R (>= 2.10.0), affy Suggests: BiocStyle, survival, xtable, sva, genefilter, logging License: Artistic-2.0 MD5sum: 7d016b8d0e68aae5bca967736fa2fafa NeedsCompilation: no Title: Bladder Cancer Gene Expression Analysis Description: The curatedBladderData package provides relevant functions and data for gene expression analysis in patients with bladder cancer. biocViews: ExperimentData, Cancer, Bladder, RNAExpressionData Author: Markus Riester Maintainer: Markus Riester source.ver: src/contrib/curatedBladderData_0.99.2.tar.gz win.binary.ver: bin/windows/contrib/3.0/curatedBladderData_0.99.2.zip mac.binary.ver: bin/macosx/contrib/3.0/curatedBladderData_0.99.2.tgz vignettes: vignettes/curatedBladderData/inst/doc/curatedBladderData_vignette.pdf vignetteTitles: curatedBladderData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: curatedOvarianData Version: 1.0.5 Depends: R (>= 2.10.0), affy Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, futile.logger, sva, xtable License: Artistic-2.0 MD5sum: 2e20ead88aea90a580dc115179e579b9 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_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/3.0/curatedOvarianData_1.0.5.zip mac.binary.ver: bin/macosx/contrib/3.0/curatedOvarianData_1.0.5.tgz vignettes: vignettes/curatedOvarianData/inst/doc/curatedOvarianData_vignette.pdf vignetteTitles: curatedOvarianData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: davidTiling Version: 1.2.19 Depends: R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db License: LGPL MD5sum: dc4965a3ab5a76fb96f70f7aead07c5a 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_1.2.19.tar.gz win.binary.ver: bin/windows/contrib/3.0/davidTiling_1.2.19.zip mac.binary.ver: bin/macosx/contrib/3.0/davidTiling_1.2.19.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: DeSousa2013 Version: 0.99.3 Depends: R (>= 2.15), Imports: affy, frma, frmaTools, hgu133plus2.db, hgu133plus2frmavecs, sva, rgl, ConsensusClusterPlus, cluster, siggenes, ROCR, pamr, survival, gplots, AnnotationDbi, Biobase License: Artistic-2.0 MD5sum: 9b8850b45d2bd953a6c9b3af1b5bc8dd NeedsCompilation: no Title: Poor prognosis colon cancer is defined by a molecularly distinct subtype and precursor lesion Description: This package reproduces the main pipeline to analyze the AMC-AJCCII-90 microarray data set in De Sousa et al. accepted by Nature Medicine in 2013. biocViews: Bioinformatics Author: Xin Wang Maintainer: Xin Wang source.ver: src/contrib/DeSousa2013_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/DeSousa2013_0.99.3.zip mac.binary.ver: bin/macosx/contrib/3.0/DeSousa2013_0.99.3.tgz vignettes: vignettes/DeSousa2013/inst/doc/DeSousa2013-Vignette.pdf vignetteTitles: Main vignette:Poor prognosis colon cancer is defined by a molecular distinct subtype and develops from serrated precursor lesions hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DeSousa2013/inst/doc/DeSousa2013-Vignette.R Package: DLBCL Version: 1.3.7 Depends: R(>= 2.11.0), Biobase License: GPL (>=2) MD5sum: 1759179b8e47f8cb826818ffe4478cec 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_1.3.7.tar.gz win.binary.ver: bin/windows/contrib/3.0/DLBCL_1.3.7.zip mac.binary.ver: bin/macosx/contrib/3.0/DLBCL_1.3.7.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: DonaPLLP2013 Version: 1.1.6 Depends: EBImage, parallel License: Artistic-2.0 MD5sum: 9f3ac5e75b0472bf6ff6664fc5a8a989 NeedsCompilation: no Title: Supplementary data package for Dona et al. (2013) containing example images and tables Description: An experiment data package associated with the publication Dona et al. (2013). Package contains runnable vignettes showing an example image segmentation for one posterior lateral line primordium, and also the data table and code used to analyze tissue-scale lifetime-ratio statistics. biocViews: ExperimentData Author: Erika Dona, Joseph D. Barry, Guillaume Valentin, Charlotte Quirin, Anton Khmelinskii, Andreas Kunze, Sevi Durdu, Lionel R. Newton, Ana Fernandez-Minan, Wolfgang Huber, Michael Knop, Darren Gilmour Maintainer: Joseph D. Barry source.ver: src/contrib/DonaPLLP2013_1.1.6.tar.gz win.binary.ver: bin/windows/contrib/3.0/DonaPLLP2013_1.1.6.zip mac.binary.ver: bin/macosx/contrib/3.0/DonaPLLP2013_1.1.6.tgz vignettes: vignettes/DonaPLLP2013/inst/doc/PLLPanalysis.pdf, vignettes/DonaPLLP2013/inst/doc/PLLPstatistics.pdf vignetteTitles: PLLP image analysis, PLLP tissue-scale ratio statistics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DonaPLLP2013/inst/doc/PLLPanalysis.R, vignettes/DonaPLLP2013/inst/doc/PLLPstatistics.R Package: DREAM4 Version: 0.99.18 Depends: R (>= 2.15.1), GenomicRanges Imports: BiocGenerics Suggests: RUnit, networkBMA License: GPL MD5sum: d05bca65e47bce5a9c98e8b3db1c78a0 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_0.99.18.tar.gz win.binary.ver: bin/windows/contrib/3.0/DREAM4_0.99.18.zip mac.binary.ver: bin/macosx/contrib/3.0/DREAM4_0.99.18.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: 0.1.9 Depends: R (>= 2.10.1), methods, Biobase (>= 2.5.5) Suggests: survival, chron License: Artistic-2.0 MD5sum: cf6a032ed27ee4d76bba339ef0c1f90a 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_0.1.9.tar.gz win.binary.ver: bin/windows/contrib/3.0/dressCheck_0.1.9.zip mac.binary.ver: bin/macosx/contrib/3.0/dressCheck_0.1.9.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: 0.99.6 Depends: R (>= 2.10) License: GPL-3 MD5sum: c1f7656166b1a6c1172aa3083a857d16 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_0.99.6.tar.gz win.binary.ver: bin/windows/contrib/3.0/DrugVsDiseasedata_0.99.6.zip mac.binary.ver: bin/macosx/contrib/3.0/DrugVsDiseasedata_0.99.6.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: 0.0.24 Depends: R (>= 2.15.0), utils, GenomicRanges, Biobase, GGBase License: Artistic-2.0 MD5sum: 5b2577226a57653d66226d5b55c8aa9c 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_0.0.24.tar.gz win.binary.ver: bin/windows/contrib/3.0/dsQTL_0.0.24.zip mac.binary.ver: bin/macosx/contrib/3.0/dsQTL_0.0.24.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: 0.99.3 Depends: R (>= 2.10) License: GPL-3 MD5sum: 3459de3e002dde406b0d2c1098eb3efe 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_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/DvDdata_0.99.3.zip mac.binary.ver: bin/macosx/contrib/3.0/DvDdata_0.99.3.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: 1.0.12 Depends: R (>= 1.4.1), marray, GEOquery Suggests: dyebias, convert, Biobase License: GPL-3 MD5sum: 1bb8c42982e41dc917422801158b582b 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_1.0.12.tar.gz win.binary.ver: bin/windows/contrib/3.0/dyebiasexamples_1.0.12.zip mac.binary.ver: bin/macosx/contrib/3.0/dyebiasexamples_1.0.12.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Package: EatonEtAlChIPseq Version: 0.0.10 Depends: GenomicRanges (>= 1.5.42), ShortRead, rtracklayer License: Artistic 2.0 MD5sum: a04a46d54c4affbd85baff62b796f188 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_0.0.10.tar.gz win.binary.ver: bin/windows/contrib/3.0/EatonEtAlChIPseq_0.0.10.zip mac.binary.ver: bin/macosx/contrib/3.0/EatonEtAlChIPseq_0.0.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ecoliLeucine Version: 1.2.11 Depends: R (>= 1.9.0), affy (>= 1.23.4), ecolicdf License: GPL (>= 2) MD5sum: 559080ac0bc26100ba560972b8cb8627 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_1.2.11.tar.gz win.binary.ver: bin/windows/contrib/3.0/ecoliLeucine_1.2.11.zip mac.binary.ver: bin/macosx/contrib/3.0/ecoliLeucine_1.2.11.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: encoDnaseI Version: 0.1.18 Depends: R (>= 2.15.0), methods, Biobase (>= 2.5.5), lattice, GGtools, GGBase Suggests: GGdata License: Artistic-2.0 MD5sum: e5efc703d448dabaea634ebdf35347bf 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_0.1.18.tar.gz win.binary.ver: bin/windows/contrib/3.0/encoDnaseI_0.1.18.zip mac.binary.ver: bin/macosx/contrib/3.0/encoDnaseI_0.1.18.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: 1.8.12 Depends: R (>= 1.9.0), affy (>= 1.4) Suggests: Biobase (>= 1.13.16), affy, vsn, hgu95av2.db, genefilter License: LGPL MD5sum: 5288ae0590015eae26a115804539c138 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_1.8.12.tar.gz win.binary.ver: bin/windows/contrib/3.0/estrogen_1.8.12.zip mac.binary.ver: bin/macosx/contrib/3.0/estrogen_1.8.12.