Package: affycompData Version: 1.2.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp License: GPL (>= 2) MD5sum: 97fae30c7164fcaf5951e53e9b4a2d84 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/affycompData_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/affycompData_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/affycompData_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: affydata Version: 1.12.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Imports: methods Suggests: hgu95av2cdf, hgu133acdf License: GPL (>= 2) MD5sum: 1a20c4d634a59d6fa915d8ffb16f10d6 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_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/affydata_1.12.0.zip mac.binary.ver: bin/macosx/contrib/3.1/affydata_1.12.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/affydata_1.12.0.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: Affyhgu133A2Expr Version: 1.0.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 453e2fe06ffd92eb7528696eed820404 NeedsCompilation: no Title: Affymetrix Human Genome U133A 2.0 Array (GPL571) Expression Data Package Description: Contains pre-built human (GPL571) databases of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: AffymetrixChIP, Homo_sapiens Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji source.ver: src/contrib/Affyhgu133A2Expr_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/Affyhgu133A2Expr_0.99.0.zip mac.binary.ver: bin/macosx/contrib/3.1/Affyhgu133A2Expr_0.99.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Affyhgu133A2Expr_0.99.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Affyhgu133aExpr Version: 1.2.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 6cabba175196df5af9bf490cf6eaef26 NeedsCompilation: no Title: Affymetrix Human hgu133a Array (GPL96) Expression Data Package Description: Contains pre-built human (GPL96) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: AffymetrixChIP, Homo_sapiens Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji source.ver: src/contrib/Affyhgu133aExpr_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/Affyhgu133aExpr_0.99.0.zip mac.binary.ver: bin/macosx/contrib/3.1/Affyhgu133aExpr_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Affyhgu133aExpr_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Affyhgu133Plus2Expr Version: 1.0.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 7e755a7f191c9bd1e99c60bc7d6a3188 NeedsCompilation: no Title: Affyhgu133Plus2Expr (GPL570) Expression Data Package Description: Contains pre-built human (GPL570) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: AffymetrixChIP, Homo_sapiens Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji source.ver: src/contrib/Affyhgu133Plus2Expr_1.0.0.tar.gz mac.binary.ver: bin/macosx/contrib/3.1/Affyhgu133Plus2Expr_0.99.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Affyhgu133Plus2Expr_0.99.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: AffymetrixDataTestFiles Version: 0.2.0 Depends: R (>= 2.5.0) License: LGPL-2.1 MD5sum: 5876d9d70fb2ed673bfacb81ae7457e8 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/AffymetrixDataTestFiles_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/AffymetrixDataTestFiles_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/AffymetrixDataTestFiles_0.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Affymoe4302Expr Version: 1.2.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 1a78301d569cf783b94b2626a43ddc9e NeedsCompilation: no Title: Affymetrix Mouse Genome 430 2.0 Array (GPL1261) Expression Data Package Description: Contains pre-built mouse (GPL1261) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: AffymetrixChIP, Mus_musculus Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji source.ver: src/contrib/Affymoe4302Expr_1.2.0.tar.gz mac.binary.ver: bin/macosx/contrib/3.1/Affymoe4302Expr_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Affymoe4302Expr_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Affymoe430Expr Version: 0.99.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 5691394e88fd08cf5e7d0c4d04d93522 NeedsCompilation: no Title: Affymetrix Mouse 430 2.0 Array (GPL1261) Expression Data Package Description: Contains pre-built mouse (GPL1261) databases of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently using fRMA. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: AffymetrixChIP, Mus_musculus Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji source.ver: src/contrib/Affymoe430Expr_0.99.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ALL Version: 1.6.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Suggests: rpart License: Artistic-2.0 MD5sum: 242cf4853bab8358755ee3c506b7ef6f 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_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/ALL_1.6.0.zip mac.binary.ver: bin/macosx/contrib/3.1/ALL_1.6.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ALL_1.6.0.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: 1.4.0 Depends: R (>= 2.10), affy (>= 1.23.4) License: GPL-2 MD5sum: 2d0ae78dfe3f42e4ac2cf6a9fe3c487d 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_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/ALLMLL_1.4.0.zip mac.binary.ver: bin/macosx/contrib/3.1/ALLMLL_1.4.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ALLMLL_1.4.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: AmpAffyExample Version: 1.4.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Suggests: hgu133acdf License: LGPL (>= 2) MD5sum: eb1f378f44ffd9ec9dce97f2d43dc269 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_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/AmpAffyExample_1.4.0.zip mac.binary.ver: bin/macosx/contrib/3.1/AmpAffyExample_1.4.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/AmpAffyExample_1.4.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: antiProfilesData Version: 1.0.0 Depends: Biobase, Suggests: frma, GEOquery, GEOmetadb License: Artistic-2.0 MD5sum: decbd7709cee033e315df041300eb4b3 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/antiProfilesData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/antiProfilesData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/antiProfilesData_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ARRmData Version: 1.0.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: de8ec31c23911211dfc82e26d5ce9e31 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/ARRmData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/ARRmData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ARRmData_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bcellViper Version: 1.0.0 Depends: R(>= 2.14.0), Biobase, methods License: GPL (>=2) MD5sum: 1151d250eb517a49313a1655e41c96bc NeedsCompilation: no Title: Human B-cell transcriptional interactome and normal human B-cell expression data Description: This package provides a human B-cell context-specific transcriptional regulatory network and a human normal B-cells dataset for the examples in package viper. biocViews: ExperimentData, Cancer Author: Mariano Javier Alvarez Maintainer: Mariano Javier Alvarez source.ver: src/contrib/bcellViper_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/bcellViper_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/bcellViper_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/bcellViper_1.0.0.tgz vignettes: vignettes/bcellViper/inst/doc/bcellViper.pdf vignetteTitles: Using bcellViper hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bcellViper/inst/doc/bcellViper.R Package: beadarrayExampleData Version: 1.2.0 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>= 2.0.0) License: GPL-2 MD5sum: aa7be71437f00166cfae27affa1f0f2e 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/beadarrayExampleData_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/beadarrayExampleData_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/beadarrayExampleData_1.2.0.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: 1.2.0 Imports: beadarray (>= 2.3.18), limma, GEOquery Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db License: GPL-2 MD5sum: caeb57a68bb77e8023c451d0f16b6417 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/BeadArrayUseCases_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/BeadArrayUseCases_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/BeadArrayUseCases_1.2.0.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: 1.2.0 Depends: R (>= 2.4.0), marray License: LGPL MD5sum: 197b601c293bf88abd43e5272d36c224 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/beta7_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/beta7_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/beta7_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bladderbatch Version: 1.2.0 Depends: Biobase License: Artistic-2.0 MD5sum: 8c5f8f7f5418ab294cea8ccaced36807 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/bladderbatch_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/bladderbatch_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/bladderbatch_1.2.0.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: 1.2.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 621a172aff3316b44f65ff1c4b234282 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/breastCancerMAINZ_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/breastCancerMAINZ_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/breastCancerMAINZ_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerNKI Version: 1.2.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 54870d703b149dceb108627ada301009 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/breastCancerNKI_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/breastCancerNKI_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/breastCancerNKI_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: seventyGeneData Package: breastCancerTRANSBIG Version: 1.2.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 56aab011cfec1956372b08d57eb93f62 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/breastCancerTRANSBIG_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/breastCancerTRANSBIG_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/breastCancerTRANSBIG_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerUNT Version: 1.2.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 7b32fff2f518009272a2630f04071a1e 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/breastCancerUNT_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/breastCancerUNT_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/breastCancerUNT_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerUPP Version: 1.2.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 58744406654c027852459a1313f08862 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/breastCancerUPP_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/breastCancerUPP_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/breastCancerUPP_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerVDX Version: 1.2.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 450f7dc1df014b609d51f156ec0b2c10 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/breastCancerVDX_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/breastCancerVDX_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/breastCancerVDX_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bronchialIL13 Version: 1.2.0 Depends: R(>= 2.10.0), affy (>= 1.23.4) License: GPL-2 MD5sum: 2755b025ea8222d42572aa80f06e55ce 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/bronchialIL13_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/bronchialIL13_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/bronchialIL13_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bsseqData Version: 0.2.0 Depends: R (>= 2.15), bsseq (>= 0.9.6) License: Artistic-2.0 MD5sum: 4c2437a6279b028b4ada139b4e35ff68 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/bsseqData_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/bsseqData_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/bsseqData_0.