Package: affycompData Version: 1.6.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp License: GPL (>= 2) MD5sum: d1ee305cb662621843a8fb2bed03a67a NeedsCompilation: no Title: affycomp data Description: Data needed by the affycomp package. biocViews: MicroarrayData Author: Rafael A. Irizarry and Zhijin Wu with contributions from Simon Cawley Maintainer: Harris Jaffee source.ver: src/contrib/affycompData_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: affydata Version: 1.16.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Imports: methods Suggests: hgu95av2cdf, hgu133acdf License: GPL (>= 2) MD5sum: 07e52d20170b455af69067bff0839943 NeedsCompilation: no Title: Affymetrix Data for Demonstration Purpose Description: Example datasets of a slightly large size. They represent 'real world examples', unlike the artificial examples included in the package affy. biocViews: ExperimentData, Tissue, MicroarrayData, TissueMicroarrayData Author: Laurent Gautier Maintainer: Harris Jaffee source.ver: src/contrib/affydata_1.16.0.tar.gz 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: 1.4.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 2b26fff3ce491ed4e02bfe5b33bbd482 NeedsCompilation: no Title: Affymetrix Human Genome U133A 2.0 Array (GPL571) Expression Data Package Description: Contains pre-built human (GPL571) databases of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji source.ver: src/contrib/Affyhgu133A2Expr_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Affyhgu133aExpr Version: 1.6.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 711dd212d366c733859db11ac2d35486 NeedsCompilation: no Title: Affymetrix Human hgu133a Array (GPL96) Expression Data Package Description: Contains pre-built human (GPL96) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji source.ver: src/contrib/Affyhgu133aExpr_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Affyhgu133Plus2Expr Version: 1.2.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: d1c21637b8f6a423c8a356e6e4e33ca4 NeedsCompilation: no Title: Affyhgu133Plus2Expr (GPL570) Expression Data Package Description: Contains pre-built human (GPL570) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji source.ver: src/contrib/Affyhgu133Plus2Expr_1.2.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: AffymetrixDataTestFiles Version: 0.6.0 Depends: R (>= 2.5.0) License: LGPL-2.1 MD5sum: efb5333c466acf64e11a9983a5b00b41 NeedsCompilation: no Title: Affymetrix data files (CEL, CDF, CHP, EXP, PGF, PSI) for testing Description: This package contains annotation data files and sample data files of Affymetrix file formats. The files originate from the Affymetrix' Fusion SDK distribution and other official sources. biocViews: ExperimentData, MicroarrayData Author: Henrik Bengtsson [aut, cre], James Bullard [aut], Kasper Daniel Hansen [aut] Maintainer: Henrik Bengtsson source.ver: src/contrib/AffymetrixDataTestFiles_0.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Affymoe4302Expr Version: 1.6.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 9ce3e59a8f1935d1e69dab109cd3ef2a NeedsCompilation: no Title: Affymetrix Mouse Genome 430 2.0 Array (GPL1261) Expression Data Package Description: Contains pre-built mouse (GPL1261) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Mus_musculus_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji source.ver: src/contrib/Affymoe4302Expr_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: airway Version: 0.102.0 Depends: R (>= 2.10), GenomicRanges Suggests: knitr, GEOquery License: LGPL MD5sum: 8133c8de64ff701d1a2a9f2afcab60b6 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, SequencingData, RNASeqData, GEO Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr source.ver: src/contrib/airway_0.102.0.tar.gz 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: 1.10.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Suggests: rpart License: Artistic-2.0 MD5sum: 9b99e422dc1acc31b59586ddb5e13163 NeedsCompilation: no Title: A data package Description: Data of T- and B-cell Acute Lymphocytic Leukemia from the Ritz Laboratory at the DFCI (includes Apr 2004 versions) biocViews: ExperimentData, CancerData, LeukemiaCancerData Author: Xiaochun Li Maintainer: Robert Gentleman source.ver: src/contrib/ALL_1.10.0.tar.gz 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: 1.8.0 Depends: R (>= 2.10), affy (>= 1.23.4) License: GPL-2 MD5sum: 8f5a3e95923e55976be1945cd4ec442b NeedsCompilation: no Title: A subset of arrays from a large acute lymphoblastic leukemia (ALL) study Description: This package provides probe-level data for 20 HGU133A and 20 HGU133B arrays which are a subset of arrays from a large ALL study. The data is for the MLL arrays. This data was published in Mary E. Ross, Xiaodong Zhou, Guangchun Song, Sheila A. Shurtleff, Kevin Girtman, W. Kent Williams, Hsi-Che Liu, Rami Mahfouz, Susana C. Raimondi, Noel Lenny, Anami Patel, and James R. Downing (2003) Classification of pediatric acute lymphoblastic leukemia by gene expression profiling Blood 102: 2951-2959 biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData Author: B. M. Bolstad source.ver: src/contrib/ALLMLL_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: AmpAffyExample Version: 1.8.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Suggests: hgu133acdf License: LGPL (>= 2) MD5sum: 12b56967a74c39eddd1f9384be1da94c NeedsCompilation: no Title: Example of Amplified Data Description: Six arrays. Three from amplified RNA, three from the typical procedure. biocViews: ExperimentData, MicroarrayData Author: Rafael A. Irizarry Maintainer: Rafael A. Irizarry source.ver: src/contrib/AmpAffyExample_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: antiProfilesData Version: 1.4.0 Depends: Biobase, Suggests: frma, GEOquery, GEOmetadb License: Artistic-2.0 MD5sum: 52a810be99da784d1abb40287178ff09 NeedsCompilation: no Title: Normal colon and cancer preprocessed affy data for antiProfile building. Description: Colon normal tissue and cancer samples used in Corrada Bravo, et al. gene expression anti-profiles paper: BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272. Measurements are z-scores obtained from the GeneExpression Barcode in the 'frma' package biocViews: ExperimentData, MicroarrayData, Tissue, CancerData, ColonCancerData Author: Hector Corrada Bravo, Matthew McCall and Rafael A. Irizarry Maintainer: Hector Corrada Bravo source.ver: src/contrib/antiProfilesData_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ARRmData Version: 1.4.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: 94b062c174d54b176f052c0b995b481e NeedsCompilation: no Title: Example dataset for normalization of Illumina 450k Methylation data Description: Raw Beta values from 36 samples across 3 groups from Illumina 450k methylation arrays biocViews: ExperimentData, MethylationArrayData Author: Jean-Philippe Fortin, Celia M.T. Greenwood, Aurelie Labbe Maintainer: Jean-Philippe Fortin source.ver: src/contrib/ARRmData_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bcellViper Version: 1.4.0 Depends: R(>= 2.14.0), Biobase, methods License: GPL (>=2) MD5sum: ccf0e8392a25e3e5030295a02ea3785b NeedsCompilation: no Title: Human B-cell transcriptional interactome and normal human B-cell expression data Description: This package provides a human B-cell context-specific transcriptional regulatory network and a human normal B-cells dataset for the examples in package viper. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData Author: Mariano Javier Alvarez Maintainer: Mariano Javier Alvarez source.ver: src/contrib/bcellViper_1.4.0.tar.gz 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: 1.6.0 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>= 2.0.0) License: GPL-2 MD5sum: 5a541417f5e5abb0e5baa49bba4a4c94 NeedsCompilation: no Title: Example data for the beadarray package Description: An small dataset that can be used to run examples from the beadarray vignette and examples biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData Author: Mark Dunning Maintainer: Mark Dunning source.ver: src/contrib/beadarrayExampleData_1.6.0.tar.gz vignettes: vignettes/beadarrayExampleData/inst/doc/beadarrayExampleData.pdf vignetteTitles: beadarrayExampleData: example data for the beadarray package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: BeadArrayUseCases Version: 1.6.0 Imports: beadarray (>= 2.3.18), limma, GEOquery Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db License: GPL-2 MD5sum: f922e336df245cf48111222ba4f7a8c6 NeedsCompilation: no Title: Analysing Illumina BeadArray expression data using Bioconductor Description: Example data files and use cases for processing Illumina BeadArray expression data using Bioconductor biocViews: MicroarrayData Author: Mark Dunning, Wei Shi, Andy Lynch, Mike Smith, Matt Ritchie Maintainer: Mike Smith source.ver: src/contrib/BeadArrayUseCases_1.6.0.tar.gz 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: 1.6.0 Depends: R (>= 2.4.0), marray License: LGPL MD5sum: ccf6f42a1645e44d771ac59c265d1768 NeedsCompilation: no Title: Rodriguez et al. (2004) Differential Gene Expression by Memory/Effector T Helper Cells Bearing the Gut-Homing Receptor Integrin alpha4 beta7. Description: Data from 6 gpr files aims to identify differential expressed genes between the beta 7+ and beta 7- memory T helper cells. biocViews: ExperimentData, Homo_sapiens_Data, CGHData, MicroarrayData Author: Jean Yang Maintainer: Jean Yang source.ver: src/contrib/beta7_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bladderbatch Version: 1.6.0 Depends: Biobase License: Artistic-2.0 MD5sum: f695655ba125d61e0cc46eaaee9d2834 NeedsCompilation: no Title: Bladder gene expression data illustrating batch effects Description: This package contains microarray gene expression data on 57 bladder samples from 5 batches. The data are used as an illustrative example for the sva package. biocViews: ExperimentData, CancerData, MicroarrayData Author: Jeffrey T. Leek Maintainer: Jeffrey T. Leek source.ver: src/contrib/bladderbatch_1.6.0.tar.gz 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: 0.102.0 Depends: R(>= 3.0.0) Suggests: blima, beadarray, illuminaHumanv4.db, BiocStyle License: GPL-3 MD5sum: b9dfa649e6cc22bcd5266a8104da5365 NeedsCompilation: no Title: Data for testing of the package blima. Description: Experiment data package. The set were prepared using microarray images of human mesenchymal cells treated with various supplements. This package is intended to provide example data to test functionality provided by blima. biocViews: MicroarrayData, ExperimentData, GEO Author: Vojtech Kulvait Maintainer: Vojtech Kulvait URL: https://bitbucket.org/kulvait/blima source.ver: src/contrib/blimaTestingData_0.102.0.tar.gz 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: 1.6.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 11e234c7182f45c754d0e05119ced25d NeedsCompilation: no Title: Gene expression dataset published by Schmidt et al. [2008] (MAINZ). Description: Gene expression data from the breast cancer study published by Schmidt et al. in 2008, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ source.ver: src/contrib/breastCancerMAINZ_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerNKI Version: 1.6.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 93ffa812c75fc29ad9a59221138ddb1e NeedsCompilation: no Title: Genexpression dataset published by van't Veer et al. [2002] and van de Vijver et al. [2002] (NKI). Description: Genexpression data from a breast cancer study published by van't Veer et al. in 2002 and van de Vijver et al. in 2002, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, CGHData, MicroarrayData, OneChannelData, ChipOnChipData Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ source.ver: src/contrib/breastCancerNKI_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: seventyGeneData Package: breastCancerTRANSBIG Version: 1.6.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: f23182e2addf69881681e8a4e56be248 NeedsCompilation: no Title: Gene expression dataset published by Desmedt et al. [2007] (TRANSBIG). Description: Gene expression data from a breast cancer study published by Desmedt et al. in 2007, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ source.ver: src/contrib/breastCancerTRANSBIG_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerUNT Version: 1.6.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 22001e1eb09401e91bdd21e0cd9a3c11 NeedsCompilation: no Title: Gene expression dataset published by Sotiriou et al. [2007] (UNT). Description: Gene expression data from a breast cancer study published by Sotiriou et al. in 2007, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, TwoChannelData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ source.ver: src/contrib/breastCancerUNT_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerUPP Version: 1.6.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 8b7a444ec4563ec6d9a5fa2425715848 NeedsCompilation: no Title: Gene expression dataset published by Miller et al. [2005] (UPP). Description: Gene expression data from a breast cancer study published by Miller et al. in 2005, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ source.ver: src/contrib/breastCancerUPP_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerVDX Version: 1.6.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 124b50e185848f4e814cbeeecb73a985 NeedsCompilation: no Title: Gene expression datasets published by Wang et al. [2005] and Minn et al. [2007] (VDX). Description: Gene expression data from a breast cancer study published by Wang et al. in 2005 and Minn et al. in 2007, provided as an eSet. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData, BreastCancerData, LungCancerData, MicroarrayData, OneChannelData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ source.ver: src/contrib/breastCancerVDX_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bronchialIL13 Version: 1.6.0 Depends: R(>= 2.10.0), affy (>= 1.23.4) License: GPL-2 MD5sum: b829d087ede477af2fc6820fd6f09392 NeedsCompilation: no Title: time course experiment involving il13 Description: derived from CNMC (pepr.cnmcresearch.org) http://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=95 Human Bronchial Cell line A549 biocViews: ExperimentData, MicroarrayData Author: Vince Carey Maintainer: Vince Carey URL: http://www.biostat.harvard.edu/~carey source.ver: src/contrib/bronchialIL13_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bsseqData Version: 0.6.0 Depends: R (>= 2.15), bsseq (>= 0.9.6) License: Artistic-2.0 MD5sum: ee7c2ca15baa2fe711c58d2270bea23f NeedsCompilation: no Title: Example whole genome bisulfite data for the bsseq package Description: Example whole genome bisulfite data for the bsseq package biocViews: Genome, CancerData, ColonCancerData, SequencingData Author: Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen source.ver: src/contrib/bsseqData_0.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cancerdata Version: 1.6.0 Depends: R (>= 2.10.1), Biobase License: GPL (>= 2) MD5sum: 8f2aefa7f15b159071d381f8c8de8b26 NeedsCompilation: no Title: Development and validation of diagnostic tests from high-dimensional molecular data: Datasets Description: Dataset for the R package cancerclass biocViews: CancerData, MicroarrayData Author: Jan Budczies, Daniel Kosztyla Maintainer: Daniel Kosztyla source.ver: src/contrib/cancerdata_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CardinalWorkflows Version: 1.0.0 Depends: R (>= 2.10), Cardinal Suggests: BiocStyle License: Artistic-2.0 MD5sum: 056063a636c9f4c23c8047c959803064 NeedsCompilation: no Title: Datasets and workflows for the Cardinal mass spectrometry imaging package Description: Datasets and workflows for Cardinal: DESI and MALDI examples including pig fetus, cardinal painting, and human RCC. biocViews: ExperimentData, MassSpectrometryData, ImagingMassSpectrometryData Author: Kyle D. Bemis Maintainer: Kyle D. Bemis source.ver: src/contrib/CardinalWorkflows_1.0.0.tar.gz vignettes: vignettes/CardinalWorkflows/inst/doc/Workflows-classification.pdf, vignettes/CardinalWorkflows/inst/doc/Workflows-clustering.pdf vignetteTitles: Classification example workflow, Clustering example workflow hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CardinalWorkflows/inst/doc/Workflows-clustering.R Package: CCl4 Version: 1.6.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), limma License: Artistic-2.0 MD5sum: 35d0f654a3bcf1bcbf36509089563b9d NeedsCompilation: no Title: Carbon Tetrachloride (CCl4) treated hepatocytes Description: NChannelSet for rat hepatocytes treated with Carbon Tetrachloride (CCl4) data from LGC company. biocViews: ExperimentData, Genome, Rattus_norvegicus_Data, MicroarrayData Author: Audrey Kauffmann, Wolfgang Huber Maintainer: Audrey Kauffmann source.ver: src/contrib/CCl4_1.6.0.tar.gz 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: 1.6.0 Depends: R (>= 2.10), Ringo(>= 1.9.8), affy(>= 1.23.4), topGO(>= 1.13.1) Imports: Biobase Suggests: biomaRt, Biobase(>= 2.5.5), xtable License: Artistic-2.0 MD5sum: ba8e10dc49a9c092614210c6abfa9330 NeedsCompilation: no Title: Data package for ChIP-chip tutorial Description: This is a data package that accompanies a ChIP-chip tutorial, which has been published in PLoS Computational Biology. The data and source code in this package allow the reader to completely reproduce the steps in the tutorial. biocViews: ExperimentData, Mus_musculus_Data, MicroarrayData, ChipOnChipData Author: Joern Toedling, Wolfgang Huber Maintainer: Joern Toedling source.ver: src/contrib/ccTutorial_1.6.0.tar.gz vignettes: vignettes/ccTutorial/inst/doc/ccTutorial.pdf, vignettes/ccTutorial/inst/doc/ccTutorialSupplement.pdf vignetteTitles: A tutorial on how to analyze ChIP-chip readouts using Bioconductor, Supplement to A tutorial on how to analyze ChIP-chip readouts using Bioconductor hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ccTutorial/inst/doc/ccTutorial.R, vignettes/ccTutorial/inst/doc/ccTutorialSupplement.R Package: ceu1kg Version: 0.6.0 Depends: R (>= 2.12.0), GGBase (>= 3.9.0), GGtools, Biobase Suggests: SNPlocs.Hsapiens.dbSNP.20101109 License: Artistic-2.0 MD5sum: 64794fac8737bb41a6b5d62408b0a965 NeedsCompilation: no Title: CEU (N=60) genotypes from 1000 genomes pilot phase I Description: CEU genotypes from 1000 genomes "low coverage" pilot phase I (approx 8 million SNP calls released July 2010); includes Wellcome trust GENEVAR expression for 43 indiv biocViews: SNPData, HapMap, Project1000genomes Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/ceu1kg_0.6.0.tar.gz 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: 0.10.0 Depends: R (>= 3.0), GGBase Imports: Biobase License: Artistic-2.0 MD5sum: 689122b3b232a22fc1d88b1595f89ade NeedsCompilation: no Title: expression + genotype on 79 unrelated CEU individuals Description: expression + genotype on 79 unrelated CEU individuals biocViews: ArrayExpress Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/ceu1kgv_0.10.0.tar.gz vignettes: vignettes/ceu1kgv/inst/doc/ceu1kgv.pdf vignetteTitles: ceu1kgv -- genotype plus expression for HapMap CEU hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ceu1kgv/inst/doc/ceu1kgv.R Package: ceuhm3 Version: 0.6.0 Depends: R (>= 2.12.0), GGBase, Biobase Imports: GGtools License: Artistic-2.0 MD5sum: d2335529ba1afec97b1ebc936b1267d9 NeedsCompilation: no Title: ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort Description: ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort biocViews: SNPData, HapMap Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/ceuhm3_0.