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: 1.2.16 Depends: xcms License: LGPL MD5sum: 4fc07d62cd3852654c94be974e373a65 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_1.2.16.tar.gz win.binary.ver: bin/windows/contrib/3.0/faahKO_1.2.16.zip mac.binary.ver: bin/macosx/contrib/3.0/faahKO_1.2.16.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fabiaData Version: 1.0.3 Depends: R (>= 2.10.0), Biobase Imports: utils Suggests: fabia License: LGPL (>= 2.1) MD5sum: b0a68a6b6baf5d85deba8fd81c1e7928 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_1.0.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/fabiaData_1.0.3.zip mac.binary.ver: bin/macosx/contrib/3.0/fabiaData_1.0.3.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: 1.4.9 Depends: R (>= 1.9.1), prada (>= 1.0.5) License: GPL-2 MD5sum: 0f39017e44bab91423de52180142c2fc 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_1.4.9.tar.gz win.binary.ver: bin/windows/contrib/3.0/facsDorit_1.4.9.zip mac.binary.ver: bin/macosx/contrib/3.0/facsDorit_1.4.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: FANTOM3and4CAGE Version: 0.99.3 Depends: R (>= 2.15.0) License: GPL-3 MD5sum: 70c246506b9bd4aa03e976fd22b74541 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_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/FANTOM3and4CAGE_0.99.3.zip mac.binary.ver: bin/macosx/contrib/3.0/FANTOM3and4CAGE_0.99.3.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: 1.0.4 Depends: R (>= 2.10.0), lumi Suggests: genefilter, affy License: GPL (>2) MD5sum: 587363490513e4a351256727cfff562d 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_1.0.4.tar.gz win.binary.ver: bin/windows/contrib/3.0/ffpeExampleData_1.0.4.zip mac.binary.ver: bin/macosx/contrib/3.0/ffpeExampleData_1.0.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fibroEset Version: 1.4.10 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: 0aff08f83abab03a3615800c421877bf 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_1.4.10.tar.gz win.binary.ver: bin/windows/contrib/3.0/fibroEset_1.4.10.zip mac.binary.ver: bin/macosx/contrib/3.0/fibroEset_1.4.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Fletcher2013a Version: 0.99.3 Depends: R (>= 2.15), limma Imports: Biobase ,VennDiagram, gplots,grid License: GPL (>= 2) MD5sum: 3f02a82031239a144d67d5eaeff0c70d NeedsCompilation: no Title: Gene expression data from breast cancer cells under FGFR2 signalling perturbation. Description: The package Fletcher2013a contains time-course gene expression data from MCF-7 cells treated under different experimental systems in order to perturb FGFR2 signalling. The data comes from Fletcher et al. (to appear in Nature Communications) where further details about the background and the experimental design of the study can be found. biocViews: ExperimentData, RNAExpressionData, Cancer Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin Meyer. Maintainer: Mauro Castro source.ver: src/contrib/Fletcher2013a_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/Fletcher2013a_0.99.3.zip mac.binary.ver: bin/macosx/contrib/3.0/Fletcher2013a_0.99.3.tgz vignettes: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.pdf vignetteTitles: Main vignette:Fletcher2013a hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.R dependsOnMe: Fletcher2013b Package: Fletcher2013b Version: 0.99.3 Depends: R (>= 2.15), Fletcher2013a, RTN, biomaRt,VennDiagram,RedeR (>= 1.8.1) Imports: RColorBrewer, corrgram License: GPL (>= 2) MD5sum: bb1db8e3b12bff9cb72203b28ada12d2 NeedsCompilation: no Title: Master regulators of FGFR2 signalling and breast cancer risk. Description: This package reproduces the systems biology analysis for the package Fletcher2013a. biocViews: ExperimentData, RNAExpressionData, Cancer Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin Meyer. Maintainer: Mauro Castro source.ver: src/contrib/Fletcher2013b_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/Fletcher2013b_0.99.3.zip mac.binary.ver: bin/macosx/contrib/3.0/Fletcher2013b_0.99.3.tgz vignettes: vignettes/Fletcher2013b/inst/doc/Fletcher2013b.pdf vignetteTitles: Main vignette:Fletcher2013b hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Fletcher2013b/inst/doc/Fletcher2013b.R Package: flowFitExampleData Version: 0.99.2 Depends: R (>= 2.12.2), flowCore Imports: methods License: Artistic-2.0 MD5sum: 3281057278eeccb721f3c3676d7be437 NeedsCompilation: no Title: Example data for the flowFit package Description: Two dataset that can be used to run examples from the flowFit vignette and examples biocViews: FlowCytometry, CellBasedAssays, Bioinformatics Author: davide Rambaldi Maintainer: Davide Rambaldi source.ver: src/contrib/flowFitExampleData_0.99.2.tar.gz win.binary.ver: bin/windows/contrib/3.0/flowFitExampleData_0.99.2.zip mac.binary.ver: bin/macosx/contrib/3.0/flowFitExampleData_0.99.2.tgz vignettes: vignettes/flowFitExampleData/inst/doc/flowFitExampleData.pdf vignetteTitles: flowFitExampleData: example data for the beadarray package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowFitExampleData/inst/doc/flowFitExampleData.R Package: FlowSorted.Blood.450k Version: 1.0.2 Depends: R (>= 2.13.0), minfi (>= 1.8.0) License: Artistic-2.0 MD5sum: e8abe00a77c109a0adf20d239e1e578a NeedsCompilation: no Title: Illumina HumanMethylation data on sorted blood cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays, and an object depicting which CpGs on the array are associated with cell type. biocViews: IlluminaChip, Homo_sapiens, DNAMethylation Author: Andrew E Jaffe Maintainer: Andrew E Jaffe source.ver: src/contrib/FlowSorted.Blood.450k_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/3.0/FlowSorted.Blood.450k_1.0.2.zip mac.binary.ver: bin/macosx/contrib/3.0/FlowSorted.Blood.450k_1.0.2.tgz vignettes: vignettes/FlowSorted.Blood.450k/inst/doc/FlowSorted.Blood.450k.pdf vignetteTitles: FlowSorted Blood 450k Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: flowWorkspaceData Version: 2.0.0 License: GPL-2 MD5sum: 0d2bbd4a7a2f3909ceb7d1a4a7652603 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_2.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.0/flowWorkspaceData_2.0.0.zip mac.binary.ver: bin/macosx/contrib/3.0/flowWorkspaceData_2.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: frmaExampleData Version: 0.99.6 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: a9ba38f5e82b6bec037d0a7852f92fed 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_0.99.6.tar.gz win.binary.ver: bin/windows/contrib/3.0/frmaExampleData_0.99.6.zip mac.binary.ver: bin/macosx/contrib/3.0/frmaExampleData_0.99.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: FunciSNP.data Version: 0.99.4 Depends: R (>= 2.14.0) Imports: rtracklayer License: GPL-3 MD5sum: 7ff2f233504f3a43318de39f35e6f5d5 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_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/3.0/FunciSNP.data_0.99.4.zip mac.binary.ver: bin/macosx/contrib/3.0/FunciSNP.data_0.99.4.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: 2.0.3 Depends: R (>= 2.10) Suggests: gage, pathview, genefilter License: GPL (>=2.0) MD5sum: 13b30888fffa1db5391002315700bf4c 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_2.0.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/gageData_2.0.3.zip mac.binary.ver: bin/macosx/contrib/3.0/gageData_2.0.3.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: gaschYHS Version: 1.0.12 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: d602f242429b73437d7b719effcf3a86 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_1.0.12.tar.gz win.binary.ver: bin/windows/contrib/3.0/gaschYHS_1.0.12.zip mac.binary.ver: bin/macosx/contrib/3.0/gaschYHS_1.0.12.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gatingMLData Version: 2.1.4 Depends: R (>= 1.9.0) Suggests: flowUtils License: GPL MD5sum: d96e8773919234cc8bc92a52f7db22dc NeedsCompilation: no Title: Data and XML files for Gating-ML Test suite Description: Test data and XML files for testing compliance of the flowUtils/flowCore packages with Gating-ML (1.5 and 2.0) standards. biocViews: ExperimentData Author: J. Spidlen, N. Gopalakrishnan Maintainer: J. Spidlen source.ver: src/contrib/gatingMLData_2.1.4.tar.gz win.binary.ver: bin/windows/contrib/3.0/gatingMLData_2.1.4.zip mac.binary.ver: bin/macosx/contrib/3.0/gatingMLData_2.1.