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cancerdata Version: 1.2.0 Depends: R (>= 2.10.1), Biobase License: GPL (>= 2) MD5sum: f5393fee171d050b1b1e8be300d6cffd 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/cancerdata_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/cancerdata_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/cancerdata_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CCl4 Version: 1.2.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), limma License: Artistic-2.0 MD5sum: ae39ec57653294f626a553f0dd3c1806 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/CCl4_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/CCl4_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/CCl4_1.2.0.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: 1.2.0 Depends: R (>= 2.10), Ringo(>= 1.9.8), affy(>= 1.23.4), topGO(>= 1.13.1) Imports: Biobase Suggests: biomaRt, Biobase(>= 2.5.5), xtable License: Artistic-2.0 MD5sum: 7ebdd8ee5b55397a71769e115105dfce 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/ccTutorial_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/ccTutorial_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ccTutorial_1.2.0.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: 0.2.0 Depends: R (>= 2.12.0), GGBase (>= 3.9.0), GGtools, Biobase Suggests: SNPlocs.Hsapiens.dbSNP.20101109 License: Artistic-2.0 MD5sum: 3fdfea5a23eeb486c0225a1845702c8d 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/ceu1kg_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/ceu1kg_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ceu1kg_0.2.0.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: 0.6.0 Depends: R (>= 3.0), GGBase Imports: Biobase License: Artistic-2.0 MD5sum: 3a5f4d7f56489fa5af2ed8cf83533310 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_0.6.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/ceu1kgv_0.6.0.zip mac.binary.ver: bin/macosx/contrib/3.1/ceu1kgv_0.6.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ceu1kgv_0.6.0.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: 0.2.0 Depends: R (>= 2.12.0), GGBase, Biobase Imports: GGtools License: Artistic-2.0 MD5sum: af0ba3d31238e7b136b654b0acb541d0 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/ceuhm3_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/ceuhm3_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ceuhm3_0.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cgdv17 Version: 0.2.0 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: 5982867883f1314f2228b3a504a4ded6 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/cgdv17_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/cgdv17_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/cgdv17_0.2.0.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: 1.0.1 Depends: R (>= 3.0.1) License: GPL-3 MD5sum: 2b7571b9105ff16dce7128cecfe24d4c NeedsCompilation: no Title: Data Packages for ChAMP package Description: Provides datasets needed for ChAMP and also a test dataset biocViews: ExpressionData, IlluminaChip Author: Tiffany Morris, Andrew Teschendorff and Lee Butcher Maintainer: Tiffany Morris source.ver: src/contrib/ChAMPdata_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/ChAMPdata_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/ChAMPdata_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ChAMPdata_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: charmData Version: 1.0.0 Depends: R(>= 2.11.0), charm, pd.charm.hg18.example License: LGPL (>= 2) MD5sum: e16c406f987903be735c7d7271179691 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/charmData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/charmData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/charmData_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cheung2010 Version: 0.2.0 Depends: R (>= 2.13.0), Biobase, GGtools, GenomicRanges, hgfocus.db Imports: AnnotationDbi Suggests: SNPlocs.Hsapiens.dbSNP.20120608 Enhances: parallel License: Artistic-2.0 MD5sum: b18bde84a99e12714d80cfd3206c9816 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/cheung2010_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/cheung2010_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/cheung2010_0.2.0.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: ChimpHumanBrainData Version: 1.2.0 Depends: affy,qvalue,limma,hexbin,statmod License: MIT MD5sum: 1b7883f3467cbed083f2746177af662c NeedsCompilation: no Title: Chimp and human brain data package Description: This data package contains chimp and human brain data extracted from the ArrayExpress accession E-AFMX-2. Both human and chimp RNAs were run on human hgu95av2 Affymetrix arrays. It is a useful dataset for tutorials. biocViews: ExpressionData, RNAExpressionData Author: Roman Jaksik, Naomi Altman, and Sean Davis Maintainer: Sean Davis source.ver: src/contrib/ChimpHumanBrainData_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/ChimpHumanBrainData_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/ChimpHumanBrainData_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ChimpHumanBrainData_1.2.0.tgz vignettes: vignettes/ChimpHumanBrainData/inst/doc/DiffExpressVignette.pdf vignetteTitles: DiffExpressVignette.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: chipenrich.data Version: 1.0.0 Depends: R (>= 2.15.0) Imports: methods, GenomicRanges (>= 1.10.0), IRanges (>= 1.16.0), BiocGenerics (>= 0.2.0) License: GPL-3 MD5sum: 36ad11bfec8b64db7e75dcbbc6d4e66b 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/chipenrich.data_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/chipenrich.data_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/chipenrich.data_1.0.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: ChIPXpressData Version: 1.2.0 Depends: bigmemory License: GPL (>=2) MD5sum: dee08b53626b6998b7563bc158fd6388 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_1.2.0.tar.gz mac.binary.ver: bin/macosx/contrib/3.1/ChIPXpressData_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ChIPXpressData_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CLL Version: 1.4.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: LGPL MD5sum: b32748cbd00f9fb29aea50d6e6f2f3f8 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_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/CLL_1.4.0.zip mac.binary.ver: bin/macosx/contrib/3.1/CLL_1.4.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/CLL_1.4.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cMap2data Version: 1.0.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 50af6a8014a3899c80933115e7c75ed8 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/cMap2data_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/cMap2data_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/cMap2data_1.0.0.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: 1.0.0 Depends: R (>= 2.10), cnvGSA License: LGPL MD5sum: 01479fdfd8977dddfa0e3cdf076c0043 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/cnvGSAdata_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/cnvGSAdata_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/cnvGSAdata_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: COHCAPanno Version: 1.0.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 3dbea0e2c3f82090322e2dabbb316fc6 NeedsCompilation: no Title: Annotations for City of Hope CpG Island Analysis Pipeline Description: Provides genomic location, nearby CpG island and nearby gene information for common Illumina methylation array platforms biocViews: DNAMethylation, Microarray, Epigenetics Author: Charles Warden Maintainer: Charles Warden source.ver: src/contrib/COHCAPanno_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/COHCAPanno_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/COHCAPanno_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/COHCAPanno_1.0.0.tgz vignettes: vignettes/COHCAPanno/inst/doc/COHCAPanno.pdf vignetteTitles: COHCAPanno Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/COHCAPanno/inst/doc/COHCAPanno.R Package: colonCA Version: 1.6.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: 8b66c2df023eb249d8d361bec0069cc3 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_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/colonCA_1.6.0.zip mac.binary.ver: bin/macosx/contrib/3.1/colonCA_1.6.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/colonCA_1.6.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ConnectivityMap Version: 1.0.0 Depends: R (>= 2.15.1) Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: c714addb696d77608f4742c08cd0dad2 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/ConnectivityMap_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/ConnectivityMap_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ConnectivityMap_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: COPDSexualDimorphism.data Version: 1.0.0 License: LGPL-2.1 MD5sum: b2d513721164eaf83f4628bd38b051ba NeedsCompilation: no Title: Data to support sexually dimorphic and COPD differential analysis for gene expression and methylation. Description: Datasets to support COPDSexaulDimorphism Package. biocViews: ExperimentData, NormalTissue, RNAExpressionData Author: J Fah Sathirapongsasuti Maintainer: J Fah Sathirapongsasuti source.ver: src/contrib/COPDSexualDimorphism.data_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/COPDSexualDimorphism.data_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/COPDSexualDimorphism.data_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/COPDSexualDimorphism.data_1.0.0.tgz vignettes: vignettes/COPDSexualDimorphism.data/inst/doc/lgrc_data.pdf vignetteTitles: SDCD Genes hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/COPDSexualDimorphism.data/inst/doc/lgrc_data.R Package: CopyNumber450kData Version: 1.0.0 Depends: R (>= 2.13.0), minfi, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 License: Artistic-2.0 MD5sum: 62e4b6b7019da091a1dda78a4c58c6ec NeedsCompilation: no Title: Example data for the Illumina Methylation 450k array Description: Data from 52 control samples from 450k methylation arrays biocViews: DNAMethylation Author: Simon Papillon-Cavanagh, Jean-Philippe Fortin, Nicolas De Jay Maintainer: Simon Papillon-Cavanagh source.ver: src/contrib/CopyNumber450kData_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/CopyNumber450kData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/CopyNumber450kData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/CopyNumber450kData_1.0.0.tgz vignettes: vignettes/CopyNumber450kData/inst/doc/CopyNumber450kData.pdf vignetteTitles: CopyNumber450kData User's Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CopyNumber450kData/inst/doc/CopyNumber450kData.R Package: COSMIC.67 Version: 1.0.0 Depends: R (>= 3.0.2) Imports: GenomicRanges, VariantAnnotation Suggests: testthat, BiocStyle, knitr License: GPL-3 MD5sum: 140fdd72dac11541b562dba3750638f0 NeedsCompilation: no Title: COSMIC.67 Description: COSMIC: Catalogue Of Somatic Mutations In Cancer, version 67 (2013-10-24) biocViews: ExperimentData, Cancer Author: Julian Gehring Maintainer: Julian Gehring VignetteBuilder: knitr source.ver: src/contrib/COSMIC.67_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/COSMIC.67_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/COSMIC.67_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/COSMIC.67_1.0.0.tgz