Package: affycompData Version: 1.3.1 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp License: GPL (>= 2) MD5sum: e7bee707d4ed3bb2659cbec30682ce4e 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/affycompData_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/affycompData_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/affycompData_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: affydata Version: 1.13.1 Depends: R (>= 2.4.0), affy (>= 1.23.4) Imports: methods Suggests: hgu95av2cdf, hgu133acdf License: GPL (>= 2) MD5sum: a224fa10026eab7bfb5352fbe2a6acfa 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_1.13.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/affydata_1.13.1.zip mac.binary.ver: bin/macosx/contrib/3.1/affydata_1.13.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/affydata_1.13.1.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: 1.1.1 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 2089f6e264122123cd9bac1242821ead 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/Affyhgu133A2Expr_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/Affyhgu133A2Expr_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Affyhgu133A2Expr_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Affyhgu133aExpr Version: 1.3.1 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 139cb656befc05dad0d432a2272c97df 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/Affyhgu133aExpr_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/Affyhgu133aExpr_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Affyhgu133aExpr_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Affyhgu133Plus2Expr Version: 1.0.1 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 35f4121e03322850adfe870caefe68f7 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_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/Affyhgu133Plus2Expr_1.0.1.zip mac.binary.ver: bin/macosx/contrib/3.1/Affyhgu133Plus2Expr_1.0.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Affyhgu133Plus2Expr_1.0.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: AffymetrixDataTestFiles Version: 0.3.1 Depends: R (>= 2.5.0) License: LGPL-2.1 MD5sum: 00095f3639b5a13b5428363e65da7494 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_0.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/AffymetrixDataTestFiles_0.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/AffymetrixDataTestFiles_0.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/AffymetrixDataTestFiles_0.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Affymoe4302Expr Version: 1.3.1 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: fea8d1d7faddd682ae7b0f80ab85a539 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/Affymoe4302Expr_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/Affymoe4302Expr_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Affymoe4302Expr_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: airway Version: 1.0.0 Depends: R (>= 2.10), GenomicRanges Suggests: knitr, GEOquery License: LGPL MD5sum: fc245bd1f806b5e5f1df73957f95b5c8 NeedsCompilation: no Title: SummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014 Description: This package provides a SummarizedExperiment object of read counts in genes for an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. Details on the gene model and read counting procedure are provided in the package vignette. The citation for the experiment is: Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri R Jr, Tantisira KG, Weiss ST, Lu Q. 'RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells.' PLoS One. 2014 Jun 13;9(6):e99625. PMID: 24926665. GEO: GSE52778. biocViews: ExperimentData, RNAseqData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr source.ver: src/contrib/airway_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/airway_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/airway_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/airway_1.0.0.tgz vignettes: vignettes/airway/inst/doc/ hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/airway/inst/doc/airway.R htmlDocs: vignettes/airway/inst/doc/airway.html htmlTitles: "Airway smooth muscle cells" Package: ALL Version: 1.7.1 Depends: R (>= 2.10), Biobase (>= 2.5.5) Suggests: rpart License: Artistic-2.0 MD5sum: 2632b583aaf3bba8ac50eb0ac7924364 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_1.7.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/ALL_1.7.1.zip mac.binary.ver: bin/macosx/contrib/3.1/ALL_1.7.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ALL_1.7.1.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: 1.5.1 Depends: R (>= 2.10), affy (>= 1.23.4) License: GPL-2 MD5sum: 6df7435a6a78e940b816689d9592db91 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_1.5.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/ALLMLL_1.5.1.zip mac.binary.ver: bin/macosx/contrib/3.1/ALLMLL_1.5.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ALLMLL_1.5.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: AmpAffyExample Version: 1.5.1 Depends: R (>= 2.4.0), affy (>= 1.23.4) Suggests: hgu133acdf License: LGPL (>= 2) MD5sum: cd5a35dcb53ab1353a7e185d4b070eca 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_1.5.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/AmpAffyExample_1.5.1.zip mac.binary.ver: bin/macosx/contrib/3.1/AmpAffyExample_1.5.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/AmpAffyExample_1.5.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: antiProfilesData Version: 1.1.1 Depends: Biobase, Suggests: frma, GEOquery, GEOmetadb License: Artistic-2.0 MD5sum: bdc8e3b0c1ea5f1927bcffda36995be1 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/antiProfilesData_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/antiProfilesData_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/antiProfilesData_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ARRmData Version: 1.1.1 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: 5c8d3b10fac1d82d1cdc7c71402f3926 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/ARRmData_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/ARRmData_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ARRmData_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bcellViper Version: 1.1.1 Depends: R(>= 2.14.0), Biobase, methods License: GPL (>=2) MD5sum: 89f740fa4a22faaec120aa4dd8c8df56 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/bcellViper_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/bcellViper_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/bcellViper_1.1.1.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: 1.3.1 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>= 2.0.0) License: GPL-2 MD5sum: 3c19ab6861454bb2a509b0c5868b2190 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/beadarrayExampleData_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/beadarrayExampleData_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/beadarrayExampleData_1.3.1.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: 1.3.1 Imports: beadarray (>= 2.3.18), limma, GEOquery Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db License: GPL-2 MD5sum: 382e28d202ae1723497338c1008b4ae6 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/BeadArrayUseCases_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/BeadArrayUseCases_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/BeadArrayUseCases_1.3.1.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: 1.3.1 Depends: R (>= 2.4.0), marray License: LGPL MD5sum: 65e478ca519d7089aa51a4f7fa66358e 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/beta7_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/beta7_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/beta7_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bladderbatch Version: 1.3.1 Depends: Biobase License: Artistic-2.0 MD5sum: e766c0cea8a583a328d1e59a57c9866c 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/bladderbatch_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/bladderbatch_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/bladderbatch_1.3.1.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: blimaTestingData Version: 1.0.0 Depends: R(>= 3.0.0) Suggests: blima, beadarray, illuminaHumanv4.db, BiocStyle License: GPL-3 MD5sum: 33443b11b593501e324c063320214e7e NeedsCompilation: no Title: Data for testing of the package blima. Description: Experiment data package. The set were prepared using microarray images of human mesenchymal cells treated with various supplements. This package is intended to provide example data to test functionality provided by blima. biocViews: RNAExpressionData Author: Vojtech Kulvait Maintainer: Vojtech Kulvait URL: https://bitbucket.org/kulvait/blima source.ver: src/contrib/blimaTestingData_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/blimaTestingData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/blimaTestingData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/blimaTestingData_1.0.0.tgz vignettes: vignettes/blimaTestingData/inst/doc/blimaTestingData.pdf vignetteTitles: blimaTestingData.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/blimaTestingData/inst/doc/blimaTestingData.R Package: breastCancerMAINZ Version: 1.3.1 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: d761c6aa54a01652eb27a4172eb991da 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/breastCancerMAINZ_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/breastCancerMAINZ_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/breastCancerMAINZ_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerNKI Version: 1.3.1 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 87e5636a01a782932df0fabdf9e5adc1 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/breastCancerNKI_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/breastCancerNKI_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/breastCancerNKI_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: seventyGeneData Package: breastCancerTRANSBIG Version: 1.3.1 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: a2539e69ecb1e8270069605acf45671d 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/breastCancerTRANSBIG_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/breastCancerTRANSBIG_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/breastCancerTRANSBIG_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerUNT Version: 1.3.1 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: dcad2cf5a0b20737d8a94d39d63a6879 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/breastCancerUNT_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/breastCancerUNT_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/breastCancerUNT_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerUPP Version: 1.3.1 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: aff56a8c0eac1691c7a32759c770b9fb 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/breastCancerUPP_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/breastCancerUPP_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/breastCancerUPP_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerVDX Version: 1.3.1 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: a625a6bdc7e47fdcfe63b6a5dc522573 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/breastCancerVDX_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/breastCancerVDX_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/breastCancerVDX_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bronchialIL13 Version: 1.3.1 Depends: R(>= 2.10.0), affy (>= 1.23.4) License: GPL-2 MD5sum: 04a71d63f065c784576b623ce7416a1d 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/bronchialIL13_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/bronchialIL13_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/bronchialIL13_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bsseqData Version: 0.3.1 Depends: R (>= 2.15), bsseq (>= 0.9.6) License: Artistic-2.0 MD5sum: 0b907030205ace128afd037cc2b01d79 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_0.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/bsseqData_0.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/bsseqData_0.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/bsseqData_0.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cancerdata Version: 1.3.1 Depends: R (>= 2.10.1), Biobase License: GPL (>= 2) MD5sum: 8960c0920cdd0d598557d8087be3f20e 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/cancerdata_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/cancerdata_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/cancerdata_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CCl4 Version: 1.3.1 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), limma License: Artistic-2.0 MD5sum: 1ed7cc8ac4df413d999c1f3ec2d209ea 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/CCl4_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/CCl4_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/CCl4_1.3.1.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: 1.3.1 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: 36f289fce0f8e46db1c11d3de14e6ddd 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/ccTutorial_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/ccTutorial_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ccTutorial_1.3.1.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: 0.3.1 Depends: R (>= 2.12.0), GGBase (>= 3.9.0), GGtools, Biobase Suggests: SNPlocs.Hsapiens.dbSNP.20101109 License: Artistic-2.0 MD5sum: 0384df0a39f18a0e3840007362094f9d 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_0.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/ceu1kg_0.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/ceu1kg_0.