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gcspikelite Version: 1.0.10 Depends: R (>= 2.5.0) License: LGPL MD5sum: 9cbcbb23a19361a68c9a82bc91eed05e 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_1.0.10.tar.gz win.binary.ver: bin/windows/contrib/3.0/gcspikelite_1.0.10.zip mac.binary.ver: bin/macosx/contrib/3.0/gcspikelite_1.0.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: geneLenDataBase Version: 0.99.12 Depends: R (>= 2.11.0) Imports: utils, rtracklayer, GenomicFeatures (>= 1.3.15) License: LGPL (>= 2) MD5sum: 8db070eb56b2ea58a353ec093f9dcd64 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_0.99.12.tar.gz win.binary.ver: bin/windows/contrib/3.0/geneLenDataBase_0.99.12.zip mac.binary.ver: bin/macosx/contrib/3.0/geneLenDataBase_0.99.12.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GGdata Version: 1.0.22 Depends: R (>= 2.12.0), methods, Biobase (>= 2.5.5), GGBase, snpStats, illuminaHumanv1.db, AnnotationDbi Enhances: GGtools License: LGPL MD5sum: f9b54b8c6fe7747a0dfcd97c79cd6751 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_1.0.22.tar.gz win.binary.ver: bin/windows/contrib/3.0/GGdata_1.0.22.zip mac.binary.ver: bin/macosx/contrib/3.0/GGdata_1.0.22.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ggtut suggestsMe: encoDnaseI Package: ggtut Version: 0.0.46 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: 98f55f798ecb6b569aaa8dc6d38cb95c 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_0.0.46.tar.gz win.binary.ver: bin/windows/contrib/3.0/ggtut_0.0.46.zip mac.binary.ver: bin/macosx/contrib/3.0/ggtut_0.0.46.tgz vignettes: vignettes/ggtut/inst/doc/ hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: golubEsets Version: 1.4.14 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: LGPL MD5sum: e26e91bb436b5ee06f8ad41afd896973 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_1.4.14.tar.gz win.binary.ver: bin/windows/contrib/3.0/golubEsets_1.4.14.zip mac.binary.ver: bin/macosx/contrib/3.0/golubEsets_1.4.14.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GSVAdata Version: 0.99.11 Depends: R (>= 2.10), Biobase, GSEABase, hgu95a.db License: GPL (>= 2) MD5sum: 2356a011a172138f0a8d5ee3961fbe40 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_0.99.11.tar.gz win.binary.ver: bin/windows/contrib/3.0/GSVAdata_0.99.11.zip mac.binary.ver: bin/macosx/contrib/3.0/GSVAdata_0.99.11.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GWASdata Version: 1.0.10 Depends: GWASTools License: Artistic-2.0 MD5sum: a016e21583d4ea47e24b55310790ca15 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 , Adrienne Stilp source.ver: src/contrib/GWASdata_1.0.10.tar.gz win.binary.ver: bin/windows/contrib/3.0/GWASdata_1.0.10.zip mac.binary.ver: bin/macosx/contrib/3.0/GWASdata_1.0.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: h5vcData Version: 1.0.0 Suggests: h5vc License: GPL (>= 3) MD5sum: 116f02497d71d7f904603a6284f34076 NeedsCompilation: no Title: Example data for the h5vc package Description: This package contains the data used in the vignettes and examples of the 'h5vc' package biocViews: HighThroughputSequencingData Author: Paul Theodor Pyl Maintainer: Paul Theodor Pyl source.ver: src/contrib/h5vcData_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.0/h5vcData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.0/h5vcData_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap100khind Version: 1.4.3 Suggests: oligo License: GPL MD5sum: 97725e76ca78282dc1b246d4d43a4e70 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_1.4.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/hapmap100khind_1.4.3.zip mac.binary.ver: bin/macosx/contrib/3.0/hapmap100khind_1.4.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap100kxba Version: 1.4.3 Suggests: oligo License: GPL MD5sum: ab85b7f27e62c102492a6f1c22573673 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_1.4.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/hapmap100kxba_1.4.3.zip mac.binary.ver: bin/macosx/contrib/3.0/hapmap100kxba_1.4.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap500knsp Version: 1.4.3 Suggests: oligo License: GPL MD5sum: d0f73b5e1d057fdf560ebc4c5fdc3da8 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_1.4.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/hapmap500knsp_1.4.3.zip mac.binary.ver: bin/macosx/contrib/3.0/hapmap500knsp_1.4.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap500ksty Version: 1.4.3 Suggests: oligo License: GPL MD5sum: 064cfbd6821de4c0b9abae36d2cc35fc 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_1.4.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/hapmap500ksty_1.4.3.zip mac.binary.ver: bin/macosx/contrib/3.0/hapmap500ksty_1.4.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmapsnp5 Version: 1.4.3 Suggests: oligo License: GPL MD5sum: 6792d4af3f1a46faecdcc823e1728eff 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_1.4.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/hapmapsnp5_1.4.3.zip mac.binary.ver: bin/macosx/contrib/3.0/hapmapsnp5_1.4.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmapsnp6 Version: 1.4.3 Depends: R (>= 2.15) Suggests: oligo, oligoClasses License: GPL MD5sum: 3127bcc2dc6888ba6eb1a207b718e26c 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_1.4.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/hapmapsnp6_1.4.3.zip mac.binary.ver: bin/macosx/contrib/3.0/hapmapsnp6_1.4.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: harbChIP Version: 1.0.12 Depends: R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5), Biostrings Imports: methods, stats License: Artistic-2.0 MD5sum: d4358ca2e4c302ae199a75cb28ecdba2 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_1.0.12.tar.gz win.binary.ver: bin/windows/contrib/3.0/harbChIP_1.0.12.zip mac.binary.ver: bin/macosx/contrib/3.0/harbChIP_1.0.12.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: 1.2.1 Depends: R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots, limma, vcd, LSD,EBImage Suggests: BiocStyle License: Artistic-2.0 MD5sum: 2d7d3ba9ea766063a16a395382f6a0cd 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_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/3.0/HD2013SGI_1.2.1.zip mac.binary.ver: bin/macosx/contrib/3.0/HD2013SGI_1.2.1.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: 1.0.6 License: LGPL MD5sum: 1fb1ac9a91862a7775d8803a971108f4 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_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/3.0/HEEBOdata_1.0.6.zip mac.binary.ver: bin/macosx/contrib/3.0/HEEBOdata_1.0.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu133abarcodevecs Version: 1.0.7 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 1497c3d2567681447392008429f81359 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_1.0.7.tar.gz win.binary.ver: bin/windows/contrib/3.0/hgu133abarcodevecs_1.0.7.zip mac.binary.ver: bin/macosx/contrib/3.0/hgu133abarcodevecs_1.0.7.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu133plus2barcodevecs Version: 1.0.7 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: b39e1cbef547c8c6cf516e50097d5433 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_1.0.7.tar.gz win.binary.ver: bin/windows/contrib/3.0/hgu133plus2barcodevecs_1.0.7.zip mac.binary.ver: bin/macosx/contrib/3.0/hgu133plus2barcodevecs_1.0.7.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu2beta7 Version: 1.2.9 Depends: R (>= 2.0.0) License: Artistic-2.0 MD5sum: 821de2fffcbb78070a7d1faee211ffba 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_1.2.9.tar.gz win.binary.ver: bin/windows/contrib/3.0/hgu2beta7_1.2.9.zip mac.binary.ver: bin/macosx/contrib/3.0/hgu2beta7_1.2.