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cgdv17 Version: 0.6.0 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: 7df03370d6b50fad1aca5093fc729144 NeedsCompilation: no Title: Complete Genomics Diversity Panel, chr17 on 46 individuals Description: Complete Genomics Diversity Panel, chr17 on 46 individuals biocViews: SequencingData, SNPData, BiocViews Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/cgdv17_0.6.0.tar.gz vignettes: vignettes/cgdv17/inst/doc/cgdv.pdf vignetteTitles: cgdv17: extract from Complete Genomics diversity panel hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cgdv17/inst/doc/cgdv.R Package: ChAMPdata Version: 1.6.0 Depends: R (>= 3.0.1) License: GPL-3 MD5sum: dc68d8e469942b46f6433fed4d4141b6 NeedsCompilation: no Title: Data Packages for ChAMP package Description: Provides datasets needed for ChAMP including a test dataset and blood controls for CNA analysis biocViews: ExperimentData Author: Tiffany Morris, Lee Butcher and Andrew Teschendorff Maintainer: Tiffany Morris source.ver: src/contrib/ChAMPdata_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: charmData Version: 1.4.0 Depends: R(>= 2.11.0), charm, pd.charm.hg18.example License: LGPL (>= 2) MD5sum: d70439b04d3b00f9698c610d5eae4649 NeedsCompilation: no Title: An example dataset for use with the charm package Description: An example dataset for use with the charm package biocViews: ExperimentData, MicroarrayData Author: Martin Aryee Maintainer: Martin Aryee source.ver: src/contrib/charmData_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cheung2010 Version: 0.6.0 Depends: R (>= 2.13.0), Biobase, GGtools, GenomicRanges, hgfocus.db Imports: AnnotationDbi Suggests: SNPlocs.Hsapiens.dbSNP.20120608 Enhances: parallel License: Artistic-2.0 MD5sum: 61a6787614bab2b3dd03bb79f4ac8d74 NeedsCompilation: no Title: resources for genetics of gene expression based on Cheung et al 2010 Description: Data resources related to the PLoS Biology paper Polymorphic Cis- and Trans-Regulation of Human Gene Expression, including small-footprint smlSet support for 147 hgfocus arrays and corresponding HapMap genotypes at 1.3 million SNP; 0.0.22+ includes cheung_eset... from Leek et al RECOUNT myrna output biocViews: Homo_sapiens_Data, SequencingData, RNASeqData, SNPData, HapMap Author: Vince Carey Maintainer: Vince Carey source.ver: src/contrib/cheung2010_0.6.0.tar.gz vignettes: vignettes/cheung2010/inst/doc/cheungTrans.pdf vignetteTitles: cheungTrans: checking trans eQTL with hgfocus arrays hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cheung2010/inst/doc/cheungTrans.R dependsOnMe: ggtut Package: ChimpHumanBrainData Version: 1.6.0 Depends: affy,qvalue,limma,hexbin,statmod License: MIT MD5sum: f09c07d3d02014dcc5f764b3000d9340 NeedsCompilation: no Title: Chimp and human brain data package Description: This data package contains chimp and human brain data extracted from the ArrayExpress accession E-AFMX-2. Both human and chimp RNAs were run on human hgu95av2 Affymetrix arrays. It is a useful dataset for tutorials. biocViews: Tissue, Homo_sapiens_Data, Pan_troglodytes_Data, MicroarrayData, TissueMicroarrayData, GEO Author: Roman Jaksik, Naomi Altman, and Sean Davis Maintainer: Sean Davis source.ver: src/contrib/ChimpHumanBrainData_1.6.0.tar.gz vignettes: vignettes/ChimpHumanBrainData/inst/doc/DiffExpressVignette.pdf vignetteTitles: DiffExpressVignette.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: chipenrich.data Version: 1.4.0 Depends: R (>= 2.15.0) Imports: methods, GenomicRanges (>= 1.10.0), IRanges (>= 1.16.0), BiocGenerics (>= 0.2.0) License: GPL-3 MD5sum: 77166c14da9c58881ffa2a2a84e86d27 NeedsCompilation: no Title: Gene set enrichment analysis for ChIP-seq data Description: Supporting data for the chipenrich package. Includes pre-defined gene sets, gene locus definitions, and mappability estimates. biocViews: ExperimentData, Genome, ChIPSeqData Author: Ryan P. Welch [aut, cre, cph], Chee Lee [aut, cre], Raymond G. Cavalcante [aut, cre], Laura J. Scott [ths], Maureen A. Sartor [ths] Maintainer: Ryan P. Welch , Chee Lee , Raymond G. Cavalcante source.ver: src/contrib/chipenrich.data_1.4.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: ChIPXpressData Version: 1.6.0 Depends: bigmemory License: GPL (>=2) MD5sum: 3a0e1648290a18da1f72a3c6517c7053 NeedsCompilation: no Title: ChIPXpress Pre-built Databases Description: Contains pre-built mouse (GPL1261) and human (GPL570) database of gene expression profiles to be used for ChIPXpress ranking. biocViews: Homo_sapiens_Data, Mus_musculus_Data, GEO Author: George Wu Maintainer: George Wu source.ver: src/contrib/ChIPXpressData_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CLL Version: 1.8.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: LGPL MD5sum: 5202eb3c760ecd253242d485d6b9545a NeedsCompilation: no Title: A Package for CLL Gene Expression Data Description: The CLL package contains the chronic lymphocytic leukemia (CLL) gene expression data. The CLL data had 24 samples that were either classified as progressive or stable in regards to disease progression. The data came from Dr. Sabina Chiaretti at Division of Hematology, Department of Cellular Biotechnologies and Hematology, University La Sapienza, Rome, Italy and Dr. Jerome Ritz at Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts. biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData Author: Elizabeth Whalen Maintainer: Robert Gentleman source.ver: src/contrib/CLL_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cMap2data Version: 1.4.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 3d193da9c37d5032de4161103da93f20 NeedsCompilation: no Title: Connectivity Map (version 2) Data Description: Data package which provides default drug profiles for the DrugVsDisease package as well as associated gene lists and data clusters used by the DrugVsDisease package. biocViews: Homo_sapiens_Data, MicroarrayData, GEO Author: C. Pacini Maintainer: J. Saez-Rodriguez source.ver: src/contrib/cMap2data_1.4.0.tar.gz 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: 1.4.0 Depends: R (>= 2.10), cnvGSA License: LGPL MD5sum: 02a662b4717d1e23e5364feecb50cb37 NeedsCompilation: no Title: Data used in the vignette of the cnvGSA package Description: This package contains the data used in the vignette of the cnvGSA package. biocViews: ExperimentData, Genome, CopyNumberVariationData Author: Joseph Lugo Maintainer: Joseph Lugo source.ver: src/contrib/cnvGSAdata_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: COHCAPanno Version: 1.4.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 7d2ab06ebc20371794efbd6d3c453f2a NeedsCompilation: no Title: Annotations for City of Hope CpG Island Analysis Pipeline Description: Provides genomic location, nearby CpG island and nearby gene information for common Illumina methylation array platforms biocViews: Homo_sapiens_Data, MicroarrayData, MethylationArrayData, CpGIslandData, GEO, ArrayExpress Author: Charles Warden Maintainer: Charles Warden source.ver: src/contrib/COHCAPanno_1.4.0.tar.gz 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: 1.10.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: a5c03ee1ceccb552294db31c00947c44 NeedsCompilation: no Title: exprSet for Alon et al. (1999) colon cancer data Description: exprSet for Alon et al. (1999) colon cancer data biocViews: ExperimentData, Tissue, CancerData, ColonCancerData, MicroarrayData, TissueMicroarrayData Author: Sylvia Merk Maintainer: W Sylvia Merk source.ver: src/contrib/colonCA_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ConnectivityMap Version: 1.4.0 Depends: R (>= 2.15.1) Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: c24b04ebef6a8d920334f3c7b5b57ed9 NeedsCompilation: no Title: Functional connections between drugs, genes and diseases as revealed by common gene-expression changes Description: The Broad Institute's Connectivity Map (cmap02) is a "large reference catalogue of gene-expression data from cultured human cells perturbed with many chemicals and genetic reagents", containing more than 7000 gene expression profiles and 1300 small molecules. biocViews: ExperimentData, CancerData, MicroarrayData Author: Paul Shannon Maintainer: Paul Shannon source.ver: src/contrib/ConnectivityMap_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: COPDSexualDimorphism.data Version: 1.4.0 License: LGPL-2.1 MD5sum: 9e6d3b387d6259c6d573c0785aede170 NeedsCompilation: no Title: Data to support sexually dimorphic and COPD differential analysis for gene expression and methylation. Description: Datasets to support COPDSexaulDimorphism Package. biocViews: ExperimentData, Tissue, COPDData Author: J Fah Sathirapongsasuti Maintainer: J Fah Sathirapongsasuti source.ver: src/contrib/COPDSexualDimorphism.data_1.4.0.tar.gz 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: CopyhelpeR Version: 1.0.1 Depends: R(>= 2.10) Suggests: BiocStyle License: GPL-2 MD5sum: 6912b134ad93b170679876a5f632cad5 NeedsCompilation: no Title: Helper files for CopywriteR Description: This package contains the helper files that are required to run the Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content and mappability files for the reference genomes hg18, hg19, hg38, mm9 and mm10. In addition, it contains a blacklist filter to remove regions that display CNV. Files are stored as GRanges objects from the GenomicRanges Bioconductor package. biocViews: Homo_sapiens, GenomicSequence Author: Thomas Kuilman Maintainer: Thomas Kuilman source.ver: src/contrib/CopyhelpeR_1.0.1.tar.gz vignettes: vignettes/CopyhelpeR/inst/doc/CopyhelpeR.pdf vignetteTitles: CopyhelpeR hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CopyhelpeR/inst/doc/CopyhelpeR.R Package: CopyNumber450kData Version: 1.4.0 Depends: R (>= 2.13.0), minfi, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 License: Artistic-2.0 MD5sum: 2a424dd23d20a1a8a1de89b6c6423283 NeedsCompilation: no Title: Example data for the Illumina Methylation 450k array Description: Data from 52 control samples from 450k methylation arrays biocViews: Tissue, Homo_sapiens_Data, MicroarrayData, MethylationArrayData, TissueMicroarrayData Author: Simon Papillon-Cavanagh, Jean-Philippe Fortin, Nicolas De Jay Maintainer: Simon Papillon-Cavanagh source.ver: src/contrib/CopyNumber450kData_1.4.0.tar.gz 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: 1.4.0 Depends: R (>= 3.0.2) Imports: GenomicRanges, VariantAnnotation Suggests: testthat, BiocStyle, knitr License: GPL-3 MD5sum: d7fc9f369ef80f467debc85612a749a3 NeedsCompilation: no Title: COSMIC.67 Description: COSMIC: Catalogue Of Somatic Mutations In Cancer, version 67 (2013-10-24) biocViews: ExperimentData, Genome, CancerData Author: Julian Gehring Maintainer: Julian Gehring VignetteBuilder: knitr source.ver: src/contrib/COSMIC.67_1.4.0.tar.gz 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: 0.102.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: f4ca6a386bb5b7313be8f42e0959a477 NeedsCompilation: no Title: CRC cell line dataset Description: colorectal cancer mRNA and miRNA on 18 cell lines biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella source.ver: src/contrib/CRCL18_0.102.0.tar.gz 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: 1.4.0 Depends: R (>= 2.10.0), affy Suggests: BiocStyle, survival, xtable, sva, genefilter, logging License: Artistic-2.0 MD5sum: 9b07641fb0a9113dcade7c73d4357d7f NeedsCompilation: no Title: Bladder Cancer Gene Expression Analysis Description: The curatedBladderData package provides relevant functions and data for gene expression analysis in patients with bladder cancer. biocViews: ExperimentData, CancerData, OvarianCancerData, MicroarrayData, ExpressionData Author: Markus Riester Maintainer: Markus Riester source.ver: src/contrib/curatedBladderData_1.4.0.tar.gz vignettes: vignettes/curatedBladderData/inst/doc/curatedBladderData_vignette.pdf vignetteTitles: curatedBladderData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: curatedBreastData Version: 1.0.0 Depends: R (>= 3.0.0), ggplot2, impute, XML, Biobase, BiocStyle License: GPL (>= 2) MD5sum: d535e3a5652df9b3359b7a5193891d25 NeedsCompilation: no Title: Curated breast gene expression data with survival and treatment information Description: Curated breast cancer S4 ExpresionSet datasets that all contain at least one type of outcomes variable and treatment information (minimum level: whether they had chemotherapy and whether they had hormonal therapy). Includes code to post-process these datasets. biocViews: GeneExpression, Microarray, ExperimentData Author: Katie Planey Maintainer: Katie Planey source.ver: src/contrib/curatedBreastData_1.0.0.tar.gz vignettes: vignettes/curatedBreastData/inst/doc/curatedBreastData-manual.pdf vignetteTitles: Manual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: curatedCRCData Version: 1.4.0 Depends: R (>= 2.10.0), nlme Suggests: survival,sva,BiocStyle, xtable, genefilter, logging, Biobase License: Artistic-2.0 MD5sum: b322bac41dbe611c4b1c7d6aa02146dc 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: ExperimentData, CancerData Author: Princy Parsana, Markus Riester, Curtis Huttenhower, Levi Waldron Maintainer: Princy Parsana URL: https://bitbucket.org/lwaldron/curatedcrcdata source.ver: src/contrib/curatedCRCData_1.4.0.tar.gz vignettes: vignettes/curatedCRCData/inst/doc/curatedCRCData_vignette.pdf vignetteTitles: curatedCRCData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: curatedOvarianData Version: 1.6.0 Depends: R (>= 2.10.0), affy Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle License: Artistic-2.0 MD5sum: d4722b1ebe52a2c1b8a7a879e8ca9c79 NeedsCompilation: no Title: Clinically Annotated Data for the Ovarian Cancer Transcriptome Description: The curatedOvarianData package provides data for gene expression analysis in patients with ovarian cancer. biocViews: ExperimentData, RNASeqData, CancerData, OvarianCancerData, MicroarrayData Author: Benjamin F. Ganzfried, Markus Riester, Steve Skates, Victoria Wang, Thomas Risch, Benjamin Haibe-Kains, Svitlana Tyekucheva, Jie Ding, Ina Jazic, Michael Birrer, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron Maintainer: Levi Waldron URL: http://bcb.dfci.harvard.edu/ovariancancer source.ver: src/contrib/curatedOvarianData_1.6.0.tar.gz vignettes: vignettes/curatedOvarianData/inst/doc/curatedOvarianData_vignette.pdf vignetteTitles: curatedOvarianData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: davidTiling Version: 1.8.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db License: LGPL MD5sum: 29806e8813157ddabdb9a954f23fc111 NeedsCompilation: no Title: Data and analysis scripts for David, Huber et al. yeast tiling array paper Description: This package contains the data for the paper by L. David et al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix genechips, an ExpressionSet object with the raw feature data, a probe annotation data structure for the chip and the yeast genome annotation (GFF file) that was used. In addition, some custom-written analysis functions are provided, as well as R scripts in the scripts directory. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, MicroarrayData Author: Wolfgang Huber , Joern Toedling Maintainer: Wolfgang Huber URL: http://www.ebi.ac.uk/huber source.ver: src/contrib/davidTiling_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: derfinderData Version: 0.102.0 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: 0e5b20e96c707dd2406235d0d82c6da0 NeedsCompilation: no Title: Processed BigWigs from BrainSpan for examples Description: Processed 22 samples from BrainSpan keeping only the information for chromosome 21. Data is stored in the BigWig format and is used for examples in other packages. biocViews: ExperimentData, Homo_sapiens_Data, RNASeqData Author: Leonardo Collado-Torres [aut, cre], Andrew Jaffe [aut], Jeffrey Leek [aut, ths] Maintainer: Leonardo Collado-Torres URL: https://github.com/lcolladotor/derfinderData VignetteBuilder: knitr BugReports: https://github.com/lcolladotor/derfinderData/issues source.ver: src/contrib/derfinderData_0.102.0.tar.gz 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: 1.4.0 Depends: R (>= 2.15), Imports: affy, frma, frmaTools, hgu133plus2.db, hgu133plus2frmavecs, sva, rgl, ConsensusClusterPlus, cluster, siggenes, ROCR, pamr, survival, gplots, AnnotationDbi, Biobase License: Artistic-2.0 MD5sum: ce40793f56f5dc619faf742d0954c618 NeedsCompilation: no Title: Poor prognosis colon cancer is defined by a molecularly distinct subtype and precursor lesion Description: This package reproduces the main pipeline to analyze the AMC-AJCCII-90 microarray data set in De Sousa et al. accepted by Nature Medicine in 2013. biocViews: CancerData, ColonCancerData, MicroarrayData Author: Xin Wang Maintainer: Xin Wang source.ver: src/contrib/DeSousa2013_1.4.0.tar.gz vignettes: vignettes/DeSousa2013/inst/doc/DeSousa2013-Vignette.pdf vignetteTitles: Main vignette:Poor prognosis colon cancer is defined by a molecular distinct subtype and develops from serrated precursor lesions hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DeSousa2013/inst/doc/DeSousa2013-Vignette.R Package: diggitdata Version: 1.0.0 Depends: R(>= 2.14.0), Biobase, methods Imports: viper License: GPL (>=2) MD5sum: 5b135d2464957a34fe32c70fcffadf0e NeedsCompilation: no Title: Example data for the diggit package Description: This package provides expression profile and CNV data for glioblastoma from TCGA, and transcriptional and post-translational regulatory networks assembled with the ARACNe and MINDy algorithms, respectively. biocViews: ExperimentData, Cancer Author: Mariano Javier Alvarez Maintainer: Mariano Javier Alvarez source.ver: src/contrib/diggitdata_1.0.0.tar.gz vignettes: vignettes/diggitdata/inst/doc/diggitdata.pdf vignetteTitles: Using bcellViper hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/diggitdata/inst/doc/diggitdata.R Package: DLBCL Version: 1.8.0 Depends: R(>= 2.11.0), Biobase License: GPL (>=2) MD5sum: f6b9e8b2834584e95c8132bf8af01e4e NeedsCompilation: no Title: Diffuse large B-cell lymphoma expression data Description: This package provides additional expression data on diffuse large B-cell lymphomas for the BioNet package. biocViews: ExperimentData, CancerData, MicroarrayData, ChipOnChipData Author: Marcus Dittrich and Daniela Beisser Maintainer: Marcus Dittrich URL: http://bionet.bioapps.biozentrum.uni-wuerzburg.de/ source.ver: src/contrib/DLBCL_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: DmelSGI Version: 1.0.0 Depends: R (>= 3.0) Imports: grid, TSP, limma, rhdf5, knitr, abind, gplots, igraph Suggests: BiocStyle, EBImage, RColorBrewer, RNAinteractMAPK, RSVGTipsDevice, cgdsr, hwriter, xtable, beeswarm License: Artistic-2.0 MD5sum: 2f2cca69389f2da4388887795ea53f11 NeedsCompilation: no Title: Experimental data and documented source code for the paper "A Map of Directional Genetic Interactions in a Metazoan Cell" Description: The package contains the experimental data and documented source code of the manuscript "Fischer et al., A Map of Directional Genetic Interactions in a Metazoan Cell, eLife, 2015, in Press.". The vignette code generates all figures in the paper. biocViews: MicrotitrePlateAssayData, CellCulture, Drosophila_melanogaster_Data, ExperimentData, HighThroughputImagingData Author: Bernd Fischer Maintainer: Bernd Fischer VignetteBuilder: knitr source.ver: src/contrib/DmelSGI_1.0.0.tar.gz vignettes: vignettes/DmelSGI/inst/doc/DmelSGI.pdf vignetteTitles: DmelSGI hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DmelSGI/inst/doc/DmelSGI.R Package: DMRcatedata Version: 1.4.0 Depends: R (>= 3.0.2) License: GPL-3 MD5sum: c6195e430df98e0c2a60727460170ed6 NeedsCompilation: no Title: Data Package for DMRcate package Description: This package contains 3 data objects supporting functionality and examples of DMRcate biocViews: SNPData Author: Tim Peters Maintainer: Tim Peters VignetteBuilder: knitr source.ver: src/contrib/DMRcatedata_1.4.0.tar.gz 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: 1.6.0 Depends: EBImage, parallel License: Artistic-2.0 MD5sum: 0a5b55ca1858969ea4285219483441ad NeedsCompilation: no Title: Supplementary data package for Dona et al. (2013) containing example images and tables Description: An experiment data package associated with the publication Dona et al. (2013). Package contains runnable vignettes showing an example image segmentation for one posterior lateral line primordium, and also the data table and code used to analyze tissue-scale lifetime-ratio statistics. biocViews: ExperimentData, Tissue Author: Erika Dona, Joseph D. Barry, Guillaume Valentin, Charlotte Quirin, Anton Khmelinskii, Andreas Kunze, Sevi Durdu, Lionel R. Newton, Ana Fernandez-Minan, Wolfgang Huber, Michael Knop, Darren Gilmour Maintainer: Joseph D. Barry source.ver: src/contrib/DonaPLLP2013_1.6.0.tar.gz vignettes: vignettes/DonaPLLP2013/inst/doc/PLLPanalysis.pdf, vignettes/DonaPLLP2013/inst/doc/PLLPstatistics.pdf vignetteTitles: PLLP image analysis, PLLP tissue-scale ratio statistics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DonaPLLP2013/inst/doc/PLLPanalysis.R, vignettes/DonaPLLP2013/inst/doc/PLLPstatistics.R Package: DREAM4 Version: 1.4.0 Depends: R (>= 2.15.1), GenomicRanges Imports: BiocGenerics Suggests: RUnit, networkBMA License: GPL MD5sum: c0196c6d3e01058794d005a4d056811c NeedsCompilation: no Title: Synthetic Expression Data for Gene Regulatory Network Inference from the 2009 DREAM4 challenge Description: Simulated expression data for five 10-node, and five 100-node networks, with associated data (including solutions) from the 2009 DREAM4 challenge. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, SequencingData Author: Paul Shannon Maintainer: Paul Shannon source.ver: src/contrib/DREAM4_1.4.0.tar.gz vignettes: vignettes/DREAM4/inst/doc/DREAM4_InSilico_Description.pdf, vignettes/DREAM4/inst/doc/DREAM4.pdf vignetteTitles: DREAM4_InSilico_Description.pdf, DREAM4 Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DREAM4/inst/doc/DREAM4.R Package: dressCheck Version: 0.6.0 Depends: R (>= 2.10.1), methods, Biobase (>= 2.5.5) Suggests: survival, chron License: Artistic-2.0 MD5sum: f409a6a8e1f0f27d691f74a120602587 NeedsCompilation: no Title: data and software for checking Dressman JCO 25(5) 2007 Description: data and software for checking Dressman JCO 25(5) 2007 biocViews: ExperimentData, Genome Author: Vincent Carey Maintainer: Vincent Carey source.ver: src/contrib/dressCheck_0.6.0.tar.gz 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: 1.4.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 892e5bce496c42120a23e6d6e9319178 NeedsCompilation: no Title: Drug versus Disease Data Description: Data package which provides default disease expression profiles, clusters and annotation information for use with the DrugVsDisease package. biocViews: Homo_sapiens_Data, MicroarrayData Author: C. Pacini Maintainer: J. Saez-Rodriguez source.ver: src/contrib/DrugVsDiseasedata_1.4.0.tar.gz 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: 0.6.0 Depends: R (>= 2.15.0), utils, GenomicRanges, Biobase, GGBase License: Artistic-2.0 MD5sum: 596ef6b51eea9d2d237976c16d096d86 NeedsCompilation: no Title: dsQTL, data excerpt from Degner et al. 2012 Nature letter Description: dsQTL, excerpt from Degner et al. 2012 Nature letter on DNA variants associated with DnaseI hypersensitivity biocViews: ExperimentData, Genome, SequencingData, DNASeqData, NCI, Project1000genomes, BiocViews Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/dsQTL_0.6.0.tar.gz vignettes: vignettes/dsQTL/inst/doc/dsq.pdf vignetteTitles: dsQTL,, data excerpt from Degner et al. 2012 Nature letter hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/dsQTL/inst/doc/dsq.R Package: DvDdata Version: 1.4.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 71c1357e6df06e7250ae51a5739185b0 NeedsCompilation: no Title: Drug versus Disease Data Description: Data package which provides default drug and disease expression profiles for the DvD package. biocViews: GEO Author: C. Pacini Maintainer: J. Saez-Rodriguez source.ver: src/contrib/DvDdata_1.4.0.tar.gz 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: 1.6.0 Depends: R (>= 1.4.1), marray, GEOquery Suggests: dyebias, convert, Biobase License: GPL-3 MD5sum: de265248c0a0152c7332b826364465f1 NeedsCompilation: no Title: Example data for the dyebias package, which implements the GASSCO method. Description: Data for the dyebias package, consisting of 4 self-self hybrizations of self-spotted yeast slides, as well as data from Array Express accession E-MTAB-32 biocViews: ExperimentData, SAGEData, CGHData, MicroarrayData, TwoChannelData, ArrayExpress Author: Philip Lijnzaad and Thanasis Margaritis Maintainer: Philip Lijnzaad URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad source.ver: src/contrib/dyebiasexamples_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Package: EatonEtAlChIPseq Version: 0.6.0 Depends: GenomicRanges (>= 1.5.42), ShortRead, rtracklayer License: Artistic 2.0 MD5sum: 96d40f297476f62788ff0c4d9fe3c16e NeedsCompilation: no Title: ChIP-seq data of ORC-binding sites in Yeast excerpted from Eaton et al. 2010 Description: ChIP-seq analysis subset from "Conserved nucleosome positioning defines replication origins" (PMID 20351051) biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, ChIPSeqData, GEO Author: Patrick Aboyoun Maintainer: Patrick Aboyoun source.ver: src/contrib/EatonEtAlChIPseq_0.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ecoliLeucine Version: 1.8.0 Depends: R (>= 1.9.0), affy (>= 1.23.4), ecolicdf License: GPL (>= 2) MD5sum: ad2eb4659c686e61654eec49e9e0f7b5 NeedsCompilation: no Title: Experimental data with Affymetrix E. coli chips Description: Experimental data with Affymetrix E. coli chips, as reported in She-pin Hung, Pierre Baldi, and G. Wesley Hatfield, J. Biol. Chem., Vol. 277, Issue 43, 40309-40323, October 25, 2002 biocViews: ExperimentData, MicroarrayData Author: Laurent Gautier Maintainer: Laurent Gautier source.ver: src/contrib/ecoliLeucine_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: encoDnaseI Version: 0.6.0 Depends: R (>= 2.15.0), methods, Biobase (>= 2.5.5), lattice, GGtools, GGBase Suggests: GGdata License: Artistic-2.0 MD5sum: 049521519b0807289f5fa4641588dfec NeedsCompilation: no Title: data provided by UCSC for Cd4 raw measures of DnaseI hypersensitivity Description: data provided by UCSC for Cd4 raw measures of DnaseI hypersensitivity biocViews: ExperimentData, Genome, Homo_sapiens_Data, SNPData, ENCODE Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/encoDnaseI_0.6.0.tar.gz vignettes: vignettes/encoDnaseI/inst/doc/dnaseUse.pdf vignetteTitles: ENCODE/hg18 track demo: DNaseI hypersensitivity hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/encoDnaseI/inst/doc/dnaseUse.R Package: estrogen Version: 1.14.0 Depends: R (>= 1.9.0), affy (>= 1.4) Suggests: Biobase (>= 1.13.16), affy, vsn, hgu95av2.db, genefilter License: LGPL MD5sum: e246f71ac9d497f0f8bf1697574152dc NeedsCompilation: no Title: 2x2 factorial design exercise for the Bioconductor short course Description: Data from 8 Affymetrix genechips, looking at a 2x2 factorial design (with 2 repeats per level) biocViews: ExperimentData, MicroarrayData Author: Wolfgang Huber, Robert Gentleman Maintainer: R. Gentleman source.ver: src/contrib/estrogen_1.14.0.tar.gz 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: 1.8.0 Depends: xcms License: LGPL MD5sum: 7a989c19075d1cb6b0e1a9abe9d37b60 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_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fabiaData Version: 1.6.0 Depends: R (>= 2.10.0), Biobase Imports: utils Suggests: fabia License: LGPL (>= 2.1) MD5sum: 91fd45cba4b2d1b50c0b9a5f55ed37b6 NeedsCompilation: no Title: Data sets for FABIA (Factor Analysis for Bicluster Acquisition) Description: Supplying gene expression data sets for the demos of the biclustering method "Factor Analysis for Bicluster Acquisition" (FABIA). The following three data sets are provided: A) breast cancer (van't Veer, Nature, 2002), B) multiple tissues (Su, PNAS, 2002), and C) diffuse large-B-cell lymphoma (Rosenwald, N Engl J Med, 2002). biocViews: CancerData, BreastCancerData, MicroarrayData Author: Sepp Hochreiter Maintainer: Sepp Hochreiter URL: http://www.bioinf.jku.at/software/fabia/fabia.html source.ver: src/contrib/fabiaData_1.6.0.tar.gz vignettes: vignettes/fabiaData/inst/doc/fabiaData.pdf vignetteTitles: fabiaData: Manual for the R Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/fabiaData/inst/doc/fabiaData.R Package: facopy.annot Version: 0.102.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 749107128161f64f6fa3395998e03112 NeedsCompilation: no Title: Annotation for the copy number alteration association and enrichment analyses with facopy Description: Provides facopy with genome annotation on chromosome arms, genomic features and copy number alterations. biocViews: Genome Author: David Mosen-Ansorena Maintainer: David Mosen-Ansorena source.ver: src/contrib/facopy.annot_0.102.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: facsDorit Version: 1.10.0 Depends: R (>= 1.9.1), prada (>= 1.0.5) License: GPL-2 MD5sum: c032d6125445c7de8167c7ba5ab8c8dc NeedsCompilation: no Title: DKFZ FACS example data Description: FACS example data for cell-based assays. This data is used in the examples and vignettes of the package prada. biocViews: ExperimentData, MicrotitrePlateAssayData Author: Florian Hahne Maintainer: Florian Hahne URL: http://www.dkfz.de/mga source.ver: src/contrib/facsDorit_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: FANTOM3and4CAGE Version: 1.4.0 Depends: R (>= 2.15.0) License: GPL-3 MD5sum: c80f06e207947c17b06988459100ce64 NeedsCompilation: no Title: CAGE data from FANTOM3 and FANTOM4 projects Description: CAGE (Cap Analysis Gene Expression) data from FANTOM3 and FANTOM4 projects produced by RIKEN Omics Science Center. biocViews: ExperimentData, Tissue Author: Vanja Haberle, Department of Biology, University of Bergen, Norway Maintainer: Vanja Haberle source.ver: src/contrib/FANTOM3and4CAGE_1.4.0.tar.gz 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: 1.6.0 Depends: R (>= 2.10.0), lumi Suggests: genefilter, affy License: GPL (>2) MD5sum: 6b803cc985fdff889c265df3f105197a NeedsCompilation: no Title: Illumina DASL example microarray data Description: A subset of GSE17565 (April et al. 2009) containing 32 FFPE samples of Burkitts Lymphoma and Breast Adenocarcinoma, with a dilution series in technical duplicate. biocViews: Tissue, Genome, MicroarrayData, TissueMicroarrayData, GEO Author: Levi Waldron Maintainer: Levi Waldron source.ver: src/contrib/ffpeExampleData_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fibroEset Version: 1.10.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: f9d5f75f3d617e4398de9ad0f921731c NeedsCompilation: no Title: exprSet for Karaman et al. (2003) fibroblasts data Description: exprSet for Karaman et al. (2003) human, bonobo and gorilla fibroblasts data biocViews: ExperimentData, Genome, Homo_sapiens_Data, MicroarrayData, ChipOnChipData Author: Sylvia Merk Maintainer: Sylvia Merk source.ver: src/contrib/fibroEset_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fission Version: 0.102.0 Depends: R (>= 2.10), GenomicRanges Suggests: knitr License: LGPL MD5sum: 0262ec2851da550150996385d2d83dcc 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, Genome, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData, GEO Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr source.ver: src/contrib/fission_0.102.0.tar.gz 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: 1.4.0 Depends: R (>= 2.15), limma Imports: Biobase ,VennDiagram, gplots,grid License: GPL (>= 2) MD5sum: 4173fecef572f66af92925edaf07d497 NeedsCompilation: no Title: Gene expression data from breast cancer cells under FGFR2 signalling perturbation. Description: The package Fletcher2013a contains time-course gene expression data from MCF-7 cells treated under different experimental systems in order to perturb FGFR2 signalling. The data comes from Fletcher et al. (Nature Comms 4:2464, 2013) where further details about the background and the experimental design of the study can be found. biocViews: ExperimentData, ExpressionData, CancerData, BreastCancerData, MicroarrayData Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin Meyer. Maintainer: Mauro Castro URL: http://dx.doi.org/10.1038/ncomms3464 source.ver: src/contrib/Fletcher2013a_1.4.0.tar.gz 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: 1.4.0 Depends: R (>= 2.15), Fletcher2013a, biomaRt, VennDiagram, RTN (>= 1.1.2), RedeR (>= 1.8.1) Imports: RColorBrewer, corrgram License: GPL (>= 2) MD5sum: 9de0bbffd69733ef40b5a809c5baec00 NeedsCompilation: no Title: Master regulators of FGFR2 signalling and breast cancer risk. Description: This package reproduces the systems biology analysis for the data in package Fletcher2013a using RTN. biocViews: ExperimentData, ChIPSeqData, CancerData, BreastCancerData, SNPData Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin Meyer. Maintainer: Mauro Castro URL: http://dx.doi.org/10.1038/ncomms3464 source.ver: src/contrib/Fletcher2013b_1.4.0.tar.gz 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: 1.4.0 Depends: R (>= 2.12.2), flowCore Imports: methods License: Artistic-2.0 MD5sum: 60df31eb77af62eeffebbbaabdd13855 NeedsCompilation: no Title: Example data for the flowFit package Description: Two dataset that can be used to run examples from the flowFit vignette and examples biocViews: FlowCytometryData Author: davide Rambaldi Maintainer: Davide Rambaldi source.ver: src/contrib/flowFitExampleData_1.4.0.tar.gz vignettes: vignettes/flowFitExampleData/inst/doc/flowFitExampleData.pdf vignetteTitles: flowFitExampleData: example data for the beadarray package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowFitExampleData/inst/doc/flowFitExampleData.R Package: FlowSorted.Blood.450k Version: 1.6.0 Depends: R (>= 2.13.0), minfi (>= 1.8.0) License: Artistic-2.0 MD5sum: b6f47bae8936e6fccd6c457bc9407925 NeedsCompilation: no Title: Illumina HumanMethylation data on sorted blood cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays, and an object depicting which CpGs on the array are associated with cell type. biocViews: Homo_sapiens_Data, MicroarrayData, MethylationArrayData Author: Andrew E Jaffe Maintainer: Andrew E Jaffe source.ver: src/contrib/FlowSorted.Blood.450k_1.6.0.tar.gz vignettes: vignettes/FlowSorted.Blood.450k/inst/doc/FlowSorted.Blood.450k.pdf vignetteTitles: FlowSorted Blood 450k Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: FlowSorted.DLPFC.450k Version: 1.4.0 Depends: R (>= 2.13.0), minfi License: Artistic-2.0 MD5sum: 8b22924a122d2981faa16abad9010351 NeedsCompilation: no Title: Illumina HumanMethylation data on sorted frontal cortex cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays. biocViews: Homo_sapiens_Data, MicroarrayData Author: Andrew E Jaffe, Zachary A. Kaminsky Maintainer: Andrew E Jaffe source.ver: src/contrib/FlowSorted.DLPFC.450k_1.4.0.tar.gz vignettes: vignettes/FlowSorted.DLPFC.450k/inst/doc/FlowSorted.DLPFC.450k.pdf vignetteTitles: FlowSorted DLPFC 450k Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: flowWorkspaceData Version: 2.4.0 License: GPL-2 MD5sum: a42004e1e2ce4cbe187b6014a11778d7 NeedsCompilation: no Title: A data package containing two flowJo xml workspaces and associated fcs files for testing the flowWorkspace and openCyto packages. Description: The necessary external data to run the flowWorkspace and openCyto vignette is found in this package. biocViews: ExperimentData, FlowCytometryData Author: Greg Finak Maintainer: Mike Jiang source.ver: src/contrib/flowWorkspaceData_2.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: frmaExampleData Version: 1.4.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: baee6ec0428b61f319efa2f35ed78c21 NeedsCompilation: no Title: Frma Example Data Description: Data files used by the examples in frma and frmaTools packages biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall Maintainer: Matthew N. McCall source.ver: src/contrib/frmaExampleData_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: FunciSNP.data Version: 1.4.0 Depends: R (>= 2.14.0), IRanges Imports: rtracklayer License: GPL-3 MD5sum: 80d5d16b208d176bbb8f57893d314c27 NeedsCompilation: no Title: Various data sets for use with the FunciSNP package Description: Data sets needed for FunciSNP to integrate information from GWAS, 1000genomes and chromatin feature, in order to identify functional SNP in coding or non-coding regions. biocViews: SNPData, Project1000genomes, ENCODE Author: Simon G. Coetzee and Houtan Noushmehr, PhD Maintainer: Simon G. Coetzee URL: http://coetzeeseq.usc.edu/publication/Coetzee_SG_et_al_2012/ source.ver: src/contrib/FunciSNP.data_1.4.0.tar.gz 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: 2.6.0 Depends: R (>= 2.10) Suggests: gage, pathview, genefilter License: GPL (>=2.0) MD5sum: 06939548075fc52c6e967dd20abe0c57 NeedsCompilation: no Title: Auxillary data for gage package Description: This is a supportive data package for the software package, gage. However, the data supplied here are also useful for gene set or pathway analysis or microarray data analysis in general. In this package, we provide two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and BMP6 (originally published as an demo dataset for GAGE, also registered as GSE13604 in GEO). This package also includes commonly used gene set data based on KEGG pathways and GO terms for major research species, including human, mouse, rat and budding yeast. Mapping data between common gene IDs for budding yeast are also included. biocViews: ExperimentData, StemCell, CancerData, BreastCancerData, MicroarrayData, GEO Author: Weijun Luo Maintainer: Weijun Luo source.ver: src/contrib/gageData_2.6.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: gaschYHS Version: 1.6.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 152e9f9d32a519b8025b9a60c243c61e NeedsCompilation: no Title: ExpressionSet for response of yeast to heat shock and other environmental stresses Description: Data from PMID 11102521 biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data Author: Audrey Gasch and colleagues Maintainer: Vince Carey URL: http://genome-www.stanford.edu/yeast_stress/data/rawdata/complete_dataset.txt source.ver: src/contrib/gaschYHS_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gatingMLData Version: 2.8.0 Depends: R (>= 1.9.0) Suggests: flowUtils License: GPL MD5sum: 64f2d306bbb7392e955badf67c3538a2 NeedsCompilation: no Title: Data and XML files for Gating-ML Test suite Description: Test data and XML files for testing compliance of the flowUtils/flowCore packages with Gating-ML (1.5 and 2.0) standards. biocViews: ExperimentData, FlowCytometryData Author: J. Spidlen, N. Gopalakrishnan Maintainer: J. Spidlen source.ver: src/contrib/gatingMLData_2.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gcspikelite Version: 1.6.0 Depends: R (>= 2.5.0) License: LGPL MD5sum: ac1f4200eb2fb1b77bb88bbc4c3bf6f6 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_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: geneLenDataBase Version: 1.4.0 Depends: R (>= 2.11.0) Imports: utils, rtracklayer, GenomicFeatures (>= 1.3.15) License: LGPL (>= 2) MD5sum: 4dc071feb26871e15f216da34cda27d2 NeedsCompilation: no Title: Lengths of mRNA transcripts for a number of genomes Description: Length of mRNA transcripts for a number of genomes and gene ID formats, largely based on UCSC table browser biocViews: ExperimentData, Genome Author: Matthew Young Maintainer: Nadia Davidson source.ver: src/contrib/geneLenDataBase_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: genomationData Version: 1.0.0 Suggests: knitr License: GPL-3 MD5sum: 4affbc224a013d3266c54c18f5714f8d NeedsCompilation: no Title: Experimental data for showing functionalities of the genomation package Description: The package contains Chip Seq, Methylation and Cage data, downloaded from Encode biocViews: ExperimentData, Genome, StemCell, SequencingData, ChIPSeqData, ChipOnChipData, ENCODE Author: Altuna Akalin, Vedran Franke Maintainer: Vedran Franke VignetteBuilder: knitr source.ver: src/contrib/genomationData_1.0.0.tar.gz vignettes: vignettes/genomationData/inst/doc/genomationData-knitr.pdf vignetteTitles: genomationData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/genomationData/inst/doc/genomationData-knitr.R Package: geuvPack Version: 1.0.0 Depends: GenomicRanges License: Artistic-2.0 MD5sum: a4836920eb3bd0ec06af3eb285682c4d NeedsCompilation: no Title: summarized experiment with expression data from GEUVADIS Description: FPKM from GEUVADIS, annotated to gencode regions biocViews: ExperimentData, Genome, SequencingData, MicroarrayData, ArrayExpress Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/geuvPack_1.0.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: geuvStore Version: 1.0.0 Depends: BatchJobs, GenomicRanges Suggests: Homo.sapiens, knitr (>= 1.7), rmarkdown License: Artistic-2.0 MD5sum: 66668d30868d8737e960a18638c4ce5e NeedsCompilation: no Title: demonstrate storage discipline for eQTL enumerations Description: demonstrate storage discipline for eQTL enumerations and analyses based on a selection of GEUVADIS results biocViews: ExperimentData, SequencingData, MicroarrayData Author: VJ Carey Maintainer: VJ Carey VignetteBuilder: knitr source.ver: src/contrib/geuvStore_1.0.0.tar.gz vignettes: vignettes/geuvStore/inst/doc/geuvStore.pdf vignetteTitles: geuvStore.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GGdata Version: 1.6.0 Depends: R (>= 2.12.0), methods, Biobase (>= 2.5.5), GGBase, snpStats, illuminaHumanv1.db, AnnotationDbi Enhances: GGtools License: LGPL MD5sum: 7a24938a0b6a837249714e2968bcde8a NeedsCompilation: no Title: all 90 hapmap CEU samples, 47K expression, 4mm SNP Description: data exemplars dealing with hapmap SNP reports, GWAS, etc. biocViews: ExperimentData, HapMap, Genome, SequencingData, MicroarrayData, SNPData Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/GGdata_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ggtut suggestsMe: encoDnaseI Package: ggtut Version: 0.6.0 Depends: R (>= 2.14.0), GGtools (>= 3.11.32), ff, GenomicRanges, snpStats, GGdata, GenomicFeatures, ChIPpeakAnno, Rsamtools(>= 1.5.35), cheung2010, SNPlocs.Hsapiens.dbSNP.20120608, hmyriB36 Suggests: rtracklayer, GenomicFeatures, ChIPpeakAnno, TxDb.Hsapiens.UCSC.hg18.knownGene License: Artistic-2.0 MD5sum: 75aff10b49b7d0f1c95b1864ac2d88f0 NeedsCompilation: no Title: support for tutorial on genetics of gene expression ISMB 2011 Description: various resources for genetics of expression with R/bioc biocViews: SequencingData, MicroarrayData, SNPData Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/ggtut_0.6.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: golubEsets Version: 1.10.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: LGPL MD5sum: eec660acfc12182a524ab39ab498daa3 NeedsCompilation: no Title: exprSets for golub leukemia data Description: representation of public golub data with some covariate data of provenance unknown to the maintainer at present; now employs ExpressionSet format biocViews: ExperimentData, Genome, CancerData, LeukemiaCancerData Author: Todd Golub Maintainer: Vince Carey source.ver: src/contrib/golubEsets_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: grndata Version: 1.0.0 Depends: R (>= 2.10) Suggests: RUnit, BiocGenerics, knitr License: GPL-3 MD5sum: 00997df37d1de2c1c274534bda076f75 NeedsCompilation: no Title: Synthetic Expression Data for Gene Regulatory Network Inference Description: Simulated expression data for five large Gene Regulatory Networks from different simulators biocViews: ExperimentData, NetworkInference, GeneExpression, Microarray, GeneRegulation, Network Author: Pau Bellot, Catharina Olsen, Patrick E Meyer Maintainer: Pau Bellot VignetteBuilder: knitr source.ver: src/contrib/grndata_1.0.0.tar.gz vignettes: vignettes/grndata/inst/doc/ hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE htmlDocs: vignettes/grndata/inst/doc/grndata.html htmlTitles: "GRNdata" Package: GSBenchMark Version: 0.102.0 Depends: R (>= 2.13.1) License: GPL-2 MD5sum: 2322677884f26a0f3e0dc823dda0663b NeedsCompilation: no Title: Gene Set Benchmark Description: Benchmarks for Machine Learning Analysis of the Gene Sets. The package contains a list of pathways and gene expression data sets used in "Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)" (2010) by Eddy et al. biocViews: MicroarrayData Author: Bahman Afsari , Elana J. Fertig Maintainer: Bahman Afsari source.ver: src/contrib/GSBenchMark_0.102.0.tar.gz 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: gskb Version: 1.0.0 Depends: R (>= 3.2.0) License: Artistic-2.0 MD5sum: 84c9dc39ca35eeda1cfe3871aa17484a NeedsCompilation: no Title: Gene Set data for pathway analysis in mouse Description: Gene Set Knowledgebase (GSKB) is a comprehensive knowledgebase for pathway analysis in mouse. Interpretation of high-throughput genomics data based on biological pathways constitutes a constant challenge, partly because of the lack of supporting pathway database. We created a functional genomics knowledgebase in mouse, which includes 33,261 pathways and gene sets compiled from 40 sources such as Gene Ontology, KEGG, GeneSetDB, PANTHER, microRNA and transcription factor target genes, etc. In addition, we also manually collected and curated 8,747 lists of differentially expressed genes from 2,526 published gene expression studies to enable the detection of similarity to previously reported gene expression signatures. These two types of data constitute a comprehensive Gene Set Knowledgebase (GSKB), which can be readily used by various pathway analysis software such as gene set enrichment analysis (GSEA). As a first step, we gathered annotation information from 40 existing databases for mouse-related gene sets. These gene sets are divided into 7 categories, namely, Gene Ontology, Curated pathways, Metabolic Pathways, Transcription Factor (TF) and microRNA target genes, location (cytogenetics band), and others. We used information in GeneSetDB for some of the databases. Detailed information on these 40 sources and the citations is available http://bioinformatics.sdstate.edu/gskb/db/Table%201-sources.pdf . The gene lists from literature were retrieved manually from individual gene expression studies through a process similar to the one used to create AraPath, a similar resource for Arabidopsis[12]. As most expression studies upload raw data to repositories like GEO and ArrayExpress, we used the meta-data in these databases to search for publications. We scanned all datasets we can found and retrieved 4,313 potentially useful papers reporting gene expression studies in mouse. These papers were individually read by curators to identify lists of differentially expressed genes in various conditions. We compiled a total of 8,747 lists of differently expressed genes from 2,518 of papers. Each gene list was annotated with a unique name, brief description, and publication information, similar to the protocol used in MSigDB and Arapath. These gene lists constitute a large collection of published gene expression signatures that form a foundation for interpret new gene lists and expression profiles. More information about this data is available here http://bioinformatics.sdstate.edu/gskb/. There is also a paper describing these data are currently in revision by Database: The Journal of Biological Databases and Curation. biocViews: ExperimentData, Mus_musculus Author: Valerie Bares, Xijin Ge Maintainer: Valerie Bares source.ver: src/contrib/gskb_1.0.0.tar.gz vignettes: vignettes/gskb/inst/doc/gskb.pdf vignetteTitles: gskb: mouse data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GSVAdata Version: 1.4.0 Depends: R (>= 2.10), Biobase, GSEABase, hgu95a.db License: GPL (>= 2) MD5sum: f05a47ad65b30ec789d8078b53f92611 NeedsCompilation: no Title: Data employed in the vignette of the GSVA package Description: This package stores the data employed in the vignette of the GSVA package. These data belong to the following publications: Armstrong et al. Nat Genet 30:41-47, 2002; Cahoy et al. J Neurosci 28:264-278, 2008; Carrel and Willard, Nature, 434:400-404, 2005; Huang et al. PNAS, 104:9758-9763, 2007; Pickrell et al. Nature, 464:768-722, 2010; Skaletsky et al. Nature, 423:825-837; Verhaak et al. Cancer Cell 17:98-110, 2010 biocViews: ExperimentData, RNASeqData, Homo_sapiens_Data, CancerData, LeukemiaCancerData Author: Robert Castelo Maintainer: Robert Castelo source.ver: src/contrib/GSVAdata_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GWASdata Version: 1.6.0 Depends: GWASTools License: Artistic-2.0 MD5sum: b79528cbc8529bcf93f4962a7e55c251 NeedsCompilation: no Title: Data used in the examples and vignettes of the GWASTools package Description: Selected Affymetrix and Illlumina SNP data for HapMap subjects. Data provided by the Center for Inherited Disease Research at Johns Hopkins University and the Broad Institute of MIT and Harvard University. biocViews: ExperimentData, MicroarrayData, SNPData, HapMap Author: Stephanie Gogarten Maintainer: Stephanie Gogarten , Adrienne Stilp source.ver: src/contrib/GWASdata_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: h5vcData Version: 1.102.0 Suggests: h5vc License: GPL (>= 3) MD5sum: cfdf642ffc9e32a045b0a6065fbf9e30 NeedsCompilation: no Title: Example data for the h5vc package Description: This package contains the data used in the vignettes and examples of the 'h5vc' package biocViews: CancerData Author: Paul Theodor Pyl Maintainer: Paul Theodor Pyl source.ver: src/contrib/h5vcData_1.102.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap100khind Version: 1.10.0 Suggests: oligo License: GPL MD5sum: f4a7e183d34a82d19ff50e42f7b181c0 NeedsCompilation: no Title: Sample data - Hapmap 100K HIND Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho source.ver: src/contrib/hapmap100khind_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap100kxba Version: 1.10.0 Suggests: oligo License: GPL MD5sum: 88d63033fe43b090ca6c99dcdaf3a78b NeedsCompilation: no Title: Sample data - Hapmap 100K XBA Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho source.ver: src/contrib/hapmap100kxba_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap500knsp Version: 1.10.0 Suggests: oligo License: GPL MD5sum: 75e99449eb426063e8c77d501fcb8852 NeedsCompilation: no Title: Sample data - Hapmap 500K NSP Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho source.ver: src/contrib/hapmap500knsp_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap500ksty Version: 1.10.0 Suggests: oligo License: GPL MD5sum: c0a20cec1e962dacbc470ed794133a10 NeedsCompilation: no Title: Sample data - Hapmap 500K STY Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho source.ver: src/contrib/hapmap500ksty_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmapsnp5 Version: 1.10.0 Suggests: oligo License: GPL MD5sum: 57e481964196452bea64bb8fe7883fd2 NeedsCompilation: no Title: Sample data - Hapmap SNP 5.0 Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData, SNPData Author: Hapmap Consortium Maintainer: Benilton Carvalho source.ver: src/contrib/hapmapsnp5_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmapsnp6 Version: 1.10.0 Depends: R (>= 2.15) Suggests: oligo, oligoClasses License: GPL MD5sum: 0f48e2c0fbbdcc84548e5898e84a7e26 NeedsCompilation: no Title: Sample data - Hapmap SNP 6.0 Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, SNPData Author: Hapmap Consortium Maintainer: Benilton Carvalho source.ver: src/contrib/hapmapsnp6_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: harbChIP Version: 1.6.0 Depends: R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5), Biostrings Imports: methods, stats License: Artistic-2.0 MD5sum: fb42e0734e43e7358d3776c7c31b4e4d NeedsCompilation: no Title: Experimental Data Package: harbChIP Description: data from a yeast ChIP-chip experiment biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/harbChIP_1.6.0.tar.gz 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: 1.8.0 Depends: R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots, limma, vcd, LSD,EBImage Suggests: BiocStyle License: Artistic-2.0 MD5sum: 4a31136076acd8479ee7c7f4956f4537 NeedsCompilation: no Title: Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping Description: This package contains the experimental data and a complete executable transcript (vignette) of the analysis of the HCT116 genetic interaction matrix presented in the paper "Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping" by C. Laufer, B. Fischer, M. Billmann, W. Huber, M. Boutros; Nature Methods (2013) 10:427-31. doi: 10.1038/nmeth.2436. biocViews: ExperimentData, CancerData, ColonCancerData, MicrotitrePlateAssayData, CellCulture, Homo_sapiens_Data, HighThroughputImagingData Author: Bernd Fischer Maintainer: Bernd Fischer SystemRequirements: GNU make source.ver: src/contrib/HD2013SGI_1.8.0.tar.gz 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: 1.6.0 Depends: R (>= 2.15.0), flowCore Imports: methods License: Artistic-2.0 MD5sum: c002ef0cbc75543c12becd3633132d8f NeedsCompilation: no Title: Healthy dataset used by the flowMatch package Description: A healthy dataset with 20 flow cytometry samples used by the flowMatch package. biocViews: FlowCytometryData Author: Ariful Azad Maintainer: Ariful Azad source.ver: src/contrib/healthyFlowData_1.6.0.tar.gz vignettes: vignettes/healthyFlowData/inst/doc/healthyFlowData.pdf vignetteTitles: healthyFlowData: A healthy dataset with 20 flow cytometry samples used by the flowMatch package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/healthyFlowData/inst/doc/healthyFlowData.R Package: HEEBOdata Version: 1.6.0 License: LGPL MD5sum: d24dc2d8b877a86204b937417b405c67 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_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu133abarcodevecs Version: 1.6.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 1a08e8f1e6b1676a504aec30e42b352a NeedsCompilation: no Title: hgu133a data for barcode Description: Data used by the barcode package for microarrays of type hgu133a. biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall source.ver: src/contrib/hgu133abarcodevecs_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu133plus2barcodevecs Version: 1.6.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: aa60fb5638a3834f12565796c8687349 NeedsCompilation: no Title: hgu133plus2 data for barcode Description: Data used by the barcode package for microarrays of type hgu133plus2. biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall source.ver: src/contrib/hgu133plus2barcodevecs_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu2beta7 Version: 1.8.0 Depends: R (>= 2.0.0) License: Artistic-2.0 MD5sum: e75ef86ff21879407dbc1f85d56f02a7 NeedsCompilation: no Title: A data package containing annotation data for hgu2beta7 Description: Annotation data file for hgu2beta7 assembled using data from public data repositories biocViews: Genome Author: Chenwei Lin Maintainer: Bioconductor Package Maintainer source.ver: src/contrib/hgu2beta7_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: HiCDataHumanIMR90 Version: 0.102.0 Depends: R (>= 2.10) Suggests: HiTC License: GPL-3 MD5sum: bbf94b1092209c5e2b422211982aa22f NeedsCompilation: no Title: Human IMR90 Fibroblast HiC data from Dixon et al. 2012 Description: The HiC data from Human Fibroblast IMR90 cell line (HindIII restriction) was retrieved from the GEO website, accession number GSE35156 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35156). The raw reads were processed as explained in Dixon et al. (Nature 2012). biocViews: ExperimentData, Genome, Homo_sapiens_Data, GEO Author: Nicolas Servant Maintainer: Nicolas Servant source.ver: src/contrib/HiCDataHumanIMR90_0.102.0.tar.gz vignettes: vignettes/HiCDataHumanIMR90/inst/doc/HiC_Human_IMR90.pdf vignetteTitles: HiC Data Human Fibroblast Dixon et al. 2012 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HiCDataHumanIMR90/inst/doc/HiC_Human_IMR90.R Package: HiCDataLymphoblast Version: 1.4.0 Suggests: GOTHiC, ShortRead License: GPL-3 MD5sum: 8e105107e4f0cafe90795b0c05f3e385 NeedsCompilation: no Title: Human lymphoblastoid HiC data from Lieberman-Aiden et al. 2009 Description: The HiC data from human lymphoblastoid cell line (HindIII restriction) was retrieved from the sequence read archive and two ends of the paired reads were aligned separately with bowtie. biocViews: ExperimentData, Homo_sapiens_Data Author: Borbala Mifsud Maintainer: Borbala Mifsud source.ver: src/contrib/HiCDataLymphoblast_1.4.0.tar.gz vignettes: vignettes/HiCDataLymphoblast/inst/doc/package_vignettes.pdf vignetteTitles: package_vignettes.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Hiiragi2013 Version: 1.4.0 Depends: R (>= 3.0.0), affy, Biobase, boot, clue, cluster, genefilter, geneplotter, gplots, gtools, KEGGREST, MASS, mouse4302.db, RColorBrewer, xtable Imports: grid, lattice, latticeExtra Suggests: ArrayExpress, BiocStyle License: Artistic-2.0 MD5sum: 126d443021c266596be66929971e348c NeedsCompilation: no Title: Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages Description: This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881." biocViews: ExperimentData, MicroarrayData, qPCRData Author: Andrzej Oles, Wolfgang Huber Maintainer: Andrzej Oles source.ver: src/contrib/Hiiragi2013_1.4.0.tar.gz 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: 1.8.0 License: GPL (>= 2) MD5sum: f1df198a92cdc317e5e72ea17b6d01ba NeedsCompilation: no Title: T cell line infections with HIV-1 LAI (BRU) Description: The expression levels of approximately 4600 cellular RNA transcripts were assessed in CD4+ T cell lines at different times after infection with HIV-1BRU using DNA microarrays. This data corresponds to the first block of a 12 block array image (001030_08_1.GEL) in the first data set (2000095918 A) in the first experiment (CEM LAI vs HI-LAI 24hr). There are two data sets, which are part of a dye-swap experiment with replicates, representing the Cy3 (green) absorption intensities for channel 1 (hiv1raw) and the Cy5 (red) absorption intensities for channel 2 (hiv2raw). biocViews: ExperimentData, MicroarrayData, TwoChannelData, HIVData Author: Dr. Angelique van't Wout, Department of Microbiology, University of Washington Maintainer: Chris Fraley URL: http://expression.microslu.washington.edu/expression/vantwoutjvi2002.html source.ver: src/contrib/HIVcDNAvantWout03_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hmyriB36 Version: 1.4.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.5.5), GGBase Suggests: GGtools, illuminaHumanv1.db License: Artistic-2.0 MD5sum: 985da5acf94fb5988b56c28451633c60 NeedsCompilation: no Title: YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes Description: YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes biocViews: ExperimentData, Genome, SNPData, HapMap Author: Vincent Carey Maintainer: Vincent Carey source.ver: src/contrib/hmyriB36_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ggtut suggestsMe: ind1KG Package: HSMMSingleCell Version: 0.102.0 Depends: R (>= 2.10) License: Artistic-2.0 MD5sum: 12151b43a87c86e90c8b0d8e483fa615 NeedsCompilation: no Title: Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM) Description: Skeletal myoblasts undergo a well-characterized sequence of morphological and transcriptional changes during differentiation. In this experiment, primary human skeletal muscle myoblasts (HSMM) were expanded under high mitogen conditions (GM) and then differentiated by switching to low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several hundred cells taken over a time-course of serum-induced differentiation. Between 49 and 77 cells were captured at each of four time points (0, 24, 48, 72 hours) following serum switch using the Fluidigm C1 microfluidic system. RNA from each cell was isolated and used to construct mRNA-Seq libraries, which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell. biocViews: ExperimentData, RNASeqData Author: Cole Trapnell Maintainer: Cole Trapnell source.ver: src/contrib/HSMMSingleCell_0.102.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: humanStemCell Version: 0.8.0 Depends: Biobase (>= 2.5.5), hgu133plus2.db License: Artistic-2.0 MD5sum: 6a04180b449b5972463c5aab1b5b1202 NeedsCompilation: no Title: Human Stem Cells time course experiment Description: Affymetrix time course experiment on human stem cells (two time points: undifferentiated and differentiated). biocViews: ExperimentData, Homo_sapiens_Data Author: R. Gentleman, N. Le Meur, M. Tewari Maintainer: R. Gentleman source.ver: src/contrib/humanStemCell_0.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Illumina450ProbeVariants.db Version: 1.4.0 Depends: R (>= 3.0.1) License: GPL-3 MD5sum: a98fc8e7dfef06b4c05c53aac8e8ba8d NeedsCompilation: no Title: Annotation Package combining variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes Description: Includes details on variants for each probe on the 450k bead chip for each of the four populations (Asian, American, African and European)License: GPL-3 biocViews: Homo_sapiens_Data, CancerData, ChipOnChipData, SNPData Author: Lee Butcher Maintainer: Tiffany Morris source.ver: src/contrib/Illumina450ProbeVariants.db_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: IlluminaDataTestFiles Version: 1.6.0 License: Artistic-2.0 MD5sum: 6dde4509d097395f8cbe175e3dc9953f NeedsCompilation: no Title: Illumina microarray files (IDAT) for testing Description: Example data for Illumina microarray output files, for testing purposes biocViews: MicroarrayData Author: Kasper Daniel Hansen, Mike L. Smith Maintainer: Kasper Daniel Hansen source.ver: src/contrib/IlluminaDataTestFiles_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ind1KG Version: 0.6.0 Depends: R (>= 2.10.1), chopsticks Suggests: Rsamtools, rtracklayer, GenomicFeatures, org.Hs.eg.db, SNPlocs.Hsapiens.dbSNP.20090506, TxDb.Hsapiens.UCSC.hg18.knownGene, lumiHumanIDMapping, GGBase, GGtools, hmyriB36 License: Artistic-2.0 MD5sum: 547099a4d233756c2b6e7c4c2c9eb363 NeedsCompilation: no Title: Data from 1000 Genomes, NA19240 (female) chr6 excerpt Description: Elements of samtools/bioc workflow for dealing with personal sequence focusing on identification and interpretation of rare variants biocViews: Genome, MicroarrayData, SNPData Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/ind1KG_0.6.0.tar.gz vignettes: vignettes/ind1KG/inst/doc/ind1KG.pdf, vignettes/ind1KG/inst/doc/nov09rv.pdf vignetteTitles: ind1KG -- 1000 genomes data demo, Notes for eSet developers hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ind1KG/inst/doc/ind1KG.R, vignettes/ind1KG/inst/doc/nov09rv.R Package: iontreeData Version: 1.4.0 License: GPL-2 MD5sum: becfc83a86c92940c8fbf08637ccf4cd NeedsCompilation: no Title: Data provided to show the usage of functions in iontree package Description: Raw MS2, MS3 scans from direct infusion mass spectrometry (DIMS) and a demo ion tree database 'mzDB' derived from the DIMS data are included. The demo database is used to show the functionalities provided by the 'iontree' package, not for the purpose of compound identification by any means. biocViews: ExperimentData, MassSpectrometryData Author: Mingshu Cao Maintainer: Mingshu Cao source.ver: src/contrib/iontreeData_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ITALICSData Version: 2.6.0 Depends: R (>= 2.0.0) License: GPL MD5sum: 204ad9d26609f9b202a1698f1a467494 NeedsCompilation: no Title: ITALICSData Description: Data needed to use the ITALICS package biocViews: ExperimentData, HapMap Author: Guillem Rigaill Maintainer: Guillem Rigaill URL: http://bioinfo.curie.fr source.ver: src/contrib/ITALICSData_2.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Iyer517 Version: 1.10.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: c92acc97a23f16adc8e9f2347cad2448 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_1.10.0.tar.gz 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: 1.4.0 Depends: R (>= 3.0.1), methods, Biostrings (>= 2.29.19) License: GPL-2 MD5sum: 959110604bf4c6cfd171ed5a7e585101 NeedsCompilation: no Title: Data package for JASPAR Description: Data package for JASPAR 2014. To search this databases, please use the package TFBSTools. biocViews: ExperimentData, SequencingData Author: Ge Tan Maintainer: Ge Tan URL: http://jaspar.genereg.net/ source.ver: src/contrib/JASPAR2014_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: KEGGandMetacoreDzPathwaysGEO Version: 0.102.0 Depends: R (>= 2.15.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: 76c129b2d81f2e9b57c35c7473d51e59 NeedsCompilation: no Title: Disease Datasets from GEO Description: This is a collection of 18 data sets for which the phenotype is a disease with a corresponding pathway in either KEGG or metacore database.This collection of datasets were used as gold standard in comparing gene set analysis methods. biocViews: ExperimentData, GEO Author: Gaurav Bhatti Maintainer: Gaurav Bhatti source.ver: src/contrib/KEGGandMetacoreDzPathwaysGEO_0.102.0.tar.gz vignettes: vignettes/KEGGandMetacoreDzPathwaysGEO/inst/doc/KEGGandMetacoreDzPathwaysGEO.pdf vignetteTitles: KEGGandMetacoreDzPathwaysGEO Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: KEGGdzPathwaysGEO Version: 1.6.0 Depends: R (>= 2.13.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: dcb40fa726c45389051f5fbfb3b2057e NeedsCompilation: no Title: KEGG Disease Datasets from GEO Description: This is a collection of 24 data sets for which the phenotype is a disease with a corresponding pathway in the KEGG database.This collection of datasets were used as gold standard in comparing gene set analysis methods by the PADOG package. biocViews: MicroarrayData, GEO, ExperimentData Author: Gaurav Bhatti, Adi L. Tarca Maintainer: Gaurav Bhatti source.ver: src/contrib/KEGGdzPathwaysGEO_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: kidpack Version: 1.10.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5) License: GPL-2 MD5sum: 6f6aaa9adf35fc4de8dddb89af58d95a NeedsCompilation: no Title: DKFZ kidney package Description: kidney microarray data biocViews: ExperimentData, CancerData, KidneyCancerData, MicroarrayData, ArrayExpress Author: Wolfgang Huber Maintainer: Wolfgang Huber URL: http://www.dkfz.de/mga source.ver: src/contrib/kidpack_1.10.0.tar.gz vignettes: vignettes/kidpack/inst/doc/kidpack.pdf vignetteTitles: kidpack - overview over the DKFZ kidney data package hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/kidpack/inst/doc/kidpack.R Package: leeBamViews Version: 1.4.0 Depends: R (>= 2.15.0), Biobase, Rsamtools (>= 0.1.50), BSgenome Imports: GenomicRanges, GenomicAlignments, methods Suggests: GenomeGraphs, biomaRt, org.Sc.sgd.db, edgeR Enhances: multicore License: Artistic 2.0 MD5sum: 9ebb9c7cfcf6bb7ed0c65afafb8b92ba NeedsCompilation: no Title: leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009 Description: data from PMID 19096707; prototype for managing multiple NGS samples biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData, SNPData Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/leeBamViews_1.4.0.tar.gz vignettes: vignettes/leeBamViews/inst/doc/leeViews.pdf vignetteTitles: managing multiple NGS samples with bamViews hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/leeBamViews/inst/doc/leeViews.R Package: leukemiasEset Version: 1.4.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 1a3093d057c155f3fc4150ac9186c3de NeedsCompilation: no Title: Leukemia's microarray gene expression data (expressionSet). Description: Expressionset containing gene expresion data from 60 bone marrow samples of patients with one of the four main types of leukemia (ALL, AML, CLL, CML) or non-leukemia. biocViews: Tissue, Genome, Homo_sapiens_Data, CancerData, LeukemiaCancerData, MicroarrayData, ChipOnChipData, TissueMicroarrayData, GEO Author: Sara Aibar, Celia Fontanillo and Javier De Las Rivas. Bioinformatics and Functional Genomics Group. Cancer Research Center (CiC-IBMCC, CSIC/USAL). Salamanca. Spain. Maintainer: Sara Aibar source.ver: src/contrib/leukemiasEset_1.4.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: LiebermanAidenHiC2009 Version: 0.6.0 Depends: KernSmooth, IRanges License: LGPL MD5sum: 4ac4ee2d567963d6b424e5a017c9f830 NeedsCompilation: no Title: Selected data from the HiC paper of E. Lieberman-Aiden et al. in Science (2009) Description: This package provides data that were presented in the article "Comprehensive mapping of long-range interactions reveals folding principles of the human genome", Science 2009 Oct 9;326(5950):289-93. PMID: 19815776 biocViews: ExperimentData, Genome, SequencingData, DNASeqData, ChIPSeqData, miRNAData, SmallRNAData, ChipOnChipData, GEO, NCI, ENCODE Author: Wolfgang Huber, Felix Klein Maintainer: Felix Klein source.ver: src/contrib/LiebermanAidenHiC2009_0.6.0.tar.gz vignettes: vignettes/LiebermanAidenHiC2009/inst/doc/LiebermanAidenHiC2009.pdf vignetteTitles: Exploration of HiC data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ListerEtAlBSseq Version: 1.0.0 Depends: R (>= 3.1.1), methylPipe Suggests: BSgenome.Hsapiens.UCSC.hg18 License: Artistic 2.0 MD5sum: d70ade53f20059d0245117d05bf8550d NeedsCompilation: no Title: BS-seq data of H1 and IMR90 cell line excerpted from Lister et al. 2009 Description: Base resolution bisulfite sequencing data of Human DNA methylomes biocViews: ExperimentData, Homo_sapiens_Data, SequencingData Author: Kamal Kishore Maintainer: Kamal Kishore source.ver: src/contrib/ListerEtAlBSseq_1.0.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: lumiBarnes Version: 1.8.0 Depends: R (>= 2.0), Biobase (>= 2.5.5), lumi (>= 1.1.0) License: LGPL MD5sum: 2ebdc46a1956222788270c9064b25b53 NeedsCompilation: no Title: Barnes Benchmark Illumina Tissues Titration Data Description: The Barnes benchmark dataset can be used to evaluate the algorithms for Illumina microarrays. It measured a titration series of two human tissues, blood and placenta, and includes six samples with the titration ratio of blood and placenta as 100:0, 95:5, 75:25, 50:50, 25:75 and 0:100. The samples were hybridized on HumanRef-8 BeadChip (Illumina, Inc) in duplicate. The data is loaded as an LumiBatch Object (see documents in the lumi package). biocViews: ExperimentData, Tissue, MicroarrayData, ChipOnChipData Author: Pan Du Maintainer: Pan Du source.ver: src/contrib/lumiBarnes_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: LungCancerACvsSCCGEO Version: 1.4.0 Depends: R (>= 2.15.0) License: GPL-2 MD5sum: ff03214d4d895af7b8d944cca098ec12 NeedsCompilation: no Title: A lung cancer dataset that can be used with maPredictDSC package for developing outcome prediction models from Affymetrix CEL files. Description: This package contains 30 Affymetrix CEL files for 7 Adenocarcinoma (AC) and 8 Squamous cell carcinoma (SCC) lung cancer samples taken at random from 3 GEO datasets (GSE10245, GSE18842 and GSE2109) and other 15 samples from a dataset produced by the organizers of the IMPROVER Diagnostic Signature Challenge available from GEO (GSE43580). biocViews: CancerData, LungCancerData, MicroarrayData, GEO Author: Adi Laurentiu Tarca Maintainer: Adi Laurentiu Tarca URL: http://bioinformaticsprb.med.wayne.edu/ source.ver: src/contrib/LungCancerACvsSCCGEO_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: LungCancerLines Version: 0.6.0 Imports: Rsamtools License: Artistic-2.0 MD5sum: 96f3a1ba4c8b55bd1d437c06548b5e9f NeedsCompilation: no Title: Reads from Two Lung Cancer Cell Lines Description: Reads from an RNA-seq experiment between two lung cancer cell lines: H1993 (met) and H2073 (primary). The reads are stored as Fastq files and are meant for use with the TP53Genome object in the gmapR package. biocViews: ExperimentData, Genome, CancerData, LungCancerData, RNASeqData Author: Cory Barr, Michael Lawrence Maintainer: Cory Barr source.ver: src/contrib/LungCancerLines_0.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: lungExpression Version: 0.6.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 56f66e8816c4de734dba8dbb502b9384 NeedsCompilation: no Title: ExpressionSets for Parmigiani et al., 2004 Clinical Cancer Research paper Description: Data from three large lung cancer studies provided as ExpressionSets biocViews: ExperimentData, CancerData, LungCancerData Author: Robert Scharpf , Simens Zhong , Giovanni Parmigiani Maintainer: Robert Scharpf source.ver: src/contrib/lungExpression_0.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mammaPrintData Version: 1.4.0 Depends: R (>= 2.13.0) Suggests: Biobase, gdata, limma License: Artistic-2.0 MD5sum: 088812269e00941493a0e870750775aa NeedsCompilation: no Title: RGLists from the Glas and Buyse breast cancer studies Description: Gene expression data for the two breast cancer cohorts published by Glas and Buyse in 2006 biocViews: ExperimentData, ExpressionData, CancerData, BreastCancerData, MicroarrayData, TwoChannelData Author: Luigi Marchionni Maintainer: Luigi Marchionni URL: http://luigimarchionni.org/breastTSP.html source.ver: src/contrib/mammaPrintData_1.4.0.tar.gz 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: mAPKLData Version: 1.0.0 Depends: R (>= 3.2.0) Suggests: Biobase License: Artistic-2.0 MD5sum: 2c9e3f108fab10d363f81f751fe094bf NeedsCompilation: no Title: Gene expression data for testing of the package mAPKL. Description: Gene expression data from a breast cancer study published by Turashvili et al. in 2007, provided as an eSet. biocViews: ExperimentData, ExpressionData, Cancer, Breast Author: Argiris Sakellariou Maintainer: Argiris Sakellariou source.ver: src/contrib/mAPKLData_1.0.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: maqcExpression4plex Version: 1.12.0 Suggests: oligo, pdInfoBuilder License: GPL MD5sum: 62b2176a7e387a8cd56b83dbefe8597b NeedsCompilation: no Title: Sample Expression Data - MAQC / HG18 - NimbleGen Description: Data from human (HG18) 4plex NimbleGen array. It has 24k genes with 3 60mer probes per gene. biocViews: ExperimentData, CancerData Author: NimbleGen Systems Maintainer: Benilton Carvalho source.ver: src/contrib/maqcExpression4plex_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MAQCsubset Version: 1.6.0 Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), lumi, methods Suggests: genefilter, codelink License: Artistic-2.0 MD5sum: b0584cbba0291be1d62b7e21ed588cfe NeedsCompilation: no Title: Experimental Data Package: MAQCsubset Description: Data Package automatically created on Sun Nov 19 15:59:29 2006. biocViews: ExperimentData, MicroarrayData, GEO Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/MAQCsubset_1.6.0.tar.gz 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: 1.6.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 1265e33deafcccbb45914b077a914835 NeedsCompilation: no Title: MAQC data subset for the Affymetrix platform Description: MAQC data subset for the Affymetrix platform biocViews: ExperimentData, Genome, Homo_sapiens_Data, MicroarrayData Author: Laurent Gatto Maintainer: Laurent Gatto source.ver: src/contrib/MAQCsubsetAFX_1.6.0.tar.gz vignettes: vignettes/MAQCsubsetAFX/inst/doc/MAQCsubsetAFX.pdf vignetteTitles: MAQCsubsetAFX: MAQC data subset for the Affymetrix platform hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MAQCsubsetAFX/inst/doc/MAQCsubsetAFX.R Package: MAQCsubsetILM Version: 1.6.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), lumi License: Artistic-2.0 MD5sum: fffcc7c5b10a3b961e8e6e48ee442cef NeedsCompilation: no Title: MAQC data subset for the Illumina platform Description: MAQC data subset for the Illumina platform biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData Author: Laurent Gatto Maintainer: Laurent Gatto source.ver: src/contrib/MAQCsubsetILM_1.6.0.tar.gz vignettes: vignettes/MAQCsubsetILM/inst/doc/MAQCsubsetILM.pdf vignetteTitles: MAQCsubsetILM: MAQC data subset for the Illumina platform hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MAQCsubsetILM/inst/doc/MAQCsubsetILM.R Package: MEDIPSData Version: 1.4.0 Depends: R (>= 2.15.0) License: GPL (>= 2) MD5sum: 578b894c7dae8c48af1ff2bad28056fb NeedsCompilation: no Title: Example data for the MEDIPS package. Description: Data for the MEDIPS package, consisting of chromosome 22 MeDIP and control/Input sample data from DNA methylation analysis of human embryonic stem cells and mapped to the human genome hg19 using bowtie. biocViews: ExperimentData, Genome, SequencingData Author: Lukas Chavez Maintainer: Lukas Chavez source.ver: src/contrib/MEDIPSData_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MEEBOdata Version: 1.6.0 License: LGPL MD5sum: 89d9cdd61fbcf741248edafc5970f5cb 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_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: metaMSdata Version: 1.4.0 License: GPL (>= 2) MD5sum: ad43465c94b01030016cd20942e378f7 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_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MethylAidData Version: 1.0.0 Depends: MethylAid, R (>= 3.2) Suggests: BiocParallel, BiocStyle, knitr License: GPL (>= 2) MD5sum: 8febce820d398bac74c4464ad9588273 NeedsCompilation: no Title: MethylAid-summarized data on 2800 Illumina 450k array samples Description: A data package containing summarized Illumina 450k array data on 2800 samples. The data can be use as a background data set in the interactive application. biocViews: ExperimentData Author: Maarten van Iterson, Elmar. Tobi, Roderick Slieker, Wouter den Hollander, Rene Luijk and Bas Heijmans Maintainer: M. van Iterson URL: http://shiny.bioexp.nl/MethylAid VignetteBuilder: knitr source.ver: src/contrib/MethylAidData_1.0.0.tar.gz vignettes: vignettes/MethylAidData/inst/doc/MethylAidData.pdf vignetteTitles: hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: minfiData Version: 0.10.0 Depends: R (>= 2.13.0), minfi, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 License: Artistic-2.0 MD5sum: 15d1a22715241d3364e4e99c00a8c751 NeedsCompilation: no Title: Example data for the Illumina Methylation 450k array Description: Data from 6 samples across 2 groups from 450k methylation arrays biocViews: Homo_sapiens_Data, MethylationArrayData Author: Kasper Daniel Hansen, Martin Aryee, Winston Timp Maintainer: Kasper Daniel Hansen source.ver: src/contrib/minfiData_0.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: miRNATarget Version: 1.6.0 Depends: R (>= 2.10), Biobase License: GPL MD5sum: e8f299358ce3e3af23940bcf1c3336d8 NeedsCompilation: no Title: gene target tabale of miRNA for human/mouse used for MiRaGE package Description: gene target tabale of miRNA for human/mouse used for MiRaGE package biocViews: ExperimentData, Homo_sapiens_Data Author: Y-h. Taguchi Maintainer: Y-h. Taguchi source.ver: src/contrib/miRNATarget_1.6.0.tar.gz 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: 1.4.0 Depends: R (>= 2.14.0) License: LGPL MD5sum: 6f00442733326e199627cede500218e8 NeedsCompilation: no Title: Experimental data associated to the paper "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay" (submitted). Description: This package contains the experimental data (assay annotation, siRNA annotation, time-lapse cell counts) associated to the paper "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay" (submitted). The data ultimately come from the Mitocheck assay reported in "Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes" (Neumann, Walter et al, Nature 2010). biocViews: ExperimentData, Genome Author: Gregoire Pau Maintainer: Gregoire Pau SystemRequirements: source.ver: src/contrib/mitoODEdata_1.4.0.tar.gz 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: 1.4.0 Suggests: MMDiff License: LGPL MD5sum: f20caa6b376a7c80390953ad1163b7e5 NeedsCompilation: no Title: Example ChIP-Seq data for the MMDiff package Description: Subset of BAM files, including WT_2.bam, Null_2.bam, Resc_2.bam, Input.bam from the "Cfp1" experiment (see Clouaire et al., Genes Dev. 2012). Data is available under ArrayExpress accession numbers E-ERAD-79. Additionally, corresponding subset of peaks called by MACS biocViews: ExperimentData, Genome, StemCell, Mus_musculus_Data, DNASeqData, ChIPSeqData, ArrayExpress Author: Gabriele Schweikert Maintainer: Gabriele Schweikert source.ver: src/contrib/MMDiffBamSubset_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mosaicsExample Version: 1.4.0 Depends: R (>= 2.11.1) License: GPL (>= 2) MD5sum: cfa86cce0a4f02a7b307a20b3b1d0c8c NeedsCompilation: no Title: Example data for the mosaics package, which implements MOSAiCS, a statistical framework to analyze one-sample or two-sample ChIP-seq data Description: Data for the mosaics package, consisting of chromosome 21 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding, with mappability, GC content, and sequence ambiguity scores of human genome HG18. biocViews: ExperimentData, Genome, Homo_sapiens_Data, ChIPSeqData Author: Dongjun Chung, Pei Fen Kuan, Sunduz Keles Maintainer: Dongjun Chung URL: http://groups.google.com/group/mosaics_user_group source.ver: src/contrib/mosaicsExample_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mouse4302barcodevecs Version: 1.6.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: f05d065cf72b3a1f03b6af1140a90468 NeedsCompilation: no Title: mouse4302 data for barcode Description: Data used by the barcode package for microarrays of type mouse4302. biocViews: Mus_musculus_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall source.ver: src/contrib/mouse4302barcodevecs_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MSBdata Version: 0.6.0 License: LGPL MD5sum: 53afd169b36730b9b6f50c2ea5284de4 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_0.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: msd16s Version: 0.102.0 Depends: R (>= 2.10), Biobase, metagenomeSeq, License: Artistic-2.0 MD5sum: 8c3bbb8bd59f22ebb04b21a33bd182a0 NeedsCompilation: no Title: Healthy and moderate to severe diarrhea 16S expression data Description: Gut 16S sequencing expression data from 992 healthy and moderate-to-severe diarrhetic samples used in 'Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition'. biocViews: ExperimentData, SequencingData, MicrobiomeData Author: Joseph N. Paulson, Hector Corrada Bravo, Mihai Pop Maintainer: Joseph N. Paulson URL: http://www.cbcb.umd.edu/research/projects/GEMS-pathogen-discovery source.ver: src/contrib/msd16s_0.102.0.tar.gz 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: 0.6.0 Suggests: xcms License: GPL (>= 2) MD5sum: 643661e03f85bcca71682cbfcb73679c 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_0.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics Package: MUGAExampleData Version: 0.102.0 Depends: R (>= 2.10.0) License: GPL-3 MD5sum: a0a19c4945541ecd14bec2ff170d4e7e NeedsCompilation: no Title: Example {M}ouse {U}niversal {G}enotyping {A}rray data for genome reconstruction and quantitative trait locus mapping. Description: This package contains example data for the MUGA array that is used by the R package DOQTL. biocViews: ExperimentData, Mus_musculus_Data Author: Daniel Gatti Maintainer: Daniel Gatti source.ver: src/contrib/MUGAExampleData_0.102.0.tar.gz 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: 0.8.0 Depends: R (>= 2.14), org.Hs.eg.db, KEGG.db Imports: igraph, HTSanalyzeR, PANR, RedeR, pvclust, MASS Suggests: snow License: Artistic-2.0 MD5sum: aad54e0c15b41473776c67fba6b5ce5c NeedsCompilation: no Title: Predicting functional networks and modules of chromatin factors controlling adult stem cell fate from RNA interference screens Description: This package provides functions to reproduce results and figures in Mulder K. et. al. published in Nature Cell Biology 2012 and Wang X. et. al. published in PLoS Computational Biology 2012. biocViews: StemCell, CancerData Author: Xin Wang , Florian Markowetz Maintainer: Xin Wang source.ver: src/contrib/Mulder2012_0.8.0.tar.gz vignettes: vignettes/Mulder2012/inst/doc/Mulder2012-Vignette.pdf vignetteTitles: Main vignette:Posterior association network and enriched functional gene modules inferred from rich phenotypes of gene perturbations hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Mulder2012/inst/doc/Mulder2012-Vignette.R Package: mvoutData Version: 1.4.0 Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4), lumi License: Artistic-2.0 MD5sum: f10c7d0caacaf4c6fa0585a4a05fd765 NeedsCompilation: no Title: affy and illumina raw data for assessing outlier detector performance Description: affy and illumina raw data for assessing outlier detector performance biocViews: ExperimentData, MicroarrayData Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/mvoutData_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: NCIgraphData Version: 1.4.0 Depends: R (>= 2.10.0) Suggests: Rgraphviz License: GPL-3 MD5sum: c36900a3da54c8bf89790cbb92971f1a NeedsCompilation: no Title: Data for the NCIgraph software package Description: Provides pathways from the NCI Pathways Database as R graph objects biocViews: NCI Author: Laurent Jacob Maintainer: Laurent Jacob source.ver: src/contrib/NCIgraphData_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Neve2006 Version: 0.6.0 Depends: R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0), hgu133a.db, annotate License: Artistic-2.0 MD5sum: 21ddc01ebb33ce0cbd637a50c22726ae NeedsCompilation: no Title: expression and CGH data on breast cancer cell lines Description: Experimental organization of combined expression and CGH data biocViews: ExperimentData, CancerData, BreastCancerData Author: M. Neve et al. in Gray Lab at LBL Maintainer: VJ Carey source.ver: src/contrib/Neve2006_0.6.0.tar.gz vignettes: vignettes/Neve2006/inst/doc/neve06notes.pdf vignetteTitles: Neve 2006: combined CGH and expression data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Neve2006/inst/doc/neve06notes.R Package: NGScopyData Version: 0.102.0 License: GPL (>=2) MD5sum: 7eed981f3e5dfb39e19a25638482bb88 NeedsCompilation: no Title: Subset of BAM files of human tumor and pooled normal sequencing data (Zhao et al. 2014) for the NGScopy package Description: Subset of BAM files of human lung tumor and pooled normal samples by targeted panel sequencing. [Zhao et al 2014. Targeted Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using the University of North Carolina (UNC) Sequencing Assay Captures Most Previously Described Genetic Aberrations in NSCLC. In preparation.] Each sample is a 10 percent random subsample drawn from the original sequencing data. The pooled normal sample has been rescaled accroding to the total number of normal samples in the "pool". Here provided is the subsampled data on chr6 (hg19). biocViews: ExperimentData, CancerData, LungCancerData, SequencingData Author: Xiaobei Zhao [aut, cre, cph] Maintainer: Xiaobei Zhao URL: http://www.bioconductor.org/packages/release/data/experiment/html/NGScopyData.html source.ver: src/contrib/NGScopyData_0.102.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: parathyroidSE Version: 1.6.0 Depends: GenomicRanges, R (>= 2.10) Suggests: Rsamtools, GenomicAlignments, GEOquery, SRAdb, GenomicFeatures, BiocStyle License: LGPL MD5sum: 91155d8deed1fe258e4f05e402066ee7 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, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love source.ver: src/contrib/parathyroidSE_1.6.0.tar.gz 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: 0.8.0 Suggests: locfit, edgeR, xtable, DEXSeq, DESeq License: LGPL MD5sum: 41e36bbfd851d4d720b0d84356f53de5 NeedsCompilation: no Title: Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011. Description: This package provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in the article "Conservation of an RNA regulatory map between Drosophila and mammals" by Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR, Genome Res. 2011 Feb;21(2):193-202, Epub 2010 Oct 4, PMID: 20921232. The experiment studied the effect of RNAi knockdown of Pasilla, the Drosophila melanogaster ortholog of mammalian NOVA1 and NOVA2, on the transcriptome. The package vignette describes how the data provided here were derived from the RNA-Seq read sequence data that is provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181 biocViews: ExperimentData, Genome, Drosophila_melanogaster_Data, RNASeqData Author: Wolfgang Huber, Alejandro Reyes Maintainer: Alejandro Reyes source.ver: src/contrib/pasilla_0.8.0.tar.gz vignettes: vignettes/pasilla/inst/doc/create_objects.pdf vignetteTitles: Data preprocessing and creation of the data objects pasillaGenes and pasillaExons hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pasilla/inst/doc/create_objects.R suggestsMe: pasillaBamSubset Package: pasillaBamSubset Version: 0.6.0 Suggests: pasilla License: LGPL MD5sum: 4331c9fbdbaf8a8fee0f655b740fff00 NeedsCompilation: no Title: Subset of BAM files from "Pasilla" experiment Description: Subset of BAM files untreated1.bam (single-end reads) and untreated3.bam (paired-end reads) from "Pasilla" experiment (Pasilla knock-down by Brooks et al., Genome Research 2011). See the vignette in the pasilla data package for how BAM files untreated1.bam and untreated3.bam were obtained from the RNA-Seq read sequence data that is provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. Also contains the DNA sequence for fly chromosome 4 to which the reads can be mapped. biocViews: ExperimentData, Genome, DNASeqData, RNASeqData Author: H. Pages Maintainer: H. Pages source.ver: src/contrib/pasillaBamSubset_0.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: PathNetData Version: 1.4.0 Depends: R (>= 1.14.0) License: GPL-3 MD5sum: 19128254feec04021d5ad339fdbe7d93 NeedsCompilation: no Title: Experimental data for the PathNet package Description: This package contains the data employed in the vignette of the PathNet package. These data belong to the following publication: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J., Source Code for Biology and Medicine 2012 Sep 24;7(1):10. biocViews: ExperimentData, PathwayInteractionDatabase Author: Bhaskar Dutta , Anders Wallqvist , and Jaques Reifman Maintainer: Jason B. Smith source.ver: src/contrib/PathNetData_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Hs.hg19 Version: 1.4.0 License: GPL (>= 2) MD5sum: 824f2831e763abc8089d46db349a07b0 NeedsCompilation: no Title: pcaGoPromoter.Hs.hg19 is a data package used by pcaGoPromoter Description: Contains the data for transciption factors analysis of organism Homo Sapiens with package pcaGoPromoter biocViews: Homo_sapiens_Data Author: Morten Hansen, Maintainer: Morten Hansen, source.ver: src/contrib/pcaGoPromoter.Hs.hg19_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Mm.mm9 Version: 1.4.0 License: GPL (>= 2) MD5sum: 5d88576f978bb53512d496408a874e16 NeedsCompilation: no Title: pcaGoPromoter.Mm.mm9 is a data package used by pcaGoPromoter Description: Contains the data for transciption factors analysis of organism Mus musculus with package pcaGoPromoter biocViews: Mus_musculus_Data Author: Morten Hansen, Maintainer: Morten Hansen, source.ver: src/contrib/pcaGoPromoter.Mm.mm9_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Rn.rn4 Version: 1.4.0 License: GPL (>= 2) MD5sum: f025a76690b79e11c0c7d683ca35c542 NeedsCompilation: no Title: pcaGoPromoter.Rn.rn4 is a data package used by pcaGoPromoter Description: Contains the data for transciption factors analysis of organism Rattus norvegicus with package pcaGoPromoter biocViews: Rattus_norvegicus_Data Author: Morten Hansen, Maintainer: Morten Hansen, source.ver: src/contrib/pcaGoPromoter.Rn.rn4_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pd.atdschip.tiling Version: 0.6.0 Depends: R (>= 2.14.0), methods, RSQLite (>= 0.10.0), oligoClasses (>= 1.15.58), oligo (>= 1.17.3), DBI Imports: Biostrings (>= 2.21.11), IRanges (>= 1.11.31), S4Vectors License: Artistic-2.0 MD5sum: add36a1d7b152186debe6b965425c7f8 NeedsCompilation: no Title: Platform Design Info for Affymetrix Atdschip_tiling Description: Platform Design Info for Affymetrix Atdschip_tiling biocViews: Arabidopsis_thaliana_Data, MicroarrayData, SNPData Author: Kristof De Beuf Maintainer: Kristof De Beuf source.ver: src/contrib/pd.atdschip.tiling_0.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pepDat Version: 0.102.0 Depends: R(>= 3.0.0) Imports: GenomicRanges Suggests: knitr License: Artistic-2.0 MD5sum: 308732d1611e14c45a118eb751b32276 NeedsCompilation: no Title: Peptide microarray data package Description: Provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV. biocViews: MicroarrayData Author: Renan Sauteraud, Raphael Gottardo Maintainer: Renan Sauteraud VignetteBuilder: knitr source.ver: src/contrib/pepDat_0.102.0.tar.gz 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: ppiData Version: 0.6.0 Depends: graph Imports: AnnotationDbi Suggests: org.Sc.sgd.db, ppiStats License: Artistic-2.0 MD5sum: 7dac4ed93703730007acfc9b46b9b49a 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_0.6.0.tar.gz 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: 1.4.0 Depends: R (>= 2.14.0) License: Artistic-2.0 MD5sum: 6db3717fee54790c9c1e6604de215106 NeedsCompilation: no Title: Data for 'prebs' package Description: This package contains data required to run examples in 'prebs' package. The data files include: 1) Small sample bam files for demonstration purposes 2) Probe sequence mappings for Custom CDF (taken from http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp) 3) Probe sequence mappings for manufacturer's CDF (manually created using bowtie) biocViews: ExperimentData, SequencingData, RNASeqData Author: Karolis Uziela and Antti Honkela Maintainer: Karolis Uziela source.ver: src/contrib/prebsdata_1.4.0.tar.gz 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: 0.8.0 Depends: R (>= 2.9.0), methods, PREDA, Biobase, affy, annotate, gahgu133plus2.db, gahgu133plus2cdf Suggests: hgu133plus2.db, hgu133plus2cdf License: Artistic-2.0 MD5sum: 05d863e5f562803cffcec4394aaaf297 NeedsCompilation: no Title: expression and copy number data on clear cell renal carcinoma samples Description: Sample data for PREDA package. (annotations objects synchronized with GeneAnnot custom CDFs version 2.2.0) biocViews: ExperimentData, Tissue, CancerData, KidneyCancerData, MicroarrayData, TissueMicroarrayData, ArrayExpress Author: I. Cifola et al. in Cristina Battaglia Lab, University of Milan Maintainer: Francesco Ferrari source.ver: src/contrib/PREDAsampledata_0.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ProData Version: 1.6.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL MD5sum: 8afdd9473cd7ecd4264b8bfcafc0b60c NeedsCompilation: no Title: SELDI-TOF data of Breast cancer samples Description: A data package of SELDI-TOF protein mass spectrometry data of 167 breast cancer and normal samples. biocViews: ExperimentData, CancerData, BreastCancerData, MassSpectrometryData, NCI Author: Xiaochun Li Maintainer: Xiaochun Li source.ver: src/contrib/ProData_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pRolocdata Version: 1.6.0 Depends: R (>= 2.15), MSnbase Imports: Biobase Suggests: pRoloc License: GPL-2 MD5sum: a8de1018d81b8bf42afed85c95ba705f NeedsCompilation: no Title: Data accompanying the pRoloc package Description: Mass-spectrometry based spatial proteomics data sets from Dunkley et al. (2006), Foster et al. (2006), Tan et al. (2009), Hall et al. (2009), Trotter et al. (2010), Ferro et al. (2010), Nikolovski et al. (2012, 2014), Breckels et al. (2013) and Groen et al. (2014) and protein complex separation data from Kristensen et al. (2012), Havugimana et al. (2012), Kirkwood et al. (2013) and Fabre et al. (2015). biocViews: ExperimentData, Homo_sapiens_Data, MassSpectrometryData, Arabidopsis_thaliana_Data, Drosophila_melanogaster_Data, Mus_musculus_Data, StemCell Author: Laurent Gatto and Lisa M. Breckels Maintainer: Laurent Gatto URL: https://github.com/lgatto/pRolocdata BugReports: https://github.com/lgatto/pRolocdata/issues source.ver: src/contrib/pRolocdata_1.6.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics Package: pumadata Version: 2.4.0 Depends: R (>= 3.0.0), affy (>= 1.41.3), Biobase (>= 2.5.5), puma,oligo License: LGPL MD5sum: 521cb2d6b9eed201f53925ec7cf0aefd NeedsCompilation: no Title: Various data sets for use with the puma package Description: This is a simple data package including various data sets derived from the estrogen data for use with the puma (Propagating Uncertainty in Microarray Analysis) package. biocViews: ExperimentData, MicroarrayData, SNPData Author: Richard Pearson Maintainer: Richard Pearson URL: http://umber.sbs.man.ac.uk/resources/puma source.ver: src/contrib/pumadata_2.4.0.tar.gz 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: 4.2.0 Depends: methods, PWMEnrich License: GPL-3 MD5sum: dc47b249a92fba4c2f1168a6643441a5 NeedsCompilation: no Title: D. melanogaster background for PWMEnrich Description: PWMEnrich pre-compiled background objects for Drosophila melanogaster and MotifDb D. melanogaster motifs. biocViews: Drosophila_melanogaster_Data Author: Robert Stojnic Maintainer: Robert Stojnic source.ver: src/contrib/PWMEnrich.Dmelanogaster.background_4.2.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: PWMEnrich.Hsapiens.background Version: 4.2.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: c3339e97aa9aab4730f3e058f1997564 NeedsCompilation: no Title: H. sapiens background for PWMEnrich Description: PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs. biocViews: Homo_sapiens_Data, CGHData Author: Robert Stojnic Maintainer: Robert Stojnic source.ver: src/contrib/PWMEnrich.Hsapiens.background_4.2.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: PWMEnrich.Mmusculus.background Version: 4.2.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: c08b9dd545b32ee0fb5c5967a90bc7b5 NeedsCompilation: no Title: M. musculus background for PWMEnrich Description: PWMEnrich pre-compiled background objects for M.musculus (mouse) and MotifDb M. musculus motifs. biocViews: Mus_musculus_Data Author: Robert Stojnic Maintainer: Robert Stojnic source.ver: src/contrib/PWMEnrich.Mmusculus.background_4.2.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: rcellminerData Version: 1.0.0 Depends: R (>= 3.1.1), Biobase Suggests: knitr, testthat, BiocStyle, rcellminer License: LGPL-3 MD5sum: f8c8859554f7c204058f931500085753 NeedsCompilation: no Title: rcellminerData: Molecular Profiles and Drug Response for the NCI-60 Cell Lines Description: The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data. biocViews: CancerData, CopyNumberVariationData, ExpressionData, SNPData, NCI, MicroarrayData, miRNAData Author: Augustin Luna, Vinodh Rajapakse, Fabricio Sousa Maintainer: Augustin Luna , Vinodh Rajapakse VignetteBuilder: knitr source.ver: src/contrib/rcellminerData_1.0.0.tar.gz vignettes: vignettes/rcellminerData/inst/doc/ hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/rcellminerData/inst/doc/rcellminerDataUsage.R htmlDocs: vignettes/rcellminerData/inst/doc/rcellminerDataUsage.html htmlTitles: "Accessing CellMiner Data" Package: RforProteomics Version: 1.6.0 Depends: MSnbase Imports: R.utils, Biobase, rpx, biocViews, BiocInstaller, interactiveDisplay, shiny Suggests: knitr, rmarkdown, BiocStyle, 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, MSGFplus, MSGFgui, MSnID, msmsTests, msmsEDA, corrplot, Heatplus, gplots, VennDiagram Enhances: cleaver License: Artistic-2.0 MD5sum: 79557caf6c407335e4473c7f4be2de5e NeedsCompilation: no Title: Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication Description: This package contains code to illustrate the 'Using R and Bioconductor for proteomics data analysis' paper. Two vignettes describe the code and data needed to reproduce the examples and figures descibed in the paper and functionality for proteomics visualisation. biocViews: ExperimentData, MassSpectrometryData 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_1.6.0.tar.gz vignettes: vignettes/RforProteomics/inst/doc/Bioc2013poster.pdf, vignettes/RforProteomics/inst/doc/HUPO2014poster.pdf, vignettes/RforProteomics/inst/doc/RforProteomics.pdf vignetteTitles: RforProteomics Bioc2013 poster, A current perspective on using R and Bioconductor for proteomics data analysis, Using R for proteomics data analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RforProteomics/inst/doc/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: 1.6.0 Depends: R (>= 2.10.0) Suggests: genefilter, Biobase, hgu133plus2.db License: Artistic-2.0 MD5sum: 2d0ab89d460da7df219ee30e7b5dbe62 NeedsCompilation: no Title: Normalized gene expression dataset published by Wollbold et al. [2009] (WOLLBOLD). Description: Normalized gene expression data from rheumatic diseases from study published by Wollbold et al. in 2009, provided as an eSet. biocViews: ExperimentData, Tissue, MicroarrayData, MultiChannelData, ChipOnChipData, TissueMicroarrayData, GEO, ArrayExpress Author: Alejandro Quiroz-Zarate, John Quackenbush Maintainer: Alejandro Quiroz-Zarate URL: http://compbio.dfci.harvard.edu/ source.ver: src/contrib/rheumaticConditionWOLLBOLD_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RIPSeekerData Version: 1.4.0 Depends: RIPSeeker License: GPL-2 MD5sum: 1ee77edf369ce5a3c51f784c3f5855ae NeedsCompilation: no Title: test data for RIPSeeker Description: The RIP-seq data in BAM format are the test data for the package RIPSeeker. The data correspond to two RIP-seq experiments, namely PRC2 and CCNT1. Raw data from NCBI Gene Expression Omnibus under accession numbers GSE17064 for PRC2 and in-house for CCNT1. biocViews: ExperimentData, Genome, StemCell, SequencingData, RIPSeqData, GEO Author: Yue Li Maintainer: Alejandro Reyes source.ver: src/contrib/RIPSeekerData_1.4.0.tar.gz vignettes: vignettes/RIPSeekerData/inst/doc/RIPSeekerData.pdf vignetteTitles: RIP-seq datasets for testing RIPSeeker package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RIPSeekerData/inst/doc/RIPSeekerData.R Package: RMassBankData Version: 1.6.0 Suggests: RMassBank License: Artistic-2.0 MD5sum: 968142e7a6895d397107d37543b3f513 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_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RNAinteractMAPK Version: 1.6.0 Depends: R (>= 2.12.0), methods, fields, sparseLDA, RNAinteract Imports: grid, gdata, MASS, genefilter Suggests: qvalue, lattice License: Artistic-2.0 MD5sum: 0811988bd9a60de7600741d3fbe5e445 NeedsCompilation: no Title: Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi Description: This package includes all data used in the paper -Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi- by Horn, Sandmann, Fischer et al.., Nat. Methods, 2011. The package vignette shows the R code to reproduce all figures in the paper. biocViews: ExperimentData, MicrotitrePlateAssayData, Drosophila_melanogaster_Data, CellCulture Author: Bernd Fischer Maintainer: Bernd Fischer source.ver: src/contrib/RNAinteractMAPK_1.6.0.tar.gz vignettes: vignettes/RNAinteractMAPK/inst/doc/RNAinteractMAPK.pdf vignetteTitles: RNAinteractMAPK hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RNAinteractMAPK/inst/doc/RNAinteractMAPK.R suggestsMe: DmelSGI Package: RNAseqData.HNRNPC.bam.chr14 Version: 0.6.0 Suggests: GenomicAlignments, BiocInstaller License: LGPL MD5sum: d8c3e8bcab384e067a5457950370ebef NeedsCompilation: no Title: Aligned reads from RNAseq experiment: Transcription profiling by high throughput sequencing of HNRNPC knockdown and control HeLa cells Description: The package contains 8 BAM files, 1 per sequencing run. Each BAM file was obtained by (1) aligning the reads (paired-end) to the full hg19 genome with TopHat2, and then (2) subsetting to keep only alignments on chr14. See accession number E-MTAB-1147 in the ArrayExpress database for details about the experiment, including links to the published study (by Zarnack et al., 2012) and to the FASTQ files. biocViews: ExperimentData, Genome, Homo_sapiens_Data, SequencingData, GEO, NCI, RNASeqData, ArrayExpress Author: H. Pages Maintainer: H. Pages URL: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1147/ source.ver: src/contrib/RNAseqData.HNRNPC.bam.chr14_0.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RnaSeqSampleSizeData Version: 1.0.0 Depends: edgeR,R (>= 2.10) Suggests: BiocStyle, knitr License: GPL (>= 2) MD5sum: 9fcb9be2d70b5415aa7c518e651c6679 NeedsCompilation: no Title: RnaSeqSampleSizeData Description: RnaSeqSampleSizeData package provides the read counts and dispersion distribution from real RNA-seq experiments. It can be used by RnaSeqSampleSize package to estimate sample size and power for RNA-seq experiment design. biocViews: ExperimentData, CancerData, RNASeqData Author: Shilin Zhao, Chung-I Li, Yan Guo, Quanhu Sheng, Yu Shyr Maintainer: Shilin Zhao VignetteBuilder: knitr source.ver: src/contrib/RnaSeqSampleSizeData_1.0.0.tar.gz vignettes: vignettes/RnaSeqSampleSizeData/inst/doc/RnaSeqSampleSizeData.pdf vignetteTitles: RnaSeqSampleSizeData: Read counts and dispersion distribution from real data for sample size estimation of RNA-seq experiments hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: RnaSeqTutorial Version: 0.6.0 Depends: R (>= 3.0.2), methods, easyRNASeq Suggests: Rsamtools, ShortRead, BSgenome.Dmelanogaster.UCSC.dm3, GenomicAlignments, biomaRt, genomeIntervals License: Artistic-2.0 MD5sum: 1e4f160e94d3a1877ef012e2f86d58dc NeedsCompilation: no Title: RNA-Seq Tutorial (EBI Cambridge UK, October 2011) Description: A selection of RNA-Seq data to get familiar with the related Bioconductor core packages and the easyRNASeq package. biocViews: ExperimentData, Drosophila_melanogaster_Data, RNASeqData Author: Nicolas Delhomme, Ismael Padioleau Maintainer: Nicolas Delhomme source.ver: src/contrib/RnaSeqTutorial_0.6.0.tar.gz 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: RnBeads.hg19 Version: 1.0.0 Depends: R (>= 2.15), GenomicRanges Suggests: RnBeads (>= 0.99.0), BSgenome.Hsapiens.UCSC.hg19, License: GPL-3 MD5sum: 59a7cd0047b9b8f0221d812a72433a67 NeedsCompilation: no Title: RnBeads.hg19 Description: Annotation tables and mappings for hg19 used by RnBeads biocViews: Homo_sapiens Author: Yassen Assenov [aut], Pavlo Lutsik [aut], Fabian Mueller [aut, cre] Maintainer: Fabian Mueller source.ver: src/contrib/RnBeads.hg19_1.0.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RnBeads.mm10 Version: 1.0.0 Depends: R (>= 2.15), GenomicRanges Suggests: RnBeads (>= 0.99.0), BSgenome.Mmusculus.UCSC.mm10, License: GPL-3 MD5sum: 720b513b51717a12dacb99a7217a71b0 NeedsCompilation: no Title: RnBeads.mm10 Description: Annotation tables and mappings for mm10 used by RnBeads Author: Yassen Assenov [aut], Pavlo Lutsik [aut], Fabian Mueller [aut, cre] Maintainer: Fabian Mueller source.ver: src/contrib/RnBeads.mm10_1.0.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RnBeads.mm9 Version: 1.0.0 Depends: R (>= 2.15), GenomicRanges Suggests: RnBeads (>= 0.99.0), BSgenome.Mmusculus.UCSC.mm9, License: GPL-3 MD5sum: 5d162633066ae56303f7e14f824c51b5 NeedsCompilation: no Title: RnBeads.mm9 Description: Annotation tables and mappings for mm9 used by RnBeads Author: Yassen Assenov [aut], Pavlo Lutsik [aut], Fabian Mueller [aut, cre] Maintainer: Fabian Mueller source.ver: src/contrib/RnBeads.mm9_1.0.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RnBeads.rn5 Version: 1.0.0 Depends: R (>= 2.15), GenomicRanges Suggests: RnBeads (>= 0.99.0), BSgenome.Rnorvegicus.UCSC.rn5, License: GPL-3 MD5sum: 6ebe29d2d2803e1e8f073bcc326ec76b NeedsCompilation: no Title: RnBeads.rn5 Description: Annotation tables and mappings for rn5 used by RnBeads Author: Yassen Assenov [aut], Pavlo Lutsik [aut], Fabian Mueller [aut, cre] Maintainer: Fabian Mueller source.ver: src/contrib/RnBeads.rn5_1.0.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RRBSdata Version: 0.102.0 Depends: R (>= 3.1.0), BiSeq License: LGPL-3 MD5sum: 177ed3c7a88f53998c895f72ebaf2cc8 NeedsCompilation: no Title: An RRBS data set with 12 samples and 10,000 simulated DMRs. Description: RRBS data set comprising 12 samples with simulated differentially methylated regions (DMRs). biocViews: ExperimentData, CancerData, SequencingData, CpGIslandData Author: Katja Hebestreit, Hans-Ulrich Klein Maintainer: Katja Hebestreit source.ver: src/contrib/RRBSdata_0.102.0.tar.gz vignettes: vignettes/RRBSdata/inst/doc/RRBSdata.pdf vignetteTitles: An RRBS data set with 12 samples and 10,,000 simulated DMRs. hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RRBSdata/inst/doc/RRBSdata.R Package: rRDPData Version: 0.102.0 Depends: rRDP License: GPL-2 MD5sum: a657362a56a27a336ad1b9836bbf51b4 NeedsCompilation: no Title: Database for the Default RDP Classifier Description: Database used by the default RDP Classifier biocViews: SequencingData, MicrobiomeData Author: Michael Hahsler, Anurag Nagar Maintainer: Michael Hahsler SystemRequirements: Java source.ver: src/contrib/rRDPData_0.102.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RUVnormalizeData Version: 0.102.0 Depends: R (>= 2.10.0), Biobase License: GPL-3 MD5sum: 349dc1f2942755f2302b116d26396f69 NeedsCompilation: no Title: Gender data for the RUVnormalize package Description: Microarray gene expression data from the study of Vawter et al., 2004. biocViews: MicroarrayData Author: Laurent Jacob Maintainer: Laurent Jacob source.ver: src/contrib/RUVnormalizeData_0.102.0.tar.gz 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: SCLCBam Version: 1.0.0 Depends: R(>= 2.10) Suggests: BiocStyle License: GPL-2 MD5sum: 256a26285fdd5ce829ba58573c22a5b6 NeedsCompilation: no Title: Sequence data from chromosome 4 of a small-cell lung tumor Description: Whole-exome sequencing data from a murine small-cell lung tumor; only contains data of chromosome 4. biocViews: SequencingData, LungCancerData Author: Thomas Kuilman Maintainer: Thomas Kuilman source.ver: src/contrib/SCLCBam_1.0.0.tar.gz vignettes: vignettes/SCLCBam/inst/doc/SCLCBam.pdf vignetteTitles: SCLCBam hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: seq2pathway.data Version: 1.0.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 3384dd9ec348153aec8a1a2d4db76164 NeedsCompilation: no Title: data set for R package seq2pathway Description: Supporting data for the seq2patheway package. Includes modified gene sets from MsigDB and org.Hs.eg.db; gene locus definitions from GENCODE project. biocViews: ExperimentData Author: Bin Wang Maintainer: Bin Wang source.ver: src/contrib/seq2pathway.data_1.0.0.tar.gz vignettes: vignettes/seq2pathway.data/inst/doc/seq2pathway.data.pdf vignetteTitles: An R data package for sequence hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/seq2pathway.data/inst/doc/seq2pathway.data.R Package: seqc Version: 1.2.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 4caadef016483a5de354217ca772fe34 NeedsCompilation: no Title: RNA-seq data generated from SEQC (MAQC-III) study Description: The SEQC/MAQC-III Consortium has produced benchmark RNA-seq data for the assessment of RNA sequencing technologies and data analysis methods (Nat Biotechnol, 2014). Billions of sequence reads have been generated from ten different sequencing sites. This package contains the summarized read count data for ~2000 sequencing libraries. It also includes all the exon-exon junctions discovered from the study. TaqMan RT-PCR data for ~1000 genes and ERCC spike-in sequence data are included in this package as well. biocViews: ExperimentData, RNASeqData, qPCRData, SequencingData Author: Yang Liao and Wei Shi with contributions from Steve Lianoglou Maintainer: Yang Liao and Wei Shi URL: http://bioconductor.org/packages/release/data/experiment/html/seqc.html source.ver: src/contrib/seqc_1.2.0.tar.gz 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: 1.4.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: d37b1bc8326e475a521f667d14793244 NeedsCompilation: no Title: Annotation for the copy number analysis of deep sequencing cancer data with seqCNA Description: Provides annotation on GC content, mappability and genomic features for various genomes biocViews: Genome, CopyNumberVariationData Author: David Mosen-Ansorena Maintainer: David Mosen-Ansorena source.ver: src/contrib/seqCNA.annot_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: serumStimulation Version: 1.4.0 Depends: R (>= 2.10) License: GPL (>= 2) MD5sum: 4d04cbaad1834ffaaea43aa3b7aa942e NeedsCompilation: no Title: serumStimulation is a data package which is used by examples in package pcaGoPromoter Description: Contains 13 micro array data results from a serum stimulation experiment biocViews: ExperimentData, MicroarrayData Author: Morten Hansen, Maintainer: Morten Hansen, source.ver: src/contrib/serumStimulation_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: seventyGeneData Version: 1.4.0 Depends: R (>= 2.13.0) Suggests: Biobase, gdata, limma, breastCancerNKI License: Artistic-2.0 MD5sum: 783328eefe71e338eb48d3f436f0f782 NeedsCompilation: no Title: ExpressionSets from the van't Veer and Van de Vijver breast cancer studies Description: Gene expression data for the two breast cancer cohorts published by van't Veer and Van de Vijver in 2002 biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData Author: Luigi Marchionni Maintainer: Luigi Marchionni URL: http://luigimarchionni.org/breastTSP.html source.ver: src/contrib/seventyGeneData_1.4.0.tar.gz 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: 0.102.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: 45d6fe5fc03685194dfd29d6ddab75e4 NeedsCompilation: no Title: Example dataset of input data for shinyMethyl Description: Extracted data from 369 TCGA Head and Neck Cancer DNA methylation samples. The extracted data serve as an example dataset for the package shinyMethyl. Original samples are from 450k methylation arrays, and were obtained from The Cancer Genome Atlas (TCGA). 310 samples are from tumor, 50 are matched normals and 9 are technical replicates of a control cell line. biocViews: Genome, CancerData Author: Jean-Philippe Fortin [cre, aut], Kasper Daniel Hansen [aut] Maintainer: Jean-Philippe Fortin source.ver: src/contrib/shinyMethylData_0.102.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: simpIntLists Version: 1.4.0 License: GPL (>= 2) MD5sum: 6680cc89a8b9be889a8ba2a1cf639fd6 NeedsCompilation: no Title: The package contains BioGRID interactions for various organisms in a simple format Description: The package contains BioGRID interactions for arabidopsis(thale cress), c.elegans, fruit fly, human, mouse, yeast( budding yeast ) and S.pombe (fission yeast) . Entrez ids, official names and unique ids can be used to find proteins. The format of interactions are lists. For each gene/protein, there is an entry in the list with "name" containing name of the gene/protein and "interactors" containing the list of genes/proteins interacting with it. biocViews: ExperimentData, Arabidopsis_thaliana_Data Author: Kircicegi Korkmaz, Volkan Atalay, Rengul Cetin-Atalay Maintainer: Kircicegi Korkmaz source.ver: src/contrib/simpIntLists_1.4.0.tar.gz 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: 1.14.0 Depends: R (>= 2.4.0), graph Suggests: Rgraphviz License: LGPL MD5sum: e518c37951da1efeb1db078e9d4c24d9 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_1.14.0.tar.gz 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: 1.4.0 Depends: R (>= 2.6.0) Suggests: ALL, hgu95av2.db, SNAGEE License: Artistic-2.0 MD5sum: e30b4ac4b749879aab8930f6fc840490 NeedsCompilation: no Title: SNAGEE data Description: SNAGEE data - gene list and correlation matrix biocViews: MicroarrayData Author: David Venet Maintainer: David Venet URL: http://fleming.ulb.ac.be/SNAGEE source.ver: src/contrib/SNAGEEdata_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SomatiCAData Version: 1.6.0 Depends: R (>= 2.14) License: Artistic-2.0 MD5sum: 6635e7cc6e8d23db58cd15116d1e13d4 NeedsCompilation: no Title: An example cancer whole genome sequencing data for the SomatiCA package Description: An example cancer whole genome sequencing data for the SomatiCA package biocViews: ExperimentData, Genome, CancerData, SequencingData Author: Mengjie Chen Maintainer: Mengjie Chen source.ver: src/contrib/SomatiCAData_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SomaticCancerAlterations Version: 1.4.0 Depends: R (>= 3.0.0) Imports: GenomicRanges, exomeCopy, stringr, IRanges Suggests: testthat, ggbio, ggplot2, BiocStyle, knitr License: GPL-3 MD5sum: c274c09bcf3b3e3dd01233d4f8d1999d NeedsCompilation: no Title: Somatic Cancer Alterations Description: Collection of somatic cancer alteration datasets biocViews: ExperimentData, Genome, CancerData, Project1000genomes, NCI Author: Julian Gehring (EMBL Heidelberg) Maintainer: Julian Gehring VignetteBuilder: knitr source.ver: src/contrib/SomaticCancerAlterations_1.4.0.tar.gz 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: 1.10.0 Depends: R (>= 1.6), affy (>= 1.23.4) License: Artistic-2.0 MD5sum: 22d522c9720d9a497a81fac57baf8ec3 NeedsCompilation: no Title: Affymetrix Spike-In Experiment Data Description: Contains the HGU133 and HGU95 spikein experiment data. biocViews: ExperimentData, MicroarrayData Author: Rafael Irizarry Maintainer: Rafael A. Irizarry source.ver: src/contrib/SpikeIn_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SpikeInSubset Version: 1.8.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5), affy (>= 1.23.4) License: LGPL MD5sum: bc4df545be49e79008793792087d44ed NeedsCompilation: no Title: Part of Affymetrix's Spike-In Experiment Data Description: Includes probe-level and expression data for the HGU133 and HGU95 spike-in experiments biocViews: ExperimentData, MicroarrayData Author: Rafael Irizarry and Zhijin Wu Maintainer: Rafael A. Irizarry source.ver: src/contrib/SpikeInSubset_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: stemHypoxia Version: 1.4.0 Depends: R (>= 2.14.1) License: GPL (>=2) MD5sum: b4d5de9b8c6caf0a61657c95f83cd476 NeedsCompilation: no Title: Differentiation of Human Embryonic Stem Cells under Hypoxia gene expression dataset by Prado-Lopez et al. (2010) Description: Expression profiling using microarray technology to prove if 'Hypoxia Promotes Efficient Differentiation of Human Embryonic Stem Cells to Functional Endothelium' by Prado-Lopez et al. (2010) Stem Cells 28:407-418. Full data available at Gene Expression Omnibus series GSE37761. biocViews: ExperimentData, Tissue, StemCell, Homo_sapiens_Data, CancerData, MicroarrayData, TissueMicroarrayData, GEO Author: Cristobal Fresno and Elmer A. Fernandez Maintainer: Cristobal Fresno URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37761, http://onlinelibrary.wiley.com/doi/10.1002/stem.295/abstract source.ver: src/contrib/stemHypoxia_1.4.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: stjudem Version: 1.8.0 Depends: R (>= 2.10), utils License: LGPL (>= 2) MD5sum: 954b64e1df5292b80c7b9ec9b7081dfc NeedsCompilation: no Title: Microarray Data from Yeoh et al. in MACAT format Description: This is a microarray data set on acute lymphoblastic leukemia, published in 2002 (Yeoh et al.Cancer Cell 2002). The experiments were conducted in the St.Jude Children's Research Hospital, Memphis, Tenessee, USA. The raw data was preprocessed by variance stabilizing normalization (Huber et al.) on probe and subsequent summarization of probe expression values into probe set expression values using median polish. biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData, ChipOnChipData Author: Benjamin Georgi, Matthias Heinig, Sebastian Schmeier, Joern Toedling Maintainer: Joern Toedling source.ver: src/contrib/stjudem_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SVM2CRMdata Version: 1.0.0 Depends: R(>= 3.2.0) License: LGPL (>= 2) MD5sum: e657e4ae8c0cf12ec6ef2e43d908a017 NeedsCompilation: no Title: An example dataset for use with the SVM2CRM package Description: An example dataset for use with the SVM2CRM package. biocViews: ExperimentData, ChIPSeq, HistoneModification, Preprocessing, DataImport Author: Guidantonio Malagoli Tagliazucchi Maintainer: Guidantonio Malagoli Tagliazucchi source.ver: src/contrib/SVM2CRMdata_1.0.0.tar.gz vignettes: vignettes/SVM2CRMdata/inst/doc/SVM2CRMdata.pdf vignetteTitles: Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: synapterdata Version: 1.6.0 Depends: R (>= 2.10), synapter (>= 0.99.6) License: GPL-2 MD5sum: c6c937848a116180b3859742599626fb NeedsCompilation: no Title: Data accompanying the synapter package Description: Data independant acquisition of UPS1 protein mix in an E. coli background obtained on a Waters Synapt G2 instrument. biocViews: ExperimentData, MassSpectrometryData Author: Laurent Gatto, Sebastian Gibb and Pavel V. Shliaha Maintainer: Laurent Gatto source.ver: src/contrib/synapterdata_1.6.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics Package: TargetScoreData Version: 1.4.0 Suggests: TargetScore, gplots License: GPL-2 MD5sum: 333ba8772ae74b415d32b211574d5965 NeedsCompilation: no Title: TargetScoreData Description: Precompiled and processed miRNA-overexpression fold-changes from 84 Gene Expression Omnibus (GEO) series corresponding to 6 platforms, 77 human cells or tissues, and 113 distinct miRNAs. Accompanied with the data, we also included in this package the sequence feature scores from TargetScanHuman 6.1 including the context+ score and the probabilities of conserved targeting for each miRNA-mRNA interaction. Thus, the user can use these static sequence-based scores together with user-supplied tissue/cell-specific fold-change due to miRNA overexpression to predict miRNA targets using the package TargetScore (download separately) biocViews: ExperimentData, RNASeqData, miRNAData Author: Yue Li Maintainer: Yue Li source.ver: src/contrib/TargetScoreData_1.4.0.tar.gz vignettes: vignettes/TargetScoreData/inst/doc/TargetScoreData.pdf vignetteTitles: Processed human microRNA-overexpression data from GEO,, and sequence information from TargetScan,, and targetScore from TargetScore hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TargetScoreData/inst/doc/TargetScoreData.R Package: TargetSearchData Version: 1.6.0 Depends: TargetSearch License: GPL (>= 2) MD5sum: beb4ef0361cd85701bcb9b2846ec4f35 NeedsCompilation: no Title: Example GC-MS data for TargetSearch Package Description: This package provides example GC-MS data for TargetSearch Package. biocViews: ExperimentData, Escherichia_coli_Data Author: Alvaro Cuadros-Inostroza, Henning Redestig, Matt Hannah Maintainer: Alvaro Cuadros-Inostroza Henning Redestig , Matt Hannah source.ver: src/contrib/TargetSearchData_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: TBX20BamSubset Version: 1.4.0 Depends: Rsamtools (>= 1.9.8) Imports: xtable License: LGPL MD5sum: 6a95d0f28696f343a79d80f13f37d477 NeedsCompilation: no Title: Subset of BAM files from the "TBX20" experiment Description: Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. A subset of the RNA-Seq data. biocViews: ExperimentData, SequencingData, RNASeqData Author: D. Bindreither Maintainer: D. Bindreither source.ver: src/contrib/TBX20BamSubset_1.4.0.tar.gz 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: 0.102.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: dfe1db80c0136339e978cffaa2891bc9 NeedsCompilation: no Title: TCGA CRC 450 miRNA dataset Description: colorectal cancer miRNA profile provided by TCGA biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella source.ver: src/contrib/TCGAcrcmiRNA_0.102.0.tar.gz 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: 0.102.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: ffde3e1a65394e1a54f727125275dedc NeedsCompilation: no Title: TCGA CRC 450 mRNA dataset Description: colorectal cancer mRNA profile provided by TCGA biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella source.ver: src/contrib/TCGAcrcmRNA_0.102.0.tar.gz 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: 1.4.0 License: GPL-2 MD5sum: 42a4b55f301d3a129d56fecede9df256 NeedsCompilation: no Title: The Cancer Genome Atlas Illumina 450k methylation example data Description: The Cancer Genome Atlas (TCGA) is applying genomics technologies to over 20 different types of cancer. This package contains a small set of 450k array data in idat format. biocViews: Genome, CancerData, MethylationArrayData Author: Sean Davis Maintainer: Sean Davis source.ver: src/contrib/TCGAMethylation450k_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: tinesath1cdf Version: 1.6.0 License: Artistic-2.0 MD5sum: a40e1a274121d4d64d9d5090feb42119 NeedsCompilation: no Title: tinesath1cdf Description: A package containing an environment represeting the newcdf/tinesATH1.cdf.cdf file. biocViews: Arabidopsis_thaliana_Data, ChipOnChipData Author: Tine Casneuf Maintainer: Tine Casneuf source.ver: src/contrib/tinesath1cdf_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: XhybCasneuf Package: tinesath1probe Version: 1.6.0 Depends: R (>= 1.6), AnnotationDbi (>= 1.11.9) License: LGPL MD5sum: 1cafce00e124d25918a311ec887b279b NeedsCompilation: no Title: Probe sequence data for microarrays of type tinesath1 Description: This package was automatically created by package matchprobes version 1.4.0. The probe sequence data was obtained from http://www.affymetrix.com. biocViews: Arabidopsis_thaliana_Data, SequencingData, MicroarrayData Author: The Bioconductor Project www.bioconductor.org Maintainer: Tine Casneuf source.ver: src/contrib/tinesath1probe_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: tweeDEseqCountData Version: 1.6.0 Depends: Biobase, R (>= 2.10) License: GPL (>=2) MD5sum: 624b7f11bb761251522d775acb66a614 NeedsCompilation: no Title: RNA-seq count data employed in the vignette of the tweeDEseq package Description: RNA-seq count data from Pickrell et al. (2010) employed to illustrate the use of the Poisson-Tweedie family of distributions with the tweeDEseq package. biocViews: Genome, Homo_sapiens_Data, RNASeqData Author: Juan R Gonzalez and Mikel Esnaola (with contributions from Robert Castelo ) Maintainer: Juan R Gonzalez URL: http://www.creal.cat/jrgonzalez/software.htm source.ver: src/contrib/tweeDEseqCountData_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: waveTilingData Version: 1.4.0 Depends: R (>= 2.14.0) License: GPL (>= 2) MD5sum: 13744a55784b3901309eb081851fc07b NeedsCompilation: no Title: waveTiling Example Data Description: Experiment and Annotation Data files used by the examples / vignette in the waveTiling package biocViews: ExperimentData, Arabidopsis_thaliana_Data, MicroarrayData Author: Kristof De Beuf Maintainer: Kristof De Beuf source.ver: src/contrib/waveTilingData_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: WES.1KG.WUGSC Version: 1.0.0 License: GPL-2 MD5sum: d4f010fffa03b8086ae212f8ea95bbc2 NeedsCompilation: no Title: Whole Exome Sequencing (WES) of chromosome 22 401st to 500th exon from the 1000 Genomes (1KG) Project by the Washington University Genome Sequencing Center (WUGSC). Description: The assembled .bam files of whole exome sequencing data from the 1000 Genomes Project. 46 samples sequenced by the Washington University Genome Sequencing Center are included. biocViews: ExperimentData, Project1000genomes, SequencingData, DNASeqData, Homo_sapiens_Data Author: Yuchao Jiang, Nancy R. Zhang Maintainer: Yuchao Jiang source.ver: src/contrib/WES.1KG.WUGSC_1.0.0.tar.gz vignettes: vignettes/WES.1KG.WUGSC/inst/doc/WES.1KG.WUGSC_vignettes.pdf vignetteTitles: Using CODEX hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/WES.1KG.WUGSC/inst/doc/WES.1KG.WUGSC_vignettes.R Package: XhybCasneuf Version: 1.6.0 Depends: R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf , RColorBrewer , methods, grid License: Artistic-2.0 MD5sum: af369a906d1de0ed2e3ba0e4007b308d NeedsCompilation: no Title: EBI/PSB cross-hybridisation study package Description: Cross-hybridisation study on the ATH1 Affymetrix GeneChip biocViews: ExperimentData, Tissue, MicroarrayData, TissueMicroarrayData Author: Tineke Casneuf Maintainer: Tineke Casneuf source.ver: src/contrib/XhybCasneuf_1.6.0.tar.gz 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: 1.8.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 6d51d9c53f8e8b8b3022c401d8ba338f NeedsCompilation: no Title: Spellman et al. (1998) and Pramila/Breeden (2006) yeast cell cycle microarray data Description: ExpressionSet for Spellman et al. (1998) yeast cell cycle microarray experiment biocViews: ExperimentData, CellCulture, Saccharomyces_cerevisiae_Data, CancerData, MicroarrayData, OneChannelData, GEO Author: Sandrine Dudoit Maintainer: Sandrine Dudoit source.ver: src/contrib/yeastCC_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastExpData Version: 0.14.0 Depends: R (>= 2.4), graph (>= 1.9.26) Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db License: GPL MD5sum: 2f10382629213bc4291de40eb58feb03 NeedsCompilation: no Title: Yeast Experimental Data Description: A collection of different sets of experimental data from yeast. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data Author: R. Gentleman Maintainer: R. Gentleman source.ver: src/contrib/yeastExpData_0.14.0.tar.gz 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: 0.6.0 License: Artistic-2.0 MD5sum: 6587a72aa1e8c11b9a2fea59fafafe3a NeedsCompilation: no Title: Yeast Gold Standard Data Description: A collection of so-called gold (and other) standard data sets biocViews: ExperimentData, Saccharomyces_cerevisiae_Data Author: R. Gentleman Maintainer: R. Gentleman source.ver: src/contrib/yeastGSData_0.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastNagalakshmi Version: 1.4.0 License: Artistic-2.0 MD5sum: af806ccef37832edc06c00cb17fa4cdb NeedsCompilation: no Title: Yeast genome RNA sequencing data based on Nagalakshmi et. al. Description: The yeast genome data was retrieved from the sequence read archive, aligned with bwa, and converted to BAM format with samtools. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, SequencingData, BiocViews, ChIPSeqData Author: Martin Morgan Maintainer: Bioconductor Package Maintainer source.ver: src/contrib/yeastNagalakshmi_1.4.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastRNASeq Version: 0.6.0 Depends: R (>= 2.4) Suggests: Biobase, ShortRead, IRanges License: GPL MD5sum: 2b255a4691e43befc5855679bc11d452 NeedsCompilation: no Title: Yeast RNA-Seq Experimental Data from Lee et al. 2008 Description: A selection of RNA-Seq data from a yeast transcriptome experiment. biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData Author: James H. Bullard and Kasper D. Hansen Maintainer: J. Bullard source.ver: src/contrib/yeastRNASeq_0.6.0.tar.gz 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: 0.10.0 Depends: GGBase Imports: Biobase License: Artistic-2.0 MD5sum: 05fdf4c23bcce73300a3097f03fc74af NeedsCompilation: no Title: expression + genotype on 79 unrelated YRI individuals Description: expression + genotype on 79 unrelated YRI individuals biocViews: ArrayExpress Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/yri1kgv_0.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: zebrafishRNASeq Version: 0.102.0 Depends: R (>= 2.10) Suggests: BiocStyle, knitr License: GPL MD5sum: 8bab577e4a90b60d345dadaefe6b58cc NeedsCompilation: no Title: Zebrafish RNA-Seq Experimental Data from Ferreira et al. (2014) Description: Gene-level read counts from RNA-Seq for gallein-treated and control zebrafish. biocViews: ExperimentData, Danio_rerio_Data, RNASeqData Author: Davide Risso Maintainer: Davide Risso VignetteBuilder: knitr source.ver: src/contrib/zebrafishRNASeq_0.102.0.tar.gz vignettes: vignettes/zebrafishRNASeq/inst/doc/preprocessing.pdf vignetteTitles: Pre-Processing for the Zebrafish RNA-Seq Gene-Level Counts hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/zebrafishRNASeq/inst/doc/preprocessing.R