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ceu1kg_0.3.1.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: 0.7.1 Depends: R (>= 3.0), GGBase Imports: Biobase License: Artistic-2.0 MD5sum: 001a6be0eb57244fd1757a3b5f673cad 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_0.7.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/ceu1kgv_0.7.1.zip mac.binary.ver: bin/macosx/contrib/3.1/ceu1kgv_0.7.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ceu1kgv_0.7.1.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: 0.3.1 Depends: R (>= 2.12.0), GGBase, Biobase Imports: GGtools License: Artistic-2.0 MD5sum: ff6a44c27555e65867fe991492077b0e 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_0.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/ceuhm3_0.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/ceuhm3_0.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ceuhm3_0.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cgdv17 Version: 0.3.2 Depends: R (>= 2.15), VariantAnnotation, org.Hs.eg.db, methods, GGtools, TxDb.Hsapiens.UCSC.hg19.knownGene, parallel Imports: Biobase, IRanges, S4Vectors License: Artistic 2.0 MD5sum: 25784c3f13995752f0b9b88e5a9f033f 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_0.3.2.tar.gz win.binary.ver: bin/windows/contrib/3.1/cgdv17_0.3.2.zip mac.binary.ver: bin/macosx/contrib/3.1/cgdv17_0.3.2.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/cgdv17_0.3.2.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: 1.1.2 Depends: R (>= 3.0.1) License: GPL-3 MD5sum: 7dc89982c83634d93bc059efa8f274d0 NeedsCompilation: no Title: Data Packages for ChAMP package Description: Provides datasets needed for ChAMP including a test dataset and blood controls for CNA analysis biocViews: ExpressionData, IlluminaChip Author: Tiffany Morris, Lee Butcher and Andrew Teschendorff Maintainer: Tiffany Morris source.ver: src/contrib/ChAMPdata_1.1.2.tar.gz win.binary.ver: bin/windows/contrib/3.1/ChAMPdata_1.1.2.zip mac.binary.ver: bin/macosx/contrib/3.1/ChAMPdata_1.1.2.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ChAMPdata_1.1.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: charmData Version: 1.1.1 Depends: R(>= 2.11.0), charm, pd.charm.hg18.example License: LGPL (>= 2) MD5sum: fb64b2d0b20830729189d86eaf560556 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/charmData_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/charmData_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/charmData_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cheung2010 Version: 0.3.2 Depends: R (>= 2.13.0), Biobase, GGtools, GenomicRanges, hgfocus.db Imports: AnnotationDbi Suggests: SNPlocs.Hsapiens.dbSNP.20120608 Enhances: parallel License: Artistic-2.0 MD5sum: ece47100241929cf4d3d360402cf7a60 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_0.3.2.tar.gz win.binary.ver: bin/windows/contrib/3.1/cheung2010_0.3.2.zip mac.binary.ver: bin/macosx/contrib/3.1/cheung2010_0.3.2.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/cheung2010_0.3.2.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: 1.3.1 Depends: affy,qvalue,limma,hexbin,statmod License: MIT MD5sum: 39736820bf2df4497221438949001070 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/ChimpHumanBrainData_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/ChimpHumanBrainData_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ChimpHumanBrainData_1.3.1.tgz vignettes: vignettes/ChimpHumanBrainData/inst/doc/DiffExpressVignette.pdf vignetteTitles: DiffExpressVignette.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: chipenrich.data Version: 1.1.8 Depends: R (>= 2.15.0) Imports: methods, GenomicRanges (>= 1.10.0), IRanges (>= 1.16.0), BiocGenerics (>= 0.2.0) License: GPL-3 MD5sum: ff408ce9d2dc9e1c17946d1b4ff9fd6e 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, cre], Raymond G. Cavalcante [aut, cre], Laura J. Scott [ths], Maureen A. Sartor [ths] Maintainer: Ryan P. Welch , Chee Lee , Raymond G. Cavalcante source.ver: src/contrib/chipenrich.data_1.1.8.tar.gz win.binary.ver: bin/windows/contrib/3.1/chipenrich.data_1.1.8.zip mac.binary.ver: bin/macosx/contrib/3.1/chipenrich.data_1.1.8.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/chipenrich.data_1.1.8.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: ChIPXpressData Version: 1.3.2 Depends: bigmemory License: GPL (>=2) OS_type: unix MD5sum: 53462e9c27ee0d7939f0171a2997628c 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_1.3.2.tar.gz mac.binary.ver: bin/macosx/contrib/3.1/ChIPXpressData_1.3.2.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ChIPXpressData_1.3.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CLL Version: 1.5.1 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: LGPL MD5sum: 488405be88090d004abb50d1a44772f4 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_1.5.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/CLL_1.5.1.zip mac.binary.ver: bin/macosx/contrib/3.1/CLL_1.5.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/CLL_1.5.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cMap2data Version: 1.1.1 Depends: R (>= 2.10) License: GPL-3 MD5sum: 4ddd6c75886466dbb02a6c906e2e850c 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/cMap2data_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/cMap2data_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/cMap2data_1.1.1.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: 1.1.1 Depends: R (>= 2.10), cnvGSA License: LGPL MD5sum: 6fc867d7fff2df97e8f6cbef266d3b9b 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/cnvGSAdata_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/cnvGSAdata_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/cnvGSAdata_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: COHCAPanno Version: 1.1.1 Depends: R (>= 2.10) License: GPL-3 MD5sum: e6fa76a841ef8ed5cb4f9fe15e54165a 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/COHCAPanno_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/COHCAPanno_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/COHCAPanno_1.1.1.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: 1.7.1 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: 1da3cd47a3a55712c00abc381c4c2486 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_1.7.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/colonCA_1.7.1.zip mac.binary.ver: bin/macosx/contrib/3.1/colonCA_1.7.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/colonCA_1.7.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ConnectivityMap Version: 1.1.1 Depends: R (>= 2.15.1) Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: ffecd181ad7509b59245940c166bb279 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/ConnectivityMap_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/ConnectivityMap_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ConnectivityMap_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: COPDSexualDimorphism.data Version: 1.1.1 License: LGPL-2.1 MD5sum: e86af3fd48e7d5a59040f9a7439d3734 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/COPDSexualDimorphism.data_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/COPDSexualDimorphism.data_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/COPDSexualDimorphism.data_1.1.1.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: 1.1.1 Depends: R (>= 2.13.0), minfi, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 License: Artistic-2.0 MD5sum: ce807b0dae43e76fbd33f0df21f9a8fc 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/CopyNumber450kData_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/CopyNumber450kData_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/CopyNumber450kData_1.1.1.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: 1.1.1 Depends: R (>= 3.0.2) Imports: GenomicRanges, VariantAnnotation Suggests: testthat, BiocStyle, knitr License: GPL-3 MD5sum: e9aa25049838845f21d366ba7528269a 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/COSMIC.67_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/COSMIC.67_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/COSMIC.67_1.1.1.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: CRCL18 Version: 1.0.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 1be18ce5a442ba24c1506c02dcc8ed76 NeedsCompilation: no Title: CRC cell line dataset Description: colorectal cancer mRNA and miRNA on 18 cell lines biocViews: ExperimentData Author: Claudio Isella Maintainer: Claudio Isella source.ver: src/contrib/CRCL18_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/CRCL18_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/CRCL18_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/CRCL18_1.0.0.tgz vignettes: vignettes/CRCL18/inst/doc/CRCL18Vignette.pdf vignetteTitles: CRCL18 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CRCL18/inst/doc/CRCL18Vignette.R Package: curatedBladderData Version: 1.1.1 Depends: R (>= 2.10.0), affy Suggests: BiocStyle, survival, xtable, sva, genefilter, logging License: Artistic-2.0 MD5sum: b6b1f4c63f6156939a6f8c032b32f8bc 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/curatedBladderData_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/curatedBladderData_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/curatedBladderData_1.1.1.tgz vignettes: vignettes/curatedBladderData/inst/doc/curatedBladderData_vignette.pdf vignetteTitles: curatedBladderData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: curatedCRCData Version: 1.1.2 Depends: R (>= 2.10.0), nlme Suggests: survival,sva,BiocStyle, xtable, genefilter, logging, Biobase License: Artistic-2.0 MD5sum: 113b9c9dc7f36b58fd6faf229feecf9e 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_1.1.2.tar.gz win.binary.ver: bin/windows/contrib/3.1/curatedCRCData_1.1.2.zip mac.binary.ver: bin/macosx/contrib/3.1/curatedCRCData_1.1.2.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/curatedCRCData_1.1.2.tgz vignettes: vignettes/curatedCRCData/inst/doc/curatedCRCData_vignette.pdf vignetteTitles: curatedCRCData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: curatedOvarianData Version: 1.3.5 Depends: R (>= 2.10.0), affy Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle License: Artistic-2.0 MD5sum: 594a0a6aa3cc6f5830505760b0d070ae 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_1.3.5.tar.gz win.binary.ver: bin/windows/contrib/3.1/curatedOvarianData_1.3.5.zip mac.binary.ver: bin/macosx/contrib/3.1/curatedOvarianData_1.3.5.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/curatedOvarianData_1.3.5.tgz vignettes: vignettes/curatedOvarianData/inst/doc/curatedOvarianData_vignette.pdf vignetteTitles: curatedOvarianData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: davidTiling Version: 1.5.1 Depends: R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db License: LGPL MD5sum: 650c044a133902656f09705f6c49a8d8 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_1.5.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/davidTiling_1.5.1.zip mac.binary.ver: bin/macosx/contrib/3.1/davidTiling_1.5.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/davidTiling_1.5.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: derfinderData Version: 1.0.0 Depends: R(>= 3.1.1) Suggests: devtools (>= 1.6), knitcitations (>= 1.0.1), knitr (>= 1.6), knitrBootstrap (>= 0.9.0), RefManageR, rmarkdown (>= 0.3.3), License: Artistic-2.0 MD5sum: d909d41f119b57fb2d721736f53eb2d0 NeedsCompilation: no Title: Processed BigWigs from BrainSpan for examples Description: Processed 22 samples from BrainSpan keeping only the information for chromosome 21. Data is stored in the BigWig format and is used for examples in other packages. biocViews: ExperimentData, RNAseqData Author: Leonardo Collado-Torres [aut, cre], Andrew Jaffe [aut], Jeffrey Leek [aut, ths] Maintainer: Leonardo Collado-Torres URL: https://github.com/lcolladotor/derfinderData VignetteBuilder: knitr source.ver: src/contrib/derfinderData_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/derfinderData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/derfinderData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/derfinderData_1.0.0.tgz vignettes: vignettes/derfinderData/inst/doc/ hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/derfinderData/inst/doc/derfinderData.R htmlDocs: vignettes/derfinderData/inst/doc/derfinderData.html htmlTitles: "Introduction to derfinderData" Package: DeSousa2013 Version: 1.1.1 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: e553037b3a0993e913b1d58e2a2e0d04 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/DeSousa2013_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/DeSousa2013_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/DeSousa2013_1.1.1.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: 1.5.1 Depends: R(>= 2.11.0), Biobase License: GPL (>=2) MD5sum: 30837b86167d2e87149a47b3d624eed5 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_1.5.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/DLBCL_1.5.1.zip mac.binary.ver: bin/macosx/contrib/3.1/DLBCL_1.5.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/DLBCL_1.5.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: DMRcatedata Version: 1.1.1 Depends: R (>= 3.0.2) License: GPL-3 MD5sum: 20edebaa0a4bca75bd11abf175040f54 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/DMRcatedata_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/DMRcatedata_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/DMRcatedata_1.1.1.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: 1.3.1 Depends: EBImage, parallel License: Artistic-2.0 MD5sum: 65cde792a66ef3fea09f0b46167d5866 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/DonaPLLP2013_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/DonaPLLP2013_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/DonaPLLP2013_1.3.1.