Package: ALLMLL Version: 1.2.11 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 source.ver: src/contrib/ALLMLL_1.2.11.tar.gz win.binary.ver: bin/windows/contrib/2.14/ALLMLL_1.2.11.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/ALLMLL_1.2.11.tgz Package: ALL Version: 1.4.11 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 source.ver: src/contrib/ALL_1.4.11.tar.gz win.binary.ver: bin/windows/contrib/2.14/ALL_1.4.11.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/ALL_1.4.11.tgz vignettes: vignettes/ALL/inst/doc/ALLintro.pdf Package: AffymetrixDataTestFiles Version: 0.1.3 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 source.ver: src/contrib/AffymetrixDataTestFiles_0.1.3.tar.gz win.binary.ver: bin/windows/contrib/2.14/AffymetrixDataTestFiles_0.1.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/AffymetrixDataTestFiles_0.1.3.tgz Package: AmpAffyExample Version: 1.2.9 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 source.ver: src/contrib/AmpAffyExample_1.2.9.tar.gz win.binary.ver: bin/windows/contrib/2.14/AmpAffyExample_1.2.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/AmpAffyExample_1.2.9.tgz Package: BeadArrayUseCases Version: 1.0.4 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 source.ver: src/contrib/BeadArrayUseCases_1.0.4.tar.gz win.binary.ver: bin/windows/contrib/2.14/BeadArrayUseCases_1.0.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/BeadArrayUseCases_1.0.4.tgz vignettes: vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.pdf, vignettes/BeadArrayUseCases/inst/doc/BeadChipSimple_old.pdf Package: CCl4 Version: 1.0.11 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 source.ver: src/contrib/CCl4_1.0.11.tar.gz win.binary.ver: bin/windows/contrib/2.14/CCl4_1.0.11.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/CCl4_1.0.11.tgz vignettes: vignettes/CCl4/inst/doc/CCl4.pdf Package: CLL Version: 1.2.11 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 source.ver: src/contrib/CLL_1.2.11.tar.gz win.binary.ver: bin/windows/contrib/2.14/CLL_1.2.11.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/CLL_1.2.11.tgz Package: DLBCL Version: 1.3.3 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/ source.ver: src/contrib/DLBCL_1.3.3.tar.gz win.binary.ver: bin/windows/contrib/2.14/DLBCL_1.3.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/DLBCL_1.3.3.tgz Package: ENCODEFig4Band4D Version: 1.0.2 Imports: Biobase, earth, randomForest License: Artistic-2.0 # modify as desired Title: Data and code package to reproduce Figure panels 4B and 4D from the ENCODE (2012) paper Description: The package provides the data and the code needed to reproduce Figure panels 4B and 4D from the ENCODE (2012) paper. The data are provided as R data objects and are documented by manual pages. The code to reproduce the figure panels is presented in the package vignette. Author: Chao Cheng and Wolfgang Huber Maintainer: Wolfgang Huber source.ver: src/contrib/ENCODEFig4Band4D_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.14/ENCODEFig4Band4D_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/ENCODEFig4Band4D_1.0.2.tgz vignettes: vignettes/ENCODEFig4Band4D/inst/doc/ENCODEFig4Band4D.pdf Package: EatonEtAlChIPseq Version: 0.0.6 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 source.ver: src/contrib/EatonEtAlChIPseq_0.0.6.tar.gz win.binary.ver: bin/windows/contrib/2.14/EatonEtAlChIPseq_0.0.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/EatonEtAlChIPseq_0.0.6.tgz Package: GGdata Version: 1.0.18 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 source.ver: src/contrib/GGdata_1.0.18.tar.gz win.binary.ver: bin/windows/contrib/2.14/GGdata_1.0.18.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/GGdata_1.0.18.tgz Package: GSVAdata Version: 0.99.3 Depends: 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; Verhaak et al. Cancer Cell 17:98-110, 2010; Cahoy et al. J Neurosci 28:264-278, 2008. biocViews: ExperimentData, Cancer, Leukemia Author: Robert Castelo Maintainer: Robert Castelo source.ver: src/contrib/GSVAdata_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/2.14/GSVAdata_0.99.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/GSVAdata_0.99.3.tgz Package: GWASdata Version: 1.0.0 Depends: GWASTools Suggests: ncdf 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 source.ver: src/contrib/GWASdata_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.14/GWASdata_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/GWASdata_1.0.0.tgz Package: HEEBOdata Version: 1.0.2 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/ source.ver: src/contrib/HEEBOdata_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.14/HEEBOdata_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/HEEBOdata_1.0.2.tgz Package: HIVcDNAvantWout03 Version: 1.2.5 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 source.ver: src/contrib/HIVcDNAvantWout03_1.2.5.tar.gz win.binary.ver: bin/windows/contrib/2.14/HIVcDNAvantWout03_1.2.