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Hiiragi2013 Version: 0.99.14 Depends: R (>= 3.0.0), affy, Biobase, boot, clue, cluster, genefilter, geneplotter, gplots, grid, gtools, KEGGREST, lattice, latticeExtra, MASS, mouse4302.db, RColorBrewer, xtable Suggests: ArrayExpress, BiocStyle License: Artistic-2.0 MD5sum: d229f1de3b7946c0cca01b5d5cf0b155 NeedsCompilation: no Title: Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages Description: This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2013). doi:10.1038/ncb2881" biocViews: ExperimentData Author: Andrzej Oles, Wolfgang Huber Maintainer: Andrzej Oles source.ver: src/contrib/Hiiragi2013_0.99.14.tar.gz win.binary.ver: bin/windows/contrib/3.0/Hiiragi2013_0.99.14.zip mac.binary.ver: bin/macosx/contrib/3.0/Hiiragi2013_0.99.14.tgz vignettes: vignettes/Hiiragi2013/inst/doc/Hiiragi2013.pdf vignetteTitles: Hiiragi2013 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Hiiragi2013/inst/doc/Hiiragi2013.R Package: HIVcDNAvantWout03 Version: 1.2.10 License: GPL (>= 2) MD5sum: 6d9403c34487cd0d19419174ee8867ac 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_1.2.10.tar.gz win.binary.ver: bin/windows/contrib/3.0/HIVcDNAvantWout03_1.2.10.zip mac.binary.ver: bin/macosx/contrib/3.0/HIVcDNAvantWout03_1.2.10.tgz vignettes: vignettes/HIVcDNAvantWout03/inst/doc/ hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hmyriB36 Version: 0.99.18 Depends: R (>= 2.13.0), methods, Biobase (>= 2.5.5), GGBase Suggests: GGtools, illuminaHumanv1.db License: Artistic-2.0 MD5sum: 4f6aefbc258475258fa7057d29a3daf6 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_0.99.18.tar.gz win.binary.ver: bin/windows/contrib/3.0/hmyriB36_0.99.18.zip mac.binary.ver: bin/macosx/contrib/3.0/hmyriB36_0.99.18.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ggtut suggestsMe: ind1KG Package: humanStemCell Version: 0.2.9 Depends: Biobase (>= 2.5.5), hgu133plus2.db License: Artistic-2.0 MD5sum: 81d432622179f557ecbfb17f3f844465 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_0.2.9.tar.gz win.binary.ver: bin/windows/contrib/3.0/humanStemCell_0.2.9.zip mac.binary.ver: bin/macosx/contrib/3.0/humanStemCell_0.2.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Illumina450ProbeVariants.db Version: 0.99.3 Depends: R (>= 3.0.1) License: GPL-3 MD5sum: 46922baa45d5c3ceb8dd6b08a20d9ce8 NeedsCompilation: no Title: Annotation Package combining variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes Description: Includes details on variants for each probe on the 450k bead chip for each of the four populations (Asian, American, African and European)License: GPL-3 biocViews: AnnotationData, SNP, Homo_sapiens, IlluminaChip, GeneticVariability Author: Butcher, Lee Maintainer: Morris, Tiffany source.ver: src/contrib/Illumina450ProbeVariants.db_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/Illumina450ProbeVariants.db_0.99.3.zip mac.binary.ver: bin/macosx/contrib/3.0/Illumina450ProbeVariants.db_0.99.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: IlluminaDataTestFiles Version: 1.0.2 License: Artistic-2.0 MD5sum: 6f0c21cfd7f27543df7380ff89c1accd NeedsCompilation: no Title: Illumina microarray files (IDAT) for testing Description: Example data for Illumina microarray output files, for testing purposes biocViews: DataImport Author: Kasper Daniel Hansen, Mike L. Smith Maintainer: Kasper Daniel Hansen source.ver: src/contrib/IlluminaDataTestFiles_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/3.0/IlluminaDataTestFiles_1.0.2.zip mac.binary.ver: bin/macosx/contrib/3.0/IlluminaDataTestFiles_1.0.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ind1KG Version: 0.1.17 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: 11814793d4fc9d133962000a2444af80 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_0.1.17.tar.gz win.binary.ver: bin/windows/contrib/3.0/ind1KG_0.1.17.zip mac.binary.ver: bin/macosx/contrib/3.0/ind1KG_0.1.17.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: 0.99.9 License: GPL-2 MD5sum: 32436c22d7c96104828a598935cca5a8 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_0.99.9.tar.gz win.binary.ver: bin/windows/contrib/3.0/iontreeData_0.99.9.zip mac.binary.ver: bin/macosx/contrib/3.0/iontreeData_0.99.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ITALICSData Version: 2.0.8 Depends: R (>= 2.0.0) License: GPL MD5sum: 3433e92d14f88c1651ee3e3958dd3c67 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_2.0.8.tar.gz win.binary.ver: bin/windows/contrib/3.0/ITALICSData_2.0.8.zip mac.binary.ver: bin/macosx/contrib/3.0/ITALICSData_2.0.8.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Iyer517 Version: 1.4.14 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: e195b9a5fab156dad5246f3bcd959953 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_1.4.14.tar.gz win.binary.ver: bin/windows/contrib/3.0/Iyer517_1.4.14.zip mac.binary.ver: bin/macosx/contrib/3.0/Iyer517_1.4.14.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: JASPAR2014 Version: 0.99.3 Depends: R (>= 3.0.1), methods, Biostrings (>= 2.29.19) License: GPL-2 MD5sum: 33650f78ae6c1b523179f3c35d150cb6 NeedsCompilation: no Title: Data package for JASPAR Description: Data package for JASPAR 2014. To search this databases, please use the package TFBSTools. biocViews: ExperimentData, MotifAnnotation, GeneRegulation Author: Ge Tan Maintainer: Ge Tan URL: http://jaspardev.genereg.net/ source.ver: src/contrib/JASPAR2014_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/JASPAR2014_0.99.3.zip mac.binary.ver: bin/macosx/contrib/3.0/JASPAR2014_0.99.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: KEGGdzPathwaysGEO Version: 1.1.3 Depends: R (>= 2.13.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: a4ac4fcc8378f47258ffe35b4f05c127 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_1.1.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/KEGGdzPathwaysGEO_1.1.3.zip mac.binary.ver: bin/macosx/contrib/3.0/KEGGdzPathwaysGEO_1.1.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: kidpack Version: 1.5.14 Depends: R (>= 2.6.0), Biobase (>= 2.5.5) License: GPL-2 MD5sum: 7beea1bee848b23b14b4bde01d2144c9 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_1.5.14.tar.gz win.binary.ver: bin/windows/contrib/3.0/kidpack_1.5.14.zip mac.binary.ver: bin/macosx/contrib/3.0/kidpack_1.5.14.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: 0.99.24 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: 6d90a6e7573022689755e768c6c2d787 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_0.99.24.tar.gz win.binary.ver: bin/windows/contrib/3.0/leeBamViews_0.99.24.zip mac.binary.ver: bin/macosx/contrib/3.0/leeBamViews_0.99.24.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: 0.99.4 Depends: R (>= 2.10.1), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: edc9722357119028054d5bf35392b3c9 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_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/3.0/leukemiasEset_0.99.4.zip mac.binary.ver: bin/macosx/contrib/3.0/leukemiasEset_0.99.4.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: LiebermanAidenHiC2009 Version: 0.1.16 Depends: KernSmooth, IRanges License: LGPL MD5sum: c1826db2195f08981c4ff1cd35d563ae 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_0.1.16.tar.gz win.binary.ver: bin/windows/contrib/3.0/LiebermanAidenHiC2009_0.1.16.zip mac.binary.ver: bin/macosx/contrib/3.0/LiebermanAidenHiC2009_0.1.16.tgz vignettes: vignettes/LiebermanAidenHiC2009/inst/doc/LiebermanAidenHiC2009.pdf vignetteTitles: Exploration of HiC data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: lumiBarnes Version: 1.3.11 Depends: R (>= 2.0), Biobase (>= 2.5.5), lumi (>= 1.1.0) License: LGPL MD5sum: aba2893af7678cb5ff8506d9f3e91a47 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_1.3.11.tar.gz win.binary.ver: bin/windows/contrib/3.0/lumiBarnes_1.3.11.zip mac.binary.ver: bin/macosx/contrib/3.0/lumiBarnes_1.3.11.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: LungCancerACvsSCCGEO Version: 0.99.1 Depends: R (>= 2.15.0) License: GPL-2 MD5sum: f6db3cb89b6341e82d841053c2e25c40 NeedsCompilation: no Title: A lung cancer dataset that can be used with maPredictDSC package for developing outcome prediction models from Affymetrix CEL files. Description: This package contains 30 Affymetrix CEL files for 7 Adenocarcinoma (AC) and 8 Squamous cell carcinoma (SCC) lung cancer samples taken at random from 3 GEO datasets (GSE10245, GSE18842 and GSE2109) and other 15 samples from a dataset produced by the organizers of the IMPROVER Diagnostic Signature Challenge available from GEO (GSE43580). biocViews: Microarray, Classification Author: Adi Laurentiu Tarca Maintainer: Adi Laurentiu Tarca URL: http://bioinformaticsprb.med.wayne.edu/ source.ver: src/contrib/LungCancerACvsSCCGEO_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/3.0/LungCancerACvsSCCGEO_0.99.1.zip mac.binary.ver: bin/macosx/contrib/3.0/LungCancerACvsSCCGEO_0.99.