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: 1.1.1 Depends: R (>= 2.15.1), GenomicRanges Imports: BiocGenerics Suggests: RUnit, networkBMA License: GPL MD5sum: be6c9ae12bf52645b378e1f09fb7ea53 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/DREAM4_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/DREAM4_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/DREAM4_1.1.1.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: 0.3.1 Depends: R (>= 2.10.1), methods, Biobase (>= 2.5.5) Suggests: survival, chron License: Artistic-2.0 MD5sum: aa04ea2a9b44ebb3e69352097b88cc0f 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_0.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/dressCheck_0.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/dressCheck_0.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/dressCheck_0.3.1.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: 1.1.1 Depends: R (>= 2.10) License: GPL-3 MD5sum: 0dccfc0c8c8fb103052020afb09b1f1c 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/DrugVsDiseasedata_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/DrugVsDiseasedata_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/DrugVsDiseasedata_1.1.1.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: 0.3.1 Depends: R (>= 2.15.0), utils, GenomicRanges, Biobase, GGBase License: Artistic-2.0 MD5sum: 1856673d4eccdaf399bfc4ab6c56e920 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_0.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/dsQTL_0.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/dsQTL_0.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/dsQTL_0.3.1.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: 1.1.1 Depends: R (>= 2.10) License: GPL-3 MD5sum: 0079a5574709c183c64b4f7b508f7c78 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/DvDdata_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/DvDdata_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/DvDdata_1.1.1.tgz vignettes: vignettes/DvDdata/inst/doc/DvDdata.pdf vignetteTitles: DvDdata hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DvDdata/inst/doc/DvDdata.R Package: dyebiasexamples Version: 1.3.1 Depends: R (>= 1.4.1), marray, GEOquery Suggests: dyebias, convert, Biobase License: GPL-3 MD5sum: 3c45374a27787d71748be4219ea6adbf 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/dyebiasexamples_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/dyebiasexamples_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/dyebiasexamples_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Package: EatonEtAlChIPseq Version: 0.3.1 Depends: GenomicRanges (>= 1.5.42), ShortRead, rtracklayer License: Artistic 2.0 MD5sum: 92b36e73386c3120711464aa1407e1d7 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_0.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/EatonEtAlChIPseq_0.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/EatonEtAlChIPseq_0.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/EatonEtAlChIPseq_0.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ecoliLeucine Version: 1.5.1 Depends: R (>= 1.9.0), affy (>= 1.23.4), ecolicdf License: GPL (>= 2) MD5sum: 964c738529f0c9aa636edd1e662345a8 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_1.5.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/ecoliLeucine_1.5.1.zip mac.binary.ver: bin/macosx/contrib/3.1/ecoliLeucine_1.5.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ecoliLeucine_1.5.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: encoDnaseI Version: 0.3.1 Depends: R (>= 2.15.0), methods, Biobase (>= 2.5.5), lattice, GGtools, GGBase Suggests: GGdata License: Artistic-2.0 MD5sum: 7f618f1fd7a9e82d0d9345c89a1d466e 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_0.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/encoDnaseI_0.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/encoDnaseI_0.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/encoDnaseI_0.3.1.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: 1.11.1 Depends: R (>= 1.9.0), affy (>= 1.4) Suggests: Biobase (>= 1.13.16), affy, vsn, hgu95av2.db, genefilter License: LGPL MD5sum: e9594ded0e5472ffb71b9bd288dddb02 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_1.11.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/estrogen_1.11.1.zip mac.binary.ver: bin/macosx/contrib/3.1/estrogen_1.11.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/estrogen_1.11.1.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: 1.5.6 Depends: xcms License: LGPL MD5sum: 9f6f9be8104b31582dd83e3e24829098 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_1.5.6.tar.gz win.binary.ver: bin/windows/contrib/3.1/faahKO_1.5.6.zip mac.binary.ver: bin/macosx/contrib/3.1/faahKO_1.5.6.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/faahKO_1.5.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fabiaData Version: 1.3.1 Depends: R (>= 2.10.0), Biobase Imports: utils Suggests: fabia License: LGPL (>= 2.1) MD5sum: f7168466184e1718b4c599f8e124ba0a 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/fabiaData_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/fabiaData_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/fabiaData_1.3.1.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: facopy.annot Version: 1.0.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: c30d6a6aa57ef486b279964bc8c9ecb9 NeedsCompilation: no Title: Annotation for the copy number alteration association and enrichment analyses with facopy Description: Provides facopy with genome annotation on chromosome arms, genomic features and copy number alterations. biocViews: AnnotationData, FunctionalAnnotation Author: David Mosen-Ansorena Maintainer: David Mosen-Ansorena source.ver: src/contrib/facopy.annot_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/facopy.annot_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/facopy.annot_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/facopy.annot_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: facsDorit Version: 1.7.1 Depends: R (>= 1.9.1), prada (>= 1.0.5) License: GPL-2 MD5sum: fff7129fffef7260b8422e8fb323b177 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_1.7.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/facsDorit_1.7.1.zip mac.binary.ver: bin/macosx/contrib/3.1/facsDorit_1.7.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/facsDorit_1.7.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: FANTOM3and4CAGE Version: 1.1.1 Depends: R (>= 2.15.0) License: GPL-3 MD5sum: 68c40771ed9c8517a036c9efdec7201c 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/FANTOM3and4CAGE_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/FANTOM3and4CAGE_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/FANTOM3and4CAGE_1.1.1.tgz vignettes: vignettes/FANTOM3and4CAGE/inst/doc/FANTOM3and4CAGE.pdf vignetteTitles: FANTOM3and4CAGE hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FANTOM3and4CAGE/inst/doc/FANTOM3and4CAGE.R Package: ffpeExampleData Version: 1.3.1 Depends: R (>= 2.10.0), lumi Suggests: genefilter, affy License: GPL (>2) MD5sum: c31fe8960d5110d1ce477cc826139495 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/ffpeExampleData_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/ffpeExampleData_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ffpeExampleData_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fibroEset Version: 1.7.1 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: 68ffaf6357cc8e0269725308b0b8b3a0 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_1.7.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/fibroEset_1.7.1.zip mac.binary.ver: bin/macosx/contrib/3.1/fibroEset_1.7.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/fibroEset_1.7.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fission Version: 1.0.0 Depends: R (>= 2.10), GenomicRanges Suggests: knitr License: LGPL MD5sum: 74ab146d2061a4265ee71cc3be2f77b0 NeedsCompilation: no Title: SummarizedExperiment for time course RNA-Seq of fission yeast in response to stress, by Leong et al., Nat Commun 2014. Description: This package provides a SummarizedExperiment object of read counts in genes for a time course RNA-Seq experiment of fission yeast (Schizosaccharomyces pombe) in response to oxidative stress (1M sorbitol treatment) at 0, 15, 30, 60, 120 and 180 mins. The samples are further divided between a wild-type group and a group with deletion of atf21. The read count matrix was prepared and provided by the author of the study: Leong HS, Dawson K, Wirth C, Li Y, Connolly Y, Smith DL, Wilkinson CR, Miller CJ. "A global non-coding RNA system modulates fission yeast protein levels in response to stress". Nat Commun 2014 May 23;5:3947. PMID: 24853205. GEO: GSE56761. biocViews: ExperimentData, RNAseqData, Yeast Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr source.ver: src/contrib/fission_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/fission_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/fission_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/fission_1.0.0.tgz vignettes: vignettes/fission/inst/doc/ hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/fission/inst/doc/fission.R htmlDocs: vignettes/fission/inst/doc/fission.html htmlTitles: "Fission yeast time course" Package: Fletcher2013a Version: 1.1.1 Depends: R (>= 2.15), limma Imports: Biobase ,VennDiagram, gplots,grid License: GPL (>= 2) MD5sum: 119f5e42982f9a4c7834f11aca50aacc 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/Fletcher2013a_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/Fletcher2013a_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Fletcher2013a_1.1.1.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: 1.1.1 Depends: R (>= 2.15), Fletcher2013a, biomaRt, VennDiagram, RTN (>= 1.1.2), RedeR (>= 1.8.1) Imports: RColorBrewer, corrgram License: GPL (>= 2) MD5sum: bb6ce43c7c2a513623704681296869c0 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/Fletcher2013b_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/Fletcher2013b_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Fletcher2013b_1.1.1.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: 1.1.1 Depends: R (>= 2.12.2), flowCore Imports: methods License: Artistic-2.0 MD5sum: c9de5fcd90b0a64840d2ee62b22d8a8b 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/flowFitExampleData_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/flowFitExampleData_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/flowFitExampleData_1.1.1.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: 1.3.1 Depends: R (>= 2.13.0), minfi (>= 1.8.0) License: Artistic-2.0 MD5sum: 3ce2cca2c41fcf9837f22393245d6f12 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/FlowSorted.Blood.450k_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/FlowSorted.Blood.450k_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/FlowSorted.Blood.450k_1.3.1.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: 1.1.1 Depends: R (>= 2.13.0), minfi License: Artistic-2.0 MD5sum: 9433e6e4447fa73c8331ce8b79f4f236 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/FlowSorted.DLPFC.450k_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/FlowSorted.DLPFC.450k_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/FlowSorted.DLPFC.450k_1.1.1.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: 2.1.1 License: GPL-2 MD5sum: a111418364340d5e2c7a713049cfab28 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_2.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/flowWorkspaceData_2.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/flowWorkspaceData_2.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/flowWorkspaceData_2.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: frmaExampleData Version: 1.1.1 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 1a620f72e50b95c68a3d5506e01e060a 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/frmaExampleData_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/frmaExampleData_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/frmaExampleData_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: FunciSNP.data Version: 1.1.0 Depends: R (>= 2.14.0) Imports: rtracklayer License: GPL-3 MD5sum: 57ec750b3746fd46892bc784706cf087 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_1.1.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/FunciSNP.data_1.1.0.zip mac.binary.ver: bin/macosx/contrib/3.1/FunciSNP.data_1.1.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/FunciSNP.data_1.1.0.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: 2.3.1 Depends: R (>= 2.10) Suggests: gage, pathview, genefilter License: GPL (>=2.0) MD5sum: eb2af827bbc42d0741fd0460059ab7ca 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_2.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/gageData_2.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/gageData_2.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/gageData_2.3.1.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: gaschYHS Version: 1.3.1 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 25d89e7d1d63c4df2025ccd2be78de9d 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/gaschYHS_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/gaschYHS_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/gaschYHS_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gatingMLData Version: 2.6.1 Depends: R (>= 1.9.0) Suggests: flowUtils License: GPL MD5sum: 1d5d8a75c5cb31b7287e088fc68ad50e 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_2.6.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/gatingMLData_2.6.1.zip mac.binary.ver: bin/macosx/contrib/3.1/gatingMLData_2.6.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/gatingMLData_2.6.