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/HIVcDNAvantWout03_1.2.5.tgz vignettes: vignettes/HIVcDNAvantWout03/inst/doc/hivData.pdf Package: ITALICSData Version: 2.0.4 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 source.ver: src/contrib/ITALICSData_2.0.4.tar.gz win.binary.ver: bin/windows/contrib/2.14/ITALICSData_2.0.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/ITALICSData_2.0.4.tgz Package: IlluminaHumanMethylation450kmanifest Version: 0.2.0 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 source.ver: src/contrib/IlluminaHumanMethylation450kmanifest_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.14/IlluminaHumanMethylation450kmanifest_0.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/IlluminaHumanMethylation450kmanifest_0.2.0.tgz Package: Iyer517 Version: 1.4.9 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 source.ver: src/contrib/Iyer517_1.4.9.tar.gz win.binary.ver: bin/windows/contrib/2.14/Iyer517_1.4.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/Iyer517_1.4.9.tgz vignettes: vignettes/Iyer517/inst/doc/Iyer517.pdf Package: LiebermanAidenHiC2009 Version: 0.1.10 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 source.ver: src/contrib/LiebermanAidenHiC2009_0.1.10.tar.gz win.binary.ver: bin/windows/contrib/2.14/LiebermanAidenHiC2009_0.1.10.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/LiebermanAidenHiC2009_0.1.10.tgz vignettes: vignettes/LiebermanAidenHiC2009/inst/doc/LiebermanAidenHiC2009.pdf Package: MAQCsubsetAFX Version: 1.0.5 Depends: 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 URL: http://www.slashhome.be/MAQCsubsetAFX.php source.ver: src/contrib/MAQCsubsetAFX_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.14/MAQCsubsetAFX_1.0.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/MAQCsubsetAFX_1.0.5.tgz vignettes: vignettes/MAQCsubsetAFX/inst/doc/MAQCsubsetAFX.pdf Package: MAQCsubsetILM Version: 1.0.4 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 URL: http://www.slashhome.be/MAQCsubsetILM.php source.ver: src/contrib/MAQCsubsetILM_1.0.4.tar.gz win.binary.ver: bin/windows/contrib/2.14/MAQCsubsetILM_1.0.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/MAQCsubsetILM_1.0.4.tgz vignettes: vignettes/MAQCsubsetILM/inst/doc/MAQCsubsetILM.pdf Package: MAQCsubset Version: 1.0.24 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 source.ver: src/contrib/MAQCsubset_1.0.24.tar.gz win.binary.ver: bin/windows/contrib/2.14/MAQCsubset_1.0.24.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/MAQCsubset_1.0.24.tgz vignettes: vignettes/MAQCsubset/inst/doc/maqcNotes.pdf Package: MEEBOdata Version: 1.0.2 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/ source.ver: src/contrib/MEEBOdata_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.14/MEEBOdata_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/MEEBOdata_1.0.2.tgz Package: NCIgraphData Version: 0.99.3 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 source.ver: src/contrib/NCIgraphData_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/2.14/NCIgraphData_0.99.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/NCIgraphData_0.99.3.tgz Package: Neve2006 Version: 0.1.13 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 source.ver: src/contrib/Neve2006_0.1.13.tar.gz win.binary.ver: bin/windows/contrib/2.14/Neve2006_0.1.13.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/Neve2006_0.1.13.tgz vignettes: vignettes/Neve2006/inst/doc/neve06notes.pdf Package: PREDAsampledata Version: 0.2.4 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 source.ver: src/contrib/PREDAsampledata_0.2.4.tar.gz win.binary.ver: bin/windows/contrib/2.14/PREDAsampledata_0.2.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/PREDAsampledata_0.2.4.tgz Package: ProData Version: 1.0.5 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 source.ver: src/contrib/ProData_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.14/ProData_1.0.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/ProData_1.0.5.tgz Package: RNAinteractMAPK Version: 1.0.3 Depends: R (>= 2.12.0), fields, sparseLDA, RNAinteract Imports: grid, gdata, crossdes, MASS, genefilter Suggests: qvalue 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 source.ver: src/contrib/RNAinteractMAPK_1.0.3.tar.gz win.binary.ver: bin/windows/contrib/2.14/RNAinteractMAPK_1.0.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/RNAinteractMAPK_1.0.3.tgz vignettes: vignettes/RNAinteractMAPK/inst/doc/RNAinteractMAPK.pdf Package: SNAData Version: 1.8.3 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 source.ver: src/contrib/SNAData_1.8.3.tar.gz win.binary.ver: bin/windows/contrib/2.14/SNAData_1.8.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/SNAData_1.8.3.tgz vignettes: vignettes/SNAData/inst/doc/SNAData.pdf Package: SpikeInSubset Version: 1.2.10 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 source.ver: src/contrib/SpikeInSubset_1.2.10.tar.gz win.binary.ver: bin/windows/contrib/2.14/SpikeInSubset_1.2.10.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/SpikeInSubset_1.2.10.tgz Package: SpikeIn Version: 1.4.7 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 source.ver: src/contrib/SpikeIn_1.4.7.tar.gz win.binary.ver: bin/windows/contrib/2.14/SpikeIn_1.4.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/SpikeIn_1.4.7.tgz Package: TCGAMethylation450k Version: 0.99.1 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 source.ver: src/contrib/TCGAMethylation450k_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/2.14/TCGAMethylation450k_0.99.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/TCGAMethylation450k_0.99.1.tgz Package: TargetSearchData Version: 1.0.5 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 source.ver: src/contrib/TargetSearchData_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.14/TargetSearchData_1.0.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/TargetSearchData_1.0.5.tgz Package: XhybCasneuf Version: 1.0.8 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 source.ver: src/contrib/XhybCasneuf_1.0.8.tar.gz win.binary.ver: bin/windows/contrib/2.14/XhybCasneuf_1.0.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/XhybCasneuf_1.0.8.tgz vignettes: vignettes/XhybCasneuf/inst/doc/Xhyb.pdf Package: affycompData Version: 1.1.2 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 source.ver: src/contrib/affycompData_1.1.2.tar.gz win.binary.ver: bin/windows/contrib/2.14/affycompData_1.1.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/affycompData_1.1.2.tgz Package: affydata Version: 1.11.15 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 source.ver: src/contrib/affydata_1.11.15.tar.gz win.binary.ver: bin/windows/contrib/2.14/affydata_1.11.15.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/affydata_1.11.15.tgz vignettes: vignettes/affydata/inst/doc/affydata.pdf Package: beadarrayExampleData Version: 1.0.3 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 source.ver: src/contrib/beadarrayExampleData_1.0.3.tar.gz win.binary.ver: bin/windows/contrib/2.14/beadarrayExampleData_1.0.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/beadarrayExampleData_1.0.3.tgz vignettes: vignettes/beadarrayExampleData/inst/doc/beadarrayExampleData.pdf Package: beta7 Version: 1.0.2 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 source.ver: src/contrib/beta7_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.14/beta7_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/beta7_1.0.2.tgz Package: bladderbatch Version: 1.0.2 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 source.ver: src/contrib/bladderbatch_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.14/bladderbatch_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/bladderbatch_1.0.2.tgz vignettes: vignettes/bladderbatch/inst/doc/bladderbatch.pdf Package: breastCancerMAINZ Version: 1.0.2 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/ source.ver: src/contrib/breastCancerMAINZ_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.14/breastCancerMAINZ_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/breastCancerMAINZ_1.0.2.tgz Package: breastCancerNKI Version: 1.0.2 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/ source.ver: src/contrib/breastCancerNKI_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.14/breastCancerNKI_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/breastCancerNKI_1.0.2.tgz Package: breastCancerTRANSBIG Version: 1.0.2 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/ source.ver: src/contrib/breastCancerTRANSBIG_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.14/breastCancerTRANSBIG_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/breastCancerTRANSBIG_1.0.2.tgz Package: breastCancerUNT Version: 1.0.2 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/ source.ver: src/contrib/breastCancerUNT_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.14/breastCancerUNT_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/breastCancerUNT_1.0.2.tgz Package: breastCancerUPP Version: 1.0.2 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/ source.ver: src/contrib/breastCancerUPP_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.14/breastCancerUPP_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/breastCancerUPP_1.0.2.tgz Package: breastCancerVDX Version: 1.0.2 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/ source.ver: src/contrib/breastCancerVDX_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.14/breastCancerVDX_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/breastCancerVDX_1.0.2.tgz Package: bronchialIL13 Version: 1.0.8 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 source.ver: src/contrib/bronchialIL13_1.0.8.tar.gz win.binary.ver: bin/windows/contrib/2.14/bronchialIL13_1.0.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/bronchialIL13_1.0.8.tgz Package: ccTutorial Version: 1.0.20 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 source.ver: src/contrib/ccTutorial_1.0.20.tar.gz win.binary.ver: bin/windows/contrib/2.14/ccTutorial_1.0.20.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/ccTutorial_1.0.20.tgz vignettes: vignettes/ccTutorial/inst/doc/ccTutorial.pdf, vignettes/ccTutorial/inst/doc/ccTutorialSupplement.pdf Package: ceu1kg Version: 0.0.29 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 source.ver: src/contrib/ceu1kg_0.0.29.tar.gz win.binary.ver: bin/windows/contrib/2.14/ceu1kg_0.0.29.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/ceu1kg_0.0.29.tgz vignettes: vignettes/ceu1kg/inst/doc/ceu1kg.pdf Package: ceuhm3 Version: 0.0.12 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 source.ver: src/contrib/ceuhm3_0.0.12.tar.gz win.binary.ver: bin/windows/contrib/2.14/ceuhm3_0.0.12.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/ceuhm3_0.0.12.tgz Package: charmData Version: 0.99.5 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 source.ver: src/contrib/charmData_0.99.5.tar.gz win.binary.ver: bin/windows/contrib/2.14/charmData_0.99.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/charmData_0.99.5.tgz Package: cheung2010 Version: 0.0.23 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 Author: Vince Carey Maintainer: Vince Carey source.ver: src/contrib/cheung2010_0.0.23.tar.gz win.binary.ver: bin/windows/contrib/2.14/cheung2010_0.0.23.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/cheung2010_0.0.23.tgz vignettes: vignettes/cheung2010/inst/doc/arr2hap.pdf, vignettes/cheung2010/inst/doc/cheungTrans.pdf Package: colonCA Version: 1.4.8 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 source.ver: src/contrib/colonCA_1.4.8.tar.gz win.binary.ver: bin/windows/contrib/2.14/colonCA_1.4.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/colonCA_1.4.8.tgz Package: davidTiling Version: 1.2.14 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 source.ver: src/contrib/davidTiling_1.2.14.tar.gz win.binary.ver: bin/windows/contrib/2.14/davidTiling_1.2.14.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/davidTiling_1.2.14.tgz Package: dressCheck Version: 0.1.4 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 source.ver: src/contrib/dressCheck_0.1.4.tar.gz win.binary.ver: bin/windows/contrib/2.14/dressCheck_0.1.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/dressCheck_0.1.4.tgz vignettes: vignettes/dressCheck/inst/doc/short.pdf Package: dyebiasexamples Version: 1.0.7 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 source.ver: src/contrib/dyebiasexamples_1.0.7.tar.gz win.binary.ver: bin/windows/contrib/2.14/dyebiasexamples_1.0.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/dyebiasexamples_1.0.7.tgz Package: ecoliLeucine Version: 1.2.7 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 source.ver: src/contrib/ecoliLeucine_1.2.7.tar.gz win.binary.ver: bin/windows/contrib/2.14/ecoliLeucine_1.2.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/ecoliLeucine_1.2.7.tgz Package: encoDnaseI Version: 0.1.9 Depends: R (>= 2.6.0), 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 source.ver: src/contrib/encoDnaseI_0.1.9.tar.gz win.binary.ver: bin/windows/contrib/2.14/encoDnaseI_0.1.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/encoDnaseI_0.1.9.tgz vignettes: vignettes/encoDnaseI/inst/doc/dnaseUse.pdf Package: estrogen Version: 1.8.7 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 source.ver: src/contrib/estrogen_1.8.7.tar.gz win.binary.ver: bin/windows/contrib/2.14/estrogen_1.8.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/estrogen_1.8.7.tgz vignettes: vignettes/estrogen/inst/doc/estrogen.pdf Package: faahKO Version: 1.2.8 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 Author: Colin A. Smith Maintainer: Colin A. Smith URL: http://dx.doi.org/10.1021/bi0480335 source.ver: src/contrib/faahKO_1.2.8.tar.gz win.binary.ver: bin/windows/contrib/2.14/faahKO_1.2.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/faahKO_1.2.8.tgz Package: facsDorit Version: 1.4.4 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 source.ver: src/contrib/facsDorit_1.4.4.tar.gz win.binary.ver: bin/windows/contrib/2.14/facsDorit_1.4.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/facsDorit_1.4.4.tgz Package: ffpeExampleData Version: 1.0.0 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 source.ver: src/contrib/ffpeExampleData_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.14/ffpeExampleData_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/ffpeExampleData_1.0.0.tgz Package: fibroEset Version: 1.4.6 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 source.ver: src/contrib/fibroEset_1.4.6.tar.gz win.binary.ver: bin/windows/contrib/2.14/fibroEset_1.4.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/fibroEset_1.4.6.tgz Package: flowWorkspaceData Version: 0.99.6 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 source.ver: src/contrib/flowWorkspaceData_0.99.6.tar.gz win.binary.ver: bin/windows/contrib/2.14/flowWorkspaceData_0.99.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/flowWorkspaceData_0.99.6.tgz Package: frmaExampleData Version: 0.99.2 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 source.ver: src/contrib/frmaExampleData_0.99.2.tar.gz win.binary.ver: bin/windows/contrib/2.14/frmaExampleData_0.99.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/frmaExampleData_0.99.2.tgz Package: gageData Version: 1.1.3 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 source.ver: src/contrib/gageData_1.1.3.tar.gz win.binary.ver: bin/windows/contrib/2.14/gageData_1.1.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/gageData_1.1.3.tgz Package: gaschYHS Version: 1.0.6 Depends: 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 source.ver: src/contrib/gaschYHS_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/2.14/gaschYHS_1.0.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/gaschYHS_1.0.6.tgz Package: gatingMLData Version: 1.0.4 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 source.ver: src/contrib/gatingMLData_1.0.4.tar.gz win.binary.ver: bin/windows/contrib/2.14/gatingMLData_1.0.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/gatingMLData_1.0.4.tgz Package: gcspikelite Version: 1.0.6 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 source.ver: src/contrib/gcspikelite_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/2.14/gcspikelite_1.0.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/gcspikelite_1.0.6.tgz Package: geneLenDataBase Version: 0.99.8 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 source.ver: src/contrib/geneLenDataBase_0.99.8.tar.gz win.binary.ver: bin/windows/contrib/2.14/geneLenDataBase_0.99.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/geneLenDataBase_0.99.8.tgz Package: ggtut Version: 0.0.41 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 source.ver: src/contrib/ggtut_0.0.41.tar.gz win.binary.ver: bin/windows/contrib/2.14/ggtut_0.0.41.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/ggtut_0.0.41.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 Package: golubEsets Version: 1.4.10 Depends: 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 source.ver: src/contrib/golubEsets_1.4.10.tar.gz win.binary.ver: bin/windows/contrib/2.14/golubEsets_1.4.10.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/golubEsets_1.4.10.tgz Package: hapmap100khind Version: 1.3.34 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 source.ver: src/contrib/hapmap100khind_1.3.34.tar.gz win.binary.ver: bin/windows/contrib/2.14/hapmap100khind_1.3.34.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/hapmap100khind_1.3.34.tgz Package: hapmap100kxba Version: 1.3.5 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 source.ver: src/contrib/hapmap100kxba_1.3.5.tar.gz win.binary.ver: bin/windows/contrib/2.14/hapmap100kxba_1.3.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/hapmap100kxba_1.3.5.tgz Package: hapmap500knsp Version: 1.3.5 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 source.ver: src/contrib/hapmap500knsp_1.3.5.tar.gz win.binary.ver: bin/windows/contrib/2.14/hapmap500knsp_1.3.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/hapmap500knsp_1.3.5.tgz Package: hapmap500ksty Version: 1.3.5 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 source.ver: src/contrib/hapmap500ksty_1.3.5.tar.gz win.binary.ver: bin/windows/contrib/2.14/hapmap500ksty_1.3.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/hapmap500ksty_1.3.5.tgz Package: hapmapsnp5 Version: 1.3.5 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 source.ver: src/contrib/hapmapsnp5_1.3.5.tar.gz win.binary.ver: bin/windows/contrib/2.14/hapmapsnp5_1.3.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/hapmapsnp5_1.3.5.tgz Package: hapmapsnp6 Version: 1.3.5 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 source.ver: src/contrib/hapmapsnp6_1.3.5.tar.gz win.binary.ver: bin/windows/contrib/2.14/hapmapsnp6_1.3.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/hapmapsnp6_1.3.5.tgz Package: harbChIP Version: 1.0.7 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 source.ver: src/contrib/harbChIP_1.0.7.tar.gz win.binary.ver: bin/windows/contrib/2.14/harbChIP_1.0.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/harbChIP_1.0.7.tgz vignettes: vignettes/harbChIP/inst/doc/yeastUpstream.pdf Package: hgu133abarcodevecs Version: 1.0.3 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 source.ver: src/contrib/hgu133abarcodevecs_1.0.3.tar.gz win.binary.ver: bin/windows/contrib/2.14/hgu133abarcodevecs_1.0.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/hgu133abarcodevecs_1.0.3.tgz Package: hgu133afrmavecs Version: 1.1.8 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 1.3.11. biocViews: AnnotationData, AffymetrixChip, hgu133a, Homo_sapiens Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall source.ver: src/contrib/hgu133afrmavecs_1.1.8.tar.gz win.binary.ver: bin/windows/contrib/2.14/hgu133afrmavecs_1.1.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/hgu133afrmavecs_1.1.8.tgz Package: hgu133plus2barcodevecs Version: 1.0.3 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 source.ver: src/contrib/hgu133plus2barcodevecs_1.0.3.tar.gz win.binary.ver: bin/windows/contrib/2.14/hgu133plus2barcodevecs_1.0.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/hgu133plus2barcodevecs_1.0.3.tgz Package: hgu133plus2frmavecs Version: 1.1.8 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 1.3.4. biocViews: AnnotationData, AffymetrixChip, hgu133plus2, Homo_sapiens Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall source.ver: src/contrib/hgu133plus2frmavecs_1.1.8.tar.gz win.binary.ver: bin/windows/contrib/2.14/hgu133plus2frmavecs_1.1.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/hgu133plus2frmavecs_1.1.8.tgz Package: hgu2beta7 Version: 1.2.5 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 source.ver: src/contrib/hgu2beta7_1.2.5.tar.gz win.binary.ver: bin/windows/contrib/2.14/hgu2beta7_1.2.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/hgu2beta7_1.2.5.tgz Package: hmyriB36 Version: 0.99.14 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 source.ver: src/contrib/hmyriB36_0.99.14.tar.gz win.binary.ver: bin/windows/contrib/2.14/hmyriB36_0.99.14.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/hmyriB36_0.99.14.tgz Package: humanStemCell Version: 0.2.5 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 source.ver: src/contrib/humanStemCell_0.2.5.tar.gz win.binary.ver: bin/windows/contrib/2.14/humanStemCell_0.2.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/humanStemCell_0.2.5.tgz Package: ind1KG Version: 0.1.12 Depends: R (>= 2.10.1), Rsamtools, TxDb.Hsapiens.UCSC.hg18.knownGene Suggests: GenomicFeatures, rtracklayer, org.Hs.eg.db, chopsticks, SNPlocs.Hsapiens.dbSNP.20090506, 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 source.ver: src/contrib/ind1KG_0.1.12.tar.gz win.binary.ver: bin/windows/contrib/2.14/ind1KG_0.1.12.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/ind1KG_0.1.12.tgz vignettes: vignettes/ind1KG/inst/doc/ind1KG.pdf, vignettes/ind1KG/inst/doc/nov09rv.pdf Package: iontreeData Version: 0.99.5 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 source.ver: src/contrib/iontreeData_0.99.5.tar.gz win.binary.ver: bin/windows/contrib/2.14/iontreeData_0.99.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/iontreeData_0.99.5.tgz Package: kidpack Version: 1.5.9 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 source.ver: src/contrib/kidpack_1.5.9.tar.gz win.binary.ver: bin/windows/contrib/2.14/kidpack_1.5.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/kidpack_1.5.9.tgz vignettes: vignettes/kidpack/inst/doc/kidpack.pdf Package: leeBamViews Version: 0.99.13 Depends: 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 Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/leeBamViews_0.99.13.tar.gz win.binary.ver: bin/windows/contrib/2.14/leeBamViews_0.99.13.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/leeBamViews_0.99.13.tgz vignettes: vignettes/leeBamViews/inst/doc/leeFull-dol.pdf, vignettes/leeBamViews/inst/doc/leeViews.pdf Package: lumiBarnes Version: 1.3.7 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 source.ver: src/contrib/lumiBarnes_1.3.7.tar.gz win.binary.ver: bin/windows/contrib/2.14/lumiBarnes_1.3.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/lumiBarnes_1.3.7.tgz Package: lungExpression Version: 0.0.12 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 source.ver: src/contrib/lungExpression_0.0.12.tar.gz win.binary.ver: bin/windows/contrib/2.14/lungExpression_0.0.12.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/lungExpression_0.0.12.tgz Package: maqcExpression4plex Version: 1.4.1 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 source.ver: src/contrib/maqcExpression4plex_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.14/maqcExpression4plex_1.4.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/maqcExpression4plex_1.4.1.tgz Package: minfiData Version: 0.2.0 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 source.ver: src/contrib/minfiData_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.14/minfiData_0.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/minfiData_0.2.0.tgz Package: mosaicsExample Version: 0.99.5 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 source.ver: src/contrib/mosaicsExample_0.99.5.tar.gz win.binary.ver: bin/windows/contrib/2.14/mosaicsExample_0.99.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/mosaicsExample_0.99.5.tgz Package: mouse4302barcodevecs Version: 1.0.3 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 source.ver: src/contrib/mouse4302barcodevecs_1.0.3.tar.gz win.binary.ver: bin/windows/contrib/2.14/mouse4302barcodevecs_1.0.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/mouse4302barcodevecs_1.0.3.tgz Package: mouse4302frmavecs Version: 1.1.8 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 1.3.4. biocViews: AnnotationData, AffymetrixChip, mouse4302, Mus_musculus Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall source.ver: src/contrib/mouse4302frmavecs_1.1.8.tar.gz win.binary.ver: bin/windows/contrib/2.14/mouse4302frmavecs_1.1.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/mouse4302frmavecs_1.1.8.tgz Package: msdata Version: 0.1.7 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 Author: Steffen Neumann Maintainer: Steffen Neumann source.ver: src/contrib/msdata_0.1.7.tar.gz win.binary.ver: bin/windows/contrib/2.14/msdata_0.1.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/msdata_0.1.7.tgz Package: mvoutData Version: 0.99.7 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 source.ver: src/contrib/mvoutData_0.99.7.tar.gz win.binary.ver: bin/windows/contrib/2.14/mvoutData_0.99.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/mvoutData_0.99.7.tgz Package: pasillaBamSubset Version: 0.0.1 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. biocViews: ExperimentData, RNAseqData Author: H. Pages Maintainer: H. Pages source.ver: src/contrib/pasillaBamSubset_0.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.14/pasillaBamSubset_0.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/pasillaBamSubset_0.0.1.tgz Package: pasilla Version: 0.2.11 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 source.ver: src/contrib/pasilla_0.2.11.tar.gz win.binary.ver: bin/windows/contrib/2.14/pasilla_0.2.11.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/pasilla_0.2.11.tgz vignettes: vignettes/pasilla/inst/doc/create_objects.pdf Package: pcaGoPromoter.Hs.hg19 Version: 0.99.1 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, source.ver: src/contrib/pcaGoPromoter.Hs.hg19_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/2.14/pcaGoPromoter.Hs.hg19_0.99.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/pcaGoPromoter.Hs.hg19_0.99.1.tgz Package: pcaGoPromoter.Mm.mm9 Version: 0.99.1 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, source.ver: src/contrib/pcaGoPromoter.Mm.mm9_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/2.14/pcaGoPromoter.Mm.mm9_0.99.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/pcaGoPromoter.Mm.mm9_0.99.1.tgz Package: pcaGoPromoter.Rn.rn4 Version: 0.99.1 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, source.ver: src/contrib/pcaGoPromoter.Rn.rn4_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/2.14/pcaGoPromoter.Rn.rn4_0.99.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/pcaGoPromoter.Rn.rn4_0.99.1.tgz Package: ppiData Version: 0.1.16 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 source.ver: src/contrib/ppiData_0.1.16.tar.gz win.binary.ver: bin/windows/contrib/2.14/ppiData_0.1.16.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/ppiData_0.1.16.tgz vignettes: vignettes/ppiData/inst/doc/ Package: pumadata Version: 1.0.5 Depends: R (>= 2.4.0), 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 source.ver: src/contrib/pumadata_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.14/pumadata_1.0.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/pumadata_1.0.5.tgz vignettes: vignettes/pumadata/inst/doc/pumadata.pdf Package: rfcdmin Version: 1.6.11 Depends: R (>= 2.4.0) Suggests: rflowcyt License: GPL-2 Title: Minimal Data Library for RFlowCyt examples Description: Provides basic data sets for examples and should be loaded before the package 'rflowcyt' and 'rfcprim'. biocViews: ExperimentData, FlowCytData Author: A.J. Rossini, J.Y. Wan, N. Le Meur and Zoe Moodie Maintainer: N. Le Meur URL: http://www.analytics.washington.edu/downloads/rflowcyt/ source.ver: src/contrib/rfcdmin_1.6.11.tar.gz win.binary.ver: bin/windows/contrib/2.14/rfcdmin_1.6.11.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/rfcdmin_1.6.11.tgz Package: rheumaticConditionWOLLBOLD Version: 1.0.0 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/ source.ver: src/contrib/rheumaticConditionWOLLBOLD_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.14/rheumaticConditionWOLLBOLD_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/rheumaticConditionWOLLBOLD_1.0.0.tgz Package: serumStimulation Version: 0.99.1 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, source.ver: src/contrib/serumStimulation_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/2.14/serumStimulation_0.99.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/serumStimulation_0.99.1.tgz Package: simpIntLists Version: 0.99.1 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 source.ver: src/contrib/simpIntLists_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/2.14/simpIntLists_0.99.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/simpIntLists_0.99.1.tgz vignettes: vignettes/simpIntLists/inst/doc/simpIntLists.pdf Package: stjudem Version: 1.2.6 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 source.ver: src/contrib/stjudem_1.2.6.tar.gz win.binary.ver: bin/windows/contrib/2.14/stjudem_1.2.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/stjudem_1.2.6.tgz Package: tinesath1cdf Version: 1.0.6 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 source.ver: src/contrib/tinesath1cdf_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/2.14/tinesath1cdf_1.0.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/tinesath1cdf_1.0.6.tgz Package: tinesath1probe Version: 1.0.6 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 source.ver: src/contrib/tinesath1probe_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/2.14/tinesath1probe_1.0.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/tinesath1probe_1.0.6.tgz Package: tweeDEseqCountData Version: 1.0.5 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 source.ver: src/contrib/tweeDEseqCountData_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.14/tweeDEseqCountData_1.0.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/tweeDEseqCountData_1.0.5.tgz Package: yeastCC Version: 1.2.15 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 source.ver: src/contrib/yeastCC_1.2.15.tar.gz win.binary.ver: bin/windows/contrib/2.14/yeastCC_1.2.15.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/yeastCC_1.2.15.tgz vignettes: vignettes/yeastCC/inst/doc/Spellmanetal.pdf Package: yeastExpData Version: 0.9.19 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 source.ver: src/contrib/yeastExpData_0.9.19.tar.gz win.binary.ver: bin/windows/contrib/2.14/yeastExpData_0.9.19.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/yeastExpData_0.9.19.tgz vignettes: vignettes/yeastExpData/inst/doc/yeastExample.pdf Package: yeastGSData Version: 0.1.7 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 source.ver: src/contrib/yeastGSData_0.1.7.tar.gz win.binary.ver: bin/windows/contrib/2.14/yeastGSData_0.1.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/yeastGSData_0.1.7.tgz Package: yeastNagalakshmi Version: 0.99.3 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 source.ver: src/contrib/yeastNagalakshmi_0.99.3.tar.gz win.binary.ver: bin/windows/contrib/2.14/yeastNagalakshmi_0.99.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/yeastNagalakshmi_0.99.3.tgz Package: yeastRNASeq Version: 0.0.5 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 source.ver: src/contrib/yeastRNASeq_0.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.14/yeastRNASeq_0.0.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.14/yeastRNASeq_0.0.5.tgz vignettes: vignettes/yeastRNASeq/inst/doc/yeastRNASeq.pdf