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: LungCancerLines Version: 0.0.10 Imports: Rsamtools License: Artistic-2.0 MD5sum: e36a765f31892ac00942935498486993 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_0.0.10.tar.gz win.binary.ver: bin/windows/contrib/3.0/LungCancerLines_0.0.10.zip mac.binary.ver: bin/macosx/contrib/3.0/LungCancerLines_0.0.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: lungExpression Version: 0.0.16 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 951c97b832dd945170fccc953f94ca72 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_0.0.16.tar.gz win.binary.ver: bin/windows/contrib/3.0/lungExpression_0.0.16.zip mac.binary.ver: bin/macosx/contrib/3.0/lungExpression_0.0.16.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mammaPrintData Version: 0.99.9 Depends: R (>= 2.13.0) Suggests: Biobase, gdata, limma License: Artistic-2.0 MD5sum: 388c3874c57307014c2fe63f6d5a222f NeedsCompilation: no Title: RGLists from the Glas and Buyse breast cancer studies Description: Gene expression data for the two breast cancer cohorts published by Glas and Buyse in 2006 biocViews: ExperimentData, Cancer, RNAExpressionData Author: Luigi Marchionni Maintainer: Luigi Marchionni URL: http://luigimarchionni.org/breastTSP.html source.ver: src/contrib/mammaPrintData_0.99.9.tar.gz win.binary.ver: bin/windows/contrib/3.0/mammaPrintData_0.99.9.zip mac.binary.ver: bin/macosx/contrib/3.0/mammaPrintData_0.99.9.tgz vignettes: vignettes/mammaPrintData/inst/doc/mammaPrintData.pdf vignetteTitles: Working with the mammaPrintData package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mammaPrintData/inst/doc/mammaPrintData.R Package: maqcExpression4plex Version: 1.6.3 Suggests: oligo, pdInfoBuilder License: GPL MD5sum: d7c2ed823c3973cd484a46fdb87c07e0 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_1.6.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/maqcExpression4plex_1.6.3.zip mac.binary.ver: bin/macosx/contrib/3.0/maqcExpression4plex_1.6.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MAQCsubset Version: 1.0.29 Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), lumi, methods Suggests: genefilter, codelink License: Artistic-2.0 MD5sum: 3caa9dc6585b5c6323b58b5f5e445607 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_1.0.29.tar.gz win.binary.ver: bin/windows/contrib/3.0/MAQCsubset_1.0.29.zip mac.binary.ver: bin/macosx/contrib/3.0/MAQCsubset_1.0.29.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: 1.0.13 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 5988cc9094a02c33586038db4c500a85 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_1.0.13.tar.gz win.binary.ver: bin/windows/contrib/3.0/MAQCsubsetAFX_1.0.13.zip mac.binary.ver: bin/macosx/contrib/3.0/MAQCsubsetAFX_1.0.13.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: 1.0.12 Depends: R (>= 2.10), Biobase (>= 2.5.5), lumi License: Artistic-2.0 MD5sum: 1acb7214e054f39ea7058a2d3d11a992 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_1.0.12.tar.gz win.binary.ver: bin/windows/contrib/3.0/MAQCsubsetILM_1.0.12.zip mac.binary.ver: bin/macosx/contrib/3.0/MAQCsubsetILM_1.0.12.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: 0.99.5 Depends: R (>= 2.15.0) License: GPL (>= 2) MD5sum: f01de8a699735536b5beeb888902d970 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_0.99.5.tar.gz win.binary.ver: bin/windows/contrib/3.0/MEDIPSData_0.99.5.zip mac.binary.ver: bin/macosx/contrib/3.0/MEDIPSData_0.99.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MEEBOdata Version: 1.0.6 License: LGPL MD5sum: 282b01a51dcee2683a88e11918f11448 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_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/3.0/MEEBOdata_1.0.6.zip mac.binary.ver: bin/macosx/contrib/3.0/MEEBOdata_1.0.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: minfiData Version: 0.4.2 Depends: R (>= 2.13.0), minfi, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 License: Artistic-2.0 MD5sum: b2288193a9f3d286926acf3df1d3f45d 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_0.4.2.tar.gz win.binary.ver: bin/windows/contrib/3.0/minfiData_0.4.2.zip mac.binary.ver: bin/macosx/contrib/3.0/minfiData_0.4.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: miRNATarget Version: 1.1.2 Depends: R (>= 2.10), Biobase License: GPL MD5sum: baf9684a7f3a2d3ad65716d382ec7e2f 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_1.1.2.tar.gz win.binary.ver: bin/windows/contrib/3.0/miRNATarget_1.1.2.zip mac.binary.ver: bin/macosx/contrib/3.0/miRNATarget_1.1.2.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: mitoODEdata Version: 0.99.6 Depends: R (>= 2.14.0) License: LGPL MD5sum: 90dab78630cdd63dae70ccc3c0a33ba0 NeedsCompilation: no Title: Experimental data associated to the paper "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay" (submitted). Description: This package contains the experimental data (assay annotation, siRNA annotation, time-lapse cell counts) associated to the paper "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay" (submitted). The data ultimately come from the Mitocheck assay reported in "Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes" (Neumann, Walter et al, Nature 2010). biocViews: ExperimentData, TimeCourse, CellBasedAssays, Preprocessing Author: Gregoire Pau Maintainer: Gregoire Pau SystemRequirements: source.ver: src/contrib/mitoODEdata_0.99.6.tar.gz win.binary.ver: bin/windows/contrib/3.0/mitoODEdata_0.99.6.zip mac.binary.ver: bin/macosx/contrib/3.0/mitoODEdata_0.99.6.tgz vignettes: vignettes/mitoODEdata/inst/doc/mitoODEdata-introduction.pdf vignetteTitles: Mitoode data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mitoODEdata/inst/doc/mitoODEdata-introduction.R Package: MMDiffBamSubset Version: 0.99.4 Suggests: MMDiff License: LGPL MD5sum: aefe3b3c489b6649189419858d245d95 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_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/3.0/MMDiffBamSubset_0.99.4.zip mac.binary.ver: bin/macosx/contrib/3.0/MMDiffBamSubset_0.99.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mosaicsExample Version: 0.99.9 Depends: R (>= 2.11.1) License: GPL (>= 2) MD5sum: bf07974d1f5f568dc2f6a964c5302c5d 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_0.99.9.tar.gz win.binary.ver: bin/windows/contrib/3.0/mosaicsExample_0.99.9.zip mac.binary.ver: bin/macosx/contrib/3.0/mosaicsExample_0.99.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mouse4302barcodevecs Version: 1.0.7 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: e9aba0421fb858b13027d6aee91f495d 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_1.0.7.tar.gz win.binary.ver: bin/windows/contrib/3.0/mouse4302barcodevecs_1.0.7.zip mac.binary.ver: bin/macosx/contrib/3.0/mouse4302barcodevecs_1.0.7.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: msdata Version: 0.1.15 Suggests: xcms License: GPL (>= 2) MD5sum: dfe7a6f9422c9f5f7e92512efbee9bdf 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_0.1.15.tar.gz win.binary.ver: bin/windows/contrib/3.0/msdata_0.1.15.zip mac.binary.ver: bin/macosx/contrib/3.0/msdata_0.1.15.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics Package: Mulder2012 Version: 0.2.5 Depends: R (>= 2.14), org.Hs.eg.db, KEGG.db Imports: igraph, HTSanalyzeR, PANR, RedeR, pvclust, MASS Suggests: snow License: Artistic-2.0 MD5sum: 8af5e80d5837859b03378ac4f585429f 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_0.2.5.tar.gz win.binary.ver: bin/windows/contrib/3.0/Mulder2012_0.2.5.zip mac.binary.ver: bin/macosx/contrib/3.0/Mulder2012_0.2.5.tgz vignettes: vignettes/Mulder2012/inst/doc/Mulder2012-Vignette.pdf vignetteTitles: Main vignette:Posterior association network and enriched functional gene modules inferred from rich phenotypes of gene perturbations hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Mulder2012/inst/doc/Mulder2012-Vignette.R Package: mvoutData Version: 0.99.11 Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4), lumi License: Artistic-2.0 MD5sum: 68122f459ba3a997ddd870eb483e79e9 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_0.99.11.tar.gz win.binary.ver: bin/windows/contrib/3.0/mvoutData_0.99.11.zip mac.binary.ver: bin/macosx/contrib/3.0/mvoutData_0.99.11.