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gcspikelite Version: 1.3.1 Depends: R (>= 2.5.0) License: LGPL MD5sum: 68b492ed1ead5fcc5eea663a0d5d7421 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/gcspikelite_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/gcspikelite_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/gcspikelite_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: geneLenDataBase Version: 1.1.1 Depends: R (>= 2.11.0) Imports: utils, rtracklayer, GenomicFeatures (>= 1.3.15) License: LGPL (>= 2) MD5sum: 68c80e3478111bea670701b38611c75a 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/geneLenDataBase_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/geneLenDataBase_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/geneLenDataBase_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GGdata Version: 1.3.1 Depends: R (>= 2.12.0), methods, Biobase (>= 2.5.5), GGBase, snpStats, illuminaHumanv1.db, AnnotationDbi Enhances: GGtools License: LGPL MD5sum: 7fcf28485f5923fb0f7aabc283f3a8bb 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/GGdata_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/GGdata_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/GGdata_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ggtut suggestsMe: encoDnaseI Package: ggtut Version: 0.3.2 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: 66e620916f8e53bbf2336a449a7ca23f 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_0.3.2.tar.gz win.binary.ver: bin/windows/contrib/3.1/ggtut_0.3.2.zip mac.binary.ver: bin/macosx/contrib/3.1/ggtut_0.3.2.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ggtut_0.3.2.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: golubEsets Version: 1.7.1 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: LGPL MD5sum: 7bebabeefc7a6b9d95074f99e894ca77 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_1.7.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/golubEsets_1.7.1.zip mac.binary.ver: bin/macosx/contrib/3.1/golubEsets_1.7.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/golubEsets_1.7.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GSBenchMark Version: 1.0.0 Depends: R (>= 2.13.1) License: GPL-2 MD5sum: df247c44d2d0554692f755f90f9e48c3 NeedsCompilation: no Title: Gene Set Benchmark Description: Benchmarks for Machine Learning Analysis of the Gene Sets. The package contains a list of pathways and gene expression data sets used in "Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)" (2010) by Eddy et al. biocViews: GeneRegulation, Pathways, Microarray, GeneExpression Author: Bahman Afsari , Elana J. Fertig Maintainer: Bahman Afsari source.ver: src/contrib/GSBenchMark_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/GSBenchMark_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/GSBenchMark_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/GSBenchMark_1.0.0.tgz vignettes: vignettes/GSBenchMark/inst/doc/GSBenchMark.pdf vignetteTitles: Working with the GSBenchMark package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GSBenchMark/inst/doc/GSBenchMark.R Package: GSVAdata Version: 1.1.1 Depends: R (>= 2.10), Biobase, GSEABase, hgu95a.db License: GPL (>= 2) MD5sum: 6b34fd05b9514c702d5578b615f2d16c 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/GSVAdata_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/GSVAdata_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/GSVAdata_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GWASdata Version: 1.3.2 Depends: GWASTools License: Artistic-2.0 MD5sum: 41c1f4f79feec4d34a2d40f8ac8a5725 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_1.3.2.tar.gz win.binary.ver: bin/windows/contrib/3.1/GWASdata_1.3.2.zip mac.binary.ver: bin/macosx/contrib/3.1/GWASdata_1.3.2.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/GWASdata_1.3.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: h5vcData Version: 1.99.1 Suggests: h5vc License: GPL (>= 3) MD5sum: 12a680d7d8db0664a6e57c3f5e0b8c52 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_1.99.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/h5vcData_1.99.1.zip mac.binary.ver: bin/macosx/contrib/3.1/h5vcData_1.99.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/h5vcData_1.99.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap100khind Version: 1.7.1 Suggests: oligo License: GPL MD5sum: b8b0a0a434646bc6cdc54b86a011f4aa 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_1.7.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/hapmap100khind_1.7.1.zip mac.binary.ver: bin/macosx/contrib/3.1/hapmap100khind_1.7.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/hapmap100khind_1.7.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap100kxba Version: 1.7.1 Suggests: oligo License: GPL MD5sum: 53da81519750562aa38d8cf0b5e948bf 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_1.7.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/hapmap100kxba_1.7.1.zip mac.binary.ver: bin/macosx/contrib/3.1/hapmap100kxba_1.7.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/hapmap100kxba_1.7.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap500knsp Version: 1.7.1 Suggests: oligo License: GPL MD5sum: 64325d945277d6c63bfcd0d2d8e3e63f 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_1.7.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/hapmap500knsp_1.7.1.zip mac.binary.ver: bin/macosx/contrib/3.1/hapmap500knsp_1.7.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/hapmap500knsp_1.7.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap500ksty Version: 1.7.1 Suggests: oligo License: GPL MD5sum: a7f36301f31ff0004e3c0ed17def6a71 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_1.7.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/hapmap500ksty_1.7.1.zip mac.binary.ver: bin/macosx/contrib/3.1/hapmap500ksty_1.7.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/hapmap500ksty_1.7.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmapsnp5 Version: 1.7.1 Suggests: oligo License: GPL MD5sum: 022d311ec89f93eff38532d4358088d5 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_1.7.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/hapmapsnp5_1.7.1.zip mac.binary.ver: bin/macosx/contrib/3.1/hapmapsnp5_1.7.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/hapmapsnp5_1.7.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmapsnp6 Version: 1.7.1 Depends: R (>= 2.15) Suggests: oligo, oligoClasses License: GPL MD5sum: 849edc1235024bc938052f5038b10e0e 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_1.7.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/hapmapsnp6_1.7.1.zip mac.binary.ver: bin/macosx/contrib/3.1/hapmapsnp6_1.7.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/hapmapsnp6_1.7.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: harbChIP Version: 1.3.1 Depends: R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5), Biostrings Imports: methods, stats License: Artistic-2.0 MD5sum: 2cc7479ae1b431face28ea48f5d7794b 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/harbChIP_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/harbChIP_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/harbChIP_1.3.1.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: 1.5.1 Depends: R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots, limma, vcd, LSD,EBImage Suggests: BiocStyle License: Artistic-2.0 MD5sum: 851470a25441a61581bfc87cdaf488e2 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_1.5.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/HD2013SGI_1.5.1.zip mac.binary.ver: bin/macosx/contrib/3.1/HD2013SGI_1.5.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/HD2013SGI_1.5.1.tgz vignettes: vignettes/HD2013SGI/inst/doc/HD2013SGI.pdf vignetteTitles: HD2013SGI hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HD2013SGI/inst/doc/HD2013SGI.R Package: healthyFlowData Version: 1.3.1 Depends: R (>= 2.15.0), flowCore Imports: methods License: Artistic-2.0 MD5sum: 69f8c7acb2e0bef0ae3616b6f477a8c8 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/healthyFlowData_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/healthyFlowData_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/healthyFlowData_1.3.1.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: 1.3.1 License: LGPL MD5sum: d9bed90046d876e010d8ea787da8624c 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/HEEBOdata_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/HEEBOdata_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/HEEBOdata_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu133abarcodevecs Version: 1.3.1 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: a7e1e7190d60df8980df03924155723e 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/hgu133abarcodevecs_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/hgu133abarcodevecs_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/hgu133abarcodevecs_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu133plus2barcodevecs Version: 1.3.1 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 98a0d99a2f1d8f3967660a32daf8470a 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/hgu133plus2barcodevecs_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/hgu133plus2barcodevecs_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/hgu133plus2barcodevecs_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu2beta7 Version: 1.5.1 Depends: R (>= 2.0.0) License: Artistic-2.0 MD5sum: 1528a90247e4d06e4aa937cfb1f619d8 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_1.5.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/hgu2beta7_1.5.1.zip mac.binary.ver: bin/macosx/contrib/3.1/hgu2beta7_1.5.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/hgu2beta7_1.5.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: HiCDataHumanIMR90 Version: 1.0.0 Depends: R (>= 2.10) Suggests: HiTC License: GPL-3 MD5sum: af1c264664242546fef1e9d8ec19af28 NeedsCompilation: no Title: Human IMR90 Fibroblast HiC data from Dixon et al. 2012 Description: The HiC data from Human Fibroblast IMR90 cell line (HindIII restriction) was retrieved from the GEO website, accession number GSE35156 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35156). The raw reads were processed as explained in Dixon et al. (Nature 2012). biocViews: ExperimentData, HighThroughputSequencingData Author: Nicolas Servant Maintainer: Nicolas Servant source.ver: src/contrib/HiCDataHumanIMR90_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/HiCDataHumanIMR90_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/HiCDataHumanIMR90_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/HiCDataHumanIMR90_1.0.0.tgz vignettes: vignettes/HiCDataHumanIMR90/inst/doc/HiC_Human_IMR90.pdf vignetteTitles: HiC Data Human Fibroblast Dixon et al. 2012 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HiCDataHumanIMR90/inst/doc/HiC_Human_IMR90.R Package: HiCDataLymphoblast Version: 1.1.1 Suggests: GOTHiC, ShortRead License: GPL-3 MD5sum: 75f581b9651fa2bdc40039ca4a156b6e 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/HiCDataLymphoblast_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/HiCDataLymphoblast_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/HiCDataLymphoblast_1.1.1.tgz vignettes: vignettes/HiCDataLymphoblast/inst/doc/package_vignettes.pdf vignetteTitles: package_vignettes.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Hiiragi2013 Version: 1.1.3 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: 75bcdc453dbc23b60e1f3b543ac3a15f 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_1.1.3.tar.gz win.binary.ver: bin/windows/contrib/3.1/Hiiragi2013_1.1.3.zip mac.binary.ver: bin/macosx/contrib/3.1/Hiiragi2013_1.1.3.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Hiiragi2013_1.1.3.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: 1.5.1 License: GPL (>= 2) MD5sum: cba98413e923a2fb4f1b402d9268fb6b 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_1.5.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/HIVcDNAvantWout03_1.5.1.zip mac.binary.ver: bin/macosx/contrib/3.1/HIVcDNAvantWout03_1.5.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/HIVcDNAvantWout03_1.5.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hmyriB36 Version: 1.1.1 Depends: R (>= 2.13.0), methods, Biobase (>= 2.5.5), GGBase Suggests: GGtools, illuminaHumanv1.db License: Artistic-2.0 MD5sum: 75bedb6e9a3ca2a9166d9c89e64769c3 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/hmyriB36_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/hmyriB36_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/hmyriB36_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ggtut suggestsMe: ind1KG Package: HSMMSingleCell Version: 1.0.0 Depends: R (>= 2.10), VGAM (>= 0.9-5) License: Artistic-2.0 MD5sum: 08ee795141fe5c25c487d5939b598964 NeedsCompilation: no Title: Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM) Description: Skeletal myoblasts undergo a well-characterized sequence of morphological and transcriptional changes during differentiation. In this experiment, primary human skeletal muscle myoblasts (HSMM) were expanded under high mitogen conditions (GM) and then differentiated by switching to low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several hundred cells taken over a time-course of serum-induced differentiation. Between 49 and 77 cells were captured at each of four time points (0, 24, 48, 72 hours) following serum switch using the Fluidigm C1 microfluidic system. RNA from each cell was isolated and used to construct mRNA-Seq libraries, which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell. biocViews: HighThroughputSequencingData, RNAseqData Author: Cole Trapnell Maintainer: Cole Trapnell source.ver: src/contrib/HSMMSingleCell_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/HSMMSingleCell_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/HSMMSingleCell_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/HSMMSingleCell_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: humanStemCell Version: 0.5.1 Depends: Biobase (>= 2.5.5), hgu133plus2.db License: Artistic-2.0 MD5sum: 853e1b9f8e0dcebe4d6249d78433a72c 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_0.5.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/humanStemCell_0.5.1.zip mac.binary.ver: bin/macosx/contrib/3.1/humanStemCell_0.5.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/humanStemCell_0.5.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Illumina450ProbeVariants.db Version: 1.1.1 Depends: R (>= 3.0.1) License: GPL-3 MD5sum: 04b750ef2086700bd53c9f6b1b3ea66a 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: Lee Butcher Maintainer: Tiffany Morris source.ver: src/contrib/Illumina450ProbeVariants.db_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/Illumina450ProbeVariants.db_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/Illumina450ProbeVariants.db_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Illumina450ProbeVariants.db_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: IlluminaDataTestFiles Version: 1.3.1 License: Artistic-2.0 MD5sum: 6e81a9bcc6df3d8e663c4698996595f5 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/IlluminaDataTestFiles_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/IlluminaDataTestFiles_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/IlluminaDataTestFiles_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ind1KG Version: 0.3.1 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: cca1a8a5f6e83d54c7cdc0aa2cb5dd53 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_0.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/ind1KG_0.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/ind1KG_0.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ind1KG_0.3.1.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: 1.1.1 License: GPL-2 MD5sum: fb3dec5120149f4e070848a59346245f 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/iontreeData_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/iontreeData_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/iontreeData_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ITALICSData Version: 2.3.1 Depends: R (>= 2.0.0) License: GPL MD5sum: 246821810e95b79841ef9f1fb3056553 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_2.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/ITALICSData_2.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/ITALICSData_2.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ITALICSData_2.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Iyer517 Version: 1.7.1 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 6e4b5c6dacfadb4f38fd07f981a40530 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_1.7.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/Iyer517_1.7.1.zip mac.binary.ver: bin/macosx/contrib/3.1/Iyer517_1.7.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Iyer517_1.7.1.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: 1.1.1 Depends: R (>= 3.0.1), methods, Biostrings (>= 2.29.19) License: GPL-2 MD5sum: bf999d85140c2ee57ecfbfebcdae6b0c 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/JASPAR2014_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/JASPAR2014_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/JASPAR2014_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: KEGGandMetacoreDzPathwaysGEO Version: 1.0.0 Depends: R (>= 2.15.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: c7abb1e9f59ce5d017da382a42d80486 NeedsCompilation: no Title: Disease Datasets from GEO Description: This is a collection of 18 data sets for which the phenotype is a disease with a corresponding pathway in either KEGG or metacore database.This collection of datasets were used as gold standard in comparing gene set analysis methods. biocViews: ExperimentData Author: Gaurav Bhatti Maintainer: Gaurav Bhatti source.ver: src/contrib/KEGGandMetacoreDzPathwaysGEO_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/KEGGandMetacoreDzPathwaysGEO_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/KEGGandMetacoreDzPathwaysGEO_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/KEGGandMetacoreDzPathwaysGEO_1.0.0.tgz vignettes: vignettes/KEGGandMetacoreDzPathwaysGEO/inst/doc/KEGGandMetacoreDzPathwaysGEO.pdf vignetteTitles: KEGGandMetacoreDzPathwaysGEO Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: KEGGdzPathwaysGEO Version: 1.3.1 Depends: R (>= 2.13.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: 498ab83d9602e6b9818fb2c46624ce85 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/KEGGdzPathwaysGEO_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/KEGGdzPathwaysGEO_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/KEGGdzPathwaysGEO_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: kidpack Version: 1.7.1 Depends: R (>= 2.6.0), Biobase (>= 2.5.5) License: GPL-2 MD5sum: 48863b112b430019084d411d3acc4112 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_1.7.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/kidpack_1.7.1.zip mac.binary.ver: bin/macosx/contrib/3.1/kidpack_1.7.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/kidpack_1.7.1.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: 1.1.1 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: a93a14009b0efb67d9c945c99750610e 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/leeBamViews_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/leeBamViews_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/leeBamViews_1.1.1.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: 1.1.1 Depends: R (>= 2.10.1), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 5ec77635d87776096c1509bd915ff2b4 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/leukemiasEset_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/leukemiasEset_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/leukemiasEset_1.1.1.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: LiebermanAidenHiC2009 Version: 0.3.1 Depends: KernSmooth, IRanges License: LGPL MD5sum: d12bb7fdbe10a8309dc94b580bc5d464 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_0.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/LiebermanAidenHiC2009_0.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/LiebermanAidenHiC2009_0.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/LiebermanAidenHiC2009_0.3.1.tgz vignettes: vignettes/LiebermanAidenHiC2009/inst/doc/LiebermanAidenHiC2009.pdf vignetteTitles: Exploration of HiC data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ListerEtAlBSseq Version: 1.0.1 Depends: R (>= 3.1.1), methylPipe License: Artistic 2.0 MD5sum: 2e5fac3cf047b775c6079b2589e33541 NeedsCompilation: no Title: BS-seq data of H1 and IMR90 cell line excerpted from Lister et al. 2009 Description: Base resolution bisulfite sequencing data of Human DNA methylomes biocViews: ExperimentData Author: Kamal Kishore Maintainer: Kamal Kishore source.ver: src/contrib/ListerEtAlBSseq_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/ListerEtAlBSseq_1.0.1.zip mac.binary.ver: bin/macosx/contrib/3.1/ListerEtAlBSseq_1.0.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ListerEtAlBSseq_1.0.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: lumiBarnes Version: 1.5.1 Depends: R (>= 2.0), Biobase (>= 2.5.5), lumi (>= 1.1.0) License: LGPL MD5sum: 85395ae79168e82787cb8f621389a37c 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_1.5.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/lumiBarnes_1.5.1.zip mac.binary.ver: bin/macosx/contrib/3.1/lumiBarnes_1.5.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/lumiBarnes_1.5.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: LungCancerACvsSCCGEO Version: 1.1.1 Depends: R (>= 2.15.0) License: GPL-2 MD5sum: a170fc474a9c57bf6e130af9c9606048 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/LungCancerACvsSCCGEO_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/LungCancerACvsSCCGEO_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/LungCancerACvsSCCGEO_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: LungCancerLines Version: 0.3.1 Imports: Rsamtools License: Artistic-2.0 MD5sum: c8f3a4a55f37d3314d413445adc997c5 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_0.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/LungCancerLines_0.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/LungCancerLines_0.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/LungCancerLines_0.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: lungExpression Version: 0.3.1 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: b2aa945d353f5c5ea9d0d1c3f877f934 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_0.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/lungExpression_0.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/lungExpression_0.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/lungExpression_0.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MafDb.ALL.wgs.phase1.release.v3.20101123 Version: 1.1.0 Depends: R (>= 3.0.0), VariantFiltering Imports: RSQLite (>= 0.8-1), Biobase, AnnotationDbi, IRanges, Biostrings, Rsamtools, GenomicRanges, VariantAnnotation License: Artistic-2.0 MD5sum: e7fa17272f95916a8ecd2053663f724d 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_1.1.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/MafDb.ALL.wgs.phase1.release.v3.20101123_1.1.0.zip mac.binary.ver: bin/macosx/contrib/3.1/MafDb.ALL.wgs.phase1.release.v3.20101123_1.1.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/MafDb.ALL.wgs.phase1.release.v3.20101123_1.1.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MafDb.ESP6500SI.V2.SSA137.dbSNP138 Version: 1.1.0 Depends: R (>= 3.0.0), VariantFiltering Imports: RSQLite (>= 0.8-1), Biobase, AnnotationDbi, IRanges, Biostrings, GenomicRanges, VariantAnnotation License: Artistic-2.0 MD5sum: b16db95835f9617070046f8fa674fb13 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_1.1.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/MafDb.ESP6500SI.V2.SSA137.dbSNP138_1.1.0.zip mac.binary.ver: bin/macosx/contrib/3.1/MafDb.ESP6500SI.V2.SSA137.dbSNP138_1.1.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/MafDb.ESP6500SI.V2.SSA137.dbSNP138_1.1.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mammaPrintData Version: 1.1.1 Depends: R (>= 2.13.0) Suggests: Biobase, gdata, limma License: Artistic-2.0 MD5sum: dd6e6d24d7c6c4bb5f2b802d61a22f1e 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/mammaPrintData_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/mammaPrintData_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/mammaPrintData_1.1.1.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: 1.9.1 Suggests: oligo, pdInfoBuilder License: GPL MD5sum: c111fda496c4033aa1e4fedc64b72661 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_1.9.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/maqcExpression4plex_1.9.1.zip mac.binary.ver: bin/macosx/contrib/3.1/maqcExpression4plex_1.9.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/maqcExpression4plex_1.9.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MAQCsubset Version: 1.3.1 Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), lumi, methods Suggests: genefilter, codelink License: Artistic-2.0 MD5sum: 62d2d6a7e7ce5c605e6f270530345baf 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/MAQCsubset_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/MAQCsubset_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/MAQCsubset_1.3.1.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: 1.3.1 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 35a4727f1c79f2ebb22bbca34bc5df95 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/MAQCsubsetAFX_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/MAQCsubsetAFX_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/MAQCsubsetAFX_1.3.1.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: 1.3.1 Depends: R (>= 2.10), Biobase (>= 2.5.5), lumi License: Artistic-2.0 MD5sum: 0f58a16fbefd1c32885cced77d2c0d74 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/MAQCsubsetILM_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/MAQCsubsetILM_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/MAQCsubsetILM_1.3.1.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: 1.1.1 Depends: R (>= 2.15.0) License: GPL (>= 2) MD5sum: 76bb974429e647f9567bc31b387bc75e 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/MEDIPSData_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/MEDIPSData_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/MEDIPSData_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MEEBOdata Version: 1.3.1 License: LGPL MD5sum: 13593f423a92410767e4f34e194c35d8 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/MEEBOdata_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/MEEBOdata_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/MEEBOdata_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: metaMSdata Version: 1.1.1 License: GPL (>= 2) MD5sum: 95d66db52d1f22d43c2c8c7644c39eda 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/metaMSdata_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/metaMSdata_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/metaMSdata_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: minfiData Version: 0.7.1 Depends: R (>= 2.13.0), minfi, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 License: Artistic-2.0 MD5sum: 9fd688d72986dfeceff038e6dbd2130f 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_0.7.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/minfiData_0.7.1.zip mac.binary.ver: bin/macosx/contrib/3.1/minfiData_0.7.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/minfiData_0.7.