vignettes: vignettes/COSMIC.67/inst/doc/COSMIC.67.pdf vignetteTitles: COSMIC.67 - PDF hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/COSMIC.67/inst/doc/COSMIC.67.R Package: curatedBladderData Version: 1.0.0 Depends: R (>= 2.10.0), affy Suggests: BiocStyle, survival, xtable, sva, genefilter, logging License: Artistic-2.0 MD5sum: 37365e60c2121d0cb58ebd32b3ce154c 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/curatedBladderData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/curatedBladderData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/curatedBladderData_1.0.0.tgz vignettes: vignettes/curatedBladderData/inst/doc/curatedBladderData_vignette.pdf vignetteTitles: curatedBladderData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: curatedCRCData Version: 1.0.0 Depends: R (>= 2.10.0), nlme Suggests: survival,sva,BiocStyle, xtable, genefilter, logging License: Artistic-2.0 MD5sum: 7f57e4c7c82244c3faab2a69c4473937 NeedsCompilation: no Title: Colorectal Cancer Gene Expression Analysis Description: The curatedCRC package provides relevant functions and data for gene expression analysis in patients with colorectal cancer. biocViews: Colorectal, Cancer, TCGA, ExperimentData Author: Princy Parsana, Markus Riester, Curtis Huttenhower, Levi Waldron Maintainer: Princy Parsana URL: https://bitbucket.org/lwaldron/curatedcrcdata source.ver: src/contrib/curatedCRCData_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/curatedCRCData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/curatedCRCData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/curatedCRCData_1.0.0.tgz vignettes: vignettes/curatedCRCData/inst/doc/curatedCRCData_vignette.pdf vignetteTitles: curatedCRCData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: curatedOvarianData Version: 1.2.0 Depends: R (>= 2.10.0), affy Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, futile.logger, sva, xtable License: Artistic-2.0 MD5sum: f54de41112d145fe90b422c9e2787158 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/curatedOvarianData_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/curatedOvarianData_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/curatedOvarianData_1.2.0.tgz vignettes: vignettes/curatedOvarianData/inst/doc/curatedOvarianData_vignette.pdf vignetteTitles: curatedOvarianData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: davidTiling Version: 1.4.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db License: LGPL MD5sum: 24a9747aa48cc459c89d184fddbe44c3 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_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/davidTiling_1.4.0.zip mac.binary.ver: bin/macosx/contrib/3.1/davidTiling_1.4.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/davidTiling_1.4.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: DeSousa2013 Version: 1.0.0 Depends: R (>= 2.15), Imports: affy, frma, frmaTools, hgu133plus2.db, hgu133plus2frmavecs, sva, rgl, ConsensusClusterPlus, cluster, siggenes, ROCR, pamr, survival, gplots, AnnotationDbi, Biobase License: Artistic-2.0 MD5sum: 72b88695928b749c9657abd5d008cc3d 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/DeSousa2013_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/DeSousa2013_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/DeSousa2013_1.0.0.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: 1.4.0 Depends: R(>= 2.11.0), Biobase License: GPL (>=2) MD5sum: f4f67842b0a840e33929b06bbd29560d 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_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/DLBCL_1.4.0.zip mac.binary.ver: bin/macosx/contrib/3.1/DLBCL_1.4.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/DLBCL_1.4.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: DMRcatedata Version: 1.0.0 Depends: R (>= 3.0.2) License: GPL-3 MD5sum: f26bc42551b3a38965155f3d60efc869 NeedsCompilation: no Title: Data Package for DMRcate package Description: This package contains 3 data objects supporting functionality and examples of DMRcate biocViews: IlluminaChip Author: Tim Peters Maintainer: Tim Peters VignetteBuilder: knitr source.ver: src/contrib/DMRcatedata_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/DMRcatedata_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/DMRcatedata_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/DMRcatedata_1.0.0.tgz vignettes: vignettes/DMRcatedata/inst/doc/DMRcatedata.pdf vignetteTitles: The DMRcate package user's guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DMRcatedata/inst/doc/DMRcatedata.R Package: DonaPLLP2013 Version: 1.2.0 Depends: EBImage, parallel License: Artistic-2.0 MD5sum: d622395c67ed37eb62b2654645ef20a4 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/DonaPLLP2013_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/DonaPLLP2013_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/DonaPLLP2013_1.2.0.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: 1.0.0 Depends: R (>= 2.15.1), GenomicRanges Imports: BiocGenerics Suggests: RUnit, networkBMA License: GPL MD5sum: a66c35f9187cc6bb2f334acee8be4aa1 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/DREAM4_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/DREAM4_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/DREAM4_1.0.0.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: 0.2.0 Depends: R (>= 2.10.1), methods, Biobase (>= 2.5.5) Suggests: survival, chron License: Artistic-2.0 MD5sum: 61f7b4b291f735ff4e78492c28e4aceb 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/dressCheck_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/dressCheck_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/dressCheck_0.2.0.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: 1.0.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 0d4c16a16434aa217ef748a31e702de0 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/DrugVsDiseasedata_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/DrugVsDiseasedata_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/DrugVsDiseasedata_1.0.0.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: 0.2.0 Depends: R (>= 2.15.0), utils, GenomicRanges, Biobase, GGBase License: Artistic-2.0 MD5sum: 8e70215543b06bbd5e142b237f308fb7 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/dsQTL_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/dsQTL_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/dsQTL_0.2.0.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: 1.0.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 7762f4b5f39f7a42f83197b3ba1f027e 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/DvDdata_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/DvDdata_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/DvDdata_1.0.0.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: 1.2.0 Depends: R (>= 1.4.1), marray, GEOquery Suggests: dyebias, convert, Biobase License: GPL-3 MD5sum: 733f4723abaee2df7c4fb7191f656843 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/dyebiasexamples_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/dyebiasexamples_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/dyebiasexamples_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Package: EatonEtAlChIPseq Version: 0.2.0 Depends: GenomicRanges (>= 1.5.42), ShortRead, rtracklayer License: Artistic 2.0 MD5sum: d875fe745c66e76f0dc50f1ccef4d766 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/EatonEtAlChIPseq_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/EatonEtAlChIPseq_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/EatonEtAlChIPseq_0.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ecoliLeucine Version: 1.4.0 Depends: R (>= 1.9.0), affy (>= 1.23.4), ecolicdf License: GPL (>= 2) MD5sum: a9ef1b31a48512952d9c5247bcccc53e 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_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/ecoliLeucine_1.4.0.zip mac.binary.ver: bin/macosx/contrib/3.1/ecoliLeucine_1.4.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ecoliLeucine_1.4.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: encoDnaseI Version: 0.2.0 Depends: R (>= 2.15.0), methods, Biobase (>= 2.5.5), lattice, GGtools, GGBase Suggests: GGdata License: Artistic-2.0 MD5sum: 41150ad36bdfa3746fd361ebf5e97da4 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/encoDnaseI_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/encoDnaseI_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/encoDnaseI_0.2.0.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: 1.10.0 Depends: R (>= 1.9.0), affy (>= 1.4) Suggests: Biobase (>= 1.13.16), affy, vsn, hgu95av2.db, genefilter License: LGPL MD5sum: b4cd0cd952daef46039bd5e8b48c3c48 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_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/estrogen_1.10.0.zip mac.binary.ver: bin/macosx/contrib/3.1/estrogen_1.10.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/estrogen_1.10.0.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: 1.4.4 Depends: xcms License: LGPL MD5sum: 32c9e9ec2809d4a71cb03b4180358b02 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_1.4.4.tar.gz win.binary.ver: bin/windows/contrib/3.1/faahKO_1.4.4.zip mac.binary.ver: bin/macosx/contrib/3.1/faahKO_1.4.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/faahKO_1.4.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fabiaData Version: 1.2.0 Depends: R (>= 2.10.0), Biobase Imports: utils Suggests: fabia License: LGPL (>= 2.1) MD5sum: 626a58e339e0359d5e9cf3a8f474fc49 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/fabiaData_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/fabiaData_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/fabiaData_1.2.0.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: 1.6.0 Depends: R (>= 1.9.1), prada (>= 1.0.5) License: GPL-2 MD5sum: c66ede10970a52f5d9da3378c439fc84 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_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/facsDorit_1.6.0.zip mac.binary.ver: bin/macosx/contrib/3.1/facsDorit_1.6.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/facsDorit_1.6.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: FANTOM3and4CAGE Version: 1.0.0 Depends: R (>= 2.15.0) License: GPL-3 MD5sum: e3fbef8cc642e10431110cd897bbbd06 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/FANTOM3and4CAGE_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/FANTOM3and4CAGE_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/FANTOM3and4CAGE_1.0.0.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: 1.2.0 Depends: R (>= 2.10.0), lumi Suggests: genefilter, affy License: GPL (>2) MD5sum: 3be4f84741e5b15a1c478168c7ffb426 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/ffpeExampleData_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/ffpeExampleData_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ffpeExampleData_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fibroEset Version: 1.6.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: 54949cc45cff98eb700c33a1f628e3cd 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_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/fibroEset_1.6.0.zip mac.binary.ver: bin/macosx/contrib/3.1/fibroEset_1.6.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/fibroEset_1.6.