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: NCIgraphData Version: 0.99.7 Depends: R (>= 2.10.0) Suggests: Rgraphviz License: GPL-3 MD5sum: 2c03778107d25ec96ed6e852031f4f9f 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_0.99.7.tar.gz win.binary.ver: bin/windows/contrib/3.0/NCIgraphData_0.99.7.zip mac.binary.ver: bin/macosx/contrib/3.0/NCIgraphData_0.99.7.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Neve2006 Version: 0.1.18 Depends: R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0), hgu133a.db, annotate License: Artistic-2.0 MD5sum: 2b4134ed3f63c097018d7a8fc212f335 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_0.1.18.tar.gz win.binary.ver: bin/windows/contrib/3.0/Neve2006_0.1.18.zip mac.binary.ver: bin/macosx/contrib/3.0/Neve2006_0.1.18.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: 0.99.8 Depends: DEXSeq, DESeq, R (>= 2.10) Suggests: GEOquery, SRAdb License: LGPL MD5sum: 304b0fceaee161b958e883bab6f69b94 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_0.99.8.tar.gz win.binary.ver: bin/windows/contrib/3.0/parathyroid_0.99.8.zip mac.binary.ver: bin/macosx/contrib/3.0/parathyroid_0.99.8.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: 1.0.4 Depends: GenomicRanges, R (>= 2.10) Suggests: Rsamtools, GEOquery, SRAdb, GenomicFeatures, BiocStyle License: LGPL MD5sum: 4fb71e9a8db917fb8a001d8810100d88 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. biocViews: ExperimentData, RNAseqData Author: Michael Love Maintainer: Michael Love source.ver: src/contrib/parathyroidSE_1.0.4.tar.gz win.binary.ver: bin/windows/contrib/3.0/parathyroidSE_1.0.4.zip mac.binary.ver: bin/macosx/contrib/3.0/parathyroidSE_1.0.4.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: 0.2.19 Suggests: locfit, edgeR, xtable, DEXSeq, DESeq License: LGPL MD5sum: b02c7992312fa31730260f9bb7c13b78 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_0.2.19.tar.gz win.binary.ver: bin/windows/contrib/3.0/pasilla_0.2.19.zip mac.binary.ver: bin/macosx/contrib/3.0/pasilla_0.2.19.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: 0.0.8 Suggests: pasilla License: LGPL MD5sum: 6808bd2267648317dcf34462f9dc2024 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_0.0.8.tar.gz win.binary.ver: bin/windows/contrib/3.0/pasillaBamSubset_0.0.8.zip mac.binary.ver: bin/macosx/contrib/3.0/pasillaBamSubset_0.0.8.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: PathNetData Version: 0.99.3 Depends: R (>= 1.14.0) License: GPL-3 MD5sum: c9390e0b9b5b81dfa41a35855b2f0827 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_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/PathNetData_0.99.3.zip mac.binary.ver: bin/macosx/contrib/3.0/PathNetData_0.99.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Hs.hg19 Version: 0.99.5 License: GPL (>= 2) MD5sum: 1210cacbec71230e92eaa0b4e66abfd2 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_0.99.5.tar.gz win.binary.ver: bin/windows/contrib/3.0/pcaGoPromoter.Hs.hg19_0.99.5.zip mac.binary.ver: bin/macosx/contrib/3.0/pcaGoPromoter.Hs.hg19_0.99.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Mm.mm9 Version: 0.99.5 License: GPL (>= 2) MD5sum: fb2241a1419c062136ae2d6897a79020 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_0.99.5.tar.gz win.binary.ver: bin/windows/contrib/3.0/pcaGoPromoter.Mm.mm9_0.99.5.zip mac.binary.ver: bin/macosx/contrib/3.0/pcaGoPromoter.Mm.mm9_0.99.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Rn.rn4 Version: 0.99.5 License: GPL (>= 2) MD5sum: 70b30f24205161ae6acf072ac54cba8f 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_0.99.5.tar.gz win.binary.ver: bin/windows/contrib/3.0/pcaGoPromoter.Rn.rn4_0.99.5.zip mac.binary.ver: bin/macosx/contrib/3.0/pcaGoPromoter.Rn.rn4_0.99.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pd.atdschip.tiling Version: 0.0.6 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: d4ab4f186f766ac749afc1bd7f071c82 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_0.0.6.tar.gz win.binary.ver: bin/windows/contrib/3.0/pd.atdschip.tiling_0.0.6.zip mac.binary.ver: bin/macosx/contrib/3.0/pd.atdschip.tiling_0.0.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ppiData Version: 0.1.24 Depends: graph Imports: AnnotationDbi Suggests: org.Sc.sgd.db, ppiStats License: Artistic-2.0 MD5sum: 49a24830969147a6db481dca452ace7d 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_0.1.24.tar.gz win.binary.ver: bin/windows/contrib/3.0/ppiData_0.1.24.zip mac.binary.ver: bin/macosx/contrib/3.0/ppiData_0.1.24.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: 0.99.5 Depends: R (>= 2.14.0) License: Artistic-2.0 MD5sum: a04e1070c0dabeabf5f530dfa4486887 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_0.99.5.tar.gz win.binary.ver: bin/windows/contrib/3.0/prebsdata_0.99.5.zip mac.binary.ver: bin/macosx/contrib/3.0/prebsdata_0.99.5.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: 0.2.8 Depends: R (>= 2.9.0), methods, PREDA, Biobase, affy, annotate, gahgu133plus2.db, gahgu133plus2cdf Suggests: hgu133plus2.db, hgu133plus2cdf License: Artistic-2.0 MD5sum: f8abd53f1c986b5adbba98dfc5bc1349 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_0.2.8.tar.gz win.binary.ver: bin/windows/contrib/3.0/PREDAsampledata_0.2.8.zip mac.binary.ver: bin/macosx/contrib/3.0/PREDAsampledata_0.2.8.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ProData Version: 1.0.9 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL MD5sum: a1be7030061fa781ad1da389d0821e0b 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_1.0.9.tar.gz win.binary.ver: bin/windows/contrib/3.0/ProData_1.0.9.zip mac.binary.ver: bin/macosx/contrib/3.0/ProData_1.0.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pRolocdata Version: 1.0.3 Depends: R (>= 2.15), MSnbase Suggests: pRoloc License: GPL-2 MD5sum: 19bf41aadf37d4c992f0e2060f169976 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_1.0.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/pRolocdata_1.0.3.zip mac.binary.ver: bin/macosx/contrib/3.0/pRolocdata_1.0.3.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: pumadata Version: 1.99.7 Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), puma License: LGPL MD5sum: b91d4efcfb07289d84c030781575aa5e 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_1.99.7.tar.gz win.binary.ver: bin/windows/contrib/3.0/pumadata_1.99.7.zip mac.binary.ver: bin/macosx/contrib/3.0/pumadata_1.99.7.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: 2.1.1 Depends: methods, PWMEnrich License: GPL-3 MD5sum: cb453def2ee0fa49aa1853113fb4d3e1 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_2.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.0/PWMEnrich.Dmelanogaster.background_2.1.1.zip mac.binary.ver: bin/macosx/contrib/3.0/PWMEnrich.Dmelanogaster.background_2.1.1.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: PWMEnrich.Hsapiens.background Version: 0.99.1 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: e39e4cc8374c1a46646dcb98a8de32b7 NeedsCompilation: no Title: H. sapiens background for PWMEnrich Description: PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs. biocViews: AnnotationData, Organism, Homo_sapiens Author: Robert Stojnic Maintainer: Robert Stojnic source.ver: src/contrib/PWMEnrich.Hsapiens.background_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/3.0/PWMEnrich.Hsapiens.background_0.99.1.zip mac.binary.ver: bin/macosx/contrib/3.0/PWMEnrich.Hsapiens.background_0.99.1.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: PWMEnrich.Mmusculus.background Version: 0.99.1 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: f5d8f77b7d4599ba4b7704589767d615 NeedsCompilation: no Title: M. musculus background for PWMEnrich Description: PWMEnrich pre-compiled background objects for M.musculus (mouse) and MotifDb M. musculus motifs. biocViews: AnnotationData, Organism, Mus_musculus Author: Robert Stojnic Maintainer: Robert Stojnic source.ver: src/contrib/PWMEnrich.Mmusculus.background_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/3.0/PWMEnrich.Mmusculus.background_0.99.1.zip mac.binary.ver: bin/macosx/contrib/3.0/PWMEnrich.Mmusculus.background_0.99.1.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: RforProteomics Version: 1.0.14 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: f32b6e955080644c763565be65f6f628 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/ VignetteBuilder: knitr source.ver: src/contrib/RforProteomics_1.0.14.tar.gz win.binary.ver: bin/windows/contrib/3.0/RforProteomics_1.0.14.zip mac.binary.ver: bin/macosx/contrib/3.0/RforProteomics_1.0.14.