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: miRNATarget Version: 1.3.1 Depends: R (>= 2.10), Biobase License: GPL MD5sum: 319e033a034359118778f97c53366da9 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/miRNATarget_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/miRNATarget_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/miRNATarget_1.3.1.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: 1.1.1 Depends: R (>= 2.14.0) License: LGPL MD5sum: 0c842884b38623833833a335d3dc8082 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/mitoODEdata_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/mitoODEdata_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/mitoODEdata_1.1.1.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: 1.1.1 Suggests: MMDiff License: LGPL MD5sum: 2bdd045bc9978b965acb138fae4f2f89 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/MMDiffBamSubset_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/MMDiffBamSubset_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/MMDiffBamSubset_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mosaicsExample Version: 1.1.1 Depends: R (>= 2.11.1) License: GPL (>= 2) MD5sum: bc6ea9fa64e8d3e63b03d4966c83cfad 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/mosaicsExample_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/mosaicsExample_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/mosaicsExample_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mouse4302barcodevecs Version: 1.3.1 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 88e250e22057b48a0556a5a4eb6f7cf4 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/mouse4302barcodevecs_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/mouse4302barcodevecs_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/mouse4302barcodevecs_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MSBdata Version: 0.3.2 License: LGPL MD5sum: 193ea37f78ff966d96fde6f84741d63f 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_0.3.2.tar.gz win.binary.ver: bin/windows/contrib/3.1/MSBdata_0.3.2.zip mac.binary.ver: bin/macosx/contrib/3.1/MSBdata_0.3.2.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/MSBdata_0.3.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: msd16s Version: 1.0.0 Depends: R (>= 2.10), Biobase, metagenomeSeq, License: Artistic-2.0 MD5sum: ae89a280a4eecefae903004e578a2aae NeedsCompilation: no Title: Healthy and moderate to severe diarrhea 16S expression data Description: Gut 16S sequencing expression data from 992 healthy and moderate-to-severe diarrhetic samples used in 'Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition'. biocViews: ExperimentData, metagenomics Author: Joseph N. Paulson, Hector Corrada Bravo, Mihai Pop Maintainer: Joseph N. Paulson URL: http://www.cbcb.umd.edu/research/projects/GEMS-pathogen-discovery source.ver: src/contrib/msd16s_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/msd16s_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/msd16s_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/msd16s_1.0.0.tgz vignettes: vignettes/msd16s/inst/doc/msd16s.pdf vignetteTitles: msd16s hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/msd16s/inst/doc/msd16s.R Package: msdata Version: 0.3.3 Suggests: xcms License: GPL (>= 2) MD5sum: 939dc13d3ab6c3f4e5e583aeab085ea4 NeedsCompilation: no Title: Various Mass Spectrometry raw data example files Description: Ion Trap positive ionization mode data in mzData file format. Subset from 500-850 m/z and 1190-1310 seconds, incl. MS2 and MS3, intensity threshold 100.000. Extracts from FTICR Apex III, m/z 400-450. Subset of UPLC - Bruker micrOTOFq data, both mzData, mzML and mz5. PSI mzIdentML example files for various search engines. biocViews: ExperimentData, MassSpectrometryData Author: Steffen Neumann Maintainer: Steffen Neumann source.ver: src/contrib/msdata_0.3.3.tar.gz win.binary.ver: bin/windows/contrib/3.1/msdata_0.3.3.zip mac.binary.ver: bin/macosx/contrib/3.1/msdata_0.3.3.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/msdata_0.3.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics Package: MUGAExampleData Version: 1.0.0 Depends: R (>= 2.10.0) License: GPL-3 MD5sum: 8d9a9dbc7011b89f7e6b19b89e334165 NeedsCompilation: no Title: Example {M}ouse {U}niversal {G}enotyping {A}rray data for genome reconstruction and quantitative trait locus mapping. Description: This package contains example data for the MUGA array that is used by the R package DOQTL. biocViews: Experiment Data Author: Daniel Gatti Maintainer: Daniel Gatti source.ver: src/contrib/MUGAExampleData_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/MUGAExampleData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/MUGAExampleData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/MUGAExampleData_1.0.0.tgz vignettes: vignettes/MUGAExampleData/inst/doc/MUGAExampleData.pdf vignetteTitles: User Manual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MUGAExampleData/inst/doc/MUGAExampleData.R Package: Mulder2012 Version: 0.5.1 Depends: R (>= 2.14), org.Hs.eg.db, KEGG.db Imports: igraph, HTSanalyzeR, PANR, RedeR, pvclust, MASS Suggests: snow License: Artistic-2.0 MD5sum: 9e0e0fa3baa9d26b24e9bb8d28c79094 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_0.5.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/Mulder2012_0.5.1.zip mac.binary.ver: bin/macosx/contrib/3.1/Mulder2012_0.5.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Mulder2012_0.5.1.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: 1.1.1 Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4), lumi License: Artistic-2.0 MD5sum: 4ebaa75c1bbd5ddff2e8030f43959163 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/mvoutData_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/mvoutData_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/mvoutData_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: NCIgraphData Version: 1.1.1 Depends: R (>= 2.10.0) Suggests: Rgraphviz License: GPL-3 MD5sum: fa5aa864924e4a7103730d6fb2138170 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/NCIgraphData_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/NCIgraphData_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/NCIgraphData_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Neve2006 Version: 0.3.1 Depends: R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0), hgu133a.db, annotate License: Artistic-2.0 MD5sum: 4ebb65fb06cb35f91b1f5b1acc9bd38d 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_0.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/Neve2006_0.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/Neve2006_0.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/Neve2006_0.3.1.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: NGScopyData Version: 0.99.2 License: GPL (>=2) MD5sum: 719c5eff1eef08656a101628cedc2bf9 NeedsCompilation: no Title: Subset of BAM files of human tumor and pooled normal sequencing data (Zhao et al. 2014) for the NGScopy package Description: Subset of BAM files of human lung tumor and pooled normal samples by targeted panel sequencing. [Zhao et al 2014. Targeted Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using the University of North Carolina (UNC) Sequencing Assay Captures Most Previously Described Genetic Aberrations in NSCLC. In preparation.] Each sample is a 10 percent random subsample drawn from the original sequencing data. The pooled normal sample has been rescaled accroding to the total number of normal samples in the "pool". Here provided is the subsampled data on chr6 (hg19). biocViews: ExperimentData, DNASeq, TargetedResequencing, Sequencing Author: Xiaobei Zhao [aut, cre, cph] Maintainer: Xiaobei Zhao URL: http://www.bioconductor.org/packages/release/data/experiment/html/NGScopyData.html source.ver: src/contrib/NGScopyData_0.99.2.tar.gz win.binary.ver: bin/windows/contrib/3.1/NGScopyData_0.99.2.zip mac.binary.ver: bin/macosx/contrib/3.1/NGScopyData_0.99.2.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/NGScopyData_0.99.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: parathyroid Version: 1.1.1 Depends: DEXSeq, DESeq, R (>= 2.10) Suggests: GEOquery, SRAdb License: LGPL MD5sum: 9cf3d610910806e7161d48c9568fba47 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/parathyroid_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/parathyroid_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/parathyroid_1.1.1.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: 1.3.2 Depends: GenomicRanges, R (>= 2.10) Suggests: Rsamtools, GenomicAlignments, GEOquery, SRAdb, GenomicFeatures, BiocStyle License: LGPL MD5sum: f068c0375ffb607948ed07067543e549 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_1.3.2.tar.gz win.binary.ver: bin/windows/contrib/3.1/parathyroidSE_1.3.2.zip mac.binary.ver: bin/macosx/contrib/3.1/parathyroidSE_1.3.2.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/parathyroidSE_1.3.2.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: 0.5.1 Suggests: locfit, edgeR, xtable, DEXSeq, DESeq License: LGPL MD5sum: 1f30fa3addb9cd78e8939d02578e8d3d 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_0.5.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/pasilla_0.5.1.zip mac.binary.ver: bin/macosx/contrib/3.1/pasilla_0.5.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/pasilla_0.5.1.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: 0.3.1 Suggests: pasilla License: LGPL MD5sum: d0fa2c0d90c82f4ddf8a262f28f5ed5a 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_0.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/pasillaBamSubset_0.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/pasillaBamSubset_0.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/pasillaBamSubset_0.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: PathNetData Version: 1.1.1 Depends: R (>= 1.14.0) License: GPL-3 MD5sum: c716d87a0f5c534b133fcdc0e8ea53f8 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/PathNetData_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/PathNetData_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/PathNetData_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Hs.hg19 Version: 1.1.1 License: GPL (>= 2) MD5sum: 8945d4b06108af2aa4707ea3f6dc1427 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/pcaGoPromoter.Hs.hg19_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/pcaGoPromoter.Hs.hg19_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/pcaGoPromoter.Hs.hg19_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Mm.mm9 Version: 1.1.1 License: GPL (>= 2) MD5sum: b69a3b6b2aa1f69c773949e73418f011 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/pcaGoPromoter.Mm.mm9_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/pcaGoPromoter.Mm.mm9_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/pcaGoPromoter.Mm.mm9_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Rn.rn4 Version: 1.1.1 License: GPL (>= 2) MD5sum: a352f5fe46b6d04803291fdbe4ebb1b0 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/pcaGoPromoter.Rn.rn4_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/pcaGoPromoter.Rn.rn4_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/pcaGoPromoter.Rn.rn4_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pd.atdschip.tiling Version: 0.3.4 Depends: R (>= 2.14.0), methods, RSQLite (>= 0.10.0), oligoClasses (>= 1.15.58), oligo (>= 1.17.3), DBI Imports: Biostrings (>= 2.21.11), IRanges (>= 1.11.31), S4Vectors License: Artistic-2.0 MD5sum: 508144e6df3cdcc56d75e853213153df 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_0.3.4.tar.gz win.binary.ver: bin/windows/contrib/3.1/pd.atdschip.tiling_0.3.4.zip mac.binary.ver: bin/macosx/contrib/3.1/pd.atdschip.tiling_0.3.4.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/pd.atdschip.tiling_0.3.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pepDat Version: 1.0.0 Depends: R(>= 3.0.0) Imports: GenomicRanges Suggests: knitr License: Artistic-2.0 MD5sum: 735e8f5e46f453522b82e47a02e38c2a NeedsCompilation: no Title: Peptide microarray data package Description: Provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV. biocViews: Microarray Author: Renan Sauteraud, Raphael Gottardo Maintainer: Renan Sauteraud VignetteBuilder: knitr source.ver: src/contrib/pepDat_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/pepDat_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/pepDat_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/pepDat_1.0.0.tgz vignettes: vignettes/pepDat/inst/doc/pepDat.pdf vignetteTitles: The pepDat users guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pepDat/inst/doc/pepDat.R Package: phastCons100way.UCSC.hg19 Version: 1.1.0 Depends: R (>= 3.0.0), VariantFiltering Imports: utils, IRanges, GenomicRanges, BSgenome License: Artistic-2.0 MD5sum: b88e7586eb9f7d60dba163963281da2f 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_1.1.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/phastCons100way.UCSC.hg19_1.1.0.zip mac.binary.ver: bin/macosx/contrib/3.1/phastCons100way.UCSC.hg19_1.1.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/phastCons100way.UCSC.hg19_1.1.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ppiData Version: 0.3.1 Depends: graph Imports: AnnotationDbi Suggests: org.Sc.sgd.db, ppiStats License: Artistic-2.0 MD5sum: 903ac270938ea291421a9826e8247cba 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_0.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/ppiData_0.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/ppiData_0.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ppiData_0.3.1.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: 1.1.1 Depends: R (>= 2.14.0) License: Artistic-2.0 MD5sum: 0f3a6ea3d72260ff5b03830abaabad6a 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/prebsdata_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/prebsdata_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/prebsdata_1.1.1.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: 0.5.1 Depends: R (>= 2.9.0), methods, PREDA, Biobase, affy, annotate, gahgu133plus2.db, gahgu133plus2cdf Suggests: hgu133plus2.db, hgu133plus2cdf License: Artistic-2.0 MD5sum: 35647d8fe9a6d5389db139700af6b170 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_0.5.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/PREDAsampledata_0.5.1.zip mac.binary.ver: bin/macosx/contrib/3.1/PREDAsampledata_0.5.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/PREDAsampledata_0.5.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ProData Version: 1.3.1 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL MD5sum: 1fbd06035d56b58373a9ca0d63d2e827 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/ProData_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/ProData_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/ProData_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pRolocdata Version: 1.4.1 Depends: R (>= 2.15), MSnbase Suggests: pRoloc License: GPL-2 MD5sum: 6b4cf84d1edd0151e27fc3172ef681d2 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, 2014), Breckels et al. (2013) and Groen et al. (2014) biocViews: ExperimentData, MassSpectrometry, Proteomics Author: Laurent Gatto and Lisa M. Breckels Maintainer: Laurent Gatto URL: https://github.com/lgatto/pRolocdata source.ver: src/contrib/pRolocdata_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/pRolocdata_1.4.1.zip mac.binary.ver: bin/macosx/contrib/3.1/pRolocdata_1.4.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/pRolocdata_1.4.1.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics Package: pumadata Version: 2.1.1 Depends: R (>= 3.0.0), affy (>= 1.41.3), Biobase (>= 2.5.5), puma,oligo License: LGPL MD5sum: 6bf632b8c2a41bd21371dc0b829f11bb 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_2.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/pumadata_2.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/pumadata_2.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/pumadata_2.1.1.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: 4.0.3 Depends: methods, PWMEnrich License: GPL-3 MD5sum: 1a800cee0ca3646f2c1ab534b59912da NeedsCompilation: no Title: D. melanogaster background for PWMEnrich Description: PWMEnrich pre-compiled background objects for Drosophila melanogaster and MotifDb D. melanogaster motifs. biocViews: AnnotationData, Organism, Drosophila_melanogaster Author: Robert Stojnic Maintainer: Robert Stojnic source.ver: src/contrib/PWMEnrich.Dmelanogaster.background_4.0.3.tar.gz win.binary.ver: bin/windows/contrib/3.1/PWMEnrich.Dmelanogaster.background_4.0.3.zip mac.binary.ver: bin/macosx/contrib/3.1/PWMEnrich.Dmelanogaster.background_4.0.3.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/PWMEnrich.Dmelanogaster.background_4.0.3.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: PWMEnrich.Hsapiens.background Version: 4.0.1 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: 68a5497bd75049d8459abebbe8b755f3 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_4.0.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/PWMEnrich.Hsapiens.background_4.0.1.zip mac.binary.ver: bin/macosx/contrib/3.1/PWMEnrich.Hsapiens.background_4.0.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/PWMEnrich.Hsapiens.background_4.0.1.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: PWMEnrich.Mmusculus.background Version: 4.0.1 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: 9b1f42bd48093eddee91a64228355b41 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_4.0.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/PWMEnrich.Mmusculus.background_4.0.1.zip mac.binary.ver: bin/macosx/contrib/3.1/PWMEnrich.Mmusculus.background_4.0.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/PWMEnrich.Mmusculus.background_4.0.1.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: RforProteomics Version: 1.4.1 Depends: MSnbase Imports: R.utils, Biobase, rpx, biocViews, BiocInstaller, interactiveDisplay, shiny Suggests: mzR, xcms, msdata, isobar, MALDIquant (>= 1.11), MALDIquantForeign, readBrukerFlexData, rTANDEM, synapter, synapterdata, IPPD, Rdisop, OrgMassSpecR, BRAIN, rols, hpar, GO.db, org.Hs.eg.db, biomaRt, RColorBrewer, ggplot2, reshape2, xtable, lattice, mzID, pRoloc, pRolocdata, knitr, BiocStyle, MSGFplus, MSGFgui, MSnID Enhances: cleaver License: Artistic-2.0 MD5sum: 3685a3bc3d0b803fb8cbd12641d6306e NeedsCompilation: no Title: Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication Description: This package contains code to illustrate the 'Using R and Bioconductor for proteomics data analysis' paper. Two vignettes describe the code and data needed to reproduce the examples and figures descibed in the paper and functionality for proteomics visualisation. biocViews: ExperimentData, MassSpectrometry, Proteomics, MassSpectrometryData Author: Laurent Gatto [aut, cre], Thomas Lin Pedersen [ctb], Sebastian Gibb [ctb], Vlad Petyuk [ctb] Maintainer: Laurent Gatto URL: http://lgatto.github.com/RforProteomics/ VignetteBuilder: knitr source.ver: src/contrib/RforProteomics_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/RforProteomics_1.4.1.zip mac.binary.ver: bin/macosx/contrib/3.1/RforProteomics_1.4.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/RforProteomics_1.4.1.tgz vignettes: vignettes/RforProteomics/inst/doc/Bioc2013poster.pdf, vignettes/RforProteomics/inst/doc/HUPO2014poster.pdf, vignettes/RforProteomics/inst/doc/RforProteomics.pdf vignetteTitles: RforProteomics Bioc2013 poster, A current perspective on using R and Bioconductor for proteomics data analysis, Using R for proteomics data analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RforProteomics/inst/doc/Bioc2013_poster.R, vignettes/RforProteomics/inst/doc/Bioc2013poster.R, vignettes/RforProteomics/inst/doc/HUPO2014poster.R, vignettes/RforProteomics/inst/doc/RforProteomics.R, vignettes/RforProteomics/inst/doc/RProtVis.R htmlDocs: vignettes/RforProteomics/inst/doc/RProtVis.html htmlTitles: "Visualisation of proteomics data using R and Bioconductor" Package: rheumaticConditionWOLLBOLD Version: 1.3.1 Depends: R (>= 2.10.0) Suggests: genefilter, Biobase, hgu133plus2.db License: Artistic-2.0 MD5sum: a08dbc0202f725dae0e613b944aea2b7 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/rheumaticConditionWOLLBOLD_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/rheumaticConditionWOLLBOLD_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/rheumaticConditionWOLLBOLD_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RIPSeekerData Version: 1.1.1 Depends: RIPSeeker License: GPL-2 MD5sum: 4a7fe261bfe35b857cfba1ac9043f7ed 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/RIPSeekerData_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/RIPSeekerData_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/RIPSeekerData_1.1.1.tgz vignettes: vignettes/RIPSeekerData/inst/doc/RIPSeekerData.pdf vignetteTitles: RIP-seq datasets for testing RIPSeeker package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RIPSeekerData/inst/doc/RIPSeekerData.R Package: RMassBankData Version: 1.3.1 Suggests: RMassBank License: Artistic-2.0 MD5sum: 670bd48c642d8556547ed0ea6256d0d0 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/RMassBankData_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/RMassBankData_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/RMassBankData_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RNAinteractMAPK Version: 1.3.1 Depends: R (>= 2.12.0), methods, fields, sparseLDA, RNAinteract Imports: grid, gdata, MASS, genefilter Suggests: qvalue, lattice License: Artistic-2.0 MD5sum: f77b60611a1524ba4b3b63713c4ceae5 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/RNAinteractMAPK_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/RNAinteractMAPK_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/RNAinteractMAPK_1.3.1.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.HNRNPC.bam.chr14 Version: 0.3.2 Suggests: GenomicAlignments, BiocInstaller License: LGPL MD5sum: d1c65f7a61c35fb1226adea52b0b5e8c 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_0.3.2.tar.gz win.binary.ver: bin/windows/contrib/3.1/RNAseqData.HNRNPC.bam.chr14_0.3.2.zip mac.binary.ver: bin/macosx/contrib/3.1/RNAseqData.HNRNPC.bam.chr14_0.3.2.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/RNAseqData.HNRNPC.bam.chr14_0.3.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RnaSeqTutorial Version: 0.3.1 Depends: R (>= 3.0.2), methods, easyRNASeq Suggests: Rsamtools, ShortRead, BSgenome.Dmelanogaster.UCSC.dm3, GenomicAlignments, biomaRt, genomeIntervals License: Artistic-2.0 MD5sum: 2d5a314e1293ef5dcf4a0b8042917552 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_0.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/RnaSeqTutorial_0.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/RnaSeqTutorial_0.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/RnaSeqTutorial_0.3.1.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: RRBSdata Version: 1.0.0 Depends: R (>= 3.1.0), BiSeq License: LGPL-3 MD5sum: e9d38fe8029a1c5b8c6ac7609e0731f1 NeedsCompilation: no Title: An RRBS data set with 12 samples and 10,000 simulated DMRs. Description: RRBS data set comprising 12 samples with simulated differentially methylated regions (DMRs). biocViews: ExperimentData, DNAmethylationData Author: Katja Hebestreit, Hans-Ulrich Klein Maintainer: Katja Hebestreit source.ver: src/contrib/RRBSdata_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/RRBSdata_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/RRBSdata_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/RRBSdata_1.0.0.tgz vignettes: vignettes/RRBSdata/inst/doc/RRBSdata.pdf vignetteTitles: An RRBS data set with 12 samples and 10,,000 simulated DMRs. hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RRBSdata/inst/doc/RRBSdata.R Package: rRDPData Version: 1.0.0 Depends: rRDP License: GPL-2 MD5sum: e67f1c45ccb502820c60d3097fd56845 NeedsCompilation: no Title: Database for the Default RDP Classifier Description: Database used by the default RDP Classifier biocViews: Genetics, Sequencing, Infrastructure, Classification Author: Michael Hahsler, Anurag Nagar Maintainer: Michael Hahsler SystemRequirements: Java source.ver: src/contrib/rRDPData_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/rRDPData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/rRDPData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/rRDPData_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RUVnormalizeData Version: 1.0.0 Depends: R (>= 2.10.0), Biobase License: GPL-3 MD5sum: 0ae813b982182df52f39e011f62edc72 NeedsCompilation: no Title: Gender data for the RUVnormalize package Description: Microarray gene expression data from the study of Vawter et al., 2004. biocViews: ExpressionData Author: Laurent Jacob Maintainer: Laurent Jacob source.ver: src/contrib/RUVnormalizeData_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/RUVnormalizeData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/RUVnormalizeData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/RUVnormalizeData_1.0.0.tgz vignettes: vignettes/RUVnormalizeData/inst/doc/RUVnormalizeData.pdf vignetteTitles: RUVnormalizeData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RUVnormalizeData/inst/doc/RUVnormalizeData.R Package: seqc Version: 1.0.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 7b5ef181b8325d3f8536f60c792029d9 NeedsCompilation: no Title: RNA-seq data generated from SEQC (MAQC-III) study Description: The SEQC/MAQC-III Consortium has produced benchmark RNA-seq data for the assessment of RNA sequencing technologies and data analysis methods (Nat Biotechnol, 2014). Billions of sequence reads have been generated from ten different sequencing sites. This package contains the summarized read count data for ~2000 sequencing libraries. It also includes all the exon-exon junctions discovered from the study. TaqMan RT-PCR data for ~1000 genes and ERCC spike-in sequence data are included in this package as well. biocViews: ExperimentData, RNAseqData, ExpressionData, HighThroughputSequencingData, RNAExpressionData, Sequencing, RNASeq, GeneExpression Author: Yang Liao and Wei Shi Maintainer: Yang Liao and Wei Shi URL: http://bioconductor.org/packages/release/data/experiment/html/seqc.html source.ver: src/contrib/seqc_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/seqc_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/seqc_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/seqc_1.0.0.tgz vignettes: vignettes/seqc/inst/doc/seqc.pdf vignetteTitles: SEQC Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/seqc/inst/doc/seqc.R Package: seqCNA.annot Version: 1.1.1 Depends: R (>= 2.10) License: GPL-3 MD5sum: fe30a8cc798ab44c00740c973df2d4e2 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/seqCNA.annot_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/seqCNA.annot_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/seqCNA.annot_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: serumStimulation Version: 1.1.1 Depends: R (>= 2.10) License: GPL (>= 2) MD5sum: d2d60e79f5f2f7f0dc53808b37f16f8a 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/serumStimulation_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/serumStimulation_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/serumStimulation_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: seventyGeneData Version: 1.1.1 Depends: R (>= 2.13.0) Suggests: Biobase, gdata, limma, breastCancerNKI License: Artistic-2.0 MD5sum: b09428fa7f4ddd9ade9e87e171b06bdb 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/seventyGeneData_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/seventyGeneData_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/seventyGeneData_1.1.1.