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Fletcher2013a Version: 1.0.0 Depends: R (>= 2.15), limma Imports: Biobase ,VennDiagram, gplots,grid License: GPL (>= 2) MD5sum: 98924bf9c8432acabf1c025b3266777e NeedsCompilation: no Title: Gene expression data from breast cancer cells under FGFR2 signalling perturbation. Description: The package Fletcher2013a contains time-course gene expression data from MCF-7 cells treated under different experimental systems in order to perturb FGFR2 signalling. The data comes from Fletcher et al. (Nature Comms 4:2464, 2013) where further details about the background and the experimental design of the study can be found. biocViews: ExperimentData, RNAExpressionData, Cancer Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin Meyer. Maintainer: Mauro Castro URL: http://dx.doi.org/10.1038/ncomms3464 source.ver: src/contrib/Fletcher2013a_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/Fletcher2013a_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/Fletcher2013a_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Fletcher2013a_1.0.0.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: 1.0.0 Depends: R (>= 2.15), Fletcher2013a, biomaRt, VennDiagram, RTN (>= 1.1.2), RedeR (>= 1.8.1) Imports: RColorBrewer, corrgram License: GPL (>= 2) MD5sum: 46ff2edf38eb4739aaff1074f064d006 NeedsCompilation: no Title: Master regulators of FGFR2 signalling and breast cancer risk. Description: This package reproduces the systems biology analysis for the data in package Fletcher2013a using RTN. biocViews: ExperimentData, RNAExpressionData, Cancer Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin Meyer. Maintainer: Mauro Castro URL: http://dx.doi.org/10.1038/ncomms3464 source.ver: src/contrib/Fletcher2013b_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/Fletcher2013b_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/Fletcher2013b_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Fletcher2013b_1.0.0.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: 1.0.0 Depends: R (>= 2.12.2), flowCore Imports: methods License: Artistic-2.0 MD5sum: 5abc84011b49a4c1793219e8b88357b1 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/flowFitExampleData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/flowFitExampleData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/flowFitExampleData_1.0.0.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: 1.2.0 Depends: R (>= 2.13.0), minfi (>= 1.8.0) License: Artistic-2.0 MD5sum: 29fb1c5561337424ef6567e1ddae3abe 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/FlowSorted.Blood.450k_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/FlowSorted.Blood.450k_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/FlowSorted.Blood.450k_1.2.0.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: FlowSorted.DLPFC.450k Version: 1.0.0 Depends: R (>= 2.13.0), minfi License: Artistic-2.0 MD5sum: 664a35385cf4415dd3b80b46b0f4483e NeedsCompilation: no Title: Illumina HumanMethylation data on sorted frontal cortex cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays. biocViews: IlluminaChip, Homo_sapiens, DNAMethylation Author: Andrew E Jaffe, Zachary A. Kaminsky Maintainer: Andrew E Jaffe source.ver: src/contrib/FlowSorted.DLPFC.450k_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/FlowSorted.DLPFC.450k_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/FlowSorted.DLPFC.450k_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/FlowSorted.DLPFC.450k_1.0.0.tgz vignettes: vignettes/FlowSorted.DLPFC.450k/inst/doc/FlowSorted.DLPFC.450k.pdf vignetteTitles: FlowSorted DLPFC 450k Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: flowWorkspaceData Version: 2.0.0 License: GPL-2 MD5sum: 6daf6c1ad2d33986ec25ade341e0895d 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/3.1/flowWorkspaceData_2.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/flowWorkspaceData_2.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/flowWorkspaceData_2.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: frmaExampleData Version: 1.0.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 70076e591244f68154c2b1d5afb34a7e 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/frmaExampleData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/frmaExampleData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/frmaExampleData_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: FunciSNP.data Version: 1.0.0 Depends: R (>= 2.14.0) Imports: rtracklayer License: GPL-3 MD5sum: ad20c19b57191f446cd0992b10004b0c 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/FunciSNP.data_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/FunciSNP.data_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/FunciSNP.data_1.0.0.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: 2.2.0 Depends: R (>= 2.10) Suggests: gage, pathview, genefilter License: GPL (>=2.0) MD5sum: 67e7a00aa62f2b2930be6f643e95d637 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_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/gageData_2.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/gageData_2.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/gageData_2.2.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: gaschYHS Version: 1.2.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: daaad815453bbe3bdd09434f34ae7534 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/gaschYHS_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/gaschYHS_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/gaschYHS_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gatingMLData Version: 2.4.0 Depends: R (>= 1.9.0) Suggests: flowUtils License: GPL MD5sum: e827bdf1a5319dd0a88898563206efcb 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_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/gatingMLData_2.4.0.zip mac.binary.ver: bin/macosx/contrib/3.1/gatingMLData_2.4.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/gatingMLData_2.4.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gcspikelite Version: 1.2.0 Depends: R (>= 2.5.0) License: LGPL MD5sum: faa08606a15d7acb08bb79a5de19e4c1 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/gcspikelite_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/gcspikelite_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/gcspikelite_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: geneLenDataBase Version: 1.0.0 Depends: R (>= 2.11.0) Imports: utils, rtracklayer, GenomicFeatures (>= 1.3.15) License: LGPL (>= 2) MD5sum: 87fe2204e370c52994385d0176a529c3 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/geneLenDataBase_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/geneLenDataBase_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/geneLenDataBase_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GGdata Version: 1.2.0 Depends: R (>= 2.12.0), methods, Biobase (>= 2.5.5), GGBase, snpStats, illuminaHumanv1.db, AnnotationDbi Enhances: GGtools License: LGPL MD5sum: f2a5d3396941e545ae517df279331df8 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/GGdata_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/GGdata_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/GGdata_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ggtut suggestsMe: encoDnaseI Package: ggtut Version: 0.2.0 Depends: R (>= 2.14.0), GGtools (>= 3.11.32), ff, GenomicRanges, snpStats, GGdata, GenomicFeatures, ChIPpeakAnno, Rsamtools(>= 1.5.35), cheung2010, SNPlocs.Hsapiens.dbSNP.20120608, hmyriB36 Suggests: rtracklayer, GenomicFeatures, ChIPpeakAnno, TxDb.Hsapiens.UCSC.hg18.knownGene License: Artistic-2.0 MD5sum: 1777e16e28fb5823fe43e5f9ffec427f 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/ggtut_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/ggtut_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ggtut_0.2.0.tgz vignettes: vignettes/ggtut/inst/doc/ hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: golubEsets Version: 1.6.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: LGPL MD5sum: 2f95d0fb194c2505673f661231a7a23b 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_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/golubEsets_1.6.0.zip mac.binary.ver: bin/macosx/contrib/3.1/golubEsets_1.6.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/golubEsets_1.6.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GSVAdata Version: 1.0.0 Depends: R (>= 2.10), Biobase, GSEABase, hgu95a.db License: GPL (>= 2) MD5sum: 77c1ad31dde6c2ce32affe6a8c457ab1 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/GSVAdata_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/GSVAdata_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/GSVAdata_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GWASdata Version: 1.2.0 Depends: GWASTools License: Artistic-2.0 MD5sum: 7657f18be08441bcc49970b993d08456 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/GWASdata_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/GWASdata_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/GWASdata_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: h5vcData Version: 1.2.0 Suggests: h5vc License: GPL (>= 3) MD5sum: bcdd06919d0307ae737a9b212010050a 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/h5vcData_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/h5vcData_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/h5vcData_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap100khind Version: 1.6.0 Suggests: oligo License: GPL MD5sum: 406f60499749488cd9b9a7a1dc24e20b 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_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/hapmap100khind_1.6.0.zip mac.binary.ver: bin/macosx/contrib/3.1/hapmap100khind_1.6.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/hapmap100khind_1.6.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap100kxba Version: 1.6.0 Suggests: oligo License: GPL MD5sum: 4cbbf592ddc5a9afdc2bf3eef5e44362 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_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/hapmap100kxba_1.6.0.zip mac.binary.ver: bin/macosx/contrib/3.1/hapmap100kxba_1.6.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/hapmap100kxba_1.6.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap500knsp Version: 1.6.0 Suggests: oligo License: GPL MD5sum: bd403a5f4e72ab6ffc98501000b1e616 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_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/hapmap500knsp_1.6.0.zip mac.binary.ver: bin/macosx/contrib/3.1/hapmap500knsp_1.6.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/hapmap500knsp_1.6.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap500ksty Version: 1.6.0 Suggests: oligo License: GPL MD5sum: 453f3d505cdae19ec4405fd40b83d54d 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_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/hapmap500ksty_1.6.0.zip mac.binary.ver: bin/macosx/contrib/3.1/hapmap500ksty_1.6.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/hapmap500ksty_1.6.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmapsnp5 Version: 1.6.0 Suggests: oligo License: GPL MD5sum: e6178db38ee17b32935ae8637e9b7f3f 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_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/hapmapsnp5_1.6.0.zip mac.binary.ver: bin/macosx/contrib/3.1/hapmapsnp5_1.6.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/hapmapsnp5_1.6.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmapsnp6 Version: 1.6.0 Depends: R (>= 2.15) Suggests: oligo, oligoClasses License: GPL MD5sum: 549c12b861fe1fb05bb9b0006226da50 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_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/hapmapsnp6_1.6.0.zip mac.binary.ver: bin/macosx/contrib/3.1/hapmapsnp6_1.6.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/hapmapsnp6_1.6.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: harbChIP Version: 1.2.0 Depends: R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5), Biostrings Imports: methods, stats License: Artistic-2.0 MD5sum: 87c120fce1d53a04cdd843417ba3081d 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/harbChIP_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/harbChIP_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/harbChIP_1.2.0.