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: 1.0.4 Depends: R (>= 2.10.0) Suggests: genefilter, Biobase, hgu133plus2.db License: Artistic-2.0 MD5sum: 3fc726e00be8c4c13fd4e37ac4b4dad0 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_1.0.4.tar.gz win.binary.ver: bin/windows/contrib/3.0/rheumaticConditionWOLLBOLD_1.0.4.zip mac.binary.ver: bin/macosx/contrib/3.0/rheumaticConditionWOLLBOLD_1.0.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RIPSeekerData Version: 0.99.3 Depends: RIPSeeker License: GPL-2 MD5sum: 4af08fdc14f054fd146f4d71e1aaf8d2 NeedsCompilation: no Title: test data for RIPSeeker Description: The RIP-seq data in BAM format are the test data for the package RIPSeeker. The data correspond to two RIP-seq experiments, namely PRC2 and CCNT1. Raw data from NCBI Gene Expression Omnibus under accession numbers GSE17064 for PRC2 and in-house for CCNT1. biocViews: ExperimentData, RIPseqData Author: Yue Li Maintainer: Alejandro Reyes source.ver: src/contrib/RIPSeekerData_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/RIPSeekerData_0.99.3.zip mac.binary.ver: bin/macosx/contrib/3.0/RIPSeekerData_0.99.3.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: 0.99.3 Suggests: RMassBank License: Artistic-2.0 MD5sum: 7001f89b190a24573391d3f28086fb85 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_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/RMassBankData_0.99.3.zip mac.binary.ver: bin/macosx/contrib/3.0/RMassBankData_0.99.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RNAinteractMAPK Version: 1.0.13 Depends: R (>= 2.12.0), methods, fields, sparseLDA, RNAinteract Imports: grid, gdata, MASS, genefilter Suggests: qvalue, lattice License: Artistic-2.0 MD5sum: e9caad15ff4fd3c886d6ef7e6fcf2b61 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_1.0.13.tar.gz win.binary.ver: bin/windows/contrib/3.0/RNAinteractMAPK_1.0.13.zip mac.binary.ver: bin/macosx/contrib/3.0/RNAinteractMAPK_1.0.13.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: 0.1.5 Depends: RNAseqData.HNRNPC.bam.chr14 Imports: RNAseqData.HNRNPC.bam.chr14 License: LGPL MD5sum: 6a2191851c9d58675b3debc619a21731 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_0.1.5.tar.gz win.binary.ver: bin/windows/contrib/3.0/RNAseqData.HeLa.bam.chr14_0.1.5.zip mac.binary.ver: bin/macosx/contrib/3.0/RNAseqData.HeLa.bam.chr14_0.1.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RNAseqData.HNRNPC.bam.chr14 Version: 0.1.4 Suggests: Rsamtools, BiocInstaller License: LGPL MD5sum: 3db68006d389fb17c03621a8dddee8c3 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_0.1.4.tar.gz win.binary.ver: bin/windows/contrib/3.0/RNAseqData.HNRNPC.bam.chr14_0.1.4.zip mac.binary.ver: bin/macosx/contrib/3.0/RNAseqData.HNRNPC.bam.chr14_0.1.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: RNAseqData.HeLa.bam.chr14 importsMe: RNAseqData.HeLa.bam.chr14 Package: RnaSeqTutorial Version: 0.0.14 Depends: R (>= 2.15.0), methods, easyRNASeq Suggests: Rsamtools, ShortRead, BSgenome.Dmelanogaster.UCSC.dm3, GenomicRanges, biomaRt, genomeIntervals License: Artistic-2.0 MD5sum: 1a98445e36699e0946a5646bc20cacce 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_0.0.14.tar.gz win.binary.ver: bin/windows/contrib/3.0/RnaSeqTutorial_0.0.14.zip mac.binary.ver: bin/macosx/contrib/3.0/RnaSeqTutorial_0.0.14.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: seqCNA.annot Version: 0.99.1 Depends: R (>= 2.10) License: GPL-3 MD5sum: 99915cc0001c409d2c807590f9f4bde7 NeedsCompilation: no Title: Annotation for the copy number analysis of deep sequencing cancer data with seqCNA Description: Provides annotation on GC content, mappability and genomic features for various genomes biocViews: Bioinformatics, CopyNumberVariants, Genetics, HighThroughputSequencing Author: David Mosen-Ansorena Maintainer: David Mosen-Ansorena source.ver: src/contrib/seqCNA.annot_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/3.0/seqCNA.annot_0.99.1.zip mac.binary.ver: bin/macosx/contrib/3.0/seqCNA.annot_0.99.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: serumStimulation Version: 0.99.5 Depends: R (>= 2.10) License: GPL (>= 2) MD5sum: 66ac6278fe1415c47c6e5f6c2fe09937 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_0.99.5.tar.gz win.binary.ver: bin/windows/contrib/3.0/serumStimulation_0.99.5.zip mac.binary.ver: bin/macosx/contrib/3.0/serumStimulation_0.99.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: seventyGeneData Version: 0.99.8 Depends: R (>= 2.13.0) Suggests: Biobase, gdata, limma, breastCancerNKI License: Artistic-2.0 MD5sum: b461eed72f0c65f0a8c046aae99916ec NeedsCompilation: no Title: ExpressionSets from the van't Veer and Van de Vijver breast cancer studies Description: Gene expression data for the two breast cancer cohorts published by van't Veer and Van de Vijver in 2002 biocViews: ExperimentData, Cancer, RNAExpressionData Author: Luigi Marchionni Maintainer: Luigi Marchionni URL: http://luigimarchionni.org/breastTSP.html source.ver: src/contrib/seventyGeneData_0.99.8.tar.gz win.binary.ver: bin/windows/contrib/3.0/seventyGeneData_0.99.8.zip mac.binary.ver: bin/macosx/contrib/3.0/seventyGeneData_0.99.8.tgz vignettes: vignettes/seventyGeneData/inst/doc/seventyGeneData.pdf vignetteTitles: Working with the seventyGeneData package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/seventyGeneData/inst/doc/seventyGeneData.R Package: simpIntLists Version: 0.99.6 License: GPL (>= 2) MD5sum: ab06773bc63f7661dd36dd5f04e2a0d0 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_0.99.6.tar.gz win.binary.ver: bin/windows/contrib/3.0/simpIntLists_0.99.6.zip mac.binary.ver: bin/macosx/contrib/3.0/simpIntLists_0.99.6.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: 1.8.8 Depends: R (>= 2.4.0), graph Suggests: Rgraphviz License: LGPL MD5sum: 3ffc63a4f5656f2d46d7a39f686a3d99 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_1.8.8.tar.gz win.binary.ver: bin/windows/contrib/3.0/SNAData_1.8.8.zip mac.binary.ver: bin/macosx/contrib/3.0/SNAData_1.8.8.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: 0.99.2 Depends: R (>= 2.6.0) Suggests: ALL, hgu95av2.db, SNAGEE License: Artistic-2.0 MD5sum: e5598724fa5652b37db8a07e49145ecf 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_0.99.2.tar.gz win.binary.ver: bin/windows/contrib/3.0/SNAGEEdata_0.99.2.zip mac.binary.ver: bin/macosx/contrib/3.0/SNAGEEdata_0.99.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SomatiCAData Version: 1.1.1 Depends: R (>= 2.14) License: Artistic-2.0 MD5sum: 2c6c8be53643cf66da1ffb90c470b000 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.0/SomatiCAData_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.0/SomatiCAData_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SomaticCancerAlterations Version: 0.99.20 Depends: R (>= 3.0.0) Imports: GenomicRanges, exomeCopy, stringr, IRanges Suggests: testthat, ggbio, ggplot2, BiocStyle, knitr License: GPL-3 MD5sum: 809bc3fc45ec2d478f3709bccb174fd2 NeedsCompilation: no Title: Somatic Cancer Alterations Description: Collection of somatic cancer alteration datasets biocViews: ExperimentData, Cancer Author: Julian Gehring (EMBL Heidelberg) Maintainer: Julian Gehring VignetteBuilder: knitr source.ver: src/contrib/SomaticCancerAlterations_0.99.20.tar.gz win.binary.ver: bin/windows/contrib/3.0/SomaticCancerAlterations_0.99.20.zip mac.binary.ver: bin/macosx/contrib/3.0/SomaticCancerAlterations_0.99.20.tgz vignettes: vignettes/SomaticCancerAlterations/inst/doc/SomaticCancerAlterations-pdf.pdf vignetteTitles: SomaticCancerAlterations - PDF hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SomaticCancerAlterations/inst/doc/SomaticCancerAlterations-html.R, vignettes/SomaticCancerAlterations/inst/doc/SomaticCancerAlterations-pdf.R htmlDocs: vignettes/SomaticCancerAlterations/inst/doc/SomaticCancerAlterations-html.html htmlTitles: "SomaticCancerAlterations - HTML" Package: SpikeIn Version: 1.4.11 Depends: R (>= 1.6), affy (>= 1.23.4) License: Artistic-2.0 MD5sum: b0d498c71f9748f62298ef52d21a7194 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_1.4.11.tar.gz win.binary.ver: bin/windows/contrib/3.0/SpikeIn_1.4.11.zip mac.binary.ver: bin/macosx/contrib/3.0/SpikeIn_1.4.11.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SpikeInSubset Version: 1.2.14 Depends: R (>= 2.4.0), Biobase (>= 2.5.5), affy (>= 1.23.4) License: LGPL MD5sum: 9a952239bc5542a0ba623c7890589d63 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_1.2.14.tar.gz win.binary.ver: bin/windows/contrib/3.0/SpikeInSubset_1.2.14.zip mac.binary.ver: bin/macosx/contrib/3.0/SpikeInSubset_1.2.14.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: stemHypoxia Version: 0.99.4 Depends: R (>= 2.14.1) License: GPL (>=2) MD5sum: 51f8cbc8ecb5f693ccd2ab6cacc9fe9e 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_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/3.0/stemHypoxia_0.99.4.zip mac.binary.ver: bin/macosx/contrib/3.0/stemHypoxia_0.99.4.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: stjudem Version: 1.2.10 Depends: R (>= 2.10), utils License: LGPL (>= 2) MD5sum: 8e2e8f3bcd571dca255b35a91cce8bbc 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_1.2.10.tar.gz win.binary.ver: bin/windows/contrib/3.0/stjudem_1.2.10.zip mac.binary.ver: bin/macosx/contrib/3.0/stjudem_1.2.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: synapterdata Version: 1.0.1 Depends: R (>= 2.10), synapter (>= 0.99.6) License: GPL-2 MD5sum: aa73a73941cc9954fe6dd32fe57fbcc4 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_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/3.0/synapterdata_1.0.1.zip mac.binary.ver: bin/macosx/contrib/3.0/synapterdata_1.0.1.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics Package: TargetScoreData Version: 0.99.6 Suggests: TargetScore, gplots License: GPL-2 MD5sum: 3a79c1bee9dad2191259f89131092c2c NeedsCompilation: no Title: TargetScoreData Description: Precompiled and processed miRNA-overexpression fold-changes from 84 Gene Expression Omnibus (GEO) series corresponding to 6 platforms, 77 human cells or tissues, and 113 distinct miRNAs. Accompanied with the data, we also included in this package the sequence feature scores from TargetScanHuman 6.1 including the context+ score and the probabilities of conserved targeting for each miRNA-mRNA interaction. Thus, the user can use these static sequence-based scores together with user-supplied tissue/cell-specific fold-change due to miRNA overexpression to predict miRNA targets using the package TargetScore (download separately) biocViews: ExperimentData,RNAExpressionData,miRNAoverexpression Author: Yue Li Maintainer: Yue Li source.ver: src/contrib/TargetScoreData_0.99.6.tar.gz win.binary.ver: bin/windows/contrib/3.0/TargetScoreData_0.99.6.zip mac.binary.ver: bin/macosx/contrib/3.0/TargetScoreData_0.99.6.tgz vignettes: vignettes/TargetScoreData/inst/doc/TargetScoreData.pdf vignetteTitles: Processed human microRNA-overexpression data from GEO,, and sequence information from TargetScan,, and targetScore from TargetScore hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TargetScoreData/inst/doc/TargetScoreData.R Package: TargetSearchData Version: 1.0.10 Depends: TargetSearch License: GPL (>= 2) MD5sum: 5329ca768df31ffe0178656d7b75c4fc 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_1.0.10.tar.gz win.binary.ver: bin/windows/contrib/3.0/TargetSearchData_1.0.10.zip mac.binary.ver: bin/macosx/contrib/3.0/TargetSearchData_1.0.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: TBX20BamSubset Version: 0.99.4 Depends: Rsamtools (>= 1.9.8) Imports: xtable License: LGPL MD5sum: ac7ef6887d4bf49b80432b4e98663f17 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_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/3.0/TBX20BamSubset_0.99.4.zip mac.binary.ver: bin/macosx/contrib/3.0/TBX20BamSubset_0.99.4.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: 0.99.5 License: GPL-2 MD5sum: d06f1b09574bc46845bce14446374573 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_0.99.5.tar.gz win.binary.ver: bin/windows/contrib/3.0/TCGAMethylation450k_0.99.5.zip mac.binary.ver: bin/macosx/contrib/3.0/TCGAMethylation450k_0.99.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: tinesath1cdf Version: 1.0.10 License: Artistic-2.0 MD5sum: e833fbe1d11ad21fe074b1f83b00ae72 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_1.0.10.tar.gz win.binary.ver: bin/windows/contrib/3.0/tinesath1cdf_1.0.10.zip mac.binary.ver: bin/macosx/contrib/3.0/tinesath1cdf_1.0.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: XhybCasneuf Package: tinesath1probe Version: 1.0.10 Depends: R (>= 1.6), AnnotationDbi (>= 1.11.9) License: LGPL MD5sum: 90221a3875ee1bb7b29ae29adeb2ed01 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_1.0.10.tar.gz win.binary.ver: bin/windows/contrib/3.0/tinesath1probe_1.0.10.zip mac.binary.ver: bin/macosx/contrib/3.0/tinesath1probe_1.0.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: tweeDEseqCountData Version: 1.0.10 Depends: Biobase, R (>= 2.10) License: GPL (>=2) MD5sum: 3b91156fd23d173647a49f00f42fc064 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_1.0.10.tar.gz win.binary.ver: bin/windows/contrib/3.0/tweeDEseqCountData_1.0.10.zip mac.binary.ver: bin/macosx/contrib/3.0/tweeDEseqCountData_1.0.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: waveTilingData Version: 0.99.3 Depends: R (>= 2.14.0) License: GPL (>= 2) MD5sum: 7cc0f6f1e90e286cd2c8e410f1b6fe41 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_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/3.0/waveTilingData_0.99.3.zip mac.binary.ver: bin/macosx/contrib/3.0/waveTilingData_0.99.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: XhybCasneuf Version: 1.0.13 Depends: R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf , RColorBrewer , methods, grid License: Artistic-2.0 MD5sum: 8868166873ae9bdfba41b937df1a64dd 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_1.0.13.tar.gz win.binary.ver: bin/windows/contrib/3.0/XhybCasneuf_1.0.13.zip mac.binary.ver: bin/macosx/contrib/3.0/XhybCasneuf_1.0.13.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: 1.2.20 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 8ff464f07a4b5d423ca00dfb2c4ce570 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_1.2.20.tar.gz win.binary.ver: bin/windows/contrib/3.0/yeastCC_1.2.20.zip mac.binary.ver: bin/macosx/contrib/3.0/yeastCC_1.2.20.tgz vignettes: vignettes/yeastCC/inst/doc/ hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastExpData Version: 0.9.24 Depends: R (>= 2.4), graph (>= 1.9.26) Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db License: GPL MD5sum: 61bbf47c9628f70004cf5a09c04f1b70 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_0.9.24.tar.gz win.binary.ver: bin/windows/contrib/3.0/yeastExpData_0.9.24.zip mac.binary.ver: bin/macosx/contrib/3.0/yeastExpData_0.9.24.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: 0.1.11 License: Artistic-2.0 MD5sum: 659445420aa573e84a136920fc451f2a 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_0.1.11.tar.gz win.binary.ver: bin/windows/contrib/3.0/yeastGSData_0.1.11.zip mac.binary.ver: bin/macosx/contrib/3.0/yeastGSData_0.1.11.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastNagalakshmi Version: 0.99.7 License: Artistic-2.0 MD5sum: 731634844aff117a3cc8a9c7043f9ac9 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_0.99.7.tar.gz win.binary.ver: bin/windows/contrib/3.0/yeastNagalakshmi_0.99.7.zip mac.binary.ver: bin/macosx/contrib/3.0/yeastNagalakshmi_0.99.7.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastRNASeq Version: 0.0.10 Depends: R (>= 2.4) Suggests: Biobase, ShortRead, IRanges License: GPL MD5sum: 1f504ce3e7bfd55e6bd587f7adc2495e 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_0.0.10.tar.gz win.binary.ver: bin/windows/contrib/3.0/yeastRNASeq_0.0.10.zip mac.binary.ver: bin/macosx/contrib/3.0/yeastRNASeq_0.0.10.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 Package: yri1kgv Version: 0.5.2 Depends: GGBase Imports: Biobase License: Artistic-2.0 MD5sum: 35ea4970557825d2dfc3f67e6bb12908 NeedsCompilation: no Title: expression + genotype on 79 unrelated YRI individuals Description: expression + genotype on 79 unrelated YRI individuals Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/yri1kgv_0.5.2.tar.gz win.binary.ver: bin/windows/contrib/3.0/yri1kgv_0.5.2.zip mac.binary.ver: bin/macosx/contrib/3.0/yri1kgv_0.5.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE