Package: ALLMLL Version: 1.2.13 Depends: R (>= 2.10), affy (>= 1.23.4) License: GPL-2 Title: A subset of arrays from a large acute lymphoblastic leukemia (ALL) study Description: This package provides probe-level data for 20 HGU133A and 20 HGU133B arrays which are a subset of arrays from a large ALL study. The data is for the MLL arrays. This data was published in Mary E. Ross, Xiaodong Zhou, Guangchun Song, Sheila A. Shurtleff, Kevin Girtman, W. Kent Williams, Hsi-Che Liu, Rami Mahfouz, Susana C. Raimondi, Noel Lenny, Anami Patel, and James R. Downing (2003) Classification of pediatric acute lymphoblastic leukemia by gene expression profiling Blood 102: 2951-2959 biocViews: ExperimentData, Cancer, Leukemia Author: B. M. Bolstad MD5sum: 3d11a244a9e2c1aad246fbb5a3f0a6d4 source.ver: src/contrib/ALLMLL_1.2.13.tar.gz win.binary.ver: bin/windows/contrib/2.15/ALLMLL_1.2.13.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ALLMLL_1.2.13.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ALL Version: 1.4.13 Depends: R (>= 2.10), Biobase (>= 2.5.5) Suggests: rpart License: Artistic-2.0 Title: A data package Description: Data of T- and B-cell Acute Lymphocytic Leukemia from the Ritz Laboratory at the DFCI (includes Apr 2004 versions) biocViews: ExperimentData, Cancer, Leukemia Author: Xiaochun Li Maintainer: Robert Gentleman MD5sum: 82a9bef4b94bf5de355f9aa0921e19b3 source.ver: src/contrib/ALL_1.4.13.tar.gz win.binary.ver: bin/windows/contrib/2.15/ALL_1.4.13.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ALL_1.4.13.tgz vignettes: vignettes/ALL/inst/doc/ALLintro.pdf vignetteTitles: ALL data intro hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ALL/inst/doc/ALLintro.R Package: AffymetrixDataTestFiles Version: 0.1.5 Depends: R (>= 2.5.0) License: LGPL-2.1 Title: Affymetrix data files (CEL, CDF, CHP, EXP, PSI) for testing Description: This package contains annotation data files and sample data files of Affymetrix file formats. The files originate from the Affymetrix' Fusion SDK distribution. biocViews: Microarray, OneChannel, AnnotationData, ExperimentData Author: Henrik Bengtsson, James Bullard, Kasper Daniel Hansen Maintainer: Henrik Bengtsson MD5sum: cf4a305543775a651cf1fd459af8fc09 source.ver: src/contrib/AffymetrixDataTestFiles_0.1.5.tar.gz win.binary.ver: bin/windows/contrib/2.15/AffymetrixDataTestFiles_0.1.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/AffymetrixDataTestFiles_0.1.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: AmpAffyExample Version: 1.2.11 Depends: R (>= 2.4.0), affy (>= 1.23.4) Suggests: hgu133acdf License: LGPL (>= 2) Title: Example of Amplified Data Description: Six arrays. Three from amplified RNA, three from the typical procedure. biocViews: ExperimentData Author: Rafael A. Irizarry Maintainer: Rafael A. Irizarry MD5sum: 284c0a5e5952f0a30b4ba9e5437b93b9 source.ver: src/contrib/AmpAffyExample_1.2.11.tar.gz win.binary.ver: bin/windows/contrib/2.15/AmpAffyExample_1.2.11.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/AmpAffyExample_1.2.11.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: BeadArrayUseCases Version: 1.0.9 Imports: beadarray (>= 2.3.18), limma, GEOquery Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db License: GPL-2 Title: Analysing Illumina BeadArray expression data using Bioconductor Description: Example data files and use cases for processing Illumina BeadArray expression data using Bioconductor biocViews: DifferentialExpression, Microarray Author: Mark Dunning, Wei Shi, Andy Lynch, Mike Smith, Matt Ritchie Maintainer: Mike Smith MD5sum: 28217cc3bcaaba4e5ccec3aa052a28cf source.ver: src/contrib/BeadArrayUseCases_1.0.9.tar.gz win.binary.ver: bin/windows/contrib/2.15/BeadArrayUseCases_1.0.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BeadArrayUseCases_1.0.9.tgz vignettes: vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.pdf, vignettes/BeadArrayUseCases/inst/doc/BeadChipSimple_old.pdf vignetteTitles: BeadArrayUseCases.pdf, BeadChipSimple_old.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.R Package: CCl4 Version: 1.0.13 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), limma License: Artistic-2.0 Title: Carbon Tetrachloride (CCl4) treated hepatocytes Description: NChannelSet for rat hepatocytes treated with Carbon Tetrachloride (CCl4) data from LGC company. biocViews: ExperimentData Author: Audrey Kauffmann, Wolfgang Huber Maintainer: Audrey Kauffmann MD5sum: 726f3fe48c36c1e6c467c4a2bf490190 source.ver: src/contrib/CCl4_1.0.13.tar.gz win.binary.ver: bin/windows/contrib/2.15/CCl4_1.0.13.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CCl4_1.0.13.tgz vignettes: vignettes/CCl4/inst/doc/CCl4.pdf vignetteTitles: CCl4 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CCl4/inst/doc/CCl4.R Package: CLL Version: 1.2.13 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: LGPL Title: A Package for CLL Gene Expression Data Description: The CLL package contains the chronic lymphocytic leukemia (CLL) gene expression data. The CLL data had 24 samples that were either classified as progressive or stable in regards to disease progression. The data came from Dr. Sabina Chiaretti at Division of Hematology, Department of Cellular Biotechnologies and Hematology, University La Sapienza, Rome, Italy and Dr. Jerome Ritz at Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts. biocViews: ExperimentData, Cancer, Leukemia Author: Elizabeth Whalen Maintainer: Robert Gentleman MD5sum: 4bdb32614e7646d2abbfa44698a6d6dc source.ver: src/contrib/CLL_1.2.13.tar.gz win.binary.ver: bin/windows/contrib/2.15/CLL_1.2.13.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CLL_1.2.13.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ChIPXpressData Version: 0.99.1 Depends: bigmemory License: GPL (>=2) Title: ChIPXpress Pre-built Databases Description: Contains pre-built mouse (GPL1261) and human (GPL570) database of gene expression profiles to be used for ChIPXpress ranking. biocViews: AffymetrixChIP, Homo_sapiens, Mus_musculus Author: George Wu Maintainer: George Wu MD5sum: 5be3e4e821b655e2a50e0fb660cdd87c source.ver: src/contrib/ChIPXpressData_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/ChIPXpressData_0.99.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ChIPXpressData_0.99.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: DLBCL Version: 1.3.5 Depends: R(>= 2.11.0), Biobase License: GPL (>=2) Title: Diffuse large B-cell lymphoma expression data Description: This package provides additional expression data on diffuse large B-cell lymphomas for the BioNet package. biocViews: ExperimentData, Cancer Author: Marcus Dittrich and Daniela Beisser Maintainer: Marcus Dittrich URL: http://bionet.bioapps.biozentrum.uni-wuerzburg.de/ MD5sum: 8889ec3c1c743b821dd1275746feacf5 source.ver: src/contrib/DLBCL_1.3.5.tar.gz win.binary.ver: bin/windows/contrib/2.15/DLBCL_1.3.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DLBCL_1.3.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: EatonEtAlChIPseq Version: 0.0.8 Depends: GenomicRanges (>= 1.5.42), ShortRead, rtracklayer License: Artistic 2.0 Title: ChIP-seq data of ORC-binding sites in Yeast excerpted from Eaton et al. 2010 Description: ChIP-seq analysis subset from "Conserved nucleosome positioning defines replication origins" (PMID 20351051) biocViews: ExperimentData, Yeast, ChIPseqData Author: Patrick Aboyoun Maintainer: Patrick Aboyoun MD5sum: c9d30af21ebc8811367df4630bfdf885 source.ver: src/contrib/EatonEtAlChIPseq_0.0.8.tar.gz win.binary.ver: bin/windows/contrib/2.15/EatonEtAlChIPseq_0.0.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/EatonEtAlChIPseq_0.0.8.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: FunciSNP.data Version: 0.99.1 Depends: R (>= 2.14.0) Imports: rtracklayer License: GPL-3 Title: Various data sets for use with the FunciSNP package Description: Data sets needed for FunciSNP to integrate information from GWAS, 1000genomes and chromatin feature, in order to identify functional SNP in coding or non-coding regions. biocViews: Infrastructure, DataRepresentation, DataImport, SequenceMatching, Annotation Author: Simon G. Coetzee and Houtan Noushmehr, PhD Maintainer: Simon G. Coetzee URL: http://coetzeeseq.usc.edu/publication/Coetzee_SG_et_al_2012/ MD5sum: ae89ef71865a5958396cc4efad5bb467 source.ver: src/contrib/FunciSNP.data_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/FunciSNP.data_0.99.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/FunciSNP.data_0.99.1.tgz vignettes: vignettes/FunciSNP.data/inst/doc/FunciSNP.data.pdf vignetteTitles: FunciSNP Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FunciSNP.data/inst/doc/FunciSNP.data.R Package: GGdata Version: 1.0.20 Depends: R (>= 2.12.0), methods, Biobase (>= 2.5.5), GGBase, snpStats, illuminaHumanv1.db, AnnotationDbi Enhances: GGtools License: LGPL Title: all 90 hapmap CEU samples, 47K expression, 4mm SNP Description: data exemplars dealing with hapmap SNP reports, GWAS, etc. biocViews: ExperimentData, HapMap Author: VJ Carey Maintainer: VJ Carey MD5sum: c7f5e1246e73991e8001cceb92c0642a source.ver: src/contrib/GGdata_1.0.20.tar.gz win.binary.ver: bin/windows/contrib/2.15/GGdata_1.0.20.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GGdata_1.0.20.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ggtut suggestsMe: encoDnaseI Package: GSVAdata Version: 0.99.9 Depends: R (>= 2.10), Biobase, GSEABase, hgu95a.db License: GPL (>= 2) Title: Data employed in the vignette of the GSVA package Description: This package stores the data employed in the vignette of the GSVA package. These data belong to the following publications: Armstrong et al. Nat Genet 30:41-47, 2002; Cahoy et al. J Neurosci 28:264-278, 2008; Carrel and Willard, Nature, 434:400-404, 2005; Huang et al. PNAS, 104:9758-9763, 2007; Pickrell et al. Nature, 464:768-722, 2010; Skaletsky et al. Nature, 423:825-837; Verhaak et al. Cancer Cell 17:98-110, 2010 biocViews: ExperimentData, RNAseqData, RNAExpressionData, Cancer, Leukemia Author: Robert Castelo Maintainer: Robert Castelo MD5sum: 3b73c1c0148607554dc252c742f56cf5 source.ver: src/contrib/GSVAdata_0.99.9.tar.gz win.binary.ver: bin/windows/contrib/2.15/GSVAdata_0.99.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GSVAdata_0.99.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GWASdata Version: 1.0.7 Depends: GWASTools License: Artistic-2.0 Title: Data used in the examples and vignettes of the GWASTools package Description: Selected Affymetrix and Illlumina SNP data for HapMap subjects. Data provided by the Center for Inherited Disease Research at Johns Hopkins University and the Broad Institute of MIT and Harvard University. biocViews: ExperimentData, SNP, Microarray Author: Stephanie Gogarten Maintainer: Stephanie Gogarten MD5sum: bf4ade53ed74bf97e417d535f1d7e6fa source.ver: src/contrib/GWASdata_1.0.7.tar.gz win.binary.ver: bin/windows/contrib/2.15/GWASdata_1.0.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GWASdata_1.0.7.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: HEEBOdata Version: 1.0.4 License: LGPL 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/ MD5sum: 6273c2678466fbcc5927e41866adbec7 source.ver: src/contrib/HEEBOdata_1.0.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/HEEBOdata_1.0.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/HEEBOdata_1.0.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: HIVcDNAvantWout03 Version: 1.2.7 License: GPL (>= 2) Title: T cell line infections with HIV-1 LAI (BRU) Description: The expression levels of approximately 4600 cellular RNA transcripts were assessed in CD4+ T cell lines at different times after infection with HIV-1BRU using DNA microarrays. This data corresponds to the first block of a 12 block array image (001030_08_1.GEL) in the first data set (2000095918 A) in the first experiment (CEM LAI vs HI-LAI 24hr). There are two data sets, which are part of a dye-swap experiment with replicates, representing the Cy3 (green) absorption intensities for channel 1 (hiv1raw) and the Cy5 (red) absorption intensities for channel 2 (hiv2raw). biocViews: ExperimentData, HIV Author: Dr. Angelique van't Wout, Department of Microbiology, University of Washington Maintainer: Chris Fraley URL: http://expression.microslu.washington.edu/expression/vantwoutjvi2002.html MD5sum: e36c9b91936f04e8913edeea85a9f9c8 source.ver: src/contrib/HIVcDNAvantWout03_1.2.7.tar.gz win.binary.ver: bin/windows/contrib/2.15/HIVcDNAvantWout03_1.2.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/HIVcDNAvantWout03_1.2.7.tgz vignettes: vignettes/HIVcDNAvantWout03/inst/doc/hivData.pdf vignetteTitles: hivData.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ITALICSData Version: 2.0.6 Depends: R (>= 2.0.0) License: GPL Title: ITALICSData Description: Data needed to use the ITALICS package biocViews: ExperimentData Author: Guillem Rigaill Maintainer: Guillem Rigaill URL: http://bioinfo.curie.fr MD5sum: 0ca0b93711a1e6be61185535041181ee source.ver: src/contrib/ITALICSData_2.0.6.tar.gz win.binary.ver: bin/windows/contrib/2.15/ITALICSData_2.0.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ITALICSData_2.0.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: IlluminaHumanMethylation450kmanifest Version: 0.2.1 Depends: R (>= 2.13.0), minfi License: Artistic-2.0 Title: Annotation for Illumina's 450k methylation arrays Description: Manifest for Illumina's 450k array data biocViews: IlluminaChip, Homo_sapiens, DNAMethylation Author: Kasper Daniel Hansen, Martin Aryee Maintainer: Kasper Daniel Hansen MD5sum: c315afc7a66c0b3d9793b76d18867444 source.ver: src/contrib/IlluminaHumanMethylation450kmanifest_0.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/IlluminaHumanMethylation450kmanifest_0.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/IlluminaHumanMethylation450kmanifest_0.2.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: minfiData Package: Iyer517 Version: 1.4.11 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 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 MD5sum: cdadd8489bca5c30809f40b7dfcd93fa source.ver: src/contrib/Iyer517_1.4.11.tar.gz win.binary.ver: bin/windows/contrib/2.15/Iyer517_1.4.11.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Iyer517_1.4.11.tgz vignettes: vignettes/Iyer517/inst/doc/Iyer517.pdf vignetteTitles: Iyer517 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Iyer517/inst/doc/Iyer517.R Package: KEGGdzPathwaysGEO Version: 1.1.1 Depends: R (>= 2.13.0) Imports: Biobase, BiocGenerics License: GPL-2 Title: KEGG Disease Datasets from GEO Description: This is a collection of 24 data sets for which the phenotype is a disease with a corresponding pathway in the KEGG database.This collection of datasets were used as gold standard in comparing gene set analysis methods by the PADOG package. Author: Gaurav Bhatti, Adi L. Tarca Maintainer: Gaurav Bhatti MD5sum: 38be40fadb76e1c9fea2178448e2cbe2 source.ver: src/contrib/KEGGdzPathwaysGEO_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/KEGGdzPathwaysGEO_1.1.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/KEGGdzPathwaysGEO_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: LiebermanAidenHiC2009 Version: 0.1.13 Depends: KernSmooth, IRanges License: LGPL Title: Selected data from the HiC paper of E. Lieberman-Aiden et al. in Science (2009) Description: This package provides data that were presented in the article "Comprehensive mapping of long-range interactions reveals folding principles of the human genome", Science 2009 Oct 9;326(5950):289-93. PMID: 19815776 biocViews: ExperimentData Author: Wolfgang Huber, Felix Klein Maintainer: Felix Klein MD5sum: 06783b16e02cfdd0cde3c407cf53fd07 source.ver: src/contrib/LiebermanAidenHiC2009_0.1.13.tar.gz win.binary.ver: bin/windows/contrib/2.15/LiebermanAidenHiC2009_0.1.13.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/LiebermanAidenHiC2009_0.1.13.tgz vignettes: vignettes/LiebermanAidenHiC2009/inst/doc/LiebermanAidenHiC2009.pdf vignetteTitles: Exploration of HiC data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: LungCancerLines Version: 0.0.7 Imports: Rsamtools License: Artistic-2.0 Title: Reads from Two Lung Cancer Cell Lines Description: Reads from an RNA-seq experiment between two lung cancer cell lines: H1993 (met) and H2073 (primary). The reads are stored as Fastq files and are meant for use with the TP53Genome object in the gmapR package. Author: Cory Barr, Michael Lawrence Maintainer: Cory Barr MD5sum: ebe2c91e3efa42d8da594878e3413834 source.ver: src/contrib/LungCancerLines_0.0.7.tar.gz win.binary.ver: bin/windows/contrib/2.15/LungCancerLines_0.0.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/LungCancerLines_0.0.7.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MAQCsubsetAFX Version: 1.0.9 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: Artistic-2.0 Title: MAQC data subset for the Affymetrix platform Description: MAQC data subset for the Affymetrix platform biocViews: Microarray, ExperimentData Author: Laurent Gatto Maintainer: Laurent Gatto MD5sum: ffb7d237a1d98c4cbbc757108910f77d source.ver: src/contrib/MAQCsubsetAFX_1.0.9.tar.gz win.binary.ver: bin/windows/contrib/2.15/MAQCsubsetAFX_1.0.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MAQCsubsetAFX_1.0.9.tgz vignettes: vignettes/MAQCsubsetAFX/inst/doc/MAQCsubsetAFX.pdf vignetteTitles: MAQCsubsetAFX: MAQC data subset for the Affymetrix platform hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MAQCsubsetAFX/inst/doc/MAQCsubsetAFX.R Package: MAQCsubsetILM Version: 1.0.7 Depends: Biobase (>= 2.5.5), lumi License: Artistic-2.0 Title: MAQC data subset for the Illumina platform Description: MAQC data subset for the Illumina platform biocViews: Microarray, ExperimentData Author: Laurent Gatto Maintainer: Laurent Gatto MD5sum: c183ed0e8008c91726879c01ec90692f source.ver: src/contrib/MAQCsubsetILM_1.0.7.tar.gz win.binary.ver: bin/windows/contrib/2.15/MAQCsubsetILM_1.0.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MAQCsubsetILM_1.0.8.tgz vignettes: vignettes/MAQCsubsetILM/inst/doc/MAQCsubsetILM.pdf vignetteTitles: MAQCsubsetILM: MAQC data subset for the Illumina platform hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MAQCsubsetILM/inst/doc/MAQCsubsetILM.R Package: MAQCsubset Version: 1.0.26 Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), lumi, methods Suggests: genefilter, codelink License: Artistic-2.0 Title: Experimental Data Package: MAQCsubset Description: Data Package automatically created on Sun Nov 19 15:59:29 2006. biocViews: ExperimentData Author: VJ Carey Maintainer: VJ Carey MD5sum: e8fc4e21697753707ca09630611b758e source.ver: src/contrib/MAQCsubset_1.0.26.tar.gz win.binary.ver: bin/windows/contrib/2.15/MAQCsubset_1.0.26.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MAQCsubset_1.0.26.tgz vignettes: vignettes/MAQCsubset/inst/doc/maqcNotes.pdf vignetteTitles: MAQC notes hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MAQCsubset/inst/doc/maqcNotes.R Package: MEDIPSData Version: 0.99.3 Depends: R (>= 2.15.0) License: GPL (>= 2) Title: Example data for the MEDIPS package. Description: Data for the MEDIPS package, consisting of chromosome 22 MeDIP and control/Input sample data from DNA methylation analysis of human embryonic stem cells and mapped to the human genome hg19 using bowtie. biocViews: ExperimentData, ChIPseq, DNAMethylation, DifferentialExpression, HighThroughputSequencing, Methylseq, Preprocessing, QualityControl, Sequencing, Software, Visualization Author: Lukas Chavez Maintainer: Lukas Chavez MD5sum: 8b98785bc99ab30fc0fe18a3d3cd14f0 source.ver: src/contrib/MEDIPSData_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/MEDIPSData_0.99.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MEDIPSData_0.99.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MEEBOdata Version: 1.0.4 License: LGPL 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/ MD5sum: 11e847c1c06145f7f6cfc15992b7b489 source.ver: src/contrib/MEEBOdata_1.0.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/MEEBOdata_1.0.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MEEBOdata_1.0.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Mulder2012 Version: 0.2.2 Depends: R (>= 2.14), org.Hs.eg.db, KEGG.db Imports: igraph, HTSanalyzeR, PANR, RedeR, pvclust, MASS Suggests: snow License: Artistic-2.0 Title: Predicting functional networks and modules of chromatin factors controlling adult stem cell fate from RNA interference screens Description: This package provides functions to reproduce results and figures in Mulder K. et. al. published in Nature Cell Biology 2012 and Wang X. et. al. published in PLoS Computational Biology 2012. biocViews: Bioinformatics Author: Xin Wang , Florian Markowetz Maintainer: Xin Wang MD5sum: 640c08345de04b418b5d9a3c6859e3f6 source.ver: src/contrib/Mulder2012_0.2.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/Mulder2012_0.2.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Mulder2012_0.2.2.tgz vignettes: vignettes/Mulder2012/inst/doc/Arora2010_PAN.pdf, vignettes/Mulder2012/inst/doc/Arora2010_sigMod.pdf, vignettes/Mulder2012/inst/doc/Mulder2012-Vignette.pdf, vignettes/Mulder2012/inst/doc/Mulder2012_PAN.pdf, vignettes/Mulder2012/inst/doc/Mulder2012_enrich.pdf, vignettes/Mulder2012/inst/doc/Mulder2012_sigMod.pdf vignetteTitles: Arora2010_PAN.pdf, Arora2010_sigMod.pdf, Main vignette:Posterior association network and enriched functional gene modules inferred from rich phenotypes of gene perturbations, Mulder2012_PAN.pdf, Mulder2012_enrich.pdf, Mulder2012_sigMod.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Mulder2012/inst/doc/Mulder2012-Vignette.R Package: NCIgraphData Version: 0.99.5 Depends: R (>= 2.10.0) Suggests: Rgraphviz License: GPL-3 Title: Data for the NCIgraph software package Description: Provides pathways from the NCI Pathways Database as R graph objects biocViews: Bioinformatics, GraphsAndNetworks Author: Laurent Jacob Maintainer: Laurent Jacob MD5sum: 16587fa96ef4f1993ed11f51f8033ff1 source.ver: src/contrib/NCIgraphData_0.99.5.tar.gz win.binary.ver: bin/windows/contrib/2.15/NCIgraphData_0.99.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/NCIgraphData_0.99.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Neve2006 Version: 0.1.15 Depends: R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0), hgu133a.db, annotate License: Artistic-2.0 Title: expression and CGH data on breast cancer cell lines Description: Experimental organization of combined expression and CGH data biocViews: ExperimentData, Cancer, Breast Author: M. Neve et al. in Gray Lab at LBL Maintainer: VJ Carey MD5sum: 6f76f6752d34c7b26a125684aff3705f source.ver: src/contrib/Neve2006_0.1.15.tar.gz win.binary.ver: bin/windows/contrib/2.15/Neve2006_0.1.15.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Neve2006_0.1.15.tgz vignettes: vignettes/Neve2006/inst/doc/neve06notes.pdf vignetteTitles: Neve 2006: combined CGH and expression data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Neve2006/inst/doc/neve06notes.R Package: PREDAsampledata Version: 0.2.6 Depends: R (>= 2.9.0), methods, PREDA, Biobase, affy, annotate, gahgu133plus2.db, gahgu133plus2cdf Suggests: hgu133plus2.db, hgu133plus2cdf License: Artistic-2.0 Title: expression and copy number data on clear cell renal carcinoma samples Description: Sample data for PREDA package. (annotations objects synchronized with GeneAnnot custom CDFs version 2.2.0) biocViews: ExperimentData, Cancer Author: I. Cifola et al. in Cristina Battaglia Lab, University of Milan Maintainer: Francesco Ferrari MD5sum: b6b5996b015c4f553000d56335d9d897 source.ver: src/contrib/PREDAsampledata_0.2.6.tar.gz win.binary.ver: bin/windows/contrib/2.15/PREDAsampledata_0.2.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PREDAsampledata_0.2.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: PWMEnrich.Dmelanogaster.background Version: 1.0.1 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 Title: D. melanogaster background for PWMEnrich Description: PWMEnrich pre-compiled background objects for Drosophila melanogaster and JASPAR insects motifs. biocViews: AnnotationData, Drosophila_melanogaster Author: Robert Stojnic Maintainer: Robert Stojnic MD5sum: 3ee55d5037e7b45311882a1683d61de7 source.ver: src/contrib/PWMEnrich.Dmelanogaster.background_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/PWMEnrich.Dmelanogaster.background_1.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PWMEnrich.Dmelanogaster.background_1.0.1.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: ProData Version: 1.0.7 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL Title: SELDI-TOF data of Breast cancer samples Description: A data package of SELDI-TOF protein mass spectrometry data of 167 breast cancer and normal samples. biocViews: ExperimentData, Cancer, Breast Author: Xiaochun Li Maintainer: Xiaochun Li MD5sum: a664210a009d502222b339e13d31c952 source.ver: src/contrib/ProData_1.0.7.tar.gz win.binary.ver: bin/windows/contrib/2.15/ProData_1.0.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ProData_1.0.7.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RMassBankData Version: 0.99.1 Suggests: RMassBank License: Artistic-2.0 Title: Test dataset for RMassBank Description: Example spectra, a example compound list and an example annotation list for a narcotics dataset; required to test RMassBank. The package is described in the man page for RMassBankData. biocViews: ExperimentData, MassSpectrometryData Author: Michael Stravs Maintainer: Michael Stravs MD5sum: 5ae7b29e8bbe635f1314cdc3d600cb1f source.ver: src/contrib/RMassBankData_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/RMassBankData_0.99.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RMassBankData_0.99.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RNASeqDataSubset Version: 0.99.1 Depends: Rsamtools (>= 1.9.8) Imports: xtable License: LGPL Title: Subset of BAM files from the "TBX20" experiment Description: Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. A subset of the RNA-Seq data. biocViews: ExperimentData, RNAseqData Author: D. Bindreither Maintainer: D. Bindreither MD5sum: e41e8da740115c5e1c2d24487be93e60 source.ver: src/contrib/RNASeqDataSubset_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/RNASeqDataSubset_0.99.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RNASeqDataSubset_0.99.1.tgz vignettes: vignettes/RNASeqDataSubset/inst/doc/RNASeqDataSubset.pdf vignetteTitles: TBX20 RNA-Seq data subset hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RNASeqDataSubset/inst/doc/RNASeqDataSubset.R Package: RNAinteractMAPK Version: 1.0.10 Depends: R (>= 2.12.0), methods, fields, sparseLDA, RNAinteract Imports: grid, gdata, MASS, genefilter Suggests: qvalue, lattice License: Artistic-2.0 Title: Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi Description: This package includes all data used in the paper -Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi- by Horn, Sandmann, Fischer et al.., Nat. Methods, 2011. The package vignette shows the R code to reproduce all figures in the paper. biocViews: ExperimentData Author: Bernd Fischer Maintainer: Bernd Fischer MD5sum: 16c2b4f2a367dbde56ef1f027661f243 source.ver: src/contrib/RNAinteractMAPK_1.0.10.tar.gz win.binary.ver: bin/windows/contrib/2.15/RNAinteractMAPK_1.0.10.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RNAinteractMAPK_1.0.10.tgz vignettes: vignettes/RNAinteractMAPK/inst/doc/RNAinteractMAPK.pdf vignetteTitles: RNAinteractMAPK hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RNAinteractMAPK/inst/doc/RNAinteractMAPK.R Package: RnaSeqTutorial Version: 0.0.11 Depends: R (>= 2.15.0), methods, easyRNASeq Suggests: Rsamtools, ShortRead, BSgenome.Dmelanogaster.UCSC.dm3, GenomicRanges, biomaRt, genomeIntervals License: Artistic-2.0 Title: RNA-Seq Tutorial (EBI Cambridge UK, October 2011) Description: A selection of RNA-Seq data to get familiar with the related Bioconductor core packages and the easyRNASeq package. biocViews: ExperimentData, RNAseqData Author: Nicolas Delhomme, Ismael Padioleau Maintainer: Nicolas Delhomme MD5sum: d88099235d9c94370826963027559d18 source.ver: src/contrib/RnaSeqTutorial_0.0.11.tar.gz win.binary.ver: bin/windows/contrib/2.15/RnaSeqTutorial_0.0.11.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RnaSeqTutorial_0.0.11.tgz vignettes: vignettes/RnaSeqTutorial/inst/doc/RnaSeqTutorial.pdf vignetteTitles: RNA-Seq Tutorial hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RnaSeqTutorial/inst/doc/RnaSeqTutorial.R Package: SNAData Version: 1.8.5 Depends: R (>= 2.4.0), graph Suggests: Rgraphviz License: LGPL Title: Social Networks Analysis Data Examples Description: Data from Wasserman & Faust (1999) "Social Network Analysis" biocViews: ExperimentData Author: Denise Scholtens Maintainer: Denise Scholtens MD5sum: 1188a8db8b01948821844e9cddd4a21b source.ver: src/contrib/SNAData_1.8.5.tar.gz win.binary.ver: bin/windows/contrib/2.15/SNAData_1.8.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SNAData_1.8.5.tgz vignettes: vignettes/SNAData/inst/doc/SNAData.pdf vignetteTitles: SNAData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SNAData/inst/doc/SNAData.R Package: SpikeInSubset Version: 1.2.12 Depends: R (>= 2.4.0), Biobase (>= 2.5.5), affy (>= 1.23.4) License: LGPL Title: Part of Affymetrix's Spike-In Experiment Data Description: Includes probe-level and expression data for the HGU133 and HGU95 spike-in experiments biocViews: ExperimentData Author: Rafael Irizarry and Zhijin Wu Maintainer: Rafael A. Irizarry MD5sum: 6d39bb5107ac0f9046e0f463fb5a647b source.ver: src/contrib/SpikeInSubset_1.2.12.tar.gz win.binary.ver: bin/windows/contrib/2.15/SpikeInSubset_1.2.12.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SpikeInSubset_1.2.12.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SpikeIn Version: 1.4.9 Depends: R (>= 1.6), affy (>= 1.23.4) License: Artistic-2.0 Title: Affymetrix Spike-In Experiment Data Description: Contains the HGU133 and HGU95 spikein experiment data. biocViews: ExperimentData Author: Rafael Irizarry Maintainer: Rafael A. Irizarry MD5sum: 7011247ecea2f4202221f09c9b4d3a2f source.ver: src/contrib/SpikeIn_1.4.9.tar.gz win.binary.ver: bin/windows/contrib/2.15/SpikeIn_1.4.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SpikeIn_1.4.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: TCGAMethylation450k Version: 0.99.3 License: GPL-2 Title: The Cancer Genome Atlas Illumina 450k methylation example data Description: The Cancer Genome Atlas (TCGA) is applying genomics technologies to over 20 different types of cancer. This package contains a small set of 450k array data in idat format. Author: Sean Davis Maintainer: Sean Davis MD5sum: 4bca595ad2d3213a2f6f133a354f4b64 source.ver: src/contrib/TCGAMethylation450k_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/TCGAMethylation450k_0.99.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/TCGAMethylation450k_0.99.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: TargetSearchData Version: 1.0.8 Depends: TargetSearch License: GPL (>= 2) Title: Example GC-MS data for TargetSearch Package Description: This package provides example GC-MS data for TargetSearch Package. biocViews: ExperimentData Author: Alvaro Cuadros-Inostroza, Henning Redestig, Matt Hannah Maintainer: Alvaro Cuadros-Inostroza Henning Redestig , Matt Hannah MD5sum: b72c685ed0a292bdbc65921efd546fd8 source.ver: src/contrib/TargetSearchData_1.0.8.tar.gz win.binary.ver: bin/windows/contrib/2.15/TargetSearchData_1.0.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/TargetSearchData_1.0.8.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: XhybCasneuf Version: 1.0.10 Depends: R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf , RColorBrewer , methods, grid License: Artistic-2.0 Title: EBI/PSB cross-hybridisation study package Description: Cross-hybridisation study on the ATH1 Affymetrix GeneChip biocViews: ExperimentData Author: Tineke Casneuf Maintainer: Tineke Casneuf MD5sum: 36b59b14b29e1e803d575360a093be85 source.ver: src/contrib/XhybCasneuf_1.0.10.tar.gz win.binary.ver: bin/windows/contrib/2.15/XhybCasneuf_1.0.10.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/XhybCasneuf_1.0.10.tgz vignettes: vignettes/XhybCasneuf/inst/doc/Xhyb.pdf vignetteTitles: Xhyb hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/XhybCasneuf/inst/doc/Xhyb.R Package: affycompData Version: 1.1.4 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp License: GPL (>= 2) Title: affycomp data Description: Data needed by the affycomp package. biocViews: OneChannel, Microarray, Preprocessing Author: Rafael A. Irizarry and Zhijin Wu with contributions from Simon Cawley Maintainer: Harris Jaffee MD5sum: 58d6650d639793d9b8483cd3d115965d source.ver: src/contrib/affycompData_1.1.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/affycompData_1.1.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affycompData_1.1.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: affydata Version: 1.11.17 Depends: R (>= 2.4.0), affy (>= 1.23.4) Imports: methods Suggests: hgu95av2cdf, hgu133acdf License: GPL (>= 2) Title: Affymetrix Data for Demonstration Purpose Description: Example datasets of a slightly large size. They represent 'real world examples', unlike the artificial examples included in the package affy. biocViews: ExperimentData, OneChannel, Microarray Author: Laurent Gautier Maintainer: Harris Jaffee MD5sum: 05607d16af3f189340ef6c38c4ec3803 source.ver: src/contrib/affydata_1.11.17.tar.gz win.binary.ver: bin/windows/contrib/2.15/affydata_1.11.17.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affydata_1.11.17.tgz vignettes: vignettes/affydata/inst/doc/affydata.pdf vignetteTitles: affydata primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/affydata/inst/doc/affydata.R Package: beadarrayExampleData Version: 1.0.5 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>= 2.0.0) License: GPL-2 Title: Example data for the beadarray package Description: An small dataset that can be used to run examples from the beadarray vignette and examples biocViews: Microarray, OneChannel, QualityControl, Preprocessing, ExperimentData Author: Mark Dunning Maintainer: Mark Dunning MD5sum: 5b81e5f2dd150a65a05d3609b145bfb0 source.ver: src/contrib/beadarrayExampleData_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.15/beadarrayExampleData_1.0.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/beadarrayExampleData_1.0.5.tgz vignettes: vignettes/beadarrayExampleData/inst/doc/beadarrayExampleData.pdf vignetteTitles: beadarrayExampleData: example data for the beadarray package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: beta7 Version: 1.0.4 Depends: R (>= 2.4.0), marray License: LGPL Title: Rodriguez et al. (2004) Differential Gene Expression by Memory/Effector T Helper Cells Bearing the Gut-Homing Receptor Integrin alpha4 beta7. Description: Data from 6 gpr files aims to identify differential expressed genes between the beta 7+ and beta 7- memory T helper cells. biocViews: ExperimentData Author: Jean Yang Maintainer: Jean Yang MD5sum: 60bccc12b51611aea96e008f7ed48968 source.ver: src/contrib/beta7_1.0.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/beta7_1.0.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/beta7_1.0.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bladderbatch Version: 1.0.4 Depends: Biobase License: Artistic-2.0 Title: Bladder gene expression data illustrating batch effects Description: This package contains microarray gene expression data on 57 bladder samples from 5 batches. The data are used as an illustrative example for the sva package. biocViews: ExperimentData,Cancer,RNAExpressionData Author: Jeffrey T. Leek Maintainer: Jeffrey T. Leek MD5sum: ac11a60b1bbb2c0b5f13e78045cc855a source.ver: src/contrib/bladderbatch_1.0.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/bladderbatch_1.0.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/bladderbatch_1.0.4.tgz vignettes: vignettes/bladderbatch/inst/doc/bladderbatch.pdf vignetteTitles: bladderbatchTutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bladderbatch/inst/doc/bladderbatch.R Package: breastCancerMAINZ Version: 1.0.4 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 Title: Gene expression dataset published by Schmidt et al. [2008] (MAINZ). Description: Gene expression data from the breast cancer study published by Schmidt et al. in 2008, provided as an eSet. biocViews: ExperimentData, Cancer, GeneExpression, Microarray Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ MD5sum: b3537c3b7310e6ba32defbd04156bf38 source.ver: src/contrib/breastCancerMAINZ_1.0.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/breastCancerMAINZ_1.0.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/breastCancerMAINZ_1.0.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerNKI Version: 1.0.4 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 Title: Genexpression dataset published by van't Veer et al. [2002] and van de Vijver et al. [2002] (NKI). Description: Genexpression data from a breast cancer study published by van't Veer et al. in 2002 and van de Vijver et al. in 2002, provided as an eSet. biocViews: ExperimentData, Cancer, GeneExpression, Microarray Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ MD5sum: 06b7c476f70762247c52a3d784423161 source.ver: src/contrib/breastCancerNKI_1.0.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/breastCancerNKI_1.0.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/breastCancerNKI_1.0.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerTRANSBIG Version: 1.0.4 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 Title: Gene expression dataset published by Desmedt et al. [2007] (TRANSBIG). Description: Gene expression data from a breast cancer study published by Desmedt et al. in 2007, provided as an eSet. biocViews: ExperimentData, Cancer, GeneExpression, Microarray Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ MD5sum: dfcbb2d08313f001df93e397ebcc7ff7 source.ver: src/contrib/breastCancerTRANSBIG_1.0.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/breastCancerTRANSBIG_1.0.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/breastCancerTRANSBIG_1.0.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerUNT Version: 1.0.4 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 Title: Gene expression dataset published by Sotiriou et al. [2007] (UNT). Description: Gene expression data from a breast cancer study published by Sotiriou et al. in 2007, provided as an eSet. biocViews: ExperimentData, Cancer, GeneExpression, Microarray Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ MD5sum: 3a58f30e6f10a8556752672535939053 source.ver: src/contrib/breastCancerUNT_1.0.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/breastCancerUNT_1.0.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/breastCancerUNT_1.0.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerUPP Version: 1.0.4 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 Title: Gene expression dataset published by Miller et al. [2005] (UPP). Description: Gene expression data from a breast cancer study published by Miller et al. in 2005, provided as an eSet. biocViews: ExperimentData, Cancer, GeneExpression, Microarray Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ MD5sum: 251093b9162e7eb439035147c8ac8012 source.ver: src/contrib/breastCancerUPP_1.0.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/breastCancerUPP_1.0.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/breastCancerUPP_1.0.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerVDX Version: 1.0.4 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 Title: Gene expression datasets published by Wang et al. [2005] and Minn et al. [2007] (VDX). Description: Gene expression data from a breast cancer study published by Wang et al. in 2005 and Minn et al. in 2007, provided as an eSet. biocViews: ExperimentData, Cancer, GeneExpression, Microarray Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ MD5sum: d516e7d4339c7c75feb7a12e5e89248b source.ver: src/contrib/breastCancerVDX_1.0.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/breastCancerVDX_1.0.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/breastCancerVDX_1.0.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bronchialIL13 Version: 1.0.10 Depends: R(>= 2.10.0), affy (>= 1.23.4) License: GPL-2 Title: time course experiment involving il13 Description: derived from CNMC (pepr.cnmcresearch.org) http://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=95 Human Bronchial Cell line A549 biocViews: ExperimentData, TimeCourse Author: Vince Carey Maintainer: Vince Carey URL: http://www.biostat.harvard.edu/~carey MD5sum: d2573a0809c0421e1db0ed42503ced87 source.ver: src/contrib/bronchialIL13_1.0.10.tar.gz win.binary.ver: bin/windows/contrib/2.15/bronchialIL13_1.0.10.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/bronchialIL13_1.0.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bsseqData Version: 0.1.2 Depends: R (>= 2.15), bsseq License: Artistic-2.0 Title: Example whole genome bisulfite data for the bsseq package Description: Example whole genome bisulfite data for the bsseq package biocViews: DNAMethylation Author: Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen MD5sum: 37a07d9a89719bbf275271bbe4b8ab8b source.ver: src/contrib/bsseqData_0.1.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/bsseqData_0.1.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/bsseqData_0.1.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cancerdata Version: 1.1.1 Depends: R (>= 2.10.1), Biobase License: GPL (>= 2) Title: Development and validation of diagnostic tests from high-dimensional molecular data: Datasets Description: Dataset for the R package cancerclass biocViews: Cancer, Microarray, Classification, Visualization Author: Jan Budczies, Daniel Kosztyla Maintainer: Daniel Kosztyla MD5sum: 486b38adf47a10a1d62afef2b9e3c691 source.ver: src/contrib/cancerdata_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/cancerdata_1.1.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cancerdata_1.1.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ccTutorial Version: 1.0.22 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 Title: Data package for ChIP-chip tutorial Description: This is a data package that accompanies a ChIP-chip tutorial, which has been published in PLoS Computational Biology. The data and source code in this package allow the reader to completely reproduce the steps in the tutorial. biocViews: ExperimentData, ChIPchipData Author: Joern Toedling, Wolfgang Huber Maintainer: Joern Toedling MD5sum: e28eba83729e6651159966f2cc7853a1 source.ver: src/contrib/ccTutorial_1.0.22.tar.gz win.binary.ver: bin/windows/contrib/2.15/ccTutorial_1.0.22.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ccTutorial_1.0.22.tgz vignettes: vignettes/ccTutorial/inst/doc/ccTutorial.pdf, vignettes/ccTutorial/inst/doc/ccTutorialSupplement.pdf vignetteTitles: A tutorial on how to analyze ChIP-chip readouts using Bioconductor, Supplement to A tutorial on how to analyze ChIP-chip readouts using Bioconductor hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ccTutorial/inst/doc/ccTutorial.R, vignettes/ccTutorial/inst/doc/ccTutorialSupplement.R Package: ceu1kg Version: 0.0.31 Depends: R (>= 2.12.0), GGBase (>= 3.9.0), GGtools, Biobase Suggests: SNPlocs.Hsapiens.dbSNP.20101109 License: Artistic-2.0 Title: CEU (N=60) genotypes from 1000 genomes pilot phase I Description: CEU genotypes from 1000 genomes "low coverage" pilot phase I (approx 8 million SNP calls released July 2010); includes Wellcome trust GENEVAR expression for 43 indiv biocViews: Genetics, SNP Author: VJ Carey Maintainer: VJ Carey MD5sum: 3a4246d9fe04ce2a5a477bd544549f64 source.ver: src/contrib/ceu1kg_0.0.31.tar.gz win.binary.ver: bin/windows/contrib/2.15/ceu1kg_0.0.31.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ceu1kg_0.0.31.tgz vignettes: vignettes/ceu1kg/inst/doc/ceu1kg.pdf vignetteTitles: ceu1kg overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ceu1kg/inst/doc/ceu1kg.R Package: ceuhm3 Version: 0.0.14 Depends: R (>= 2.12.0), GGBase, Biobase Imports: GGtools License: Artistic-2.0 Title: ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort Description: ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort biocViews: Genetics, GeneExpression, GeneticVariability, SNP Author: VJ Carey Maintainer: VJ Carey MD5sum: acf64a41cdbe20369342dfacedb1e5c2 source.ver: src/contrib/ceuhm3_0.0.14.tar.gz win.binary.ver: bin/windows/contrib/2.15/ceuhm3_0.0.14.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ceuhm3_0.0.14.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cgdv17 Version: 0.0.18 Depends: R (>= 2.15), VariantAnnotation, org.Hs.eg.db, methods, GGtools, TxDb.Hsapiens.UCSC.hg19.knownGene, parallel Imports: Biobase, IRanges License: Artistic 2.0 Title: Complete Genomics Diversity Panel, chr17 on 46 individuals Description: Complete Genomics Diversity Panel, chr17 on 46 individuals biocViews: genetics Author: VJ Carey Maintainer: VJ Carey MD5sum: 0fe56f0c6403b7c9f82b45c80f55e8da source.ver: src/contrib/cgdv17_0.0.18.tar.gz win.binary.ver: bin/windows/contrib/2.15/cgdv17_0.0.18.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cgdv17_0.0.18.tgz vignettes: vignettes/cgdv17/inst/doc/cgdv.pdf vignetteTitles: cgdv17: extract from Complete Genomics diversity panel hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cgdv17/inst/doc/cgdv.R Package: charmData Version: 0.99.7 Depends: R(>= 2.11.0), charm, pd.charm.hg18.example License: LGPL (>= 2) Title: An example dataset for use with the charm package Description: An example dataset for use with the charm package biocViews: ExperimentData Author: Martin Aryee Maintainer: Martin Aryee MD5sum: aabc6ca1cb940b416c806616568b783d source.ver: src/contrib/charmData_0.99.7.tar.gz win.binary.ver: bin/windows/contrib/2.15/charmData_0.99.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/charmData_0.99.7.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cheung2010 Version: 0.0.26 Depends: R (>= 2.13.0), Biobase, GGtools, GenomicRanges, hgfocus.db Imports: AnnotationDbi Suggests: SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, Enhances: parallel License: Artistic 2.0 Title: resources for genetics of gene expression based on Cheung et al 2010 Description: Data resources related to the PLoS Biology paper Polymorphic Cis- and Trans-Regulation of Human Gene Expression, including small-footprint smlSet support for 147 hgfocus arrays and corresponding HapMap genotypes at 1.3 million SNP; 0.0.22+ includes cheung_eset... from Leek et al RECOUNT myrna output biocViews: GeneticVariability, RNAseqData Author: Vince Carey Maintainer: Vince Carey MD5sum: 12f4e4efcc6ae71cb37c5215017d48b8 source.ver: src/contrib/cheung2010_0.0.26.tar.gz win.binary.ver: bin/windows/contrib/2.15/cheung2010_0.0.26.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cheung2010_0.0.26.tgz vignettes: vignettes/cheung2010/inst/doc/arr2hap.pdf, vignettes/cheung2010/inst/doc/cheungTrans.pdf vignetteTitles: arr2hap.pdf, cheungTrans: checking trans eQTL with hgfocus arrays hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cheung2010/inst/doc/cheungTrans.R dependsOnMe: ggtut Package: cnvGSAdata Version: 0.99.3 Depends: R (>= 2.10), cnvGSA License: LGPL Title: Data used in the vignette of the cnvGSA package Description: This package contains the data used in the vignette of the cnvGSA package. biocViews: ExperimentData Author: Robert Ziman Maintainer: Robert Ziman MD5sum: d015d66de87dccddf508616c88785b09 source.ver: src/contrib/cnvGSAdata_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/cnvGSAdata_0.99.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cnvGSAdata_0.99.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: colonCA Version: 1.4.10 Depends: Biobase (>= 2.5.5) License: LGPL Title: exprSet for Alon et al. (1999) colon cancer data Description: exprSet for Alon et al. (1999) colon cancer data biocViews: ExperimentData, Cancer, Colon Author: Sylvia Merk Maintainer: W Sylvia Merk MD5sum: 1d1227d669a025825e4f12bde49e7a6c source.ver: src/contrib/colonCA_1.4.10.tar.gz win.binary.ver: bin/windows/contrib/2.15/colonCA_1.4.10.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/colonCA_1.4.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: davidTiling Version: 1.2.16 Depends: R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db License: LGPL Title: Data and analysis scripts for David, Huber et al. yeast tiling array paper Description: This package contains the data for the paper by L. David et al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix genechips, an ExpressionSet object with the raw feature data, a probe annotation data structure for the chip and the yeast genome annotation (GFF file) that was used. In addition, some custom-written analysis functions are provided, as well as R scripts in the scripts directory. biocViews: ExperimentData, Yeast Author: Wolfgang Huber , Joern Toedling Maintainer: Wolfgang Huber URL: http://www.ebi.ac.uk/huber MD5sum: cc768c586887bb06f6c7502559308ef4 source.ver: src/contrib/davidTiling_1.2.16.tar.gz win.binary.ver: bin/windows/contrib/2.15/davidTiling_1.2.16.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/davidTiling_1.2.16.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: dressCheck Version: 0.1.6 Depends: R (>= 2.10.1), methods, Biobase (>= 2.5.5) Suggests: survival, chron License: Artistic-2.0 Title: data and software for checking Dressman JCO 25(5) 2007 Description: data and software for checking Dressman JCO 25(5) 2007 biocViews: Statistics, ExperimentData Author: Vincent Carey Maintainer: Vincent Carey MD5sum: ead3df6340deefee6ad38b5149300169 source.ver: src/contrib/dressCheck_0.1.6.tar.gz win.binary.ver: bin/windows/contrib/2.15/dressCheck_0.1.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/dressCheck_0.1.6.tgz vignettes: vignettes/dressCheck/inst/doc/short.pdf vignetteTitles: short review of dressCheck contents hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/dressCheck/inst/doc/short.R Package: dsQTL Version: 0.0.22 Depends: R (>= 2.15.0), utils, GenomicRanges, Biobase, GGBase License: Artistic-2.0 Title: dsQTL, data excerpt from Degner et al. 2012 Nature letter Description: dsQTL, excerpt from Degner et al. 2012 Nature letter on DNA variants associated with DnaseI hypersensitivity biocViews: genetics, HighThroughputSequencingData, ExperimentData Author: VJ Carey Maintainer: VJ Carey MD5sum: 39a893353d96a9b4e0f1909bedd38489 source.ver: src/contrib/dsQTL_0.0.22.tar.gz win.binary.ver: bin/windows/contrib/2.15/dsQTL_0.0.22.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/dsQTL_0.0.22.tgz vignettes: vignettes/dsQTL/inst/doc/dsq.pdf vignetteTitles: dsQTL,, data excerpt from Degner et al. 2012 Nature letter hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/dsQTL/inst/doc/dsq.R Package: dyebiasexamples Version: 1.0.9 Depends: R (>= 1.4.1), marray, GEOquery Suggests: dyebias, convert, Biobase License: GPL-3 Title: Example data for the dyebias package, which implements the GASSCO method. Description: Data for the dyebias package, consisting of 4 self-self hybrizations of self-spotted yeast slides, as well as data from Array Express accession E-MTAB-32 biocViews: Microarray, TwoChannel, ExperimentData Author: Philip Lijnzaad and Thanasis Margaritis Maintainer: Philip Lijnzaad URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad MD5sum: 04b4a386c8340b40e753cf0c0b3dae58 source.ver: src/contrib/dyebiasexamples_1.0.9.tar.gz win.binary.ver: bin/windows/contrib/2.15/dyebiasexamples_1.0.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/dyebiasexamples_1.0.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Package: ecoliLeucine Version: 1.2.9 Depends: R (>= 1.9.0), affy (>= 1.23.4), ecolicdf License: GPL (>= 2) Title: Experimental data with Affymetrix E. coli chips Description: Experimental data with Affymetrix E. coli chips, as reported in She-pin Hung, Pierre Baldi, and G. Wesley Hatfield, J. Biol. Chem., Vol. 277, Issue 43, 40309-40323, October 25, 2002 biocViews: ExperimentData, EColiData Author: Laurent Gautier Maintainer: Laurent Gautier MD5sum: 9151d4bf456fcb939108510d1ac83357 source.ver: src/contrib/ecoliLeucine_1.2.9.tar.gz win.binary.ver: bin/windows/contrib/2.15/ecoliLeucine_1.2.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ecoliLeucine_1.2.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: encoDnaseI Version: 0.1.15 Depends: R (>= 2.15.0), methods, Biobase (>= 2.5.5), lattice, GGtools, GGBase Suggests: GGdata License: Artistic-2.0 Title: data provided by UCSC for Cd4 raw measures of DnaseI hypersensitivity Description: data provided by UCSC for Cd4 raw measures of DnaseI hypersensitivity biocViews: ExperimentData Author: VJ Carey Maintainer: VJ Carey MD5sum: 74d9ca996ff945f8727492792c2d601a source.ver: src/contrib/encoDnaseI_0.1.15.tar.gz win.binary.ver: bin/windows/contrib/2.15/encoDnaseI_0.1.15.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/encoDnaseI_0.1.15.tgz vignettes: vignettes/encoDnaseI/inst/doc/dnaseUse.pdf vignetteTitles: ENCODE/hg18 track demo: DNaseI hypersensitivity hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/encoDnaseI/inst/doc/dnaseUse.R Package: estrogen Version: 1.8.9 Depends: R (>= 1.9.0), affy (>= 1.4) Suggests: Biobase (>= 1.13.16), affy, vsn, hgu95av2.db, genefilter License: LGPL Title: 2x2 factorial design exercise for the Bioconductor short course Description: Data from 8 Affymetrix genechips, looking at a 2x2 factorial design (with 2 repeats per level) biocViews: ExperimentData Author: Wolfgang Huber, Robert Gentleman Maintainer: R. Gentleman MD5sum: 798a4315c61381be9f5498fe50a5a097 source.ver: src/contrib/estrogen_1.8.9.tar.gz win.binary.ver: bin/windows/contrib/2.15/estrogen_1.8.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/estrogen_1.8.9.tgz vignettes: vignettes/estrogen/inst/doc/estrogen.pdf vignetteTitles: estrogen hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/estrogen/inst/doc/estrogen.R Package: faahKO Version: 1.2.12 Depends: xcms License: LGPL 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 MD5sum: 0949ce9f156ddc03dde092aced5ab7b8 source.ver: src/contrib/faahKO_1.2.12.tar.gz win.binary.ver: bin/windows/contrib/2.15/faahKO_1.2.12.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/faahKO_1.2.12.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fabiaData Version: 1.0.1 Depends: R (>= 2.10.0), Biobase Imports: utils Suggests: fabia License: LGPL (>= 2.1) Title: Data sets for FABIA (Factor Analysis for Bicluster Acquisition) Description: Supplying gene expression data sets for the demos of the biclustering method "Factor Analysis for Bicluster Acquisition" (FABIA). The following three data sets are provided: A) breast cancer (van't Veer, Nature, 2002), B) multiple tissues (Su, PNAS, 2002), and C) diffuse large-B-cell lymphoma (Rosenwald, N Engl J Med, 2002). biocViews: Bioinformatics, Statistics, Microarray, DifferentialExpression, MultipleComparisons, Clustering, Visualization Author: Sepp Hochreiter Maintainer: Sepp Hochreiter URL: http://www.bioinf.jku.at/software/fabia/fabia.html MD5sum: 020ead8db413d8776d4249be98468089 source.ver: src/contrib/fabiaData_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/fabiaData_1.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/fabiaData_1.0.1.tgz vignettes: vignettes/fabiaData/inst/doc/fabiaData.pdf vignetteTitles: fabiaData: Manual for the R Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/fabiaData/inst/doc/fabiaData.R Package: facsDorit Version: 1.4.6 Depends: R (>= 1.9.1), prada (>= 1.0.5) License: GPL-2 Title: DKFZ FACS example data Description: FACS example data for cell-based assays. This data is used in the examples and vignettes of the package prada. biocViews: ExperimentData Author: Florian Hahne Maintainer: Florian Hahne URL: http://www.dkfz.de/mga MD5sum: 143415b3da3f9b24b442f7058470d4f5 source.ver: src/contrib/facsDorit_1.4.6.tar.gz win.binary.ver: bin/windows/contrib/2.15/facsDorit_1.4.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/facsDorit_1.4.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ffpeExampleData Version: 1.0.2 Depends: R (>= 2.10.0), lumi Suggests: genefilter, affy License: GPL (>2) Title: Illumina DASL example microarray data Description: A subset of GSE17565 (April et al. 2009) containing 32 FFPE samples of Burkitts Lymphoma and Breast Adenocarcinoma, with a dilution series in technical duplicate. biocViews: Microarray, GeneExpression Author: Levi Waldron Maintainer: Levi Waldron MD5sum: 11f4327c77abdb4cc036f3ee5d9d06ed source.ver: src/contrib/ffpeExampleData_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/ffpeExampleData_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ffpeExampleData_1.0.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fibroEset Version: 1.4.8 Depends: Biobase (>= 2.5.5) License: LGPL Title: exprSet for Karaman et al. (2003) fibroblasts data Description: exprSet for Karaman et al. (2003) human, bonobo and gorilla fibroblasts data biocViews: ExperimentData Author: Sylvia Merk Maintainer: Sylvia Merk MD5sum: 6dc1efaed7441246d44b14a3b44c39ed source.ver: src/contrib/fibroEset_1.4.8.tar.gz win.binary.ver: bin/windows/contrib/2.15/fibroEset_1.4.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/fibroEset_1.4.8.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: flowWorkspaceData Version: 0.99.8 License: GPL-2 Title: A data package containing a flowJo xml workspace and associated fcs files for testing the flowWorkspace package. Description: The necessary external data to run the flowWorkspace vignette is found in this package. biocViews: ExperimentData Author: Greg Finak Maintainer: Greg Finak MD5sum: cf8050ad9bfbecceb9869e4c9ba5cf45 source.ver: src/contrib/flowWorkspaceData_0.99.8.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowWorkspaceData_0.99.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowWorkspaceData_0.99.8.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: frmaExampleData Version: 0.99.4 Depends: R (>= 2.10.0) License: GPL (>= 2) Title: Frma Example Data Description: Data files used by the examples in frma and frmaTools packages biocViews: Microarray, AffymetrixChip, Homo_sapiens Author: Matthew N. McCall Maintainer: Matthew N. McCall MD5sum: 2610fc6cbac9cc57d35befaa01c57218 source.ver: src/contrib/frmaExampleData_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/frmaExampleData_0.99.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/frmaExampleData_0.99.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gageData Version: 1.1.5 Suggests: gage, genefilter License: GPL (>=2.0) Title: Auxillary data for gage package Description: This is a supportive data package for the software package, gage. However, the data supplied here are also useful for gene set or pathway analysis or microarray data analysis in general. In this package, we provide two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and BMP6 (originally published as an demo dataset for GAGE, also registered as GSE13604 in GEO). This package also includes commonly used gene set data based on KEGG pathways and GO terms for major research species, including human, mouse, rat and budding yeast. Mapping data between common gene IDs for budding yeast are also included. biocViews: ExperimentData, Cancer Author: Weijun Luo Maintainer: Weijun Luo MD5sum: 6f5b68abe7c67dc000f6ef63ab9db8ef source.ver: src/contrib/gageData_1.1.5.tar.gz win.binary.ver: bin/windows/contrib/2.15/gageData_1.1.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gageData_1.1.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gaschYHS Version: 1.0.10 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: Artistic-2.0 Title: ExpressionSet for response of yeast to heat shock and other environmental stresses Description: Data from PMID 11102521 biocViews: ExperimentData, Yeast Author: Audrey Gasch and colleagues Maintainer: Vince Carey URL: http://genome-www.stanford.edu/yeast_stress/data/rawdata/complete_dataset.txt MD5sum: 77e8c1fed946b6e5348e74fcd8beac5c source.ver: src/contrib/gaschYHS_1.0.10.tar.gz win.binary.ver: bin/windows/contrib/2.15/gaschYHS_1.0.10.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gaschYHS_1.0.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gatingMLData Version: 1.0.6 Depends: R (>= 1.9.0) Suggests: flowUtils License: GPL Title: Data and XML files for GatingML Test suite Description: Test data & XML files for Testing compliance with the GatingML 1.5 standards in package flowUtils. biocViews: ExperimentData Author: Nishant Gopalakrishnan Maintainer: Nishant Gopalakrishnan MD5sum: b4d3030bdff64ac4e2f10c20d7098c53 source.ver: src/contrib/gatingMLData_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/2.15/gatingMLData_1.0.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gatingMLData_1.0.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gcspikelite Version: 1.0.8 Depends: R (>= 2.5.0) License: LGPL 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 MD5sum: f05aed2968966680bd61f659a1cb1983 source.ver: src/contrib/gcspikelite_1.0.8.tar.gz win.binary.ver: bin/windows/contrib/2.15/gcspikelite_1.0.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gcspikelite_1.0.8.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: geneLenDataBase Version: 0.99.10 Depends: R (>= 2.11.0) Imports: utils, rtracklayer, GenomicFeatures (>= 1.3.15) License: LGPL (>= 2) Title: Lengths of mRNA transcripts for a number of genomes Description: Length of mRNA transcripts for a number of genomes and gene ID formats, largely based on UCSC table browser biocViews: HighThroughputSequencingData, ExperimentData, Transcription, RNAseq Author: Matthew Young Maintainer: Matthew Young , Nadia Davidson MD5sum: 27426f2b64ee116d57acdeb51bf584f9 source.ver: src/contrib/geneLenDataBase_0.99.10.tar.gz win.binary.ver: bin/windows/contrib/2.15/geneLenDataBase_0.99.10.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/geneLenDataBase_0.99.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ggtut Version: 0.0.43 Depends: R (>= 2.14.0), GGtools (>= 3.11.32), ff, GenomicRanges, snpStats, GGdata, GenomicFeatures, ChIPpeakAnno, Rsamtools(>= 1.5.35), cheung2010, SNPlocs.Hsapiens.dbSNP.20090506, hmyriB36 Suggests: rtracklayer, GenomicFeatures, ChIPpeakAnno, TxDb.Hsapiens.UCSC.hg18.knownGene License: Artistic-2.0 Title: support for tutorial on genetics of gene expression ISMB 2011 Description: various resources for genetics of expression with R/bioc Author: VJ Carey Maintainer: VJ Carey MD5sum: 517b906a283f23f2e7093f48ca06aa92 source.ver: src/contrib/ggtut_0.0.43.tar.gz win.binary.ver: bin/windows/contrib/2.15/ggtut_0.0.43.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ggtut_0.0.43.tgz vignettes: vignettes/ggtut/inst/doc/careyGGtutslides.pdf, vignettes/ggtut/inst/doc/extras.pdf, vignettes/ggtut/inst/doc/tut11.pdf, vignettes/ggtut/inst/doc/tut12.pdf vignetteTitles: careyGGtutslides.pdf, extras.pdf, tut11.pdf, tut12.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: golubEsets Version: 1.4.12 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: LGPL Title: exprSets for golub leukemia data Description: representation of public golub data with some covariate data of provenance unknown to the maintainer at present; now employs ExpressionSet format biocViews: ExperimentData, Cancer, Leukemia Author: Todd Golub Maintainer: Vince Carey MD5sum: 710f544de4147ff46561f9062e78a5d4 source.ver: src/contrib/golubEsets_1.4.12.tar.gz win.binary.ver: bin/windows/contrib/2.15/golubEsets_1.4.12.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/golubEsets_1.4.12.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap100khind Version: 1.4.1 Suggests: oligo License: GPL Title: Sample data - Hapmap 100K HIND Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap Author: Hapmap Consortium Maintainer: Benilton Carvalho MD5sum: 90bb0d3ee1f2608528b48ec2c9a03930 source.ver: src/contrib/hapmap100khind_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/hapmap100khind_1.4.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hapmap100khind_1.4.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap100kxba Version: 1.4.1 Suggests: oligo License: GPL Title: Sample data - Hapmap 100K XBA Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap Author: Hapmap Consortium Maintainer: Benilton Carvalho MD5sum: 0bbe24e0a59d8c4863f45a8b6018f760 source.ver: src/contrib/hapmap100kxba_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/hapmap100kxba_1.4.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hapmap100kxba_1.4.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap500knsp Version: 1.4.1 Suggests: oligo License: GPL Title: Sample data - Hapmap 500K NSP Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap Author: Hapmap Consortium Maintainer: Benilton Carvalho MD5sum: 940b1a5de5a889127c217f487b3ef8cd source.ver: src/contrib/hapmap500knsp_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/hapmap500knsp_1.4.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hapmap500knsp_1.4.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap500ksty Version: 1.4.1 Suggests: oligo License: GPL Title: Sample data - Hapmap 500K STY Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap Author: Hapmap Consortium Maintainer: Benilton Carvalho MD5sum: 15d8aeadc63a50c7ff74451732387908 source.ver: src/contrib/hapmap500ksty_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/hapmap500ksty_1.4.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hapmap500ksty_1.4.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmapsnp5 Version: 1.4.1 Suggests: oligo License: GPL Title: Sample data - Hapmap SNP 5.0 Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap Author: Hapmap Consortium Maintainer: Benilton Carvalho MD5sum: 00632863cad40f16c800d76b6ea48323 source.ver: src/contrib/hapmapsnp5_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/hapmapsnp5_1.4.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hapmapsnp5_1.4.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmapsnp6 Version: 1.4.1 Depends: R (>= 2.15) Suggests: oligo, oligoClasses License: GPL Title: Sample data - Hapmap SNP 6.0 Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap Author: Hapmap Consortium Maintainer: Benilton Carvalho MD5sum: ed23f0e2c0638bda4f7cbc507b6c0849 source.ver: src/contrib/hapmapsnp6_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/hapmapsnp6_1.4.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hapmapsnp6_1.4.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: harbChIP Version: 1.0.9 Depends: R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5), Biostrings Imports: methods, stats License: Artistic-2.0 Title: Experimental Data Package: harbChIP Description: data from a yeast ChIP-chip experiment biocViews: ExperimentData, Yeast, ChIPchip Author: VJ Carey Maintainer: VJ Carey MD5sum: 3dd761e532920f7c734a3bb92d55626b source.ver: src/contrib/harbChIP_1.0.9.tar.gz win.binary.ver: bin/windows/contrib/2.15/harbChIP_1.0.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/harbChIP_1.0.9.tgz vignettes: vignettes/harbChIP/inst/doc/yeastUpstream.pdf vignetteTitles: upstream sequence management for yeast hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/harbChIP/inst/doc/yeastUpstream.R Package: hgu133abarcodevecs Version: 1.0.5 Depends: R (>= 2.10.0) License: GPL (>= 2) Title: hgu133a data for barcode Description: Data used by the barcode package for microarrays of type hgu133a. biocViews: AnnotationData, AffymetrixChip, hgu133a, Homo_sapiens Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall MD5sum: d6317e163a823f743e92baeed3d383c0 source.ver: src/contrib/hgu133abarcodevecs_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.15/hgu133abarcodevecs_1.0.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hgu133abarcodevecs_1.0.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu133afrmavecs Version: 1.1.10 Depends: R (>= 2.10.0) License: GPL (>= 2) Title: Vectors used by frma for microarrays of type hgu133a Description: This package was created by frmaTools version 1.9.1. biocViews: AnnotationData, AffymetrixChip, hgu133a, Homo_sapiens Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall MD5sum: 9408a62f173a117a2c88246a79d76c9e source.ver: src/contrib/hgu133afrmavecs_1.1.10.tar.gz win.binary.ver: bin/windows/contrib/2.15/hgu133afrmavecs_1.1.10.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hgu133afrmavecs_1.1.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu133plus2barcodevecs Version: 1.0.5 Depends: R (>= 2.10.0) License: GPL (>= 2) Title: hgu133plus2 data for barcode Description: Data used by the barcode package for microarrays of type hgu133plus2. biocViews: AnnotationData, AffymetrixChip, hgu133plus2, Homo_sapiens Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall MD5sum: a53aa05904a0550fb67d2789722c4c67 source.ver: src/contrib/hgu133plus2barcodevecs_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.15/hgu133plus2barcodevecs_1.0.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hgu133plus2barcodevecs_1.0.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu133plus2frmavecs Version: 1.1.10 Depends: R (>= 2.10.0) License: GPL (>= 2) Title: Vectors used by frma for microarrays of type hgu133plus2 Description: This package was created by frmaTools version 1.9.1. biocViews: AnnotationData, AffymetrixChip, hgu133plus2, Homo_sapiens Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall MD5sum: 36d778aa26421b55eca6dc44e2a06cd3 source.ver: src/contrib/hgu133plus2frmavecs_1.1.10.tar.gz win.binary.ver: bin/windows/contrib/2.15/hgu133plus2frmavecs_1.1.10.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hgu133plus2frmavecs_1.1.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu2beta7 Version: 1.2.7 Depends: R (>= 2.0.0) License: Artistic-2.0 Title: A data package containing annotation data for hgu2beta7 Description: Annotation data file for hgu2beta7 assembled using data from public data repositories biocViews: AnnotationData Author: Chenwei Lin Maintainer: Bioconductor Package Maintainer MD5sum: e9d5700fbb5df7e74308a75a8296f321 source.ver: src/contrib/hgu2beta7_1.2.7.tar.gz win.binary.ver: bin/windows/contrib/2.15/hgu2beta7_1.2.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hgu2beta7_1.2.7.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hmyriB36 Version: 0.99.16 Depends: R (>= 2.13.0), methods, Biobase (>= 2.5.5), GGBase Suggests: GGtools, illuminaHumanv1.db License: Artistic-2.0 Title: YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes Description: YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes biocViews: Statistics, ExperimentData Author: Vincent Carey Maintainer: Vincent Carey MD5sum: 7ff01207211dcb929ee55181d9e8e381 source.ver: src/contrib/hmyriB36_0.99.16.tar.gz win.binary.ver: bin/windows/contrib/2.15/hmyriB36_0.99.16.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hmyriB36_0.99.16.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ggtut suggestsMe: ind1KG Package: humanStemCell Version: 0.2.7 Depends: Biobase (>= 2.5.5), hgu133plus2.db License: Artistic-2.0 Title: Human Stem Cells time course experiment Description: Affymetrix time course experiment on human stem cells (two time points: undifferentiated and differentiated). biocViews: ExperimentData, StemCells Author: R. Gentleman, N. Le Meur, M. Tewari Maintainer: R. Gentleman MD5sum: 4feccf2c8ea4e8ccc9466c4f5e0ed19a source.ver: src/contrib/humanStemCell_0.2.7.tar.gz win.binary.ver: bin/windows/contrib/2.15/humanStemCell_0.2.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/humanStemCell_0.2.7.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ind1KG Version: 0.1.14 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 Title: Data from 1000 Genomes, NA19240 (female) chr6 excerpt Description: Elements of samtools/bioc workflow for dealing with personal sequence focusing on identification and interpretation of rare variants biocViews: Genetics, HighThroughputSequencing Author: VJ Carey Maintainer: VJ Carey MD5sum: 4163c74fba5f9cff677827416d3f27e3 source.ver: src/contrib/ind1KG_0.1.14.tar.gz win.binary.ver: bin/windows/contrib/2.15/ind1KG_0.1.14.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ind1KG_0.1.14.tgz vignettes: vignettes/ind1KG/inst/doc/ind1KG.pdf, vignettes/ind1KG/inst/doc/nov09rv.pdf vignetteTitles: ind1KG -- 1000 genomes data demo, Notes for eSet developers hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ind1KG/inst/doc/ind1KG.R, vignettes/ind1KG/inst/doc/nov09rv.R Package: iontreeData Version: 0.99.7 License: GPL-2 Title: Data provided to show the usage of functions in iontree package Description: Raw MS2, MS3 scans from direct infusion mass spectrometry (DIMS) and a demo ion tree database 'mzDB' derived from the DIMS data are included. The demo database is used to show the functionalities provided by the 'iontree' package, not for the purpose of compound identification by any means. biocViews: ExperimentData, Metabolomics Author: Mingshu Cao Maintainer: Mingshu Cao MD5sum: aa0dffc3ed90fa0d7c6724664a8e0cc3 source.ver: src/contrib/iontreeData_0.99.7.tar.gz win.binary.ver: bin/windows/contrib/2.15/iontreeData_0.99.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/iontreeData_0.99.7.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: kidpack Version: 1.5.11 Depends: R (>= 2.6.0), Biobase (>= 2.5.5) License: GPL-2 Title: DKFZ kidney package Description: kidney microarray data biocViews: ExperimentData, Cancer, Kidney Author: Wolfgang Huber Maintainer: Wolfgang Huber URL: http://www.dkfz.de/mga MD5sum: d22c4a447cd6cc7593b82cc7ee968353 source.ver: src/contrib/kidpack_1.5.11.tar.gz win.binary.ver: bin/windows/contrib/2.15/kidpack_1.5.11.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/kidpack_1.5.11.tgz vignettes: vignettes/kidpack/inst/doc/kidpack.pdf vignetteTitles: kidpack - overview over the DKFZ kidney data package hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/kidpack/inst/doc/kidpack.R Package: leeBamViews Version: 0.99.20 Depends: R (>= 2.15.0), Biobase, Rsamtools (>= 0.1.50), BSgenome Imports: GenomicRanges, methods Suggests: GenomeGraphs, biomaRt, org.Sc.sgd.db, edgeR Enhances: multicore License: Artistic 2.0 Title: leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009 Description: data from PMID 19096707; prototype for managing multiple NGS samples biocViews: HighThroughputSequencing, RNAseq, CellBiology, Genetics, DifferentialExpression, RNAseqData Author: VJ Carey Maintainer: VJ Carey MD5sum: 95f6ec79289dbce2c9c8158d6bbe4022 source.ver: src/contrib/leeBamViews_0.99.20.tar.gz win.binary.ver: bin/windows/contrib/2.15/leeBamViews_0.99.20.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/leeBamViews_0.99.20.tgz vignettes: vignettes/leeBamViews/inst/doc/leeViews.pdf vignetteTitles: managing multiple NGS samples with bamViews hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/leeBamViews/inst/doc/leeViews.R Package: lumiBarnes Version: 1.3.9 Depends: R (>= 2.0), Biobase (>= 2.5.5), lumi (>= 1.1.0) License: LGPL Title: Barnes Benchmark Illumina Tissues Titration Data Description: The Barnes benchmark dataset can be used to evaluate the algorithms for Illumina microarrays. It measured a titration series of two human tissues, blood and placenta, and includes six samples with the titration ratio of blood and placenta as 100:0, 95:5, 75:25, 50:50, 25:75 and 0:100. The samples were hybridized on HumanRef-8 BeadChip (Illumina, Inc) in duplicate. The data is loaded as an LumiBatch Object (see documents in the lumi package). biocViews: ExperimentData, OneChannel, RNAExpressionData, NormalTissue Author: Pan Du Maintainer: Pan Du MD5sum: 2833c447dded2ec91d6ac959ed37cc6e source.ver: src/contrib/lumiBarnes_1.3.9.tar.gz win.binary.ver: bin/windows/contrib/2.15/lumiBarnes_1.3.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/lumiBarnes_1.3.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: lungExpression Version: 0.0.14 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL (>= 2) Title: ExpressionSets for Parmigiani et al., 2004 Clinical Cancer Research paper Description: Data from three large lung cancer studies provided as ExpressionSets biocViews: ExperimentData, Cancer, Lung Author: Robert Scharpf , Simens Zhong , Giovanni Parmigiani Maintainer: Robert Scharpf MD5sum: 3509fe2c15027a69ad84f5e4428f54fb source.ver: src/contrib/lungExpression_0.0.14.tar.gz win.binary.ver: bin/windows/contrib/2.15/lungExpression_0.0.14.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/lungExpression_0.0.14.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: maqcExpression4plex Version: 1.6.1 Suggests: oligo, pdInfoBuilder License: GPL Title: Sample Expression Data - MAQC / HG18 - NimbleGen Description: Data from human (HG18) 4plex NimbleGen array. It has 24k genes with 3 60mer probes per gene. biocViews: ExperimentData Author: NimbleGen Systems Maintainer: Benilton Carvalho MD5sum: 031eaf937ae6c1dfff490e8460f7f985 source.ver: src/contrib/maqcExpression4plex_1.6.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/maqcExpression4plex_1.6.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/maqcExpression4plex_1.6.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: miRNATarget Version: 0.99.2 Depends: R (>= 2.10), Biobase License: GPL Title: gene target tabale of miRNA for human/mouse used for MiRaGE package Description: gene target tabale of miRNA for human/mouse used for MiRaGE package biocViews: ExperimentData, Author: Y-h. Taguchi Maintainer: Y-h. Taguchi MD5sum: a361580afde690924326033289f6ae7a source.ver: src/contrib/miRNATarget_0.99.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/miRNATarget_0.99.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/miRNATarget_0.99.2.tgz vignettes: vignettes/miRNATarget/inst/doc/miRNATarget.pdf vignetteTitles: miRNATargetTutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/miRNATarget/inst/doc/miRNATarget.R Package: minfiData Version: 0.3.1 Depends: R (>= 2.13.0), minfi, IlluminaHumanMethylation450kmanifest License: Artistic-2.0 Title: Example data for the Illumina Methylation 450k array Description: Data from 6 samples across 2 groups from 450k methylation arrays biocViews: DNAMethylation Author: Kasper Daniel Hansen, Martin Aryee, Winston Timp Maintainer: Kasper Daniel Hansen MD5sum: e89877821218a03f1e0bfc191681d44d source.ver: src/contrib/minfiData_0.3.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/minfiData_0.3.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/minfiData_0.3.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mosaicsExample Version: 0.99.7 Depends: R (>= 2.11.1) License: GPL (>= 2) Title: Example data for the mosaics package, which implements MOSAiCS, a statistical framework to analyze one-sample or two-sample ChIP-seq data Description: Data for the mosaics package, consisting of chromosome 21 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding, with mappability, GC content, and sequence ambiguity scores of human genome HG18. biocViews: ExperimentData, ChIPseqData, Homo_sapiens Author: Dongjun Chung, Pei Fen Kuan, Sunduz Keles Maintainer: Dongjun Chung URL: http://groups.google.com/group/mosaics_user_group MD5sum: 226c39c6fa72b70120445f14098dc271 source.ver: src/contrib/mosaicsExample_0.99.7.tar.gz win.binary.ver: bin/windows/contrib/2.15/mosaicsExample_0.99.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/mosaicsExample_0.99.7.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mouse4302barcodevecs Version: 1.0.5 Depends: R (>= 2.10.0) License: GPL (>= 2) Title: mouse4302 data for barcode Description: Data used by the barcode package for microarrays of type mouse4302. biocViews: AnnotationData, AffymetrixChip, mouse4302, Mus_musculus Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall MD5sum: 7efcd3d6812334fa2c351cb06ee8abb5 source.ver: src/contrib/mouse4302barcodevecs_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.15/mouse4302barcodevecs_1.0.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/mouse4302barcodevecs_1.0.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mouse4302frmavecs Version: 1.1.10 Depends: R (>= 2.10.0) License: GPL (>= 2) Title: Vectors used by frma for microarrays of type mouse4302 Description: This package was created by frmaTools version 1.9.1. biocViews: AnnotationData, AffymetrixChip, mouse4302, Mus_musculus Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall MD5sum: 31f0f4306f18580d74596be16c1bedc0 source.ver: src/contrib/mouse4302frmavecs_1.1.10.tar.gz win.binary.ver: bin/windows/contrib/2.15/mouse4302frmavecs_1.1.10.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/mouse4302frmavecs_1.1.10.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: msdata Version: 0.1.12 Suggests: xcms License: GPL (>= 2) Title: Various Mass Spectrometry raw data example files Description: Ion Trap positive ionization mode data in mzData file format. Subset from 500-850 m/z and 1190-1310 seconds, incl. MS2 and MS3, intensity threshold 100.000. Extracts from FTICR Apex III, m/z 400-450. Subset of UPLC - Bruker micrOTOFq data, both mzData and mzML. biocViews: ExperimentData, MassSpectrometryData Author: Steffen Neumann Maintainer: Steffen Neumann MD5sum: 4396c1ce3cf1cc4acaff2efcc8bf134e source.ver: src/contrib/msdata_0.1.12.tar.gz win.binary.ver: bin/windows/contrib/2.15/msdata_0.1.12.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/msdata_0.1.12.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mvoutData Version: 0.99.9 Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4), lumi License: Artistic-2.0 Title: affy and illumina raw data for assessing outlier detector performance Description: affy and illumina raw data for assessing outlier detector performance biocViews: ExperimentData Author: VJ Carey Maintainer: VJ Carey MD5sum: 61a59cd7bd16f62d54ed197499d6b996 source.ver: src/contrib/mvoutData_0.99.9.tar.gz win.binary.ver: bin/windows/contrib/2.15/mvoutData_0.99.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/mvoutData_0.99.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pasillaBamSubset Version: 0.0.6 Suggests: pasilla License: LGPL Title: Subset of BAM files from "Pasilla" experiment Description: Subset of BAM files untreated1.bam (single-end reads) and untreated3.bam (paired-end reads) from "Pasilla" experiment (Pasilla knock-down by Brooks et al., Genome Research 2011). See the vignette in the pasilla data package for how BAM files untreated1.bam and untreated3.bam were obtained from the RNA-Seq read sequence data that is provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. Also contains the DNA sequence for fly chromosome 4 to which the reads can be mapped. biocViews: ExperimentData, RNAseqData Author: H. Pages Maintainer: H. Pages MD5sum: 8296c5e83acc2dabb8c13c3fd0c7f8dc source.ver: src/contrib/pasillaBamSubset_0.0.6.tar.gz win.binary.ver: bin/windows/contrib/2.15/pasillaBamSubset_0.0.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pasillaBamSubset_0.0.6.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pasilla Version: 0.2.15 Depends: DEXSeq, DESeq Suggests: locfit, edgeR, xtable License: LGPL Title: Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011. Description: This package provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in the article "Conservation of an RNA regulatory map between Drosophila and mammals" by Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR, Genome Res. 2011 Feb;21(2):193-202, Epub 2010 Oct 4, PMID: 20921232. The experiment studied the effect of RNAi knockdown of Pasilla, the Drosophila melanogaster ortholog of mammalian NOVA1 and NOVA2, on the transcriptome. The package vignette describes how the data provided here were derived from the RNA-Seq read sequence data that is provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181 biocViews: ExperimentData, RNAseqData Author: Wolfgang Huber, Alejandro Reyes Maintainer: Alejandro Reyes MD5sum: e15e7e01bfba489f4eed3a8f9b81e5b0 source.ver: src/contrib/pasilla_0.2.15.tar.gz win.binary.ver: bin/windows/contrib/2.15/pasilla_0.2.15.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pasilla_0.2.15.tgz vignettes: vignettes/pasilla/inst/doc/create_objects.pdf vignetteTitles: Data preprocessing and creation of the data objects pasillaGenes and pasillaExons hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pasilla/inst/doc/create_objects.R suggestsMe: pasillaBamSubset Package: pcaGoPromoter.Hs.hg19 Version: 0.99.3 License: GPL (>= 2) Title: pcaGoPromoter.Hs.hg19 is a data package used by pcaGoPromoter Description: Contains the data for transciption factors analysis of organism Homo Sapiens with package pcaGoPromoter biocViews: AnnotationData, Homo_sapiens Author: Morten Hansen, Maintainer: Morten Hansen, MD5sum: c272b922c542f988295bf26c79c26764 source.ver: src/contrib/pcaGoPromoter.Hs.hg19_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/pcaGoPromoter.Hs.hg19_0.99.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pcaGoPromoter.Hs.hg19_0.99.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Mm.mm9 Version: 0.99.3 License: GPL (>= 2) Title: pcaGoPromoter.Mm.mm9 is a data package used by pcaGoPromoter Description: Contains the data for transciption factors analysis of organism Mus musculus with package pcaGoPromoter biocViews: AnnotationData, Mus_musculus Author: Morten Hansen, Maintainer: Morten Hansen, MD5sum: e636e88d6940809ed0a96681967b5343 source.ver: src/contrib/pcaGoPromoter.Mm.mm9_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/pcaGoPromoter.Mm.mm9_0.99.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pcaGoPromoter.Mm.mm9_0.99.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Rn.rn4 Version: 0.99.3 License: GPL (>= 2) Title: pcaGoPromoter.Rn.rn4 is a data package used by pcaGoPromoter Description: Contains the data for transciption factors analysis of organism Rattus norvegicus with package pcaGoPromoter biocViews: AnnotationData, Rattus_norvegicus Author: Morten Hansen, Maintainer: Morten Hansen, MD5sum: deeebabcd4e8c89b83bec661f3d761af source.ver: src/contrib/pcaGoPromoter.Rn.rn4_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/pcaGoPromoter.Rn.rn4_0.99.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pcaGoPromoter.Rn.rn4_0.99.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pd.atdschip.tiling Version: 0.0.4 Depends: R (>= 2.14.0), methods, RSQLite (>= 0.10.0), oligoClasses (>= 1.15.58), oligo (>= 1.17.3), DBI Imports: Biostrings (>= 2.21.11), IRanges (>= 1.11.31) License: Artistic-2.0 Title: Platform Design Info for Affymetrix Atdschip_tiling Description: Platform Design Info for Affymetrix Atdschip_tiling biocViews: AnnotationData Author: Kristof De Beuf Maintainer: Kristof De Beuf MD5sum: 983b90f0eb34efb9a5a0f079cf99c7c7 source.ver: src/contrib/pd.atdschip.tiling_0.0.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/pd.atdschip.tiling_0.0.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pd.atdschip.tiling_0.0.4.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ppiData Version: 0.1.18 Depends: graph Suggests: org.Sc.sgd.db, ppiStats License: Artistic-2.0 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: Tony Chiang MD5sum: 5950fc41e0a8e2735a11fbc2b6c6517c source.ver: src/contrib/ppiData_0.1.18.tar.gz win.binary.ver: bin/windows/contrib/2.15/ppiData_0.1.18.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ppiData_0.1.18.tgz vignettes: vignettes/ppiData/inst/doc/ hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pumadata Version: 1.99.4 Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), puma License: LGPL Title: Various data sets for use with the puma package Description: This is a simple data package including various data sets derived from the estrogen data for use with the puma (Propagating Uncertainty in Microarray Analysis) package. biocViews: ExperimentData Author: Richard Pearson Maintainer: Richard Pearson URL: http://umber.sbs.man.ac.uk/resources/puma MD5sum: 14910e60fb36b75b99206ed3f9d482d1 source.ver: src/contrib/pumadata_1.99.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/pumadata_1.99.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pumadata_1.99.4.tgz vignettes: vignettes/pumadata/inst/doc/pumadata.pdf vignetteTitles: pumadata User Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pumadata/inst/doc/pumadata.R Package: rheumaticConditionWOLLBOLD Version: 1.0.2 Depends: R (>= 2.10.0) Suggests: genefilter, Biobase, hgu133plus2.db License: Artistic-2.0 Title: Normalized gene expression dataset published by Wollbold et al. [2009] (WOLLBOLD). Description: Normalized gene expression data from rheumatic diseases from study published by Wollbold et al. in 2009, provided as an eSet. biocViews: ExperimentData, Rheumatic diseases,Arthritis, Osteoarthritis, GeneExpression, Microarray Author: Alejandro Quiroz-Zarate, John Quackenbush Maintainer: Alejandro Quiroz-Zarate URL: http://compbio.dfci.harvard.edu/ MD5sum: ff5f6575eb08ba7e51b69b780f8bd786 source.ver: src/contrib/rheumaticConditionWOLLBOLD_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/rheumaticConditionWOLLBOLD_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rheumaticConditionWOLLBOLD_1.0.2.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: serumStimulation Version: 0.99.3 Depends: R (>= 2.10) License: GPL (>= 2) Title: serumStimulation is a data package which is used by examples in package pcaGoPromoter Description: Contains 13 micro array data results from a serum stimulation experiment biocViews: ExperimentData Author: Morten Hansen, Maintainer: Morten Hansen, MD5sum: 64383a692c1c87ab53e67d1bff192dba source.ver: src/contrib/serumStimulation_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/serumStimulation_0.99.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/serumStimulation_0.99.3.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: simpIntLists Version: 0.99.3 License: GPL (>= 2) Title: The package contains BioGRID interactions for various organisms in a simple format Description: The package contains BioGRID interactions for arabidopsis(thale cress), c.elegans, fruit fly, human, mouse, yeast( budding yeast ) and S.pombe (fission yeast) . Entrez ids, official names and unique ids can be used to find proteins. The format of interactions are lists. For each gene/protein, there is an entry in the list with "name" containing name of the gene/protein and "interactors" containing the list of genes/proteins interacting with it. biocViews: ExperimentData Author: Kircicegi Korkmaz, Volkan Atalay, Rengul Cetin-Atalay Maintainer: Kircicegi Korkmaz MD5sum: 61a217cd004afd4d9f469dd275e0bd56 source.ver: src/contrib/simpIntLists_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/simpIntLists_0.99.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/simpIntLists_0.99.3.tgz vignettes: vignettes/simpIntLists/inst/doc/simpIntLists.pdf vignetteTitles: simpIntLists hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/simpIntLists/inst/doc/simpIntLists.R Package: stemHypoxia Version: 0.99.2 Depends: R (>= 2.14.1) License: GPL (>=2) Title: Differentiation of Human Embryonic Stem Cells under Hypoxia gene expression dataset by Prado-Lopez et al. (2010) Description: Expression profiling using microarray technology to prove if 'Hypoxia Promotes Efficient Differentiation of Human Embryonic Stem Cells to Functional Endothelium' by Prado-Lopez et al. (2010) Stem Cells 28:407-418. Full data available at Gene Expression Omnibus series GSE37761. biocViews: ExperimentData, Cancer, GeneExpression, Microarray Author: Cristobal Fresno and Elmer A. Fernandez Maintainer: Cristobal Fresno URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37761, http://onlinelibrary.wiley.com/doi/10.1002/stem.295/abstract MD5sum: 4f7ac05ef4de5b50a40a0eedb3ee699c source.ver: src/contrib/stemHypoxia_0.99.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/stemHypoxia_0.99.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/stemHypoxia_0.99.2.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: stjudem Version: 1.2.8 Depends: R (>= 2.10), utils License: LGPL (>= 2) Title: Microarray Data from Yeoh et al. in MACAT format Description: This is a microarray data set on acute lymphoblastic leukemia, published in 2002 (Yeoh et al.Cancer Cell 2002). The experiments were conducted in the St.Jude Children's Research Hospital, Memphis, Tenessee, USA. The raw data was preprocessed by variance stabilizing normalization (Huber et al.) on probe and subsequent summarization of probe expression values into probe set expression values using median polish. biocViews: ExperimentData Author: Benjamin Georgi, Matthias Heinig, Sebastian Schmeier, Joern Toedling Maintainer: Joern Toedling MD5sum: e8e9f98e898724957958894ec39ee220 source.ver: src/contrib/stjudem_1.2.8.tar.gz win.binary.ver: bin/windows/contrib/2.15/stjudem_1.2.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/stjudem_1.2.8.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: synapterdata Version: 0.99.3 Depends: R (>= 2.10), synapter (>= 0.99.6) License: GPL-2 Title: Data accompanying the synapter package Description: Data independant acquisition of UPS1 protein mix in an E. coli background obtained on a Waters Synapt G2 instrument. biocViews: ExperimentData, MassSpectrometry, MassSpectrometryData, Proteomics Author: Laurent Gatto and Pavel V. Shliaha Maintainer: Laurent Gatto MD5sum: ffd5e483ef866b7b1520fbfbc9a7f09a source.ver: src/contrib/synapterdata_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/synapterdata_0.99.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/synapterdata_0.99.3.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: tinesath1cdf Version: 1.0.8 License: Artistic-2.0 Title: tinesath1cdf Description: A package containing an environment represeting the newcdf/tinesATH1.cdf.cdf file. biocViews: AnnotationData, AffymetrixChip, ath1121501, Arabidopsis_thaliana Author: Tine Casneuf Maintainer: Tine Casneuf MD5sum: e4046e640954166a6126ef2ae9c0a347 source.ver: src/contrib/tinesath1cdf_1.0.8.tar.gz win.binary.ver: bin/windows/contrib/2.15/tinesath1cdf_1.0.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/tinesath1cdf_1.0.8.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: XhybCasneuf Package: tinesath1probe Version: 1.0.8 Depends: R (>= 1.6), AnnotationDbi (>= 1.11.9) License: LGPL Title: Probe sequence data for microarrays of type tinesath1 Description: This package was automatically created by package matchprobes version 1.4.0. The probe sequence data was obtained from http://www.affymetrix.com. biocViews: AnnotationData, AffymetrixChip, tinesath1, Arabidopsis_thaliana Author: The Bioconductor Project www.bioconductor.org Maintainer: Tine Casneuf MD5sum: f891c02f8996f19880f133c0f792ac8c source.ver: src/contrib/tinesath1probe_1.0.8.tar.gz win.binary.ver: bin/windows/contrib/2.15/tinesath1probe_1.0.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/tinesath1probe_1.0.8.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: tweeDEseqCountData Version: 1.0.8 Depends: Biobase, R (>= 2.10) License: GPL (>=2) Title: RNA-seq count data employed in the vignette of the tweeDEseq package Description: RNA-seq count data from Pickrell et al. (2010) employed to illustrate the use of the Poisson-Tweedie family of distributions with the tweeDEseq package. biocViews: HighThroughputSequencingData, RNAseqData Author: Juan R Gonzalez and Mikel Esnaola (with contributions from Robert Castelo ) Maintainer: Juan R Gonzalez URL: http://www.creal.cat/jrgonzalez/software.htm MD5sum: e96ac3facd8bbb0ae025b3222df015d5 source.ver: src/contrib/tweeDEseqCountData_1.0.8.tar.gz win.binary.ver: bin/windows/contrib/2.15/tweeDEseqCountData_1.0.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/tweeDEseqCountData_1.0.8.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: waveTilingData Version: 0.99.1 Depends: R (>= 2.14.0) License: GPL (>= 2) Title: waveTiling Example Data Description: Experiment and Annotation Data files used by the examples / vignette in the waveTiling package biocViews: Microarray, AnnotationData, ExperimentData Author: Kristof De Beuf Maintainer: Kristof De Beuf MD5sum: 7ca49b9b0866fb9f055daba0b5ab9782 source.ver: src/contrib/waveTilingData_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/waveTilingData_0.99.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/waveTilingData_0.99.1.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastCC Version: 1.2.17 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 Title: Spellman et al. (1998) and Pramila/Breeden (2006) yeast cell cycle microarray data Description: ExpressionSet for Spellman et al. (1998) yeast cell cycle microarray experiment biocViews: ExperimentData, Yeast Author: Sandrine Dudoit Maintainer: Sandrine Dudoit MD5sum: fca4de526434f2ffaadb521f81b1b0d5 source.ver: src/contrib/yeastCC_1.2.17.tar.gz win.binary.ver: bin/windows/contrib/2.15/yeastCC_1.2.17.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/yeastCC_1.2.17.tgz vignettes: vignettes/yeastCC/inst/doc/Spellmanetal.pdf vignetteTitles: Spellmanetal.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastExpData Version: 0.9.21 Depends: R (>= 2.4), graph (>= 1.9.26) Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db License: GPL Title: Yeast Experimental Data Description: A collection of different sets of experimental data from yeast. biocViews: ExperimentData, Yeast Author: R. Gentleman Maintainer: R. Gentleman MD5sum: 37841cd9eefdeba570802612d89aa0f8 source.ver: src/contrib/yeastExpData_0.9.21.tar.gz win.binary.ver: bin/windows/contrib/2.15/yeastExpData_0.9.21.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/yeastExpData_0.9.21.tgz vignettes: vignettes/yeastExpData/inst/doc/yeastExample.pdf vignetteTitles: Yeast PPI Example hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/yeastExpData/inst/doc/yeastExample.R Package: yeastGSData Version: 0.1.9 License: Artistic-2.0 Title: Yeast Gold Standard Data Description: A collection of so-called gold (and other) standard data sets biocViews: ExperimentData, Yeast Author: R. Gentleman Maintainer: R. Gentleman MD5sum: 7e876c35b0101516e3d797934d5e7466 source.ver: src/contrib/yeastGSData_0.1.9.tar.gz win.binary.ver: bin/windows/contrib/2.15/yeastGSData_0.1.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/yeastGSData_0.1.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastNagalakshmi Version: 0.99.5 License: Artistic-2.0 Title: Yeast genome RNA sequencing data based on Nagalakshmi et. al. Description: The yeast genome data was retrieved from the sequence read archive, aligned with bwa, and converted to BAM format with samtools. biocViews: ExperimentData, Yeast, ChIPseqData Author: Martin Morgan Maintainer: Bioconductor Package Maintainer MD5sum: fdf8215605e5acc2c6fa0de321bd9482 source.ver: src/contrib/yeastNagalakshmi_0.99.5.tar.gz win.binary.ver: bin/windows/contrib/2.15/yeastNagalakshmi_0.99.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/yeastNagalakshmi_0.99.5.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastRNASeq Version: 0.0.7 Depends: R (>= 2.4) Suggests: Biobase, ShortRead, IRanges License: GPL Title: Yeast RNA-Seq Experimental Data from Lee et al. 2008 Description: A selection of RNA-Seq data from a yeast transcriptome experiment. biocViews: ExperimentData, Yeast, RNAseqData Author: James H. Bullard and Kasper D. Hansen Maintainer: J. Bullard MD5sum: c88abd3b8e2b7c8d1b0eb1e9ecf471e2 source.ver: src/contrib/yeastRNASeq_0.0.7.tar.gz win.binary.ver: bin/windows/contrib/2.15/yeastRNASeq_0.0.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/yeastRNASeq_0.0.7.tgz vignettes: vignettes/yeastRNASeq/inst/doc/yeastRNASeq.pdf vignetteTitles: An overview of yeastRNASeq hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/yeastRNASeq/inst/doc/yeastRNASeq.R