Package: ALLMLL Version: 1.2.8 Depends: R (>= 2.4.0), 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_1.2.8.tar.gz win.binary.ver: bin/windows/contrib/2.11/ALLMLL_1.2.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/ALLMLL_1.2.8.tgz Package: ALL Version: 1.4.7 Depends: Biobase (>= 2.5.5) Suggests: rpart License: GPL 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: Xiaochun Li source.ver: src/contrib/ALL_1.4.7.tar.gz win.binary.ver: bin/windows/contrib/2.11/ALL_1.4.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/ALL_1.4.7.tgz vignettes: vignettes/ALL/inst/doc/ALLintro.pdf Package: AffymetrixDataTestFiles Version: 0.1.2 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_0.1.2.tar.gz win.binary.ver: bin/windows/contrib/2.11/AffymetrixDataTestFiles_0.1.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/AffymetrixDataTestFiles_0.1.2.tgz Package: AmpAffyExample Version: 1.2.5 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_1.2.5.tar.gz win.binary.ver: bin/windows/contrib/2.11/AmpAffyExample_1.2.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/AmpAffyExample_1.2.5.tgz Package: CCl4 Version: 1.0.9 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_1.0.9.tar.gz win.binary.ver: bin/windows/contrib/2.11/CCl4_1.0.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/CCl4_1.0.9.tgz vignettes: vignettes/CCl4/inst/doc/CCl4.pdf Package: CLL Version: 1.2.8 Depends: 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_1.2.8.tar.gz win.binary.ver: bin/windows/contrib/2.11/CLL_1.2.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/CLL_1.2.8.tgz Package: DLBCL Version: 1.3.1 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_1.3.1.tar.gz win.binary.ver: bin/windows/contrib/2.11/DLBCL_1.3.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/DLBCL_1.3.1.tgz Package: EatonEtAlChIPseq Version: 0.0.1 Depends: 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_0.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.11/EatonEtAlChIPseq_0.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/EatonEtAlChIPseq_0.0.1.tgz Package: GGdata Version: 1.0.4 Depends: R (>= 2.6.0), methods, Biobase (>= 2.5.5), ff, GGBase, snpMatrix, illuminaHumanv1.db, AnnotationDbi 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_1.0.4.tar.gz win.binary.ver: bin/windows/contrib/2.11/GGdata_1.0.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/GGdata_1.0.4.tgz Package: GenomicFeatures.Hsapiens.UCSC.hg18 Version: 0.1.2 Depends: GenomicFeatures (>= 0.3.32) Imports: DBI, RSQLite, GenomicFeatures License: Artistic-2.0 Title: A transient package to store various Genomic Features for Human Description: Various Genome-related features, such as gene boundaries, etc. biocViews: AnnotationData, Homo_sapiens Author: D. Sarkar, M. Lawrence Maintainer: Biocore Data Team source.ver: src/contrib/GenomicFeatures.Hsapiens.UCSC.hg18_0.1.2.tar.gz win.binary.ver: bin/windows/contrib/2.11/GenomicFeatures.Hsapiens.UCSC.hg18_0.1.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/GenomicFeatures.Hsapiens.UCSC.hg18_0.1.2.tgz Package: GenomicFeatures.Mmusculus.UCSC.mm9 Version: 0.1.2 Depends: GenomicFeatures (>= 0.3.32) Imports: DBI, RSQLite, GenomicFeatures License: Artistic-2.0 Title: A transient package to store various Genomic Features for Mouse Description: Various Genome-related features, such as gene boundaries, CpG islands, etc. biocViews: AnnotationData, Mus_musculus Author: D. Sarkar, M. Lawrence Maintainer: Biocore Data Team source.ver: src/contrib/GenomicFeatures.Mmusculus.UCSC.mm9_0.1.2.tar.gz win.binary.ver: bin/windows/contrib/2.11/GenomicFeatures.Mmusculus.UCSC.mm9_0.1.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/GenomicFeatures.Mmusculus.UCSC.mm9_0.1.2.tgz Package: GenomicFeatures Version: 0.0.9 Imports: IRanges (>= 1.3.14) License: Artistic-2.0 Title: A transient package to store various Genomic Features Description: Various Genome-related features, such as gene boundaries, CpG islands, etc. biocViews: ExperimentData Author: D. Sarkar, M. Lawrence Maintainer: Deepayan Sarkar source.ver: src/contrib/GenomicFeatures_0.0.9.tar.gz Package: HEEBOdata Version: 1.0.0 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.11/HEEBOdata_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/HEEBOdata_1.0.0.tgz Package: HIVcDNAvantWout03 Version: 1.2.3 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_1.2.3.tar.gz win.binary.ver: bin/windows/contrib/2.11/HIVcDNAvantWout03_1.2.