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: 1.4.0 Depends: R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots, limma, vcd, LSD,EBImage Suggests: BiocStyle License: Artistic-2.0 MD5sum: c570ad9eede6056affbb7c8c21fd444e 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_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/HD2013SGI_1.4.0.zip mac.binary.ver: bin/macosx/contrib/3.1/HD2013SGI_1.4.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/HD2013SGI_1.4.0.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: healthyFlowData Version: 1.2.0 Depends: R (>= 2.15.0), flowCore Imports: methods License: Artistic-2.0 MD5sum: bae2bf9ac4b4d1ce9d4cb79692289ea6 NeedsCompilation: no Title: Healthy dataset used by the flowMatch package Description: A healthy dataset with 20 flow cytometry samples used by the flowMatch package. biocViews: FlowCytometry, CellBasedAssays, Bioinformatics Author: Ariful Azad Maintainer: Ariful Azad source.ver: src/contrib/healthyFlowData_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/healthyFlowData_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/healthyFlowData_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/healthyFlowData_1.2.0.tgz vignettes: vignettes/healthyFlowData/inst/doc/healthyFlowData.pdf vignetteTitles: healthyFlowData: A healthy dataset with 20 flow cytometry samples used by the flowMatch package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/healthyFlowData/inst/doc/healthyFlowData.R Package: HEEBOdata Version: 1.2.0 License: LGPL MD5sum: 4a9d9f44a005d1e677ae87fc7f3e7ae3 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/HEEBOdata_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/HEEBOdata_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/HEEBOdata_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu133abarcodevecs Version: 1.2.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 14aab37baff8dcbc0b121c063bb49560 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/hgu133abarcodevecs_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/hgu133abarcodevecs_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/hgu133abarcodevecs_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu133plus2barcodevecs Version: 1.2.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 84672aaf8b5f44e56ac257ff663682f2 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/hgu133plus2barcodevecs_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/hgu133plus2barcodevecs_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/hgu133plus2barcodevecs_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu2beta7 Version: 1.4.0 Depends: R (>= 2.0.0) License: Artistic-2.0 MD5sum: 3b747fbe56f2b909f1ce520ba5cf6d79 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_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/hgu2beta7_1.4.0.zip mac.binary.ver: bin/macosx/contrib/3.1/hgu2beta7_1.4.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/hgu2beta7_1.4.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: HiCDataLymphoblast Version: 1.0.0 Suggests: GOTHiC, ShortRead License: GPL-3 MD5sum: 7f0b2e0cfd2a306ddd85b7a68b5ba932 NeedsCompilation: no Title: Human lymphoblastoid HiC data from Lieberman-Aiden et al. 2009 Description: The HiC data from human lymphoblastoid cell line (HindIII restriction) was retrieved from the sequence read archive and two ends of the paired reads were aligned separately with bowtie. biocViews: ExperimentData, HighThroughputSequencingData Author: Borbala Mifsud Maintainer: Borbala Mifsud source.ver: src/contrib/HiCDataLymphoblast_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/HiCDataLymphoblast_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/HiCDataLymphoblast_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/HiCDataLymphoblast_1.0.0.tgz vignettes: vignettes/HiCDataLymphoblast/inst/doc/package_vignettes.pdf vignetteTitles: package_vignettes.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Hiiragi2013 Version: 1.0.0 Depends: R (>= 3.0.0), affy, Biobase, boot, clue, cluster, genefilter, geneplotter, gplots, gtools, KEGGREST, MASS, mouse4302.db, RColorBrewer, xtable Imports: grid, lattice, latticeExtra Suggests: ArrayExpress, BiocStyle License: Artistic-2.0 MD5sum: 9d139eec19fbfdbc947c44ddc27c9ca0 NeedsCompilation: no Title: Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages Description: This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881." biocViews: ExperimentData Author: Andrzej Oles, Wolfgang Huber Maintainer: Andrzej Oles source.ver: src/contrib/Hiiragi2013_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/Hiiragi2013_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/Hiiragi2013_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Hiiragi2013_1.0.0.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: 1.4.0 License: GPL (>= 2) MD5sum: c348ec38994cb108c1b358c73b44788c 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_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/HIVcDNAvantWout03_1.4.0.zip mac.binary.ver: bin/macosx/contrib/3.1/HIVcDNAvantWout03_1.4.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/HIVcDNAvantWout03_1.4.0.tgz vignettes: vignettes/HIVcDNAvantWout03/inst/doc/ hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hmyriB36 Version: 1.0.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.5.5), GGBase Suggests: GGtools, illuminaHumanv1.db License: Artistic-2.0 MD5sum: 9c7459d3feac7016c6ec2425c76d135e 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/hmyriB36_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/hmyriB36_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/hmyriB36_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ggtut suggestsMe: ind1KG Package: humanStemCell Version: 0.4.0 Depends: Biobase (>= 2.5.5), hgu133plus2.db License: Artistic-2.0 MD5sum: 27e45ac332bde2f46a40da5e49ead718 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_0.4.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/humanStemCell_0.4.0.zip mac.binary.ver: bin/macosx/contrib/3.1/humanStemCell_0.4.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/humanStemCell_0.4.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Illumina450ProbeVariants.db Version: 1.0.0 Depends: R (>= 3.0.1) License: GPL-3 MD5sum: 5b9b47827915c4b550175b982af41465 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/Illumina450ProbeVariants.db_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/Illumina450ProbeVariants.db_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Illumina450ProbeVariants.db_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: IlluminaDataTestFiles Version: 1.2.0 License: Artistic-2.0 MD5sum: e07899c7bb05095c448542a58ba371b7 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/IlluminaDataTestFiles_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/IlluminaDataTestFiles_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/IlluminaDataTestFiles_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ind1KG Version: 0.2.0 Depends: R (>= 2.10.1), chopsticks Suggests: Rsamtools, rtracklayer, GenomicFeatures, org.Hs.eg.db, SNPlocs.Hsapiens.dbSNP.20090506, TxDb.Hsapiens.UCSC.hg18.knownGene, lumiHumanIDMapping, GGBase, GGtools, hmyriB36 License: Artistic-2.0 MD5sum: b752f23dc671dbc6ab06abaad497392d 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/ind1KG_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/ind1KG_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ind1KG_0.2.0.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: 1.0.0 License: GPL-2 MD5sum: c56b6d7c4afeb1f2b279876303ff6d60 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/iontreeData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/iontreeData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/iontreeData_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ITALICSData Version: 2.2.0 Depends: R (>= 2.0.0) License: GPL MD5sum: 3424d61226aa300553cda772ecbc5252 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_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/ITALICSData_2.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/ITALICSData_2.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ITALICSData_2.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Iyer517 Version: 1.6.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 53367d368c5a664deab670c315235ff3 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_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/Iyer517_1.6.0.zip mac.binary.ver: bin/macosx/contrib/3.1/Iyer517_1.6.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Iyer517_1.6.0.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: 1.0.0 Depends: R (>= 3.0.1), methods, Biostrings (>= 2.29.19) License: GPL-2 MD5sum: f201375577ec3483b398a7a8505a5a9f 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://jaspar.genereg.net/ source.ver: src/contrib/JASPAR2014_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/JASPAR2014_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/JASPAR2014_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/JASPAR2014_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: KEGGdzPathwaysGEO Version: 1.2.0 Depends: R (>= 2.13.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: 4200d26d445627f8a4fe1970eaf955bd 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/KEGGdzPathwaysGEO_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/KEGGdzPathwaysGEO_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/KEGGdzPathwaysGEO_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: kidpack Version: 1.6.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5) License: GPL-2 MD5sum: f38a3637ed6bd5547e9c99294a691606 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_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/kidpack_1.6.0.zip mac.binary.ver: bin/macosx/contrib/3.1/kidpack_1.6.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/kidpack_1.6.0.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: 1.0.0 Depends: R (>= 2.15.0), Biobase, Rsamtools (>= 0.1.50), BSgenome Imports: GenomicRanges, GenomicAlignments, methods Suggests: GenomeGraphs, biomaRt, org.Sc.sgd.db, edgeR Enhances: multicore License: Artistic 2.0 MD5sum: e78013d140b6629f5d210b628977f590 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/leeBamViews_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/leeBamViews_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/leeBamViews_1.0.0.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: 1.0.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: aa72d4eeb3281af6d7f83604efad12b6 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/leukemiasEset_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/leukemiasEset_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/leukemiasEset_1.0.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: LiebermanAidenHiC2009 Version: 0.2.0 Depends: KernSmooth, IRanges License: LGPL MD5sum: 18dc34a8c81be4953ce0c1b4ac9a5f67 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/LiebermanAidenHiC2009_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/LiebermanAidenHiC2009_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/LiebermanAidenHiC2009_0.2.0.tgz vignettes: vignettes/LiebermanAidenHiC2009/inst/doc/LiebermanAidenHiC2009.pdf vignetteTitles: Exploration of HiC data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: lumiBarnes Version: 1.4.0 Depends: R (>= 2.0), Biobase (>= 2.5.5), lumi (>= 1.1.0) License: LGPL MD5sum: d9cbc9a5a346542c15529d34779584e9 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_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/lumiBarnes_1.4.0.zip mac.binary.ver: bin/macosx/contrib/3.1/lumiBarnes_1.4.