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: shinyMethylData Version: 1.0.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: a2907a80cbe6bce93d0fec69cdca7098 NeedsCompilation: no Title: Example dataset of input data for shinyMethyl Description: Extracted data from 369 TCGA Head and Neck Cancer DNA methylation samples. The extracted data serve as an example dataset for the package shinyMethyl. Original samples are from 450k methylation arrays, and were obtained from The Cancer Genome Atlas (TCGA). 310 samples are from tumor, 50 are matched normals and 9 are technical replicates of a control cell line. biocViews: DNAMethylation Author: Jean-Philippe Fortin [cre, aut], Kasper Daniel Hansen [aut] Maintainer: Jean-Philippe Fortin source.ver: src/contrib/shinyMethylData_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/shinyMethylData_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/shinyMethylData_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/shinyMethylData_1.0.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: simpIntLists Version: 1.1.1 License: GPL (>= 2) MD5sum: d6f7d5eb8d967ba6f33843c992a24b9e 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/simpIntLists_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/simpIntLists_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/simpIntLists_1.1.1.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: 1.11.1 Depends: R (>= 2.4.0), graph Suggests: Rgraphviz License: LGPL MD5sum: dd0c8189025968bf8d6f423f6a146d2e 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_1.11.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/SNAData_1.11.1.zip mac.binary.ver: bin/macosx/contrib/3.1/SNAData_1.11.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/SNAData_1.11.1.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: 1.1.1 Depends: R (>= 2.6.0) Suggests: ALL, hgu95av2.db, SNAGEE License: Artistic-2.0 MD5sum: 760d0fc38bbf39675831849e57a370f9 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/SNAGEEdata_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/SNAGEEdata_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/SNAGEEdata_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SomatiCAData Version: 1.3.1 Depends: R (>= 2.14) License: Artistic-2.0 MD5sum: b023327e5d52954c1a3eb89c3d02ff4f 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/SomatiCAData_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/SomatiCAData_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/SomatiCAData_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SomaticCancerAlterations Version: 1.1.1 Depends: R (>= 3.0.0) Imports: GenomicRanges, exomeCopy, stringr, IRanges Suggests: testthat, ggbio, ggplot2, BiocStyle, knitr License: GPL-3 MD5sum: f210d807590b3ae98f8a3e962b29d70e 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/SomaticCancerAlterations_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/SomaticCancerAlterations_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/SomaticCancerAlterations_1.1.1.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: 1.7.1 Depends: R (>= 1.6), affy (>= 1.23.4) License: Artistic-2.0 MD5sum: e08e28369a29915186ff29a4bf07901e 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_1.7.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/SpikeIn_1.7.1.zip mac.binary.ver: bin/macosx/contrib/3.1/SpikeIn_1.7.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/SpikeIn_1.7.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SpikeInSubset Version: 1.5.1 Depends: R (>= 2.4.0), Biobase (>= 2.5.5), affy (>= 1.23.4) License: LGPL MD5sum: 853938853486cf776f03cad999e4d172 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_1.5.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/SpikeInSubset_1.5.1.zip mac.binary.ver: bin/macosx/contrib/3.1/SpikeInSubset_1.5.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/SpikeInSubset_1.5.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: stemHypoxia Version: 1.1.1 Depends: R (>= 2.14.1) License: GPL (>=2) MD5sum: fd66580443c3ba81a29d0e7c4c198197 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/stemHypoxia_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/stemHypoxia_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/stemHypoxia_1.1.1.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: stjudem Version: 1.5.1 Depends: R (>= 2.10), utils License: LGPL (>= 2) MD5sum: 554fb62c333cd3220577e77646923867 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_1.5.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/stjudem_1.5.1.zip mac.binary.ver: bin/macosx/contrib/3.1/stjudem_1.5.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/stjudem_1.5.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: synapterdata Version: 1.3.2 Depends: R (>= 2.10), synapter (>= 0.99.6) License: GPL-2 MD5sum: 4c97650048d7f7905b980b4d54c7924e 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, Sebastian Gibb and Pavel V. Shliaha Maintainer: Laurent Gatto source.ver: src/contrib/synapterdata_1.3.2.tar.gz win.binary.ver: bin/windows/contrib/3.1/synapterdata_1.3.2.zip mac.binary.ver: bin/macosx/contrib/3.1/synapterdata_1.3.2.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/synapterdata_1.3.2.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics Package: TargetScoreData Version: 1.1.1 Suggests: TargetScore, gplots License: GPL-2 MD5sum: 8d6d8a2f33c9df0b0f739e529f4445a5 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/TargetScoreData_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/TargetScoreData_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/TargetScoreData_1.1.1.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: 1.3.1 Depends: TargetSearch License: GPL (>= 2) MD5sum: ce0f3dd4fa421bb38c5a94716aa42691 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/TargetSearchData_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/TargetSearchData_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/TargetSearchData_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: TBX20BamSubset Version: 1.1.1 Depends: Rsamtools (>= 1.9.8) Imports: xtable License: LGPL MD5sum: d2dfc86a76d82c76710588d44e2be034 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/TBX20BamSubset_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/TBX20BamSubset_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/TBX20BamSubset_1.1.1.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: TCGAcrcmiRNA Version: 1.0.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 1f56f9b6330c43f85ca735a9ff954992 NeedsCompilation: no Title: TCGA CRC 450 miRNA dataset Description: colorectal cancer miRNA profile provided by TCGA biocViews: ExperimentData Author: Claudio Isella Maintainer: Claudio Isella source.ver: src/contrib/TCGAcrcmiRNA_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/TCGAcrcmiRNA_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/TCGAcrcmiRNA_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/TCGAcrcmiRNA_1.0.0.tgz vignettes: vignettes/TCGAcrcmiRNA/inst/doc/TcgaCrcVignette.pdf vignetteTitles: TCGAcrcmiRNA hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TCGAcrcmiRNA/inst/doc/TcgaCrcVignette.R Package: TCGAcrcmRNA Version: 1.0.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: b56d0f27c09a97917cee48f680e81200 NeedsCompilation: no Title: TCGA CRC 450 mRNA dataset Description: colorectal cancer mRNA profile provided by TCGA biocViews: ExperimentData Author: Claudio Isella Maintainer: Claudio Isella source.ver: src/contrib/TCGAcrcmRNA_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/TCGAcrcmRNA_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/TCGAcrcmRNA_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/TCGAcrcmRNA_1.0.0.tgz vignettes: vignettes/TCGAcrcmRNA/inst/doc/TcgaCrcVignette.pdf vignetteTitles: TCGAcrcmRNA hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TCGAcrcmRNA/inst/doc/TcgaCrcVignette.R Package: TCGAMethylation450k Version: 1.1.1 License: GPL-2 MD5sum: d7d49087e1fafd937a53105b3c1326c7 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/TCGAMethylation450k_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/TCGAMethylation450k_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/TCGAMethylation450k_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: tinesath1cdf Version: 1.3.1 License: Artistic-2.0 MD5sum: 89219204deec1995c1d30206258ba74d 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/tinesath1cdf_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/tinesath1cdf_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/tinesath1cdf_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: XhybCasneuf Package: tinesath1probe Version: 1.3.1 Depends: R (>= 1.6), AnnotationDbi (>= 1.11.9) License: LGPL MD5sum: fdb1348c6b87cf625aaa81c54106655a 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/tinesath1probe_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/tinesath1probe_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/tinesath1probe_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: tweeDEseqCountData Version: 1.3.1 Depends: Biobase, R (>= 2.10) License: GPL (>=2) MD5sum: 5013d79234d2f328511f8142a982ee70 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/tweeDEseqCountData_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/tweeDEseqCountData_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/tweeDEseqCountData_1.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: waveTilingData Version: 1.1.1 Depends: R (>= 2.14.0) License: GPL (>= 2) MD5sum: acae61dfe857d26f7f7c5883915a48ad 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/waveTilingData_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/waveTilingData_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/waveTilingData_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: XhybCasneuf Version: 1.3.1 Depends: R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf , RColorBrewer , methods, grid License: Artistic-2.0 MD5sum: 397005fd2f18263336f7fd8a1b426305 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/XhybCasneuf_1.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/XhybCasneuf_1.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/XhybCasneuf_1.3.1.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: 1.5.1 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: d08eafab738a9a4109944d9511dd948d 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_1.5.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/yeastCC_1.5.1.zip mac.binary.ver: bin/macosx/contrib/3.1/yeastCC_1.5.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/yeastCC_1.5.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastExpData Version: 0.11.1 Depends: R (>= 2.4), graph (>= 1.9.26) Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db License: GPL MD5sum: ddf4120564f70c7fa604ce71b2b169d2 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_0.11.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/yeastExpData_0.11.1.zip mac.binary.ver: bin/macosx/contrib/3.1/yeastExpData_0.11.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/yeastExpData_0.11.1.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: 0.3.1 License: Artistic-2.0 MD5sum: a658098fe0e3929d4180208be0461e4e 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_0.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/yeastGSData_0.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/yeastGSData_0.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/yeastGSData_0.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastNagalakshmi Version: 1.1.1 License: Artistic-2.0 MD5sum: 7e2b0cb7a991e63004b3410f2058df67 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_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/yeastNagalakshmi_1.1.1.zip mac.binary.ver: bin/macosx/contrib/3.1/yeastNagalakshmi_1.1.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/yeastNagalakshmi_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastRNASeq Version: 0.3.1 Depends: R (>= 2.4) Suggests: Biobase, ShortRead, IRanges License: GPL MD5sum: 7ad0b01b7cbbb2e7025e7af2b0a83499 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_0.3.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/yeastRNASeq_0.3.1.zip mac.binary.ver: bin/macosx/contrib/3.1/yeastRNASeq_0.3.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/yeastRNASeq_0.3.1.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: 0.7.1 Depends: GGBase Imports: Biobase License: Artistic-2.0 MD5sum: 455fab6bde80fb5b1574382ec865564f 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_0.7.1.tar.gz win.binary.ver: bin/windows/contrib/3.1/yri1kgv_0.7.1.zip mac.binary.ver: bin/macosx/contrib/3.1/yri1kgv_0.7.1.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/yri1kgv_0.7.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: zebrafishRNASeq Version: 1.0.0 Depends: R (>= 2.10) Suggests: BiocStyle, knitr License: GPL MD5sum: 7618920b3a13542ba95248a8be49e2fe NeedsCompilation: no Title: Zebrafish RNA-Seq Experimental Data from Ferreira et al. (2014) Description: Gene-level read counts from RNA-Seq for gallein-treated and control zebrafish. biocViews: ExperimentData, RNAseqData Author: Davide Risso Maintainer: Davide Risso VignetteBuilder: knitr source.ver: src/contrib/zebrafishRNASeq_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/3.1/zebrafishRNASeq_1.0.0.zip mac.binary.ver: bin/macosx/contrib/3.1/zebrafishRNASeq_1.0.0.tgz mac.binary.mavericks.ver: bin/macosx/mavericks/contrib/3.1/zebrafishRNASeq_1.0.0.tgz vignettes: vignettes/zebrafishRNASeq/inst/doc/preprocessing.pdf vignetteTitles: Pre-Processing for the Zebrafish RNA-Seq Gene-Level Counts hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/zebrafishRNASeq/inst/doc/preprocessing.R