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/HIVcDNAvantWout03_1.2.3.tgz vignettes: vignettes/HIVcDNAvantWout03/inst/doc/hivData.pdf Package: ITALICSData Version: 2.0.1 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_2.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.11/ITALICSData_2.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/ITALICSData_2.0.1.tgz Package: Iyer517 Version: 1.4.4 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_1.4.4.tar.gz win.binary.ver: bin/windows/contrib/2.11/Iyer517_1.4.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/Iyer517_1.4.4.tgz vignettes: vignettes/Iyer517/inst/doc/Iyer517.pdf Package: MAQCsubsetAFX Version: 1.0.3 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_1.0.3.tar.gz win.binary.ver: bin/windows/contrib/2.11/MAQCsubsetAFX_1.0.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/MAQCsubsetAFX_1.0.3.tgz vignettes: vignettes/MAQCsubsetAFX/inst/doc/MAQCsubsetAFX.pdf Package: MAQCsubsetILM Version: 1.0.2 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_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.11/MAQCsubsetILM_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/MAQCsubsetILM_1.0.2.tgz vignettes: vignettes/MAQCsubsetILM/inst/doc/MAQCsubsetILM.pdf Package: MAQCsubset Version: 1.0.19 Depends: affy (>= 1.23.4), Biobase (>= 2.5.5), lumi, methods Suggests: genefilter 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_1.0.19.tar.gz win.binary.ver: bin/windows/contrib/2.11/MAQCsubset_1.0.19.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/MAQCsubset_1.0.19.tgz vignettes: vignettes/MAQCsubset/inst/doc/maqcNotes.pdf Package: MEEBOdata Version: 1.0.0 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.11/MEEBOdata_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/MEEBOdata_1.0.0.tgz Package: Neve2006 Version: 0.1.9 Depends: R (>= 2.5.0), 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_0.1.9.tar.gz win.binary.ver: bin/windows/contrib/2.11/Neve2006_0.1.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/Neve2006_0.1.9.tgz vignettes: vignettes/Neve2006/inst/doc/neve06notes.pdf Package: ProData Version: 1.0.3 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_1.0.3.tar.gz win.binary.ver: bin/windows/contrib/2.11/ProData_1.0.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/ProData_1.0.3.tgz Package: SNAData Version: 1.8.1 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_1.8.1.tar.gz win.binary.ver: bin/windows/contrib/2.11/SNAData_1.8.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/SNAData_1.8.1.tgz vignettes: vignettes/SNAData/inst/doc/SNAData.pdf Package: SpikeInSubset Version: 1.2.8 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_1.2.8.tar.gz win.binary.ver: bin/windows/contrib/2.11/SpikeInSubset_1.2.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/SpikeInSubset_1.2.8.tgz Package: SpikeIn Version: 1.4.4 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_1.4.4.tar.gz win.binary.ver: bin/windows/contrib/2.11/SpikeIn_1.4.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/SpikeIn_1.4.4.tgz Package: TargetSearchData Version: 1.0.1 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_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.11/TargetSearchData_1.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/TargetSearchData_1.0.1.tgz Package: XhybCasneuf Version: 1.0.6 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_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/2.11/XhybCasneuf_1.0.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/XhybCasneuf_1.0.6.tgz vignettes: vignettes/XhybCasneuf/inst/doc/Rplots.pdf, vignettes/XhybCasneuf/inst/doc/Xhyb.pdf Package: affydata Version: 1.11.10 Depends: R (>= 2.4.0), affy (>= 1.23.4) 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: Bioconductor Maintainer: Laurent source.ver: src/contrib/affydata_1.11.10.tar.gz win.binary.ver: bin/windows/contrib/2.11/affydata_1.11.10.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/affydata_1.11.10.tgz vignettes: vignettes/affydata/inst/doc/affydata.pdf Package: beta7 Version: 1.0.0 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_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.11/beta7_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/beta7_1.0.0.tgz Package: bronchialIL13 Version: 1.0-6 Depends: 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_1.0-6.tar.gz win.binary.ver: bin/windows/contrib/2.11/bronchialIL13_1.0-6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/bronchialIL13_1.0-6.tgz Package: ccTutorial Version: 1.0.17 Depends: R (>= 2.9.0), Ringo(>= 1.9.8), affy(>= 1.23.4), topGO(>= 1.13.1) 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_1.0.17.tar.gz win.binary.ver: bin/windows/contrib/2.11/ccTutorial_1.0.17.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/ccTutorial_1.0.17.tgz vignettes: vignettes/ccTutorial/inst/doc/ccTutorial.pdf, vignettes/ccTutorial/inst/doc/ccTutorialSupplement.pdf Package: ceuhm3 Version: 0.0.3 Depends: GGBase 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 Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/ceuhm3_0.0.3.tar.gz win.binary.ver: bin/windows/contrib/2.11/ceuhm3_0.0.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/ceuhm3_0.0.3.tgz Package: charmData Version: 0.99.1 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_0.99.1.tar.gz win.binary.ver: bin/windows/contrib/2.11/charmData_0.99.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/charmData_0.99.1.tgz Package: colonCA Version: 1.4.5 Depends: Biobase (>= 2.5.5) License: unknown 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_1.4.5.tar.gz win.binary.ver: bin/windows/contrib/2.11/colonCA_1.4.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/colonCA_1.4.5.tgz Package: davidTiling Version: 1.2.12 Depends: 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_1.2.12.tar.gz win.binary.ver: bin/windows/contrib/2.11/davidTiling_1.2.12.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/davidTiling_1.2.12.tgz Package: dressCheck Version: 0.0.15 Depends: R (>= 2.6.1), methods, Biobase (>= 2.5.5) 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_0.0.15.tar.gz win.binary.ver: bin/windows/contrib/2.11/dressCheck_0.0.15.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/dressCheck_0.0.15.tgz vignettes: vignettes/dressCheck/inst/doc/jcolet.pdf, vignettes/dressCheck/inst/doc/jcolet2.pdf, vignettes/dressCheck/inst/doc/jcolet3.pdf, vignettes/dressCheck/inst/doc/jcoletLong.pdf, vignettes/dressCheck/inst/doc/postRG.pdf, vignettes/dressCheck/inst/doc/short.pdf Package: dyebiasexamples Version: 1.0.6 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_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/2.11/dyebiasexamples_1.0.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/dyebiasexamples_1.0.6.tgz Package: ecoliLeucine Version: 1.2.5 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_1.2.5.tar.gz win.binary.ver: bin/windows/contrib/2.11/ecoliLeucine_1.2.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/ecoliLeucine_1.2.5.tgz Package: encoDnaseI Version: 0.1-4 Depends: R (>= 2.6.0), methods, Biobase (>= 2.5.5), lattice, GGtools, GGBase, snpMatrix 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_0.1-4.tar.gz win.binary.ver: bin/windows/contrib/2.11/encoDnaseI_0.1-4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/encoDnaseI_0.1-4.tgz vignettes: vignettes/encoDnaseI/inst/doc/dnaseUse.pdf Package: estrogen Version: 1.8.5 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_1.8.5.tar.gz win.binary.ver: bin/windows/contrib/2.11/estrogen_1.8.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/estrogen_1.8.5.tgz vignettes: vignettes/estrogen/inst/doc/estrogen.pdf Package: faahKO Version: 1.2.5 Suggests: 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_1.2.5.tar.gz win.binary.ver: bin/windows/contrib/2.11/faahKO_1.2.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/faahKO_1.2.5.tgz Package: facsDorit Version: 1.4.2 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_1.4.2.tar.gz win.binary.ver: bin/windows/contrib/2.11/facsDorit_1.4.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/facsDorit_1.4.2.tgz Package: fibroEset Version: 1.4.4 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_1.4.4.tar.gz win.binary.ver: bin/windows/contrib/2.11/fibroEset_1.4.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/fibroEset_1.4.4.tgz Package: frmaExampleData Version: 0.99.0 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_0.99.0.tar.gz win.binary.ver: bin/windows/contrib/2.11/frmaExampleData_0.99.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/frmaExampleData_0.99.0.tgz Package: gaschYHS Version: 1.0.3 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_1.0.3.tar.gz win.binary.ver: bin/windows/contrib/2.11/gaschYHS_1.0.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/gaschYHS_1.0.3.tgz Package: gatingMLData Version: 1.0.2 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_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.11/gatingMLData_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/gatingMLData_1.0.2.tgz Package: gcspikelite Version: 1.0.2 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 Author: Mark Robinson Maintainer: Mark Robinson source.ver: src/contrib/gcspikelite_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.11/gcspikelite_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/gcspikelite_1.0.2.tgz Package: geneLenDataBase Version: 0.99.4 Depends: R (>= 2.11.0) Imports: utils, rtracklayer, Biostrings, GenomicFeatures (>= 0.5.5) 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_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/2.11/geneLenDataBase_0.99.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/geneLenDataBase_0.99.4.tgz Package: golubEsets Version: 1.4.7 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_1.4.7.tar.gz win.binary.ver: bin/windows/contrib/2.11/golubEsets_1.4.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/golubEsets_1.4.7.tgz Package: hapmap100khind Version: 1.3.32 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_1.3.32.tar.gz win.binary.ver: bin/windows/contrib/2.11/hapmap100khind_1.3.32.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/hapmap100khind_1.3.32.tgz Package: hapmap100kxba Version: 1.3.3 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_1.3.3.tar.gz win.binary.ver: bin/windows/contrib/2.11/hapmap100kxba_1.3.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/hapmap100kxba_1.3.3.tgz Package: hapmap500knsp Version: 1.3.3 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_1.3.3.tar.gz win.binary.ver: bin/windows/contrib/2.11/hapmap500knsp_1.3.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/hapmap500knsp_1.3.3.tgz Package: hapmap500ksty Version: 1.3.3 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_1.3.3.tar.gz win.binary.ver: bin/windows/contrib/2.11/hapmap500ksty_1.3.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/hapmap500ksty_1.3.3.tgz Package: hapmapsnp5 Version: 1.3.3 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_1.3.3.tar.gz win.binary.ver: bin/windows/contrib/2.11/hapmapsnp5_1.3.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/hapmapsnp5_1.3.3.tgz Package: hapmapsnp6 Version: 1.3.3 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_1.3.3.tar.gz win.binary.ver: bin/windows/contrib/2.11/hapmapsnp6_1.3.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/hapmapsnp6_1.3.3.tgz Package: harbChIP Version: 1.0.5 Depends: R (>= 2.6.0), 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_1.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.11/harbChIP_1.0.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/harbChIP_1.0.5.tgz vignettes: vignettes/harbChIP/inst/doc/yeastUpstream.pdf Package: hgu133abarcodevecs Version: 0.0.4 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_0.0.4.tar.gz win.binary.ver: bin/windows/contrib/2.11/hgu133abarcodevecs_0.0.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/hgu133abarcodevecs_0.0.4.tgz Package: hgu133afrmavecs Version: 1.0.1 Depends: R (>= 2.10.0) License: GPL (>= 2) Title: Vectors used by frma for microarrays of type hgu133a Description: This package was automatically created by package frmaTools version 1.1.1. biocViews: AnnotationData, AffymetrixChip, hgu133a, Homo_sapiens Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall source.ver: src/contrib/hgu133afrmavecs_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.11/hgu133afrmavecs_1.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/hgu133afrmavecs_1.0.1.tgz Package: hgu133plus2barcodevecs Version: 0.0.4 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_0.0.4.tar.gz win.binary.ver: bin/windows/contrib/2.11/hgu133plus2barcodevecs_0.0.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/hgu133plus2barcodevecs_0.0.4.tgz Package: hgu133plus2frmavecs Version: 0.99.0 Depends: R (>= 2.10.0), utils License: GPL (>= 2) Title: Vectors used by frma for microarrays of type hgu133plus2 Description: This package was automatically created by package frmaTools version 1.0.3. biocViews: AnnotationData, AffymetrixChip, hgu133plus2, Homo_sapiens Author: Matthew N. McCall Maintainer: Matthew N. McCall source.ver: src/contrib/hgu133plus2frmavecs_0.99.0.tar.gz win.binary.ver: bin/windows/contrib/2.11/hgu133plus2frmavecs_0.99.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/hgu133plus2frmavecs_0.99.0.tgz Package: hgu2beta7 Version: 1.2.2 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: Biocore Team c/o BioC user list source.ver: src/contrib/hgu2beta7_1.2.2.tar.gz win.binary.ver: bin/windows/contrib/2.11/hgu2beta7_1.2.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/hgu2beta7_1.2.2.tgz Package: hmyriB36 Version: 0.99.4 Depends: R (>= 2.7.0), methods, Biobase (>= 2.5.5), GGBase(>= 2.99.0) Suggests: GGtools 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_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/2.11/hmyriB36_0.99.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/hmyriB36_0.99.4.tgz Package: humanStemCell Version: 0.2.3 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_0.2.3.tar.gz win.binary.ver: bin/windows/contrib/2.11/humanStemCell_0.2.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/humanStemCell_0.2.3.tgz Package: ind1KG Version: 0.1.3 Depends: R (>= 2.9.1), Rsamtools Suggests: GenomicFeatures, rtracklayer, org.Hs.eg.db, snpMatrix, SNPlocs.Hsapiens.dbSNP.20080617, 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 Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/ind1KG_0.1.3.tar.gz win.binary.ver: bin/windows/contrib/2.11/ind1KG_0.1.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/ind1KG_0.1.3.tgz vignettes: vignettes/ind1KG/inst/doc/ind1KG.pdf, vignettes/ind1KG/inst/doc/nov09rv.pdf Package: kidpack Version: 1.5.7 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_1.5.7.tar.gz win.binary.ver: bin/windows/contrib/2.11/kidpack_1.5.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/kidpack_1.5.7.tgz vignettes: vignettes/kidpack/inst/doc/kidpack.pdf Package: leeBamViews Version: 0.99.7 Depends: Biobase, Rsamtools (>= 0.1.50), BSgenome Imports: GenomicRanges, methods Suggests: GenomeGraphs, biomaRt, org.Sc.sgd.db, edgeR 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 Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/leeBamViews_0.99.7.tar.gz win.binary.ver: bin/windows/contrib/2.11/leeBamViews_0.99.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/leeBamViews_0.99.7.tgz vignettes: vignettes/leeBamViews/inst/doc/leeFull-dol.pdf, vignettes/leeBamViews/inst/doc/leeViews.pdf Package: lumiBarnes Version: 1.3.4 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 Author: Pan Du Maintainer: Pan Du source.ver: src/contrib/lumiBarnes_1.3.4.tar.gz win.binary.ver: bin/windows/contrib/2.11/lumiBarnes_1.3.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/lumiBarnes_1.3.4.tgz Package: lungExpression Version: 0.0.10 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_0.0.10.tar.gz win.binary.ver: bin/windows/contrib/2.11/lungExpression_0.0.10.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/lungExpression_0.0.10.tgz Package: maqcExpression4plex Version: 1.2 Suggests: oligo, makePlatformDesign 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_1.2.tar.gz win.binary.ver: bin/windows/contrib/2.11/maqcExpression4plex_1.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/maqcExpression4plex_1.2.tgz Package: mouse4302barcodevecs Version: 0.0.4 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_0.0.4.tar.gz win.binary.ver: bin/windows/contrib/2.11/mouse4302barcodevecs_0.0.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/mouse4302barcodevecs_0.0.4.tgz Package: mouse4302frmavecs Version: 0.99.0 Depends: R (>= 2.10.0), utils License: GPL (>= 2) Title: Vectors used by frma for microarrays of type mouse4302 Description: This package was automatically created by package frmaTools version 1.0.3. biocViews: AnnotationData, AffymetrixChip, mouse4302, Mus_musculus Author: Matthew N. McCall Maintainer: Matthew N. McCall source.ver: src/contrib/mouse4302frmavecs_0.99.0.tar.gz win.binary.ver: bin/windows/contrib/2.11/mouse4302frmavecs_0.99.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/mouse4302frmavecs_0.99.0.tgz Package: msdata Version: 0.1.4 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 threshhold 100.000. Extracts from FTICR Apex III, m/z 400-450 biocViews: ExperimentData Author: Steffen Neumann Maintainer: Steffen Neumann source.ver: src/contrib/msdata_0.1.4.tar.gz win.binary.ver: bin/windows/contrib/2.11/msdata_0.1.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/msdata_0.1.4.tgz Package: mvoutData Version: 0.99.4 Depends: R (>= 2.6.0), 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_0.99.4.tar.gz win.binary.ver: bin/windows/contrib/2.11/mvoutData_0.99.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/mvoutData_0.99.4.tgz Package: ppiData Version: 0.1.14 Depends: Rgraphviz, 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_0.1.14.tar.gz win.binary.ver: bin/windows/contrib/2.11/ppiData_0.1.14.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/ppiData_0.1.14.tgz vignettes: vignettes/ppiData/inst/doc/ppiStats.pdf Package: pumadata Version: 1.0.3 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_1.0.3.tar.gz win.binary.ver: bin/windows/contrib/2.11/pumadata_1.0.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/pumadata_1.0.3.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/2.11/rfcdmin_1.6.11.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/rfcdmin_1.6.11.tgz Package: stjudem Version: 1.2.2 Depends: R (>= 2.0.0), 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_1.2.2.tar.gz win.binary.ver: bin/windows/contrib/2.11/stjudem_1.2.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/stjudem_1.2.2.tgz Package: tinesath1cdf Version: 1.0.3 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_1.0.3.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/tinesath1cdf_1.0.3.tgz Package: tinesath1probe Version: 1.0.2 Depends: R (>= 1.6), matchprobes (>= 1.4.0) 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_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.11/tinesath1probe_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/tinesath1probe_1.0.2.tgz Package: yeastCC Version: 1.2.11 Depends: Biobase (>= 2.5.5) License: unknown 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_1.2.11.tar.gz win.binary.ver: bin/windows/contrib/2.11/yeastCC_1.2.11.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/yeastCC_1.2.11.tgz vignettes: vignettes/yeastCC/inst/doc/Spellmanetal.pdf Package: yeastExpData Version: 0.9.17 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_0.9.17.tar.gz win.binary.ver: bin/windows/contrib/2.11/yeastExpData_0.9.17.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/yeastExpData_0.9.17.tgz vignettes: vignettes/yeastExpData/inst/doc/yeastExample.pdf Package: yeastGSData Version: 0.1.5 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_0.1.5.tar.gz win.binary.ver: bin/windows/contrib/2.11/yeastGSData_0.1.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/yeastGSData_0.1.5.tgz Package: yeastRNASeq Version: 0.0.3 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_0.0.3.tar.gz win.binary.ver: bin/windows/contrib/2.11/yeastRNASeq_0.0.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.11/yeastRNASeq_0.0.3.tgz vignettes: vignettes/yeastRNASeq/inst/doc/yeastRNASeq.pdf