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/lumiBarnes_1.4.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: LungCancerACvsSCCGEO Version: 1.0.0 Depends: R (>= 2.15.0) License: GPL-2 MD5sum: 2356cb9e257c26816bab43781f223804 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/LungCancerACvsSCCGEO_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/LungCancerACvsSCCGEO_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/LungCancerACvsSCCGEO_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: LungCancerLines Version: 0.2.0 Imports: Rsamtools License: Artistic-2.0 MD5sum: 2dbc93d3ce0990eebd0a06ea22e2d024 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/LungCancerLines_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/LungCancerLines_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/LungCancerLines_0.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: lungExpression Version: 0.2.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 729dc54269710b5d583152a9c8a95e46 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/lungExpression_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/lungExpression_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/lungExpression_0.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MafDb.ALL.wgs.phase1.release.v3.20101123 Version: 1.0.0 Depends: R (>= 3.0.0), VariantFiltering Imports: RSQLite (>= 0.8-1), Biobase, AnnotationDbi, IRanges, Biostrings, Rsamtools, GenomicRanges, VariantAnnotation License: Artistic-2.0 MD5sum: 250504936fd5fa65c8ad8eb56f5634d1 NeedsCompilation: no Title: Minimum allele frequency data from the 1000 Genomes project Description: This annotation package stores minimum allele frequency data frozen from the 1000 Genomes project biocViews: AnnotationData, Genetics, MafDb, Homo_sapiens Author: Robert Castelo, Dei M. Elurbe Maintainer: Robert Castelo source.ver: src/contrib/MafDb.ALL.wgs.phase1.release.v3.20101123_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/MafDb.ALL.wgs.phase1.release.v3.20101123_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/MafDb.ALL.wgs.phase1.release.v3.20101123_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/MafDb.ALL.wgs.phase1.release.v3.20101123_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MafDb.ESP6500SI.V2.SSA137.dbSNP138 Version: 1.0.0 Depends: R (>= 3.0.0), VariantFiltering Imports: RSQLite (>= 0.8-1), Biobase, AnnotationDbi, IRanges, Biostrings, GenomicRanges, VariantAnnotation License: Artistic-2.0 MD5sum: e4487be2addd3b2484d606537a22c8da NeedsCompilation: no Title: Minimum allele frequency data from NHLBI ESP Description: Minimum allele frequency data frozen from the NHLBI Exome Sequencing Project biocViews: AnnotationData, Genetics, MafDb, Homo_sapiens Author: Robert Castelo, Dei M. Elurbe Maintainer: Robert Castelo source.ver: src/contrib/MafDb.ESP6500SI.V2.SSA137.dbSNP138_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/MafDb.ESP6500SI.V2.SSA137.dbSNP138_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/MafDb.ESP6500SI.V2.SSA137.dbSNP138_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/MafDb.ESP6500SI.V2.SSA137.dbSNP138_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mammaPrintData Version: 1.0.0 Depends: R (>= 2.13.0) Suggests: Biobase, gdata, limma License: Artistic-2.0 MD5sum: 12f83b6e02bbbba3d62080796d2edfd0 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/mammaPrintData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/mammaPrintData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/mammaPrintData_1.0.0.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: 1.8.0 Suggests: oligo, pdInfoBuilder License: GPL MD5sum: 2f36735c70c567939060c9f7888086c8 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_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/maqcExpression4plex_1.8.0.zip mac.binary.ver: bin/macosx/contrib/3.1/maqcExpression4plex_1.8.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/maqcExpression4plex_1.8.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MAQCsubset Version: 1.2.0 Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), lumi, methods Suggests: genefilter, codelink License: Artistic-2.0 MD5sum: 76866d9f8fd0782c424c3d469703b091 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/MAQCsubset_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/MAQCsubset_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/MAQCsubset_1.2.0.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: 1.2.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 13434ea3f9767e32424725cf3561212c 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/MAQCsubsetAFX_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/MAQCsubsetAFX_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/MAQCsubsetAFX_1.2.0.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: 1.2.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), lumi License: Artistic-2.0 MD5sum: 8fd8b30dca8b0eb37e920b26ab2fe748 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/MAQCsubsetILM_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/MAQCsubsetILM_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/MAQCsubsetILM_1.2.0.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: 1.0.0 Depends: R (>= 2.15.0) License: GPL (>= 2) MD5sum: 25b699d350bc973d039a2bd182181fcc 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/MEDIPSData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/MEDIPSData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/MEDIPSData_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MEEBOdata Version: 1.2.0 License: LGPL MD5sum: 35179abb0c19ef519625fa9cae67a0d9 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/MEEBOdata_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/MEEBOdata_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/MEEBOdata_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: metaMSdata Version: 1.0.0 License: GPL (>= 2) MD5sum: 265d68aa8f7ef2162238c64eac8394c5 NeedsCompilation: no Title: Example CDF data for the metaMS package Description: Example CDF data for the metaMS package biocViews: ExperimentData, MassSpectrometryData Author: Ron Wehrens [aut, cre], Pietro Franceschi [aut], Georg Weingart [ctb] Maintainer: Ron Wehrens source.ver: src/contrib/metaMSdata_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/metaMSdata_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/metaMSdata_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/metaMSdata_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: minfiData Version: 0.6.0 Depends: R (>= 2.13.0), minfi, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 License: Artistic-2.0 MD5sum: aa50772fbc23c070ba4e43e7bb212c36 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_0.6.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/minfiData_0.6.0.zip mac.binary.ver: bin/macosx/contrib/3.1/minfiData_0.6.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/minfiData_0.6.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: miRNATarget Version: 1.2.0 Depends: R (>= 2.10), Biobase License: GPL MD5sum: c9fd4205dabdeeda54388e153209bc1e 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/miRNATarget_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/miRNATarget_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/miRNATarget_1.2.0.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: 1.0.0 Depends: R (>= 2.14.0) License: LGPL MD5sum: 12842257cb6e72c3a73d5b29415cbf72 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/mitoODEdata_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/mitoODEdata_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/mitoODEdata_1.0.0.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: 1.0.0 Suggests: MMDiff License: LGPL MD5sum: c8b412737d84a0c62c5c05720b2ce6e5 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/MMDiffBamSubset_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/MMDiffBamSubset_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/MMDiffBamSubset_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mosaicsExample Version: 1.0.0 Depends: R (>= 2.11.1) License: GPL (>= 2) MD5sum: f25cd74ad9a11574af01b098e2bd605d 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/mosaicsExample_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/mosaicsExample_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/mosaicsExample_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mouse4302barcodevecs Version: 1.2.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: d9f4c93514dc1d289e4b900bbcde0711 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/mouse4302barcodevecs_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/mouse4302barcodevecs_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/mouse4302barcodevecs_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MSBdata Version: 0.2.0 License: LGPL MD5sum: ab30e73af99c5660e838b105438602eb NeedsCompilation: no Title: Data sets for the book 'Modern Statistics for Biology' Description: Data sets for the book 'Modern Statistics for Biology' biocViews: ExperimentData Author: Wolfgang Huber and Andrzej Oles Maintainer: Wolfgang Huber source.ver: src/contrib/MSBdata_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/MSBdata_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/MSBdata_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/MSBdata_0.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: msdata Version: 0.2.0 Suggests: xcms License: GPL (>= 2) MD5sum: 27afceae2fcd538f7759508432db1c39 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/msdata_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/msdata_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/msdata_0.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics Package: Mulder2012 Version: 0.4.0 Depends: R (>= 2.14), org.Hs.eg.db, KEGG.db Imports: igraph, HTSanalyzeR, PANR, RedeR, pvclust, MASS Suggests: snow License: Artistic-2.0 MD5sum: 176a16aee34a57a5ed41d954c1d2c353 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_0.4.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/Mulder2012_0.4.0.zip mac.binary.ver: bin/macosx/contrib/3.1/Mulder2012_0.4.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Mulder2012_0.4.0.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: 1.0.0 Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4), lumi License: Artistic-2.0 MD5sum: 7c73e52fa3f4d99c4394e3a93cf0400c 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/mvoutData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/mvoutData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/mvoutData_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: NCIgraphData Version: 1.0.0 Depends: R (>= 2.10.0) Suggests: Rgraphviz License: GPL-3 MD5sum: 75bff175a03f5bd6ad0d56fb72197cf1 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/NCIgraphData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/NCIgraphData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/NCIgraphData_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Neve2006 Version: 0.2.0 Depends: R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0), hgu133a.db, annotate License: Artistic-2.0 MD5sum: 12230aef11632b4e555db34ab7e224c3 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/Neve2006_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/Neve2006_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Neve2006_0.2.0.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: 1.0.0 Depends: DEXSeq, DESeq, R (>= 2.10) Suggests: GEOquery, SRAdb License: LGPL MD5sum: 8fb406d3ecf4db3fd29492cea9ca3a2e 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/parathyroid_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/parathyroid_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/parathyroid_1.0.0.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: 1.2.0 Depends: GenomicRanges, R (>= 2.10) Suggests: Rsamtools, GenomicAlignments, GEOquery, SRAdb, GenomicFeatures, BiocStyle License: LGPL MD5sum: cb687894292cc7174922fca997505e26 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/parathyroidSE_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/parathyroidSE_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/parathyroidSE_1.2.0.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: 0.4.0 Suggests: locfit, edgeR, xtable, DEXSeq, DESeq License: LGPL MD5sum: e46c5c3f62d26e3dcca635915870072e 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_0.4.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/pasilla_0.4.0.zip mac.binary.ver: bin/macosx/contrib/3.1/pasilla_0.4.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/pasilla_0.4.0.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: 0.2.0 Suggests: pasilla License: LGPL MD5sum: afbc98b2967d1da8839291d6bfb623d2 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/pasillaBamSubset_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/pasillaBamSubset_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/pasillaBamSubset_0.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: PathNetData Version: 1.0.0 Depends: R (>= 1.14.0) License: GPL-3 MD5sum: 8bec7b511abd5f6035aeb7b51c59f220 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/PathNetData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/PathNetData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/PathNetData_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Hs.hg19 Version: 1.0.0 License: GPL (>= 2) MD5sum: f191681537f6579a4e134c96be71f1b8 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/pcaGoPromoter.Hs.hg19_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/pcaGoPromoter.Hs.hg19_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/pcaGoPromoter.Hs.hg19_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Mm.mm9 Version: 1.0.0 License: GPL (>= 2) MD5sum: 392161113d993306da1b80b6a1d3c6df 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/pcaGoPromoter.Mm.mm9_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/pcaGoPromoter.Mm.mm9_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/pcaGoPromoter.Mm.mm9_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Rn.rn4 Version: 1.0.0 License: GPL (>= 2) MD5sum: ee59f3e60664339221127008495527f1 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/pcaGoPromoter.Rn.rn4_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/pcaGoPromoter.Rn.rn4_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/pcaGoPromoter.Rn.rn4_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pd.atdschip.tiling Version: 0.2.0 Depends: R (>= 2.14.0), methods, RSQLite (>= 0.10.0), oligoClasses (>= 1.15.58), oligo (>= 1.17.3), DBI Imports: Biostrings (>= 2.21.11), IRanges (>= 1.11.31) License: Artistic-2.0 MD5sum: c53c137c8f04ba79699748be4f23ca34 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/pd.atdschip.tiling_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/pd.atdschip.tiling_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/pd.atdschip.tiling_0.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: phastCons100way.UCSC.hg19 Version: 1.0.0 Depends: R (>= 3.0.0), VariantFiltering Imports: utils, IRanges, GenomicRanges, BSgenome License: Artistic-2.0 MD5sum: 2301274848993469b08d585cb386af2d NeedsCompilation: no Title: UCSC phastCons conservation scores Description: UCSC phastCons conservation scores from alignments of 100 vertebrate species biocViews: AnnotationData, Genetics, PhastConsDb, Homo_sapiens Author: Robert Castelo Maintainer: Robert Castelo source.ver: src/contrib/phastCons100way.UCSC.hg19_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/phastCons100way.UCSC.hg19_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/phastCons100way.UCSC.hg19_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/phastCons100way.UCSC.hg19_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ppiData Version: 0.2.0 Depends: graph Imports: AnnotationDbi Suggests: org.Sc.sgd.db, ppiStats License: Artistic-2.0 MD5sum: bbab8e3bdee6bee4c19e11a02cfb6013 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/ppiData_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/ppiData_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ppiData_0.2.0.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: 1.0.0 Depends: R (>= 2.14.0) License: Artistic-2.0 MD5sum: b2811ff6d5d2341fe403034b6895354e 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/prebsdata_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/prebsdata_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/prebsdata_1.0.0.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: 0.4.0 Depends: R (>= 2.9.0), methods, PREDA, Biobase, affy, annotate, gahgu133plus2.db, gahgu133plus2cdf Suggests: hgu133plus2.db, hgu133plus2cdf License: Artistic-2.0 MD5sum: fe885b3295da6c99c148ccf9a542714a 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_0.4.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/PREDAsampledata_0.4.0.zip mac.binary.ver: bin/macosx/contrib/3.1/PREDAsampledata_0.4.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/PREDAsampledata_0.4.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ProData Version: 1.2.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL MD5sum: b758dacf4f5724cf812c6e16618310d9 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/ProData_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/ProData_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ProData_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pRolocdata Version: 1.2.0 Depends: R (>= 2.15), MSnbase Suggests: pRoloc License: GPL-2 MD5sum: 790fab3f72018909a897630f87b160b2 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), Breckels et al. (2013) and Groen et al. biocViews: ExperimentData, MassSpectrometry, Proteomics Author: Laurent Gatto and Lisa M. Breckels Maintainer: Laurent Gatto source.ver: src/contrib/pRolocdata_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/pRolocdata_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/pRolocdata_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/pRolocdata_1.2.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: pumadata Version: 2.0.0 Depends: R (>= 3.0.0), affy (>= 1.41.3), Biobase (>= 2.5.5), puma,oligo License: LGPL MD5sum: 52bc8ce4ff583b21b2c8cf10bec9bba0 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_2.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/pumadata_2.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/pumadata_2.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/pumadata_2.0.0.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: 2.2.0 Depends: methods, PWMEnrich License: GPL-3 MD5sum: 993c5d94fe4fccccae664186d5485614 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_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/PWMEnrich.Dmelanogaster.background_2.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/PWMEnrich.Dmelanogaster.background_2.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/PWMEnrich.Dmelanogaster.background_2.2.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: PWMEnrich.Hsapiens.background Version: 1.0.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: 0e8f3c6cd69af50e03ef330eac85abb7 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/PWMEnrich.Hsapiens.background_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/PWMEnrich.Hsapiens.background_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/PWMEnrich.Hsapiens.background_1.0.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: PWMEnrich.Mmusculus.background Version: 1.0.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: 25a76fb6679747da10adebd567647113 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/PWMEnrich.Mmusculus.background_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/PWMEnrich.Mmusculus.background_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/PWMEnrich.Mmusculus.background_1.0.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: RforProteomics Version: 1.2.1 Imports: R.utils, Biobase, rpx, biocViews, interactiveDisplay, BiocInstaller 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, xtable Enhances: cleaver License: Artistic-2.0 MD5sum: 174aa61f48ee96d34b489f60703e400b 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_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/RforProteomics_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/RforProteomics_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/RforProteomics_1.2.0.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: 1.2.0 Depends: R (>= 2.10.0) Suggests: genefilter, Biobase, hgu133plus2.db License: Artistic-2.0 MD5sum: 40db1f54ae71630466f6a914cbc6e55f 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/rheumaticConditionWOLLBOLD_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/rheumaticConditionWOLLBOLD_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/rheumaticConditionWOLLBOLD_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RIPSeekerData Version: 1.0.0 Depends: RIPSeeker License: GPL-2 MD5sum: a937b9dc84c190d04c05ede5059f2b9f 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/RIPSeekerData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/RIPSeekerData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/RIPSeekerData_1.0.0.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: 1.2.0 Suggests: RMassBank License: Artistic-2.0 MD5sum: 4ca035656e7b0b6ed8173cacb518ea2e NeedsCompilation: no Title: Test dataset for RMassBank Description: Example spectra, example compound list(s) and an example annotation list for a narcotics dataset; required to test RMassBank. The package is described in the man page for RMassBankData. Includes new XCMS test data. biocViews: ExperimentData, MassSpectrometryData Author: Michael Stravs, Emma Schymanski, Steffen Neumann Maintainer: Michael Stravs, Emma Schymanski source.ver: src/contrib/RMassBankData_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/RMassBankData_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/RMassBankData_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/RMassBankData_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RNAinteractMAPK Version: 1.2.0 Depends: R (>= 2.12.0), methods, fields, sparseLDA, RNAinteract Imports: grid, gdata, MASS, genefilter Suggests: qvalue, lattice License: Artistic-2.0 MD5sum: f35237a669a1278180a6665d9c0d0abe 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/RNAinteractMAPK_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/RNAinteractMAPK_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/RNAinteractMAPK_1.2.0.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: e55e8a34aeac6d426d08934360f86045 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/3.1/RNAseqData.HeLa.bam.chr14_0.1.5.zip mac.binary.ver: bin/macosx/contrib/3.1/RNAseqData.HeLa.bam.chr14_0.1.5.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/RNAseqData.HeLa.bam.chr14_0.1.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RNAseqData.HNRNPC.bam.chr14 Version: 0.2.0 Suggests: GenomicAlignments, BiocInstaller License: LGPL MD5sum: 29be928845dbd3c4b74867498ca205bb 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/RNAseqData.HNRNPC.bam.chr14_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/RNAseqData.HNRNPC.bam.chr14_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/RNAseqData.HNRNPC.bam.chr14_0.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: RNAseqData.HeLa.bam.chr14 importsMe: RNAseqData.HeLa.bam.chr14 Package: RnaSeqTutorial Version: 0.2.0 Depends: R (>= 3.0.2), methods, easyRNASeq Suggests: Rsamtools, ShortRead, BSgenome.Dmelanogaster.UCSC.dm3, GenomicAlignments, biomaRt, genomeIntervals License: Artistic-2.0 MD5sum: cf1cd686001131ea0716c5cc8b4e30c3 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/RnaSeqTutorial_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/RnaSeqTutorial_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/RnaSeqTutorial_0.2.0.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: 1.0.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 6fb7e4b0500bcdd728a3406c11d1f7ab 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/seqCNA.annot_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/seqCNA.annot_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/seqCNA.annot_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: serumStimulation Version: 1.0.0 Depends: R (>= 2.10) License: GPL (>= 2) MD5sum: 9d759f18ce54639026c7ff0dac82cb89 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/serumStimulation_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/serumStimulation_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/serumStimulation_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: seventyGeneData Version: 1.0.0 Depends: R (>= 2.13.0) Suggests: Biobase, gdata, limma, breastCancerNKI License: Artistic-2.0 MD5sum: c830472a9745767963a0d35dfd6d982f 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/seventyGeneData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/seventyGeneData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/seventyGeneData_1.0.0.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: 1.0.0 License: GPL (>= 2) MD5sum: 0aa09349c3a8d8d838e18e6aca7e8383 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/simpIntLists_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/simpIntLists_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/simpIntLists_1.0.0.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: 1.10.0 Depends: R (>= 2.4.0), graph Suggests: Rgraphviz License: LGPL MD5sum: 2ee3d31dacce1daf03bab30be25d22ec 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_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/SNAData_1.10.0.zip mac.binary.ver: bin/macosx/contrib/3.1/SNAData_1.10.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/SNAData_1.10.0.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: 1.0.0 Depends: R (>= 2.6.0) Suggests: ALL, hgu95av2.db, SNAGEE License: Artistic-2.0 MD5sum: 4466da8954b93a3e6c0bb550e9834736 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/SNAGEEdata_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/SNAGEEdata_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/SNAGEEdata_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SomatiCAData Version: 1.2.0 Depends: R (>= 2.14) License: Artistic-2.0 MD5sum: 5abdfdf384b8000a3a12594e0a52499c 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/SomatiCAData_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/SomatiCAData_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/SomatiCAData_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SomaticCancerAlterations Version: 1.0.0 Depends: R (>= 3.0.0) Imports: GenomicRanges, exomeCopy, stringr, IRanges Suggests: testthat, ggbio, ggplot2, BiocStyle, knitr License: GPL-3 MD5sum: 147c91aa86fa4e81d9902b6dc224d511 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/SomaticCancerAlterations_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/SomaticCancerAlterations_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/SomaticCancerAlterations_1.0.0.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: 1.6.0 Depends: R (>= 1.6), affy (>= 1.23.4) License: Artistic-2.0 MD5sum: a2a69bcb51cf7622c5290d467183e0b2 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_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/SpikeIn_1.6.0.zip mac.binary.ver: bin/macosx/contrib/3.1/SpikeIn_1.6.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/SpikeIn_1.6.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SpikeInSubset Version: 1.4.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5), affy (>= 1.23.4) License: LGPL MD5sum: 60465401dda0aa62e3da217c01ea2ab3 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_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/SpikeInSubset_1.4.0.zip mac.binary.ver: bin/macosx/contrib/3.1/SpikeInSubset_1.4.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/SpikeInSubset_1.4.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: stemHypoxia Version: 1.0.0 Depends: R (>= 2.14.1) License: GPL (>=2) MD5sum: 70e53af1a6f049b308195cfaa1dea808 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/stemHypoxia_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/stemHypoxia_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/stemHypoxia_1.0.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: stjudem Version: 1.4.0 Depends: R (>= 2.10), utils License: LGPL (>= 2) MD5sum: 475b376ac6c5352e1586593ee0fe0719 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_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/stjudem_1.4.0.zip mac.binary.ver: bin/macosx/contrib/3.1/stjudem_1.4.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/stjudem_1.4.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: synapterdata Version: 1.2.0 Depends: R (>= 2.10), synapter (>= 0.99.6) License: GPL-2 MD5sum: ec37a2854a066ab6d4040faf0195fa53 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/synapterdata_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/synapterdata_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/synapterdata_1.2.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics Package: TargetScoreData Version: 1.0.0 Suggests: TargetScore, gplots License: GPL-2 MD5sum: 901a8184848e501088720c699a9beef3 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/TargetScoreData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/TargetScoreData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/TargetScoreData_1.0.0.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: 1.2.0 Depends: TargetSearch License: GPL (>= 2) MD5sum: a0bb4579541d66731fef988d5ed6b742 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/TargetSearchData_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/TargetSearchData_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/TargetSearchData_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: TBX20BamSubset Version: 1.0.0 Depends: Rsamtools (>= 1.9.8) Imports: xtable License: LGPL MD5sum: 4dea296af4e0ec5776c34d7cb9df957b 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/TBX20BamSubset_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/TBX20BamSubset_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/TBX20BamSubset_1.0.0.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: 1.0.0 License: GPL-2 MD5sum: a07630639e46301dc39e2b749ccc6804 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/TCGAMethylation450k_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/TCGAMethylation450k_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/TCGAMethylation450k_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: tinesath1cdf Version: 1.2.0 License: Artistic-2.0 MD5sum: e2b7fa604e71a2713f97a3a09ab137af 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/tinesath1cdf_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/tinesath1cdf_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/tinesath1cdf_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: XhybCasneuf Package: tinesath1probe Version: 1.2.0 Depends: R (>= 1.6), AnnotationDbi (>= 1.11.9) License: LGPL MD5sum: 5dc557a50a799db1eed324b9b4eca70d 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/tinesath1probe_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/tinesath1probe_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/tinesath1probe_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: tweeDEseqCountData Version: 1.2.0 Depends: Biobase, R (>= 2.10) License: GPL (>=2) MD5sum: cf16fd3832c1216b9b639f2d8b3b258d 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/tweeDEseqCountData_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/tweeDEseqCountData_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/tweeDEseqCountData_1.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: waveTilingData Version: 1.0.0 Depends: R (>= 2.14.0) License: GPL (>= 2) MD5sum: f40ea1b9f12ec4c8c82e560e75153d48 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/waveTilingData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/waveTilingData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/waveTilingData_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: XhybCasneuf Version: 1.2.0 Depends: R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf , RColorBrewer , methods, grid License: Artistic-2.0 MD5sum: 7e2cd0955f8a19c2afc1d935512a634d 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_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/XhybCasneuf_1.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/XhybCasneuf_1.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/XhybCasneuf_1.2.0.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: 1.4.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: a159b5a2523532519fb4929f1b598828 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_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/yeastCC_1.4.0.zip mac.binary.ver: bin/macosx/contrib/3.1/yeastCC_1.4.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/yeastCC_1.4.0.tgz vignettes: vignettes/yeastCC/inst/doc/ hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastExpData Version: 0.10.0 Depends: R (>= 2.4), graph (>= 1.9.26) Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db License: GPL MD5sum: 0ca93f5bfdecda9c4f87721424453cb4 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_0.10.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/yeastExpData_0.10.0.zip mac.binary.ver: bin/macosx/contrib/3.1/yeastExpData_0.10.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/yeastExpData_0.10.0.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: 0.2.0 License: Artistic-2.0 MD5sum: faadac428be6ddea55b67dd9ddb1a495 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/yeastGSData_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/yeastGSData_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/yeastGSData_0.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastNagalakshmi Version: 1.0.0 License: Artistic-2.0 MD5sum: 013009f96b000e565fcf8189a7731c02 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/yeastNagalakshmi_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/yeastNagalakshmi_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/yeastNagalakshmi_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastRNASeq Version: 0.2.0 Depends: R (>= 2.4) Suggests: Biobase, ShortRead, IRanges License: GPL MD5sum: 333a23bb7652f35ffd4c9e94f296beab 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_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/yeastRNASeq_0.2.0.zip mac.binary.ver: bin/macosx/contrib/3.1/yeastRNASeq_0.2.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/yeastRNASeq_0.2.0.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: 0.6.0 Depends: GGBase Imports: Biobase License: Artistic-2.0 MD5sum: 990a23db48faedd2eeae08535796479b 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_0.6.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/yri1kgv_0.6.0.zip mac.binary.ver: bin/macosx/contrib/3.1/yri1kgv_0.6.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/yri1kgv_0.6.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE