Package: ABAData Version: 1.12.0 Depends: R (>= 3.2) Suggests: BiocStyle, knitr, ABAEnrichment License: GPL (>= 2) MD5sum: 617a2967ed10a6b1f90406420a28545e NeedsCompilation: no Title: Averaged gene expression in human brain regions from Allen Brain Atlas Description: Provides the data for the gene expression enrichment analysis conducted in the package 'ABAEnrichment'. The package includes three datasets which are derived from the Allen Brain Atlas: (1) Gene expression data from Human Brain (adults) averaged across donors, (2) Gene expression data from the Developing Human Brain pooled into five age categories and averaged across donors and (3) a developmental effect score based on the Developing Human Brain expression data. All datasets are restricted to protein coding genes. biocViews: ExpressionData, Homo_sapiens_Data, MicroarrayData, RNASeqData Author: Steffi Grote Maintainer: Steffi Grote VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ABAData git_branch: RELEASE_3_8 git_last_commit: 9c2f0fb git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ABAData_1.12.0.tar.gz vignettes: vignettes/ABAData/inst/doc/ABAData.html vignetteTitles: ABAData: gene expression data to use with enrichment analysis package ABAEnrichment hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ABAData/inst/doc/ABAData.R Package: affycompData Version: 1.20.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp License: GPL (>= 2) MD5sum: 7dd3ccd7ee103e5fabc1beb000d08af2 NeedsCompilation: no Title: affycomp data Description: Data needed by the affycomp package. biocViews: MicroarrayData Author: Rafael A. Irizarry and Zhijin Wu with contributions from Simon Cawley Maintainer: Harris Jaffee git_url: https://git.bioconductor.org/packages/affycompData git_branch: RELEASE_3_8 git_last_commit: 3886f62 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/affycompData_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: affydata Version: 1.30.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Imports: methods Suggests: hgu95av2cdf, hgu133acdf License: GPL (>= 2) MD5sum: c4edc5ad12670675bc7fc5b993f29a36 NeedsCompilation: no Title: Affymetrix Data for Demonstration Purpose Description: Example datasets of a slightly large size. They represent 'real world examples', unlike the artificial examples included in the package affy. biocViews: ExperimentData, Tissue, MicroarrayData, TissueMicroarrayData Author: Laurent Gautier Maintainer: Harris Jaffee git_url: https://git.bioconductor.org/packages/affydata git_branch: RELEASE_3_8 git_last_commit: d5408d8 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/affydata_1.30.0.tar.gz vignettes: vignettes/affydata/inst/doc/affydata.pdf vignetteTitles: affydata primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/affydata/inst/doc/affydata.R Package: Affyhgu133A2Expr Version: 1.18.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 5944ee99dfc56eaedd6ca8a95dfd59dc NeedsCompilation: no Title: Affymetrix Human Genome U133A 2.0 Array (GPL571) Expression Data Package Description: Contains pre-built human (GPL571) databases of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133A2Expr git_branch: RELEASE_3_8 git_last_commit: b2914b6 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/Affyhgu133A2Expr_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Affyhgu133aExpr Version: 1.20.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 9254b9cb76829110172cb80b01921ddc NeedsCompilation: no Title: Affymetrix Human hgu133a Array (GPL96) Expression Data Package Description: Contains pre-built human (GPL96) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133aExpr git_branch: RELEASE_3_8 git_last_commit: 971c1e8 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/Affyhgu133aExpr_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Affyhgu133Plus2Expr Version: 1.16.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: 86ff16e83ac8445c7242525e1cbc146a NeedsCompilation: no Title: Affyhgu133Plus2Expr (GPL570) Expression Data Package Description: Contains pre-built human (GPL570) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Homo_sapiens_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affyhgu133Plus2Expr git_branch: RELEASE_3_8 git_last_commit: c3b2542 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/Affyhgu133Plus2Expr_1.16.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: AffymetrixDataTestFiles Version: 0.20.0 Depends: R (>= 2.5.0) License: LGPL-2.1 MD5sum: 9ba84883ca62f5f7b73d9cd3fa1f36a5 NeedsCompilation: no Title: Affymetrix data files (CEL, CDF, CHP, EXP, PGF, PSI) for testing Description: This package contains annotation data files and sample data files of Affymetrix file formats. The files originate from the Affymetrix' Fusion SDK distribution and other official sources. biocViews: ExperimentData, MicroarrayData Author: Henrik Bengtsson [aut, cre], James Bullard [aut], Kasper Daniel Hansen [aut] Maintainer: Henrik Bengtsson git_url: https://git.bioconductor.org/packages/AffymetrixDataTestFiles git_branch: RELEASE_3_8 git_last_commit: c63a411 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/AffymetrixDataTestFiles_0.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Affymoe4302Expr Version: 1.20.0 Depends: R (>= 2.10) License: GPL (>=2) MD5sum: e21ed8d45f198ac957d5343b48dd8d2c NeedsCompilation: no Title: Affymetrix Mouse Genome 430 2.0 Array (GPL1261) Expression Data Package Description: Contains pre-built mouse (GPL1261) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. biocViews: Genome, Mus_musculus_Data, GEO Author: Zhicheng Ji, Hongkai Ji Maintainer: Zhicheng Ji git_url: https://git.bioconductor.org/packages/Affymoe4302Expr git_branch: RELEASE_3_8 git_last_commit: 244c0e0 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/Affymoe4302Expr_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: airway Version: 1.2.0 Depends: R (>= 2.10), SummarizedExperiment Suggests: knitr, GEOquery License: LGPL MD5sum: 1b539cecd5b5a3b3550b659ec1f21b89 NeedsCompilation: no Title: RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014 Description: This package provides a RangedSummarizedExperiment object of read counts in genes for an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. Details on the gene model and read counting procedure are provided in the package vignette. The citation for the experiment is: Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri R Jr, Tantisira KG, Weiss ST, Lu Q. 'RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells.' PLoS One. 2014 Jun 13;9(6):e99625. PMID: 24926665. GEO: GSE52778. biocViews: ExperimentData, SequencingData, RNASeqData, GEO Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/airway git_branch: RELEASE_3_8 git_last_commit: a3fc2bc git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/airway_1.2.0.tar.gz vignettes: vignettes/airway/inst/doc/airway.html vignetteTitles: Airway smooth muscle cells hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/airway/inst/doc/airway.R suggestsMe: IHWpaper, RegParallel Package: ALL Version: 1.24.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Suggests: rpart License: Artistic-2.0 MD5sum: 815e7ffa1cb6eb8d71d29a5f450ff804 NeedsCompilation: no Title: A data package Description: Data of T- and B-cell Acute Lymphocytic Leukemia from the Ritz Laboratory at the DFCI (includes Apr 2004 versions) biocViews: ExperimentData, CancerData, LeukemiaCancerData Author: Xiaochun Li Maintainer: Robert Gentleman git_url: https://git.bioconductor.org/packages/ALL git_branch: RELEASE_3_8 git_last_commit: 9076eaf git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ALL_1.24.0.tar.gz vignettes: vignettes/ALL/inst/doc/ALLintro.pdf vignetteTitles: ALL data intro hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ALL/inst/doc/ALLintro.R suggestsMe: SNAGEEdata Package: allenpvc Version: 1.0.0 Depends: R (>= 3.5.0), AnnotationHub, ExperimentHub (>= 1.7.0), SingleCellExperiment Suggests: BiocStyle, knitr, rmarkdown License: CC0 MD5sum: e77a28b830842ee034930432e95fdfaf NeedsCompilation: no Title: GEO accession data GSE71585 as a SingleCellExperiment Description: Celular taxonomy of the primary visual cortex in adult mice based on single cell RNA-sequencing from a study performed by the Allen Institute for Brain Science. In said study 49 transcriptomic cell types are identified. biocViews: ExperimentData, ExpressionData, SingleCellData, RNASeqData Author: Diogo P. P. Branco Maintainer: Diogo P. P. Branco VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/allenpvc git_branch: RELEASE_3_8 git_last_commit: b7bed86 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/allenpvc_1.0.0.tar.gz vignettes: vignettes/allenpvc/inst/doc/allenpvc.html vignetteTitles: Vignette Title hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/allenpvc/inst/doc/allenpvc.R Package: ALLMLL Version: 1.22.0 Depends: R (>= 2.10), affy (>= 1.23.4) License: GPL-2 MD5sum: fc9e850c94ac9ec9c377f5e8843e7673 NeedsCompilation: no Title: A subset of arrays from a large acute lymphoblastic leukemia (ALL) study Description: This package provides probe-level data for 20 HGU133A and 20 HGU133B arrays which are a subset of arrays from a large ALL study. The data is for the MLL arrays. This data was published in Mary E. Ross, Xiaodong Zhou, Guangchun Song, Sheila A. Shurtleff, Kevin Girtman, W. Kent Williams, Hsi-Che Liu, Rami Mahfouz, Susana C. Raimondi, Noel Lenny, Anami Patel, and James R. Downing (2003) Classification of pediatric acute lymphoblastic leukemia by gene expression profiling Blood 102: 2951-2959 biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData Author: B. M. Bolstad git_url: https://git.bioconductor.org/packages/ALLMLL git_branch: RELEASE_3_8 git_last_commit: 79c9f06 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ALLMLL_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: alpineData Version: 1.8.0 Depends: ExperimentHub, GenomicAlignments Imports: utils, AnnotationHub Suggests: GenomicAlignments, knitr License: GPL (>=2) MD5sum: 56b8097bf76942789ec2694ad0fa51e7 NeedsCompilation: no Title: Data for the alpine package vignette Description: A small subset of paired-end RNA-seq reads from four samples of the GEUVADIS project. biocViews: SequencingData, RNASeqData, ExpressionData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/alpineData git_branch: RELEASE_3_8 git_last_commit: 1a8b99e git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/alpineData_1.8.0.tar.gz vignettes: vignettes/alpineData/inst/doc/alpineData.html vignetteTitles: tximport hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/alpineData/inst/doc/alpineData.R Package: AmpAffyExample Version: 1.22.0 Depends: R (>= 2.4.0), affy (>= 1.23.4) Suggests: hgu133acdf License: LGPL (>= 2) MD5sum: 89fc3d6d5cff3852ec8b8748898bf8af NeedsCompilation: no Title: Example of Amplified Data Description: Six arrays. Three from amplified RNA, three from the typical procedure. biocViews: ExperimentData, MicroarrayData Author: Rafael A. Irizarry Maintainer: Rafael A. Irizarry git_url: https://git.bioconductor.org/packages/AmpAffyExample git_branch: RELEASE_3_8 git_last_commit: be30bf2 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/AmpAffyExample_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: AneuFinderData Version: 1.10.0 Depends: R (>= 3.3) License: file LICENSE MD5sum: aeee3783942cb420cfb1a39dbbe1b9cc NeedsCompilation: no Title: WGSCS Data for Demonstration Purposes Description: Whole-genome single cell sequencing data for demonstration purposes in the AneuFinder package. biocViews: CopyNumberVariationData, LungCancerData, Homo_sapiens_Data, SequencingData Author: Aaron Taudt Maintainer: Aaron Taudt git_url: https://git.bioconductor.org/packages/AneuFinderData git_branch: RELEASE_3_8 git_last_commit: ef7fc27 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/AneuFinderData_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Package: antiProfilesData Version: 1.18.0 Depends: Biobase, Suggests: frma, GEOquery, GEOmetadb License: Artistic-2.0 MD5sum: 6db261abb425b57ede7976f9b0a0ca90 NeedsCompilation: no Title: Normal colon and cancer preprocessed affy data for antiProfile building. Description: Colon normal tissue and cancer samples used in Corrada Bravo, et al. gene expression anti-profiles paper: BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272. Measurements are z-scores obtained from the GeneExpression Barcode in the 'frma' package biocViews: ExperimentData, MicroarrayData, Tissue, CancerData, ColonCancerData Author: Hector Corrada Bravo, Matthew McCall and Rafael A. Irizarry Maintainer: Hector Corrada Bravo git_url: https://git.bioconductor.org/packages/antiProfilesData git_branch: RELEASE_3_8 git_last_commit: db2246a git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/antiProfilesData_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: aracne.networks Version: 1.8.0 Depends: R (>= 3.3), viper License: file LICENSE MD5sum: 1dd61303e99861938db45495480b8dea NeedsCompilation: no Title: ARACNe-inferred gene networks from TCGA tumor datasets Description: This package contains ARACNe-inferred networks from TCGA tumor datasets. It also contains a function to export them into plain-text format. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData Author: Federico M. Giorgi Maintainer: Federico M. Giorgi , Mariano Alvarez git_url: https://git.bioconductor.org/packages/aracne.networks git_branch: RELEASE_3_8 git_last_commit: 23db789 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/aracne.networks_1.8.0.tar.gz vignettes: vignettes/aracne.networks/inst/doc/aracne.networks.pdf vignetteTitles: Using aracne.networks hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/aracne.networks/inst/doc/aracne.networks.R Package: ARRmData Version: 1.18.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: 16ccdc6a5bc334b90c45e81103075a58 NeedsCompilation: no Title: Example dataset for normalization of Illumina 450k Methylation data Description: Raw Beta values from 36 samples across 3 groups from Illumina 450k methylation arrays biocViews: ExperimentData, MethylationArrayData Author: Jean-Philippe Fortin, Celia M.T. Greenwood, Aurelie Labbe Maintainer: Jean-Philippe Fortin git_url: https://git.bioconductor.org/packages/ARRmData git_branch: RELEASE_3_8 git_last_commit: 2086b16 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ARRmData_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: AshkenazimSonChr21 Version: 1.12.0 Suggests: knitr, VariantAnnotation License: Artistic-2.0 MD5sum: b565b952357149f37240f4fa62dfc425 NeedsCompilation: no Title: Annotated variants on the chromosome 21, human genome 19, Ashkenazim Trio son sample Description: SonVariantsChr21 is a dataset of annotated genomic variants coming from Complete Genomics whole genome sequencing. Data comes from GIAB project, Ashkenazim Trio, sample HG002 run 1. Both vcf and annotated data frame are provided. biocViews: GenomicVariation, Sequencing, WholeGenome Author: Tomasz Stokowy Maintainer: Who to complain to VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/AshkenazimSonChr21 git_branch: RELEASE_3_8 git_last_commit: 61ae491 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/AshkenazimSonChr21_1.12.0.tar.gz vignettes: vignettes/AshkenazimSonChr21/inst/doc/AshkenazimSonChr21.pdf vignetteTitles: RareVariantVis hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/AshkenazimSonChr21/inst/doc/AshkenazimSonChr21.R Package: ASICSdata Version: 1.2.0 Depends: R (>= 3.5) Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: bb4f0522ab312de30adfa029a55e023b NeedsCompilation: no Title: Example of 1D NMR spectra data for ASICS package Description: 1D NMR example spectra and additional data for use with the ASICS package. Raw 1D Bruker spectral data files were found in the MetaboLights database (https://www.ebi.ac.uk/metabolights/, study MTBLS1). biocViews: ExperimentData, Homo_sapiens_Data Author: Gaëlle Lefort [aut, cre], Rémi Servien [aut], Nathalie Villa-Vialaneix [aut] Maintainer: Gaëlle Lefort VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ASICSdata git_branch: RELEASE_3_8 git_last_commit: e809e66 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ASICSdata_1.2.0.tar.gz vignettes: vignettes/ASICSdata/inst/doc/ASICSdata.html vignetteTitles: ASICSdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: AssessORFData Version: 1.0.0 Depends: R (>= 3.5.0) Imports: DECIPHER, utils Suggests: AssessORF, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 53b9314533795f7344f755bccd72a1ec NeedsCompilation: no Title: Data and Files for the AssessORF Package Description: This package provides access to mapping and results objects generated by the AssessORF package, as well as the genome sequences for the strains corresponding to those objects. biocViews: OrganismData, Bacillus_subtilis_Data, Escherichia_coli_Data, Pseudomonas_aeruginosa_Data, Staphylococcus_aureus_Data, Genome, Proteome, SequencingData Author: Deepank Korandla [aut, cre] Maintainer: Deepank Korandla VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/AssessORFData git_branch: RELEASE_3_8 git_last_commit: 06ac74a git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/AssessORFData_1.0.0.tar.gz vignettes: vignettes/AssessORFData/inst/doc/AssessORFDataGuide.pdf vignetteTitles: Using AssessORF hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/AssessORFData/inst/doc/AssessORFDataGuide.R Package: bcellViper Version: 1.18.0 Depends: R(>= 2.14.0), Biobase, methods License: GPL (>=2) MD5sum: 9fb04cd65ec9c1bd6673bf0e53878c28 NeedsCompilation: no Title: Human B-cell transcriptional interactome and normal human B-cell expression data Description: This package provides a human B-cell context-specific transcriptional regulatory network and a human normal B-cells dataset for the examples in package viper. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData Author: Mariano Javier Alvarez Maintainer: Mariano Javier Alvarez git_url: https://git.bioconductor.org/packages/bcellViper git_branch: RELEASE_3_8 git_last_commit: f4e2d34 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/bcellViper_1.18.0.tar.gz vignettes: vignettes/bcellViper/inst/doc/bcellViper.pdf vignetteTitles: Using bcellViper hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bcellViper/inst/doc/bcellViper.R Package: beadarrayExampleData Version: 1.20.0 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>= 2.0.0) License: GPL-2 MD5sum: 256c9a9bb54f750aba53708c59e3c132 NeedsCompilation: no Title: Example data for the beadarray package Description: An small dataset that can be used to run examples from the beadarray vignette and examples biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/beadarrayExampleData git_branch: RELEASE_3_8 git_last_commit: 24d66b7 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/beadarrayExampleData_1.20.0.tar.gz vignettes: vignettes/beadarrayExampleData/inst/doc/beadarrayExampleData.pdf vignetteTitles: beadarrayExampleData: example data for the beadarray package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/beadarrayExampleData/inst/doc/beadarrayExampleData.R Package: BeadArrayUseCases Version: 1.20.0 Imports: beadarray (>= 2.3.18), limma, GEOquery Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db License: GPL-2 MD5sum: aa5309f7583a03c59235ce459a749cd6 NeedsCompilation: no Title: Analysing Illumina BeadArray expression data using Bioconductor Description: Example data files and use cases for processing Illumina BeadArray expression data using Bioconductor biocViews: MicroarrayData Author: Mark Dunning, Wei Shi, Andy Lynch, Mike Smith, Matt Ritchie Maintainer: Mike Smith git_url: https://git.bioconductor.org/packages/BeadArrayUseCases git_branch: RELEASE_3_8 git_last_commit: b369e83 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/BeadArrayUseCases_1.20.0.tar.gz vignettes: vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.pdf vignetteTitles: BeadArrayUseCases.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.R Package: beta7 Version: 1.20.0 Depends: R (>= 2.4.0), marray License: LGPL MD5sum: 135330c43b9aa93aedc4559f15e83c76 NeedsCompilation: no Title: Rodriguez et al. (2004) Differential Gene Expression by Memory/Effector T Helper Cells Bearing the Gut-Homing Receptor Integrin alpha4 beta7. Description: Data from 6 gpr files aims to identify differential expressed genes between the beta 7+ and beta 7- memory T helper cells. biocViews: ExperimentData, Homo_sapiens_Data, CGHData, MicroarrayData Author: Jean Yang Maintainer: Jean Yang git_url: https://git.bioconductor.org/packages/beta7 git_branch: RELEASE_3_8 git_last_commit: c797d45 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/beta7_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: biotmleData Version: 1.6.0 Depends: R (>= 3.0) Suggests: Biobase, SummarizedExperiment License: file LICENSE MD5sum: 14d22102df0583c9d12c3bc003a4c544 NeedsCompilation: no Title: Example experimental microarray data set for the "biotmle" R package Description: Microarray data (from the Illumina Ref-8 BeadChips platform) and phenotype-level data from an epidemiological investigation of benzene exposure, packaged using "SummarizedExperiemnt", for use as an example with the "biotmle" R package. biocViews: GeneExpression, DifferentialExpression, Sequencing, Microarray, RNASeq Author: Nima Hejazi [aut, cre] Maintainer: Nima Hejazi git_url: https://git.bioconductor.org/packages/biotmleData git_branch: RELEASE_3_8 git_last_commit: 075e59f git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/biotmleData_1.6.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Package: bladderbatch Version: 1.20.0 Depends: Biobase License: Artistic-2.0 MD5sum: 27cf90b928cffce1c1ae3e0b3a99e687 NeedsCompilation: no Title: Bladder gene expression data illustrating batch effects Description: This package contains microarray gene expression data on 57 bladder samples from 5 batches. The data are used as an illustrative example for the sva package. biocViews: ExperimentData, CancerData, MicroarrayData Author: Jeffrey T. Leek Maintainer: Jeffrey T. Leek git_url: https://git.bioconductor.org/packages/bladderbatch git_branch: RELEASE_3_8 git_last_commit: 4bc4218 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/bladderbatch_1.20.0.tar.gz vignettes: vignettes/bladderbatch/inst/doc/bladderbatch.pdf vignetteTitles: bladderbatchTutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/bladderbatch/inst/doc/bladderbatch.R Package: blimaTestingData Version: 1.2.0 Depends: R(>= 3.0.0) Suggests: blima, beadarray, illuminaHumanv4.db, BiocStyle License: GPL-3 MD5sum: 7e41a94448ab84c270161d5e9cb5a623 NeedsCompilation: no Title: Data for testing of the package blima. Description: Experiment data package. The set were prepared using microarray images of human mesenchymal cells treated with various supplements. This package is intended to provide example data to test functionality provided by blima. biocViews: MicroarrayData, ExperimentData, GEO Author: Vojtech Kulvait Maintainer: Vojtech Kulvait URL: https://bitbucket.org/kulvait/blima git_url: https://git.bioconductor.org/packages/blimaTestingData git_branch: RELEASE_3_8 git_last_commit: fe3ee6a git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/blimaTestingData_1.2.0.tar.gz vignettes: vignettes/blimaTestingData/inst/doc/blimaTestingData.pdf vignetteTitles: blimaTestingData.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/blimaTestingData/inst/doc/blimaTestingData.R Package: BloodCancerMultiOmics2017 Version: 1.2.0 Depends: R (>= 3.5.0) Imports: beeswarm, Biobase, DESeq2, devtools, dplyr, ggdendro, ggplot2, glmnet, graphics, grDevices, grid, gtable, ipflasso, methods, RColorBrewer, reshape2, scales, stats, SummarizedExperiment, survival, tibble Suggests: BiocStyle, knitr, rmarkdown, abind, AnnotationDbi, biomaRt, broom, colorspace, cowplot, dendsort, doParallel, foreach, forestplot, genefilter, ggbeeswarm, ggtern, gridExtra, hexbin, IHW, limma, magrittr, Matrix, maxstat, nat, org.Hs.eg.db, pheatmap, piano, readxl, Rtsne, tidyr, tidyverse, xtable License: LGPL (>= 3) MD5sum: 15b928a89d53d59a59901c520a2368f6 NeedsCompilation: no Title: "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al. - experimental data and complete analysis Description: The package contains data of the Primary Blood Cancer Encyclopedia (PACE) project together with a complete executable transcript of the statistical analysis and reproduces figures presented in the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) 128(1):427-445. doi:10.1172/JCI93801. biocViews: ExperimentData, ReproducibleResearch, CancerData, LeukemiaCancerData Author: Malgorzata Oles, Sascha Dietrich, Junyan Lu, Britta Velten, Andreas Mock, Vladislav Kim, Wolfgang Huber Maintainer: Malgorzata Oles VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/BloodCancerMultiOmics2017 git_branch: RELEASE_3_8 git_last_commit: 781296c git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/BloodCancerMultiOmics2017_1.2.0.tar.gz vignettes: vignettes/BloodCancerMultiOmics2017/inst/doc/BloodCancerMultiOmics2017-dataOverview.html, vignettes/BloodCancerMultiOmics2017/inst/doc/BloodCancerMultiOmics2017.html vignetteTitles: BloodCancerMultiOmics2017 - data overview, BloodCancerMultiOmics2017 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/BloodCancerMultiOmics2017/inst/doc/BloodCancerMultiOmics2017-dataOverview.R, vignettes/BloodCancerMultiOmics2017/inst/doc/BloodCancerMultiOmics2017.R Package: brainImageRdata Version: 1.0.0 Depends: ExperimentHub Suggests: knitr License: CC BY-SA 4.0 MD5sum: 87e676b7cde0a2abb781670ade0e68d9 NeedsCompilation: no Title: Image masks and expression data for use with BrainImageR Description: brainImageRdata contains image masks for the developing human and the adult human brain. These masks can be used in conjunction with the gene expression data to generate spatial gene set enrichment plots. It also contains the expression data for the 15 pcw human brain, the adult human brain, and the developing human brain. biocViews: OrganismData, Homo_sapiens_Data, ExpressionData Author: Sara Linker Maintainer: Sara Linker VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/brainImageRdata git_branch: RELEASE_3_8 git_last_commit: 2bdb16c git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/brainImageRdata_1.0.0.tar.gz vignettes: vignettes/brainImageRdata/inst/doc/brainImageRdata.html vignetteTitles: brainImageRdata hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/brainImageRdata/inst/doc/brainImageRdata.R Package: breakpointRdata Version: 1.0.0 Depends: R (>= 3.5) Suggests: knitr, BiocStyle, License: file LICENSE MD5sum: 6484ead0a5a57fe29f9bd0edba517f10 NeedsCompilation: no Title: Strand-seq data for demonstration purposes Description: Strand-seq data to demonstrate functionalities of breakpointR package. biocViews: ExperimentData, Homo_sapiens_Data, SequencingData, DNASeqData, Genome, SingleCellData Author: David Porubsky, Aaron Taudt, Ashley Sanders Maintainer: David Porubsky URL: https://github.com/daewoooo/breakpointRdata VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/breakpointRdata git_branch: RELEASE_3_8 git_last_commit: 4cf1155 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/breakpointRdata_1.0.0.tar.gz vignettes: vignettes/breakpointRdata/inst/doc/breakpointRdata-knitr.pdf vignetteTitles: Example data for breakpointR hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/breakpointRdata/inst/doc/breakpointRdata-knitr.R Package: breastCancerMAINZ Version: 1.20.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: d3c2b64b8798cb80b9f214fcb4958dfd NeedsCompilation: no Title: Gene expression dataset published by Schmidt et al. [2008] (MAINZ). Description: Gene expression data from the breast cancer study published by Schmidt et al. in 2008, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerMAINZ git_branch: RELEASE_3_8 git_last_commit: c0f9982 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/breastCancerMAINZ_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerNKI Version: 1.20.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 2f70179c1ded047824519512d9eed41b NeedsCompilation: no Title: Genexpression dataset published by van't Veer et al. [2002] and van de Vijver et al. [2002] (NKI). Description: Genexpression data from a breast cancer study published by van't Veer et al. in 2002 and van de Vijver et al. in 2002, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, CGHData, MicroarrayData, OneChannelData, ChipOnChipData Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerNKI git_branch: RELEASE_3_8 git_last_commit: 1ed8cda git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/breastCancerNKI_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: seventyGeneData Package: breastCancerTRANSBIG Version: 1.20.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: c3fe59c8cf826647a2f11320f6b7a3bd NeedsCompilation: no Title: Gene expression dataset published by Desmedt et al. [2007] (TRANSBIG). Description: Gene expression data from a breast cancer study published by Desmedt et al. in 2007, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerTRANSBIG git_branch: RELEASE_3_8 git_last_commit: 8b25372 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/breastCancerTRANSBIG_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerUNT Version: 1.20.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: f70937326bfeab71ab497ce4ea46ff76 NeedsCompilation: no Title: Gene expression dataset published by Sotiriou et al. [2007] (UNT). Description: Gene expression data from a breast cancer study published by Sotiriou et al. in 2007, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, TwoChannelData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerUNT git_branch: RELEASE_3_8 git_last_commit: b90c844 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/breastCancerUNT_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerUPP Version: 1.20.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 8a54948ea0e0328b3035e3f4d4551960 NeedsCompilation: no Title: Gene expression dataset published by Miller et al. [2005] (UPP). Description: Gene expression data from a breast cancer study published by Miller et al. in 2005, provided as an eSet. biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerUPP git_branch: RELEASE_3_8 git_last_commit: 7ddbfb4 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/breastCancerUPP_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: breastCancerVDX Version: 1.20.0 Depends: R (>= 2.5.0) Suggests: survcomp, genefu, Biobase License: Artistic-2.0 MD5sum: 4b05a31ca8f4a0a069137dfc614039e8 NeedsCompilation: no Title: Gene expression datasets published by Wang et al. [2005] and Minn et al. [2007] (VDX). Description: Gene expression data from a breast cancer study published by Wang et al. in 2005 and Minn et al. in 2007, provided as an eSet. biocViews: ExperimentData, Genome, Homo_sapiens_Data, CancerData, BreastCancerData, LungCancerData, MicroarrayData, OneChannelData, GEO Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Markus Schroeder , Benjamin Haibe-Kains URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/breastCancerVDX git_branch: RELEASE_3_8 git_last_commit: b9e41bd git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/breastCancerVDX_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: brgedata Version: 1.4.0 Depends: R (>= 3.4), Biobase Imports: SummarizedExperiment Suggests: minfi, MultiAssayExperiment, knitr, rexposome License: MIT + file LICENSE MD5sum: d2ad8ac2f818311243fa6afe0907e93c NeedsCompilation: no Title: Exposures, Gene Expression and Methylation data for ilustration purpouses Description: This package contains several sets of omics data including Gene Expression (ExpressionSet), Methylation (GenomicRatioSet), Proteome and Exposome (ExposomeSet). This data is used in vignettes and exaples at MEAL, MultiDataSet and omicRexposome. biocViews: ExperimentData,Homo_sapiens_Data,MicroarrayData,MethylationArrayData Author: Carlos Ruiz-Arenas [aut, cre], Carles Hernandez-Ferrer [aut], Juan R. Gonzalez [aut] Maintainer: Carlos Ruiz-Arenas VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/brgedata git_branch: RELEASE_3_8 git_last_commit: 917432f git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/brgedata_1.4.0.tar.gz vignettes: vignettes/brgedata/inst/doc/general_description.html vignetteTitles: brgedata -- data R package with three omic data-set and exposome data-set from the same Spanish pupulation hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/brgedata/inst/doc/general_description.R Package: bronchialIL13 Version: 1.20.0 Depends: R(>= 2.10.0), affy (>= 1.23.4) License: GPL-2 MD5sum: 985ae91a81f525c68653969a59631523 NeedsCompilation: no Title: time course experiment involving il13 Description: derived from CNMC (pepr.cnmcresearch.org) http://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=95 Human Bronchial Cell line A549 biocViews: ExperimentData, MicroarrayData Author: Vince Carey Maintainer: Vince Carey URL: http://www.biostat.harvard.edu/~carey git_url: https://git.bioconductor.org/packages/bronchialIL13 git_branch: RELEASE_3_8 git_last_commit: bef90a2 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/bronchialIL13_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bsseqData Version: 0.20.0 Depends: R (>= 2.15), bsseq (>= 1.16.0) License: Artistic-2.0 MD5sum: fb6e98b0545c71b6447d69747244036c NeedsCompilation: no Title: Example whole genome bisulfite data for the bsseq package Description: Example whole genome bisulfite data for the bsseq package biocViews: Genome, CancerData, ColonCancerData, SequencingData Author: Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/bsseqData git_branch: RELEASE_3_8 git_last_commit: eb04e68 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/bsseqData_0.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cancerdata Version: 1.20.0 Depends: R (>= 2.10.1), Biobase License: GPL (>= 2) MD5sum: 2fb3c2815ba70f6edcf0254c19afed66 NeedsCompilation: no Title: Development and validation of diagnostic tests from high-dimensional molecular data: Datasets Description: Dataset for the R package cancerclass biocViews: CancerData, MicroarrayData Author: Jan Budczies, Daniel Kosztyla Maintainer: Daniel Kosztyla git_url: https://git.bioconductor.org/packages/cancerdata git_branch: RELEASE_3_8 git_last_commit: 19cb779 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/cancerdata_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CardinalWorkflows Version: 1.14.0 Depends: R (>= 2.10), Cardinal Suggests: BiocStyle License: Artistic-2.0 MD5sum: 5c7621b5e018a39a1dc3f2ea76532695 NeedsCompilation: no Title: Datasets and workflows for the Cardinal mass spectrometry imaging package Description: Datasets and workflows for Cardinal: DESI and MALDI examples including pig fetus, cardinal painting, and human RCC. biocViews: ExperimentData, MassSpectrometryData, ImagingMassSpectrometryData Author: Kylie A. Bemis Maintainer: Kylie A. Bemis git_url: https://git.bioconductor.org/packages/CardinalWorkflows git_branch: RELEASE_3_8 git_last_commit: bace2d8 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/CardinalWorkflows_1.14.0.tar.gz vignettes: vignettes/CardinalWorkflows/inst/doc/Workflows-classification.pdf, vignettes/CardinalWorkflows/inst/doc/Workflows-clustering.pdf vignetteTitles: Classification example workflow, Clustering example workflow hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CardinalWorkflows/inst/doc/Workflows-classification.R, vignettes/CardinalWorkflows/inst/doc/Workflows-clustering.R Package: ccdata Version: 1.8.0 Depends: R (>= 3.3) License: MIT + file LICENSE MD5sum: 43a2ecfa4bf126deb0a2ef4abf1c349e NeedsCompilation: no Title: Data for Combination Connectivity Mapping (ccmap) Package Description: This package contains microarray gene expression data generated from the Connectivity Map build 02 and LINCS l1000. The data are used by the ccmap package to find drugs and drug combinations to mimic or reverse a gene expression signature. biocViews: ExperimentData, MicroarrayData, ExpressionData Author: Alex Pickering Maintainer: Alex Pickering git_url: https://git.bioconductor.org/packages/ccdata git_branch: RELEASE_3_8 git_last_commit: d92b4e1 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ccdata_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Package: CCl4 Version: 1.20.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), limma License: Artistic-2.0 MD5sum: f8e6ef164ec15f7b8af5bfcd78fcc34b NeedsCompilation: no Title: Carbon Tetrachloride (CCl4) treated hepatocytes Description: NChannelSet for rat hepatocytes treated with Carbon Tetrachloride (CCl4) data from LGC company. biocViews: ExperimentData, Genome, Rattus_norvegicus_Data, MicroarrayData Author: Audrey Kauffmann, Wolfgang Huber Maintainer: Audrey Kauffmann git_url: https://git.bioconductor.org/packages/CCl4 git_branch: RELEASE_3_8 git_last_commit: 08be361 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/CCl4_1.20.0.tar.gz vignettes: vignettes/CCl4/inst/doc/CCl4.pdf vignetteTitles: CCl4 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CCl4/inst/doc/CCl4.R Package: ccTutorial Version: 1.20.0 Depends: R (>= 2.10), Ringo(>= 1.9.8), affy(>= 1.23.4), topGO(>= 1.13.1) Imports: Biobase Suggests: biomaRt, Biobase(>= 2.5.5), xtable License: Artistic-2.0 MD5sum: bf29fe20285bcedbd73d52a641ebb751 NeedsCompilation: no Title: Data package for ChIP-chip tutorial Description: This is a data package that accompanies a ChIP-chip tutorial, which has been published in PLoS Computational Biology. The data and source code in this package allow the reader to completely reproduce the steps in the tutorial. biocViews: ExperimentData, Mus_musculus_Data, MicroarrayData, ChipOnChipData Author: Joern Toedling, Wolfgang Huber Maintainer: Joern Toedling git_url: https://git.bioconductor.org/packages/ccTutorial git_branch: RELEASE_3_8 git_last_commit: 6d0cb0b git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ccTutorial_1.20.0.tar.gz vignettes: vignettes/ccTutorial/inst/doc/ccTutorial.pdf, vignettes/ccTutorial/inst/doc/ccTutorialSupplement.pdf vignetteTitles: A tutorial on how to analyze ChIP-chip readouts using Bioconductor, Supplement to A tutorial on how to analyze ChIP-chip readouts using Bioconductor hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ccTutorial/inst/doc/ccTutorial.R, vignettes/ccTutorial/inst/doc/ccTutorialSupplement.R Package: celarefData Version: 1.0.0 Depends: R (>= 3.5.0) Suggests: ExperimentHub, knitr, rmarkdown License: GPL-3 MD5sum: fcf4c1723f025947fa6012f02e2aa33c NeedsCompilation: no Title: Processed scRNA data for celaref Vignette - cell labelling by reference Description: This experiment data contains some processed data used in the celaref package vignette. These are publically available datasets, that have been processed by celaref package, and can be manipulated further with it. biocViews: ExperimentData, SingleCellData Author: Sarah Williams [aut, cre] Maintainer: Sarah Williams VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/celarefData git_branch: RELEASE_3_8 git_last_commit: 2c21778 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/celarefData_1.0.0.tar.gz vignettes: vignettes/celarefData/inst/doc/celarefData.html vignetteTitles: Manual hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/celarefData/inst/doc/celarefData.R Package: CellMapperData Version: 1.8.0 Depends: ExperimentHub, CellMapper Suggests: BiocStyle License: Artistic-2.0 MD5sum: ac7ff311f02953168d5cb3f829fd1e1c NeedsCompilation: no Title: Pre-processed data for use with the CellMapper package Description: Experiment data package. Contains microarray data from several large expression compendia that have been pre-processed for use with the CellMapper package. This pre-processed data is recommended for routine searches using the CellMapper package. biocViews: ExperimentData, MicroarrayData, ExpressionData Author: Brad Nelms Maintainer: Brad Nelms git_url: https://git.bioconductor.org/packages/CellMapperData git_branch: RELEASE_3_8 git_last_commit: 4a47a12 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/CellMapperData_1.8.0.tar.gz vignettes: vignettes/CellMapperData/inst/doc/CellMapperData.pdf vignetteTitles: CellMapperData Introduction hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CellMapperData/inst/doc/CellMapperData.R Package: ceu1kg Version: 0.20.0 Depends: R (>= 2.12.0), GGBase (>= 3.9.0), GGtools, Biobase Suggests: SNPlocs.Hsapiens.dbSNP.20101109 License: Artistic-2.0 MD5sum: 039d5e0ba8ee673cbd97d636f30d379e NeedsCompilation: no Title: CEU (N=60) genotypes from 1000 genomes pilot phase I Description: CEU genotypes from 1000 genomes "low coverage" pilot phase I (approx 8 million SNP calls released July 2010); includes Wellcome trust GENEVAR expression for 43 indiv biocViews: SNPData, HapMap, Project1000genomes Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/ceu1kg git_branch: RELEASE_3_8 git_last_commit: 1510069 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ceu1kg_0.20.0.tar.gz vignettes: vignettes/ceu1kg/inst/doc/ceu1kg.pdf vignetteTitles: ceu1kg overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ceu1kg/inst/doc/ceu1kg.R Package: ceu1kgv Version: 0.24.0 Depends: R (>= 3.0), GGBase Imports: Biobase License: Artistic-2.0 MD5sum: c972c7288208ef044f986bbfd8fab71c NeedsCompilation: no Title: expression + genotype on 79 unrelated CEU individuals Description: expression + genotype on 79 unrelated CEU individuals biocViews: ArrayExpress Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/ceu1kgv git_branch: RELEASE_3_8 git_last_commit: 2b8f84a git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ceu1kgv_0.24.0.tar.gz vignettes: vignettes/ceu1kgv/inst/doc/ceu1kgv.pdf vignetteTitles: ceu1kgv -- genotype plus expression for HapMap CEU hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ceu1kgv/inst/doc/ceu1kgv.R Package: ceuhm3 Version: 0.20.0 Depends: R (>= 2.12.0), GGBase, Biobase Imports: GGtools License: Artistic-2.0 MD5sum: 0255a0481a74261e5d40cbc1c00bd46f NeedsCompilation: no Title: ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort Description: ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort biocViews: SNPData, HapMap Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/ceuhm3 git_branch: RELEASE_3_8 git_last_commit: 953195b git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ceuhm3_0.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cgdv17 Version: 0.20.0 Depends: R (>= 2.15), methods, VariantAnnotation (>= 1.15.15) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biobase Suggests: parallel, GGtools, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, illuminaHumanv1.db License: Artistic-2.0 MD5sum: f099ccc73aef5fb29585a9f7a026f29f NeedsCompilation: no Title: Complete Genomics Diversity Panel, chr17 on 46 individuals Description: Complete Genomics Diversity Panel, chr17 on 46 individuals biocViews: SequencingData, SNPData, BiocViews Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/cgdv17 git_branch: RELEASE_3_8 git_last_commit: da8fe64 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/cgdv17_0.20.0.tar.gz vignettes: vignettes/cgdv17/inst/doc/cgdv.pdf vignetteTitles: cgdv17: extract from Complete Genomics diversity panel hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cgdv17/inst/doc/cgdv.R Package: ChAMPdata Version: 2.14.1 Depends: GenomicRanges (>= 1.22.4),BiocGenerics(>= 0.16.1),R (>= 3.3) License: GPL-3 MD5sum: 4bf780ba771b8bee8639aecacc014243 NeedsCompilation: no Title: Data Packages for ChAMP package Description: Provides datasets needed for ChAMP including a test dataset and blood controls for CNA analysis. biocViews: ExperimentData Author: Yuan Tian [ctb,aut], Tiffany Morris [cre,aut], Lee Stirling [ctb] and Andrew Teschendorff [ctb] Maintainer: Yuan Tian git_url: https://git.bioconductor.org/packages/ChAMPdata git_branch: RELEASE_3_8 git_last_commit: a75d97a git_last_commit_date: 2019-01-27 Date/Publication: 2019-01-29 source.ver: src/contrib/ChAMPdata_2.14.1.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: charmData Version: 1.18.0 Depends: R(>= 2.11.0), charm, pd.charm.hg18.example License: LGPL (>= 2) MD5sum: b8a33b09e3b618b0aae3f3ca0ec5acc9 NeedsCompilation: no Title: An example dataset for use with the charm package Description: An example dataset for use with the charm package biocViews: ExperimentData, MicroarrayData Author: Martin Aryee Maintainer: Martin Aryee git_url: https://git.bioconductor.org/packages/charmData git_branch: RELEASE_3_8 git_last_commit: 171210a git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/charmData_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ChIC.data Version: 1.2.0 Depends: R (>= 3.5) Imports: caret (>= 6.0-78) License: GPL-2 MD5sum: 4bee195762ecb4bfce23bc3f841cc5cb NeedsCompilation: no Title: ChIC package data Description: This package contains annotation and metagene profile data for the ChIC package. biocViews: ExperimentData, ENCODE Author: Carmen Maria Livi [aut, cre, dtc], Endre Sebestyen [aut] Maintainer: Carmen Maria Livi git_url: https://git.bioconductor.org/packages/ChIC.data git_branch: RELEASE_3_8 git_last_commit: e3d271d git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ChIC.data_1.2.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ChimpHumanBrainData Version: 1.20.0 Depends: affy,qvalue,limma,hexbin,statmod License: MIT MD5sum: ea5241df1f05ea48aa510de5a2a3efb9 NeedsCompilation: no Title: Chimp and human brain data package Description: This data package contains chimp and human brain data extracted from the ArrayExpress accession E-AFMX-2. Both human and chimp RNAs were run on human hgu95av2 Affymetrix arrays. It is a useful dataset for tutorials. biocViews: Tissue, Homo_sapiens_Data, Pan_troglodytes_Data, MicroarrayData, TissueMicroarrayData, GEO Author: Roman Jaksik, Naomi Altman, and Sean Davis Maintainer: Sean Davis git_url: https://git.bioconductor.org/packages/ChimpHumanBrainData git_branch: RELEASE_3_8 git_last_commit: e24e922 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ChimpHumanBrainData_1.20.0.tar.gz vignettes: vignettes/ChimpHumanBrainData/inst/doc/DiffExpressVignette.pdf vignetteTitles: DiffExpressVignette.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ChimpHumanBrainData/inst/doc/DiffExpressVignette.R Package: chipenrich.data Version: 2.6.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, BiocGenerics, methods, GenomicRanges, GenomeInfoDb, IRanges, readr, rtracklayer, S4Vectors, utils Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat, GO.db, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene License: GPL-3 MD5sum: cd762813ed7fcc7e0ef6d0be7de5047b NeedsCompilation: no Title: Companion package to chipenrich Description: Supporting data for the chipenrich package. Includes pre-defined gene sets, gene locus definitions, and mappability estimates. biocViews: ChIPSeq, Epigenetics, FunctionalGenomics, GeneSetEnrichment, HistoneModification, Regression Author: Ryan P. Welch [aut, cph], Chee Lee [aut], Raymond G. Cavalcante [aut, cre], Laura J. Scott [ths], Maureen A. Sartor [ths] Maintainer: Raymond G. Cavalcante VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/chipenrich.data git_branch: RELEASE_3_8 git_last_commit: 381587c git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/chipenrich.data_2.6.0.tar.gz vignettes: vignettes/chipenrich.data/inst/doc/chipenrich.data-vignette.html vignetteTitles: chipenrich.data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/chipenrich.data/inst/doc/chipenrich.data-vignette.R Package: ChIPexoQualExample Version: 1.6.0 Depends: R (>= 3.3) License: GPL (>= 2) MD5sum: 18e7a340ba4586efebd01c0eaa2de1b4 NeedsCompilation: no Title: Example data for the ChIPexoQual package, which implements a quality control pipeline for ChIP-exo data Description: Data for the ChIPexoQual package, consisting of (3) chromosome 1 aligned reads from a ChIP-exo experiment for FoxA1 in mouse liver cell lines aligned to the mm9 genome. biocViews: ExperimentData, Genome Author: Rene Welch, Dongjun Chung, Sunduz Keles Maintainer: Rene Welch URL: http://www.github.com/keleslab/ChIPexoQualExample VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ChIPexoQualExample git_branch: RELEASE_3_8 git_last_commit: 60358fc git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ChIPexoQualExample_1.6.0.tar.gz vignettes: vignettes/ChIPexoQualExample/inst/doc/vignette.html vignetteTitles: Vignette Title hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ChIPexoQualExample/inst/doc/vignette.R Package: ChIPXpressData Version: 1.20.0 Depends: bigmemory License: GPL (>=2) MD5sum: a22a580a546729aa51a3e5899c047f1e NeedsCompilation: no Title: ChIPXpress Pre-built Databases Description: Contains pre-built mouse (GPL1261) and human (GPL570) database of gene expression profiles to be used for ChIPXpress ranking. biocViews: Homo_sapiens_Data, Mus_musculus_Data, GEO Author: George Wu Maintainer: George Wu git_url: https://git.bioconductor.org/packages/ChIPXpressData git_branch: RELEASE_3_8 git_last_commit: 926ba2b git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ChIPXpressData_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: chromstaRData Version: 1.8.0 Depends: R (>= 3.3) License: GPL-3 MD5sum: 6de05adbae8cdeacaad09e20b18bbf95 NeedsCompilation: no Title: ChIP-seq data for Demonstration Purposes Description: ChIP-seq data for demonstration purposes in the chromstaR package. biocViews: Mus_musculus_Data, StemCell, ChIPSeqData Author: Aaron Taudt Maintainer: Aaron Taudt git_url: https://git.bioconductor.org/packages/chromstaRData git_branch: RELEASE_3_8 git_last_commit: 83301a7 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/chromstaRData_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CLL Version: 1.22.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: LGPL MD5sum: 3851a86f9abc1159d405cbbc03ecf405 NeedsCompilation: no Title: A Package for CLL Gene Expression Data Description: The CLL package contains the chronic lymphocytic leukemia (CLL) gene expression data. The CLL data had 24 samples that were either classified as progressive or stable in regards to disease progression. The data came from Dr. Sabina Chiaretti at Division of Hematology, Department of Cellular Biotechnologies and Hematology, University La Sapienza, Rome, Italy and Dr. Jerome Ritz at Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts. biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData Author: Elizabeth Whalen Maintainer: Robert Gentleman git_url: https://git.bioconductor.org/packages/CLL git_branch: RELEASE_3_8 git_last_commit: 55f8067 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/CLL_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CLLmethylation Version: 1.2.0 Depends: R (>= 3.5.0) Imports: SummarizedExperiment, ExperimentHub Suggests: BiocStyle, ggplot2, knitr, rmarkdown License: LGPL MD5sum: cd8a30818dd72030144bd4216d915569 NeedsCompilation: no Title: Methylation data of primary CLL samples in PACE project Description: The package includes DNA methylation data for the primary Chronic Lymphocytic Leukemia samples included in the Primary Blood Cancer Encyclopedia (PACE) project. Raw data from the 450k DNA methylation arrays is stored in the European Genome-Phenome Archive (EGA) under accession number EGAS0000100174. For more information concerning the project please refer to the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) and R/Bioconductor package BloodCancerMultiOmics2017. biocViews: ExperimentData, DiseaseModel, CancerData, LeukemiaCancerData Author: Malgorzata Oles, Andreas Mock Maintainer: Malgorzata Oles , Andreas Mock VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/CLLmethylation git_branch: RELEASE_3_8 git_last_commit: d5b3f2b git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/CLLmethylation_1.2.0.tar.gz vignettes: vignettes/CLLmethylation/inst/doc/CLLmethylation.html vignetteTitles: CLLmethylation hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CLLmethylation/inst/doc/CLLmethylation.R Package: cMap2data Version: 1.18.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: 174f2e6265ede0b5e9163d7557f9e608 NeedsCompilation: no Title: Connectivity Map (version 2) Data Description: Data package which provides default drug profiles for the DrugVsDisease package as well as associated gene lists and data clusters used by the DrugVsDisease package. biocViews: Homo_sapiens_Data, MicroarrayData, GEO Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/cMap2data git_branch: RELEASE_3_8 git_last_commit: bf5c016 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/cMap2data_1.18.0.tar.gz vignettes: vignettes/cMap2data/inst/doc/cMap2data.pdf vignetteTitles: cMap2data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/cMap2data/inst/doc/cMap2data.R Package: cnvGSAdata Version: 1.18.0 Depends: R (>= 2.10), cnvGSA License: LGPL MD5sum: 9068308f3e9af11c862659158fc77687 NeedsCompilation: no Title: Data used in the vignette of the cnvGSA package Description: This package contains the data used in the vignette of the cnvGSA package. biocViews: ExperimentData, Genome, CopyNumberVariationData Author: Joseph Lugo Maintainer: Joseph Lugo git_url: https://git.bioconductor.org/packages/cnvGSAdata git_branch: RELEASE_3_8 git_last_commit: 9ed4b89 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/cnvGSAdata_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: COHCAPanno Version: 1.18.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: b68214a25ae7726c488dd5893cf6417a NeedsCompilation: no Title: Annotations for City of Hope CpG Island Analysis Pipeline Description: Provides genomic location, nearby CpG island and nearby gene information for common Illumina methylation array platforms biocViews: Homo_sapiens_Data, MicroarrayData, MethylationArrayData, CpGIslandData, GEO, ArrayExpress Author: Charles Warden Maintainer: Charles Warden git_url: https://git.bioconductor.org/packages/COHCAPanno git_branch: RELEASE_3_8 git_last_commit: 112abe2 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/COHCAPanno_1.18.0.tar.gz vignettes: vignettes/COHCAPanno/inst/doc/COHCAPanno.pdf vignetteTitles: COHCAPanno Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/COHCAPanno/inst/doc/COHCAPanno.R Package: colonCA Version: 1.24.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: 60d8c68d5e87c89a3fb08e63169e3ab0 NeedsCompilation: no Title: exprSet for Alon et al. (1999) colon cancer data Description: exprSet for Alon et al. (1999) colon cancer data biocViews: ExperimentData, Tissue, CancerData, ColonCancerData, MicroarrayData, TissueMicroarrayData Author: Sylvia Merk Maintainer: W Sylvia Merk git_url: https://git.bioconductor.org/packages/colonCA git_branch: RELEASE_3_8 git_last_commit: 3ce3a6a git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/colonCA_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CONFESSdata Version: 1.10.0 Depends: R (>= 3.3) License: GPL-2 MD5sum: 3e44ef1d35b8701069ba3908770dbb1e NeedsCompilation: no Title: Example dataset for CONFESS package Description: Example text-converted C01 image files for use in the CONFESS Bioconductor package. biocViews: HighThroughputImagingData,CellCulture,Homo_sapiens_Data,ExpressionData Author: Diana LOW and Efthimios MOTAKIS Maintainer: Diana LOW git_url: https://git.bioconductor.org/packages/CONFESSdata git_branch: RELEASE_3_8 git_last_commit: 3e115c4 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/CONFESSdata_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ConnectivityMap Version: 1.18.0 Depends: R (>= 2.15.1) Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: ff3bb449f67cd01953a13682b3496fff NeedsCompilation: no Title: Functional connections between drugs, genes and diseases as revealed by common gene-expression changes Description: The Broad Institute's Connectivity Map (cmap02) is a "large reference catalogue of gene-expression data from cultured human cells perturbed with many chemicals and genetic reagents", containing more than 7000 gene expression profiles and 1300 small molecules. biocViews: ExperimentData, CancerData, MicroarrayData Author: Paul Shannon Maintainer: Paul Shannon git_url: https://git.bioconductor.org/packages/ConnectivityMap git_branch: RELEASE_3_8 git_last_commit: 9b2f470 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ConnectivityMap_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: COPDSexualDimorphism.data Version: 1.18.0 License: LGPL-2.1 MD5sum: 4089a6b6e4d5537d8b1c4352800ab0a4 NeedsCompilation: no Title: Data to support sexually dimorphic and COPD differential analysis for gene expression and methylation. Description: Datasets to support COPDSexaulDimorphism Package. biocViews: ExperimentData, Tissue, COPDData Author: J Fah Sathirapongsasuti Maintainer: J Fah Sathirapongsasuti git_url: https://git.bioconductor.org/packages/COPDSexualDimorphism.data git_branch: RELEASE_3_8 git_last_commit: 2ac8bfa git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/COPDSexualDimorphism.data_1.18.0.tar.gz vignettes: vignettes/COPDSexualDimorphism.data/inst/doc/lgrc_data.pdf vignetteTitles: SDCD Genes hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/COPDSexualDimorphism.data/inst/doc/lgrc_data.R Package: CopyhelpeR Version: 1.14.0 Depends: R(>= 2.10) Suggests: BiocStyle License: GPL-2 MD5sum: d1141ae0fe9aa075e083042ededcafce NeedsCompilation: no Title: Helper files for CopywriteR Description: This package contains the helper files that are required to run the Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content and mappability files for the reference genomes hg18, hg19, hg38, mm9 and mm10. In addition, it contains a blacklist filter to remove regions that display CNV. Files are stored as GRanges objects from the GenomicRanges Bioconductor package. biocViews: Homo_sapiens, GenomicSequence Author: Thomas Kuilman Maintainer: Oscar Krijgsman git_url: https://git.bioconductor.org/packages/CopyhelpeR git_branch: RELEASE_3_8 git_last_commit: 43c843e git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/CopyhelpeR_1.14.0.tar.gz vignettes: vignettes/CopyhelpeR/inst/doc/CopyhelpeR.pdf vignetteTitles: CopyhelpeR hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CopyhelpeR/inst/doc/CopyhelpeR.R Package: CopyNeutralIMA Version: 1.0.0 Depends: R (>= 3.5.0) Imports: ExperimentHub,Rdpack (>= 0.8) Suggests: BiocStyle,knitr,rmarkdown,minfi,conumee,minfiData License: Artistic-2.0 MD5sum: 88e8d2b42e4512161e2c2a7fa95b6a5b NeedsCompilation: no Title: Copy Neutral Illumina Methylation Arrays Description: Provides a set of genomic copy neutral samples hybridized using Illumina Methylation arrays (450k and EPIC). biocViews: ExperimentData,Homo_sapiens_Data,MicroarrayData,TwoChannelData,MethylationArrayData,GEO Author: Xavier Pastor Hostench [aut, cre], Moritz Przybilla [aut] Maintainer: Xavier Pastor Hostench VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/CopyNeutralIMA git_branch: RELEASE_3_8 git_last_commit: 841bdec git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/CopyNeutralIMA_1.0.0.tar.gz vignettes: vignettes/CopyNeutralIMA/inst/doc/CopyNeutralIMA.html vignetteTitles: CopyNeutralIMA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CopyNeutralIMA/inst/doc/CopyNeutralIMA.R Package: COSMIC.67 Version: 1.18.0 Depends: R (>= 3.0.2) Imports: GenomicRanges, SummarizedExperiment, VariantAnnotation Suggests: testthat, BiocStyle, knitr License: GPL-3 MD5sum: db1bb894b11d6e1f9d2675e68bdf3291 NeedsCompilation: no Title: COSMIC.67 Description: COSMIC: Catalogue Of Somatic Mutations In Cancer, version 67 (2013-10-24) biocViews: ExperimentData, Genome, CancerData Author: Julian Gehring Maintainer: Julian Gehring VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/COSMIC.67 git_branch: RELEASE_3_8 git_last_commit: f2d8bd0 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/COSMIC.67_1.18.0.tar.gz vignettes: vignettes/COSMIC.67/inst/doc/COSMIC.67.pdf vignetteTitles: COSMIC.67 - PDF hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/COSMIC.67/inst/doc/COSMIC.67.R Package: CRCL18 Version: 1.2.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 552108f3a1772e108e845fea9ac04fa8 NeedsCompilation: no Title: CRC cell line dataset Description: colorectal cancer mRNA and miRNA on 18 cell lines biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/CRCL18 git_branch: RELEASE_3_8 git_last_commit: 0b67e6e git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/CRCL18_1.2.0.tar.gz vignettes: vignettes/CRCL18/inst/doc/CRCL18Vignette.pdf vignetteTitles: CRCL18 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/CRCL18/inst/doc/CRCL18Vignette.R Package: curatedBladderData Version: 1.18.1 Depends: R (>= 2.10.0), affy Suggests: BiocStyle, survival, xtable, sva, genefilter, logging License: Artistic-2.0 MD5sum: d9f2ab021b0b87a531a585ce5ffa9b17 NeedsCompilation: no Title: Bladder Cancer Gene Expression Analysis Description: The curatedBladderData package provides relevant functions and data for gene expression analysis in patients with bladder cancer. biocViews: ExperimentData, CancerData, OvarianCancerData, MicroarrayData, ExpressionData Author: Markus Riester Maintainer: Markus Riester git_url: https://git.bioconductor.org/packages/curatedBladderData git_branch: RELEASE_3_8 git_last_commit: 14d2d1d git_last_commit_date: 2019-03-28 Date/Publication: 2019-03-31 source.ver: src/contrib/curatedBladderData_1.18.1.tar.gz vignettes: vignettes/curatedBladderData/inst/doc/curatedBladderData_vignette.pdf vignetteTitles: curatedBladderData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedBladderData/inst/doc/curatedBladderData_vignette.R Package: curatedBreastData Version: 2.10.0 Depends: R (>= 3.0.0), XML, ggplot2, impute, Biobase, BiocStyle Imports: methods, stats License: GPL (>= 2) MD5sum: f331996cfe36abc88dbc84a8fde187c5 NeedsCompilation: no Title: Curated breast cancer gene expression data with survival and treatment information Description: Curated human breast cancer tissue S4 ExpresionSet datasets from over 16 clinical trials comprising over 2,000 patients. All datasets contain at least one type of outcomes variable and treatment information (minimum level: whether they had chemotherapy and whether they had hormonal therapy). Includes code to post-process these datasets. biocViews: ExperimentData, ExpressionData, CancerData, Tissue, BreastCancerData, qPCRData, MicroarrayData, TissueMicroarrayData, GEO Author: Katie Planey Maintainer: Katie Planey git_url: https://git.bioconductor.org/packages/curatedBreastData git_branch: RELEASE_3_8 git_last_commit: 62820e1 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/curatedBreastData_2.10.0.tar.gz vignettes: vignettes/curatedBreastData/inst/doc/curatedBreastData-manual.pdf vignetteTitles: Manual hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedBreastData/inst/doc/curatedBreastData-manual.R Package: curatedCRCData Version: 2.14.0 Depends: R (>= 2.10.0), nlme Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle License: Artistic-2.0 MD5sum: 930dbdba821daa1232beb01eee233d80 NeedsCompilation: no Title: Colorectal Cancer Gene Expression Analysis Description: The curatedCRC package provides relevant functions and data for gene expression analysis in patients with colorectal cancer. biocViews: Colorectal, Cancer, TCGA, ExperimentData, RNAExpressionData Author: Princy Parsana, Markus Riester, Curtis Huttenhower, Levi Waldron Maintainer: Princy Parsana URL: https://bitbucket.org/biobakery/curatedcrcdata git_url: https://git.bioconductor.org/packages/curatedCRCData git_branch: RELEASE_3_8 git_last_commit: 29fec19 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/curatedCRCData_2.14.0.tar.gz vignettes: vignettes/curatedCRCData/inst/doc/curatedCRCData_vignette.pdf vignetteTitles: curatedCRCData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedCRCData/inst/doc/curatedCRCData_vignette.R Package: curatedMetagenomicData Version: 1.12.3 Depends: R (>= 3.4.0), dplyr (>= 0.5.0), Biobase (>= 2.37.0), ExperimentHub (>= 1.3.0), AnnotationHub (>= 2.9.0) Imports: utils, tidyr, magrittr, methods, S4Vectors Suggests: BiocManager, devtools, roxygen2, testthat, covr, knitr, rmarkdown, BiocCheck, BiocStyle, BiocParallel, readr, RISmed, ggplot2, metagenomeSeq, phyloseq, ape License: Artistic-2.0 MD5sum: 647d57c43704bee51d7d54327e419cd4 NeedsCompilation: no Title: Curated Metagenomic Data of the Human Microbiome Description: The curatedMetagenomicData package provides microbial taxonomic, functional, and gene marker abundance for samples collected from different bodysites. biocViews: Homo_sapiens_Data, ReproducibleResearch, MicrobiomeData, ExperimentHub Author: Lucas Schiffer , Edoardo Pasolli , Levi Waldron , Faizan Malik , Nicola Segata , Valerie Obenchain , Morgan Martin Maintainer: Lucas Schiffer URL: https://github.com/waldronlab/curatedMetagenomicData VignetteBuilder: knitr BugReports: https://github.com/waldronlab/curatedMetagenomicData/issues git_url: https://git.bioconductor.org/packages/curatedMetagenomicData git_branch: RELEASE_3_8 git_last_commit: a0ee22e git_last_commit_date: 2018-11-04 Date/Publication: 2018-11-06 source.ver: src/contrib/curatedMetagenomicData_1.12.3.tar.gz vignettes: vignettes/curatedMetagenomicData/inst/doc/curatedMetagenomicData.html vignetteTitles: curatedMetagenomicData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedMetagenomicData/inst/doc/curatedMetagenomicData.R suggestsMe: HMP16SData Package: curatedOvarianData Version: 1.20.1 Depends: R (>= 2.10.0), affy Imports: BiocGenerics Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle License: Artistic-2.0 MD5sum: d4051a3cd2316e680003c8efa99cdb9b NeedsCompilation: no Title: Clinically Annotated Data for the Ovarian Cancer Transcriptome Description: The curatedOvarianData package provides data for gene expression analysis in patients with ovarian cancer. biocViews: ExperimentData, RNASeqData, CancerData, OvarianCancerData, MicroarrayData Author: Benjamin F. Ganzfried, Markus Riester, Steve Skates, Victoria Wang, Thomas Risch, Benjamin Haibe-Kains, Svitlana Tyekucheva, Jie Ding, Ina Jazic, Michael Birrer, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron Maintainer: Levi Waldron URL: http://bcb.dfci.harvard.edu/ovariancancer git_url: https://git.bioconductor.org/packages/curatedOvarianData git_branch: RELEASE_3_8 git_last_commit: 42ad8c7 git_last_commit_date: 2019-03-15 Date/Publication: 2019-03-17 source.ver: src/contrib/curatedOvarianData_1.20.1.tar.gz vignettes: vignettes/curatedOvarianData/inst/doc/curatedOvarianData_vignette.pdf vignetteTitles: curatedOvarianData_vignette.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedOvarianData/inst/doc/curatedOvarianData_vignette.R Package: curatedTCGAData Version: 1.4.3 Depends: R (>= 3.5.0), MultiAssayExperiment Imports: AnnotationHub, ExperimentHub, S4Vectors, utils Suggests: BiocStyle, knitr, readr, rmarkdown, testthat License: Artistic-2.0 MD5sum: a51cab7f08a1851714f91b384127b83b NeedsCompilation: no Title: Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects Description: This package provides publicly available data from The Cancer Genome Atlas (TCGA) Bioconductor MultiAssayExperiment class objects. These objects integrate multiple assays (e.g. RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. The MultiAssayExperiment class links assay barcodes with patient IDs, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire experiment. biocViews: Homo_sapiens_Data, ReproducibleResearch, CancerData Author: Marcel Ramos [aut, cre], Levi Waldron [ctb], Lucas Schiffer [ctb], Valerie Obenchain [ctb], Martin Morgan [ctb] Maintainer: Marcel Ramos VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/curatedTCGAData git_branch: RELEASE_3_8 git_last_commit: 399d685 git_last_commit_date: 2019-01-30 Date/Publication: 2019-02-03 source.ver: src/contrib/curatedTCGAData_1.4.3.tar.gz vignettes: vignettes/curatedTCGAData/inst/doc/curatedTCGAData.html vignetteTitles: curatedTCGAData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/curatedTCGAData/inst/doc/curatedTCGAData.R Package: DAPARdata Version: 1.12.1 Depends: R (>= 3.5) Imports: utils, knitr, MSnbase Suggests: DAPAR, Prostar License: GPL-2 MD5sum: 5db15dae7303ec5f823c84377aa5c12c NeedsCompilation: no Title: Data accompanying the DAPAR and Prostar packages Description: Mass-spectrometry based UPS proteomics data sets from Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssie D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianferani S, Ferro M, Dorssaeler AV, Burlet-Schiltz O, Schaeffer C, Coute Y, Gonzalez de Peredo A. Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods. Data Brief. 2015 Dec 17;6:286-94 and Giai Gianetto, Q., Combes, F., Ramus, C., Bruley, C., Coute, Y., Burger, T. (2016). Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments. Proteomics, 16(1), 29-32. biocViews: ExperimentData, MassSpectrometryData Author: Samuel Wieczorek and Florence Combes Maintainer: Samuel Wieczorek git_url: https://git.bioconductor.org/packages/DAPARdata git_branch: RELEASE_3_8 git_last_commit: 83cc496 git_last_commit_date: 2018-11-13 Date/Publication: 2018-11-13 source.ver: src/contrib/DAPARdata_1.12.1.tar.gz vignettes: vignettes/DAPARdata/inst/doc/Exp1_R2_pept.pdf, vignettes/DAPARdata/inst/doc/Exp1_R2_prot.pdf, vignettes/DAPARdata/inst/doc/Exp1_R25_pept.pdf, vignettes/DAPARdata/inst/doc/Exp1_R25_prot.pdf, vignettes/DAPARdata/inst/doc/Exp2_R10_pept.pdf, vignettes/DAPARdata/inst/doc/Exp2_R10_prot.pdf, vignettes/DAPARdata/inst/doc/Exp2_R100_pept.pdf, vignettes/DAPARdata/inst/doc/Exp2_R100_prot.pdf, vignettes/DAPARdata/inst/doc/Exp2_R2_pept.pdf, vignettes/DAPARdata/inst/doc/Exp2_R2_prot.pdf vignetteTitles: Exp1_R2_pept.pdf, Exp1_R2_prot.pdf, Exp1_R25_pept.pdf, Exp1_R25_prot.pdf, Exp2_R10_pept.pdf, Exp2_R10_prot.pdf, Exp2_R100_pept.pdf, Exp2_R100_prot.pdf, Exp2_R2_pept.pdf, Exp2_R2_prot.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: davidTiling Version: 1.22.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db License: LGPL MD5sum: ace6b4becfd62c19a8b353de336d6ca6 NeedsCompilation: no Title: Data and analysis scripts for David, Huber et al. yeast tiling array paper Description: This package contains the data for the paper by L. David et al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix genechips, an ExpressionSet object with the raw feature data, a probe annotation data structure for the chip and the yeast genome annotation (GFF file) that was used. In addition, some custom-written analysis functions are provided, as well as R scripts in the scripts directory. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, MicroarrayData, ReproducibleResearch Author: Wolfgang Huber , Joern Toedling Maintainer: Wolfgang Huber URL: http://www.ebi.ac.uk/huber git_url: https://git.bioconductor.org/packages/davidTiling git_branch: RELEASE_3_8 git_last_commit: 4eba70d git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/davidTiling_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: derfinderData Version: 2.0.0 Depends: R(>= 3.1.1) Suggests: sessioninfo, knitcitations (>= 1.0.1), knitr (>= 1.6), knitrBootstrap (>= 0.9.0), RefManageR, rmarkdown (>= 0.3.3), License: Artistic-2.0 MD5sum: a33f63fe0dc553cdb09434a7b243535b NeedsCompilation: no Title: Processed BigWigs from BrainSpan for examples Description: Processed 22 samples from BrainSpan keeping only the information for chromosome 21. Data is stored in the BigWig format and is used for examples in other packages. biocViews: ExperimentData, Homo_sapiens_Data, RNASeqData Author: Leonardo Collado-Torres [aut, cre], Andrew Jaffe [aut], Jeffrey Leek [aut, ths] Maintainer: Leonardo Collado-Torres URL: https://github.com/leekgroup/derfinderData VignetteBuilder: knitr BugReports: https://github.com/leekgroup/derfinderData/issues git_url: https://git.bioconductor.org/packages/derfinderData git_branch: RELEASE_3_8 git_last_commit: 71314e1 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/derfinderData_2.0.0.tar.gz vignettes: vignettes/derfinderData/inst/doc/derfinderData.html vignetteTitles: Introduction to derfinderData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/derfinderData/inst/doc/derfinderData.R Package: DeSousa2013 Version: 1.18.0 Depends: R (>= 2.15), Imports: affy, frma, frmaTools, hgu133plus2.db, hgu133plus2frmavecs, sva, rgl, ConsensusClusterPlus, cluster, siggenes, ROCR, pamr, survival, gplots, AnnotationDbi, Biobase License: Artistic-2.0 MD5sum: 6059d057fb2eb7d4b64896680da57226 NeedsCompilation: no Title: Poor prognosis colon cancer is defined by a molecularly distinct subtype and precursor lesion Description: This package reproduces the main pipeline to analyze the AMC-AJCCII-90 microarray data set in De Sousa et al. accepted by Nature Medicine in 2013. biocViews: CancerData, ColonCancerData, MicroarrayData Author: Xin Wang Maintainer: Xin Wang git_url: https://git.bioconductor.org/packages/DeSousa2013 git_branch: RELEASE_3_8 git_last_commit: 59f079b git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/DeSousa2013_1.18.0.tar.gz vignettes: vignettes/DeSousa2013/inst/doc/DeSousa2013-Vignette.pdf vignetteTitles: Main vignette:Poor prognosis colon cancer is defined by a molecular distinct subtype and develops from serrated precursor lesions hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DeSousa2013/inst/doc/DeSousa2013-Vignette.R Package: diffloopdata Version: 1.10.0 Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 157263c6bb6d391cab4e51e575e014c3 NeedsCompilation: no Title: Example ChIA-PET Datasets for the diffloop Package Description: ChIA-PET example datasets and additional data for use with the diffloop package. biocViews: ExperimentData, SequencingData Author: Caleb Lareau [aut], Martin Aryee [aut, cre] Maintainer: Caleb Lareau VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/diffloopdata git_branch: RELEASE_3_8 git_last_commit: cfae493 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/diffloopdata_1.10.0.tar.gz vignettes: vignettes/diffloopdata/inst/doc/diffloopdata.html vignetteTitles: diffloopdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Package: diggitdata Version: 1.14.0 Depends: R(>= 2.14.0), Biobase, methods Imports: viper License: GPL (>=2) MD5sum: 5129f39e50ca1fa38fe4e56ef691e868 NeedsCompilation: no Title: Example data for the diggit package Description: This package provides expression profile and CNV data for glioblastoma from TCGA, and transcriptional and post-translational regulatory networks assembled with the ARACNe and MINDy algorithms, respectively. biocViews: ExperimentData, Cancer Author: Mariano Javier Alvarez Maintainer: Mariano Javier Alvarez git_url: https://git.bioconductor.org/packages/diggitdata git_branch: RELEASE_3_8 git_last_commit: cad7b51 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/diggitdata_1.14.0.tar.gz vignettes: vignettes/diggitdata/inst/doc/diggitdata.pdf vignetteTitles: Using bcellViper hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/diggitdata/inst/doc/diggitdata.R Package: DLBCL Version: 1.22.0 Depends: R(>= 2.11.0), Biobase License: GPL (>=2) MD5sum: a031da595f9e721bc23ff580d3fa5bd4 NeedsCompilation: no Title: Diffuse large B-cell lymphoma expression data Description: This package provides additional expression data on diffuse large B-cell lymphomas for the BioNet package. biocViews: ExperimentData, CancerData, MicroarrayData, ChipOnChipData Author: Marcus Dittrich and Daniela Beisser Maintainer: Marcus Dittrich URL: http://bionet.bioapps.biozentrum.uni-wuerzburg.de/ git_url: https://git.bioconductor.org/packages/DLBCL git_branch: RELEASE_3_8 git_last_commit: 1deae00 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/DLBCL_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: DmelSGI Version: 1.14.0 Depends: R (>= 3.0) Imports: grid, TSP, limma, rhdf5, knitr, abind, gplots, igraph Suggests: BiocStyle, EBImage, RColorBrewer, RNAinteractMAPK, RSVGTipsDevice, cgdsr, hwriter, xtable, beeswarm License: Artistic-2.0 MD5sum: 9eda48b2f405f9995dcd517916961e93 NeedsCompilation: no Title: Experimental data and documented source code for the paper "A Map of Directional Genetic Interactions in a Metazoan Cell" Description: The package contains the experimental data and documented source code of the manuscript "Fischer et al., A Map of Directional Genetic Interactions in a Metazoan Cell, eLife, 2015, in Press.". The vignette code generates all figures in the paper. biocViews: MicrotitrePlateAssayData, CellCulture, HighthroughputImagingData, Drosophila_melanogaster_Data, ExperimentData, HighThroughputImagingData, ReproducibleResearch Author: Bernd Fischer Maintainer: Bernd Fischer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DmelSGI git_branch: RELEASE_3_8 git_last_commit: c43680e git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/DmelSGI_1.14.0.tar.gz vignettes: vignettes/DmelSGI/inst/doc/DmelSGI.pdf vignetteTitles: DmelSGI hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DmelSGI/inst/doc/DmelSGI.R Package: DMRcatedata Version: 1.18.0 Depends: R (>= 3.2.2), GenomicRanges Suggests: knitr License: GPL-3 MD5sum: b929cb1b0888f6cbd0e41219b3807b84 NeedsCompilation: no Title: Data Package for DMRcate package Description: This package contains 8 data objects supporting functionality and examples of the Bioconductor package DMRcate. biocViews: ExperimentData, SNPData Author: Tim Peters Maintainer: Tim Peters VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DMRcatedata git_branch: RELEASE_3_8 git_last_commit: 2bf030f git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/DMRcatedata_1.18.0.tar.gz vignettes: vignettes/DMRcatedata/inst/doc/DMRcatedata.pdf vignetteTitles: The DMRcate package user's guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DMRcatedata/inst/doc/DMRcatedata.R Package: DonaPLLP2013 Version: 1.20.0 Depends: EBImage, parallel License: Artistic-2.0 MD5sum: 5a228295986fdfe1ad44a66ca2f1d947 NeedsCompilation: no Title: Supplementary data package for Dona et al. (2013) containing example images and tables Description: An experiment data package associated with the publication Dona et al. (2013). Package contains runnable vignettes showing an example image segmentation for one posterior lateral line primordium, and also the data table and code used to analyze tissue-scale lifetime-ratio statistics. biocViews: ExperimentData, Tissue Author: Erika Dona, Joseph D. Barry, Guillaume Valentin, Charlotte Quirin, Anton Khmelinskii, Andreas Kunze, Sevi Durdu, Lionel R. Newton, Ana Fernandez-Minan, Wolfgang Huber, Michael Knop, Darren Gilmour Maintainer: Joseph D. Barry git_url: https://git.bioconductor.org/packages/DonaPLLP2013 git_branch: RELEASE_3_8 git_last_commit: 4e94063 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/DonaPLLP2013_1.20.0.tar.gz vignettes: vignettes/DonaPLLP2013/inst/doc/PLLPanalysis.pdf, vignettes/DonaPLLP2013/inst/doc/PLLPstatistics.pdf vignetteTitles: PLLP image analysis, PLLP tissue-scale ratio statistics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DonaPLLP2013/inst/doc/PLLPanalysis.R, vignettes/DonaPLLP2013/inst/doc/PLLPstatistics.R Package: DREAM4 Version: 1.18.0 Depends: R (>= 2.15.1), SummarizedExperiment Suggests: RUnit, networkBMA License: GPL MD5sum: 47e37f3d98279f6f1f1e5dfa1198f1b3 NeedsCompilation: no Title: Synthetic Expression Data for Gene Regulatory Network Inference from the 2009 DREAM4 challenge Description: Simulated expression data for five 10-node, and five 100-node networks, with associated data (including solutions) from the 2009 DREAM4 challenge. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, SequencingData Author: Paul Shannon Maintainer: Paul Shannon git_url: https://git.bioconductor.org/packages/DREAM4 git_branch: RELEASE_3_8 git_last_commit: ef37c0a git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/DREAM4_1.18.0.tar.gz vignettes: vignettes/DREAM4/inst/doc/DREAM4_InSilico_Description.pdf, vignettes/DREAM4/inst/doc/DREAM4.pdf vignetteTitles: DREAM4_InSilico_Description.pdf, DREAM4 Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DREAM4/inst/doc/DREAM4.R Package: dressCheck Version: 0.20.0 Depends: R (>= 2.10.1), methods, Biobase (>= 2.5.5) Suggests: survival, chron License: Artistic-2.0 MD5sum: dad61d2a1cfae86bc1f1b9f132291ae6 NeedsCompilation: no Title: data and software for checking Dressman JCO 25(5) 2007 Description: data and software for checking Dressman JCO 25(5) 2007 biocViews: ExperimentData, Genome Author: Vincent Carey Maintainer: Vincent Carey git_url: https://git.bioconductor.org/packages/dressCheck git_branch: RELEASE_3_8 git_last_commit: 2891d99 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/dressCheck_0.20.0.tar.gz vignettes: vignettes/dressCheck/inst/doc/short.pdf vignetteTitles: short review of dressCheck contents hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/dressCheck/inst/doc/short.R Package: DrugVsDiseasedata Version: 1.18.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: e6cddb699ec1351eda47cbb3fb40e705 NeedsCompilation: no Title: Drug versus Disease Data Description: Data package which provides default disease expression profiles, clusters and annotation information for use with the DrugVsDisease package. biocViews: Homo_sapiens_Data, MicroarrayData Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/DrugVsDiseasedata git_branch: RELEASE_3_8 git_last_commit: 611d5f6 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/DrugVsDiseasedata_1.18.0.tar.gz vignettes: vignettes/DrugVsDiseasedata/inst/doc/DrugVsDiseasedata.pdf vignetteTitles: DrugVsDiseasedata hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DrugVsDiseasedata/inst/doc/DrugVsDiseasedata.R Package: dsQTL Version: 0.20.0 Depends: R (>= 2.15.0), utils, Biobase, SummarizedExperiment, GGBase (>= 3.31.1) Suggests: GGtools, rtracklayer License: Artistic-2.0 MD5sum: 077dd1342d0cc842c44937a61e90ea10 NeedsCompilation: no Title: dsQTL, data excerpt from Degner et al. 2012 Nature letter Description: dsQTL, excerpt from Degner et al. 2012 Nature letter on DNA variants associated with DnaseI hypersensitivity biocViews: ExperimentData, Genome, SequencingData, DNASeqData, NCI, Project1000genomes, BiocViews Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/dsQTL git_branch: RELEASE_3_8 git_last_commit: 04c0502 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/dsQTL_0.20.0.tar.gz vignettes: vignettes/dsQTL/inst/doc/dsq.pdf vignetteTitles: dsQTL,, data excerpt from Degner et al. 2012 Nature letter hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/dsQTL/inst/doc/dsq.R importsMe: yriMulti Package: DuoClustering2018 Version: 1.0.0 Imports: ExperimentHub, utils, magrittr, dplyr, tidyr, mclust, ggplot2, purrr, reshape2, viridis, ggthemes, stats, methods Suggests: knitr, rmarkdown, BiocStyle, iSEE, scater, SingleCellExperiment, SummarizedExperiment, plyr License: GPL (>=2) MD5sum: 533a6230137770c646ced387a5ecd4fd NeedsCompilation: no Title: Data, Clustering Results and Visualization Functions From Duò et al (2018) Description: Preprocessed experimental and simulated scRNA-seq data sets used for evaluation of clustering methods for scRNA-seq data in Duò et al (2018). Also contains results from applying several clustering methods to each of the data sets, and functions for plotting method performance. biocViews: SingleCellData, ExperimentData Author: Angelo Duò, Charlotte Soneson Maintainer: Angelo Duò VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/DuoClustering2018 git_branch: RELEASE_3_8 git_last_commit: 9b6f656 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/DuoClustering2018_1.0.0.tar.gz vignettes: vignettes/DuoClustering2018/inst/doc/combine_data_clustering.html, vignettes/DuoClustering2018/inst/doc/plot_performance.html, vignettes/DuoClustering2018/inst/doc/run_clustering.html vignetteTitles: Visualize data sets and clustering results with iSEE, Plot performance summaries, Apply clustering method hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DuoClustering2018/inst/doc/combine_data_clustering.R, vignettes/DuoClustering2018/inst/doc/plot_performance.R, vignettes/DuoClustering2018/inst/doc/run_clustering.R Package: DvDdata Version: 1.18.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: c2b58da21a872a2757fb6928e7fd155e NeedsCompilation: no Title: Drug versus Disease Data Description: Data package which provides default drug and disease expression profiles for the DvD package. biocViews: GEO Author: C. Pacini Maintainer: J. Saez-Rodriguez git_url: https://git.bioconductor.org/packages/DvDdata git_branch: RELEASE_3_8 git_last_commit: dcdbcaa git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/DvDdata_1.18.0.tar.gz vignettes: vignettes/DvDdata/inst/doc/DvDdata.pdf vignetteTitles: DvDdata hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/DvDdata/inst/doc/DvDdata.R Package: dyebiasexamples Version: 1.22.0 Depends: R (>= 1.4.1), marray, GEOquery Suggests: dyebias, convert, Biobase License: GPL-3 MD5sum: 21da0022921c7f6e6eeb997e1bc56fa4 NeedsCompilation: no Title: Example data for the dyebias package, which implements the GASSCO method. Description: Data for the dyebias package, consisting of 4 self-self hybrizations of self-spotted yeast slides, as well as data from Array Express accession E-MTAB-32 biocViews: ExperimentData, SAGEData, CGHData, MicroarrayData, TwoChannelData, ArrayExpress Author: Philip Lijnzaad and Thanasis Margaritis Maintainer: Philip Lijnzaad URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad git_url: https://git.bioconductor.org/packages/dyebiasexamples git_branch: RELEASE_3_8 git_last_commit: a7e5874 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/dyebiasexamples_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Package: EatonEtAlChIPseq Version: 0.20.0 Depends: GenomicRanges (>= 1.5.42), ShortRead, rtracklayer License: Artistic 2.0 MD5sum: 4733fad7f34d353e3dbe267587fe2198 NeedsCompilation: no Title: ChIP-seq data of ORC-binding sites in Yeast excerpted from Eaton et al. 2010 Description: ChIP-seq analysis subset from "Conserved nucleosome positioning defines replication origins" (PMID 20351051) biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, ChIPSeqData, GEO Author: Patrick Aboyoun Maintainer: Patrick Aboyoun git_url: https://git.bioconductor.org/packages/EatonEtAlChIPseq git_branch: RELEASE_3_8 git_last_commit: 91aee82 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/EatonEtAlChIPseq_0.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ecoliLeucine Version: 1.22.0 Depends: R (>= 1.9.0), affy (>= 1.23.4), ecolicdf License: GPL (>= 2) MD5sum: 8b615a131951847086512158b0d6c876 NeedsCompilation: no Title: Experimental data with Affymetrix E. coli chips Description: Experimental data with Affymetrix E. coli chips, as reported in She-pin Hung, Pierre Baldi, and G. Wesley Hatfield, J. Biol. Chem., Vol. 277, Issue 43, 40309-40323, October 25, 2002 biocViews: ExperimentData, MicroarrayData Author: Laurent Gautier Maintainer: Laurent Gautier git_url: https://git.bioconductor.org/packages/ecoliLeucine git_branch: RELEASE_3_8 git_last_commit: c93fdec git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ecoliLeucine_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: EGSEAdata Version: 1.10.0 Depends: R (>= 3.4) Suggests: EGSEA License: file LICENSE MD5sum: 666b85ee723e0125632a40a30b3f602e NeedsCompilation: no Title: Gene set collections for the EGSEA package Description: This package includes gene set collections that are used for the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. It includes Human and Mouse versions of the MSidDB (Subramanian, et al. (2005) PNAS, 102(43):15545-15550) and GeneSetDB (Araki, et al. (2012) FEBS Open Bio, 2:76-82) collections. biocViews: ExperimentData, Homo_sapiens_Data, Mus_musculus_Data, Rattus_norvegicus_Data Author: Monther Alhamdoosh, Yifang Hu and Gordon K. Smyth Maintainer: Monther Alhamdoosh git_url: https://git.bioconductor.org/packages/EGSEAdata git_branch: RELEASE_3_8 git_last_commit: 98ccb92 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/EGSEAdata_1.10.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Package: ELMER.data Version: 2.6.0 Depends: R (>= 3.2.0) Imports: GenomicRanges Suggests: BiocStyle, knitr, dplyr, devtools, DT License: GPL-3 MD5sum: 6c2fe2971cd966175cb61c146921107f NeedsCompilation: no Title: Data for the ELMER package Description: Supporting data for the ELMER package. It includes: - elmer.data.example.promoter: mae.promoter - elmer.data.example: data - EPIC.hg38.manifest - EPIC.hg19.manifest - hm450.hg38.manifest - hm450.hg19.manifest - hocomoco.table - human.TF - LUSC_meth_refined: Meth - LUSC_RNA_refined: GeneExp - Probes.motif.hg19.450K - Probes.motif.hg19.EPIC - Probes.motif.hg38.450K - Probes.motif.hg38.EPIC - TF.family - TF.subfamily biocViews: AssayDomainData, TechnologyData, OrganismData Author: Tiago Chedraoui Silva, Lijing Yao Simon Coetzee, Ben Berman Maintainer: Tiago Chedraoui Silva VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/ELMER.data git_branch: RELEASE_3_8 git_last_commit: 7cd8574 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ELMER.data_2.6.0.tar.gz vignettes: vignettes/ELMER.data/inst/doc/vignettes.html vignetteTitles: ELMER.data: Supporting data for the ELMER package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ELMER.data/inst/doc/vignettes.R Package: estrogen Version: 1.28.0 Suggests: affy, hgu95av2, hgu95av2cdf, vsn, knitr License: LGPL MD5sum: 5a2bbc25340ef7cc6c9cf4a579e4c190 NeedsCompilation: no Title: Microarray dataset that can be used as example for 2x2 factorial designs Description: Data from 8 Affymetrix genechips, looking at a 2x2 factorial design (with 2 repeats per level). biocViews: ExperimentData, MicroarrayData Author: Wolfgang Huber, Robert Gentleman Maintainer: Wolfgang Huber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/estrogen git_branch: RELEASE_3_8 git_last_commit: 9587631 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/estrogen_1.28.0.tar.gz vignettes: vignettes/estrogen/inst/doc/estrogen.pdf vignetteTitles: estrogen hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/estrogen/inst/doc/estrogen.R Package: etec16s Version: 1.10.0 Depends: R (>= 3.3), Biobase, metagenomeSeq(>= 1.12.0) License: Artistic-2.0 MD5sum: ab6de328373655b42c1915fa52fcb47e NeedsCompilation: no Title: Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment Description: 16S rRNA gene sequencing data to study changes in the faecal microbiota of 12 volunteers during a human challenge study with ETEC (H10407) and subsequent treatment with ciprofloxacin. biocViews: ExperimentData, SequencingData, MicrobiomeData Author: Joseph N. Paulson Maintainer: Joseph N. Paulson git_url: https://git.bioconductor.org/packages/etec16s git_branch: RELEASE_3_8 git_last_commit: 1231d85 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/etec16s_1.10.0.tar.gz vignettes: vignettes/etec16s/inst/doc/etec16s.pdf vignetteTitles: etec16s hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/etec16s/inst/doc/etec16s.R Package: faahKO Version: 1.22.0 Depends: xcms License: LGPL MD5sum: c59e4588f572f3b56555cfd8d905107e NeedsCompilation: no Title: Saghatelian et al. (2004) FAAH knockout LC/MS data Description: Positive ionization mode data in NetCDF file format. Centroided subset from 200-600 m/z and 2500-4500 seconds. Data originally reported in "Assignment of Endogenous Substrates to Enzymes by Global Metabolite Profiling" Biochemistry; 2004; 43(45). Also includes detected peaks in an xcmsSet. biocViews: ExperimentData, MassSpectrometryData Author: Colin A. Smith Maintainer: Colin A. Smith URL: http://dx.doi.org/10.1021/bi0480335 git_url: https://git.bioconductor.org/packages/faahKO git_branch: RELEASE_3_8 git_last_commit: 3d14219 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/faahKO_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fabiaData Version: 1.20.0 Depends: R (>= 2.10.0), Biobase Imports: utils Suggests: fabia License: LGPL (>= 2.1) MD5sum: 1e781ec38c4767dd2ab23517fae76c59 NeedsCompilation: no Title: Data sets for FABIA (Factor Analysis for Bicluster Acquisition) Description: Supplying gene expression data sets for the demos of the biclustering method "Factor Analysis for Bicluster Acquisition" (FABIA). The following three data sets are provided: A) breast cancer (van't Veer, Nature, 2002), B) multiple tissues (Su, PNAS, 2002), and C) diffuse large-B-cell lymphoma (Rosenwald, N Engl J Med, 2002). biocViews: CancerData, BreastCancerData, MicroarrayData Author: Sepp Hochreiter Maintainer: Sepp Hochreiter URL: http://www.bioinf.jku.at/software/fabia/fabia.html git_url: https://git.bioconductor.org/packages/fabiaData git_branch: RELEASE_3_8 git_last_commit: 75d5733 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/fabiaData_1.20.0.tar.gz vignettes: vignettes/fabiaData/inst/doc/fabiaData.pdf vignetteTitles: fabiaData: Manual for the R Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/fabiaData/inst/doc/fabiaData.R Package: facopy.annot Version: 1.2.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: db7545bcf43738e8ba6894a2ec423c19 NeedsCompilation: no Title: Annotation for the copy number alteration association and enrichment analyses with facopy Description: Provides facopy with genome annotation on chromosome arms, genomic features and copy number alterations. biocViews: Genome Author: David Mosen-Ansorena Maintainer: David Mosen-Ansorena git_url: https://git.bioconductor.org/packages/facopy.annot git_branch: RELEASE_3_8 git_last_commit: 63b7b0e git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/facopy.annot_1.2.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: facsDorit Version: 1.24.0 Depends: R (>= 1.9.1), prada (>= 1.0.5) License: GPL-2 MD5sum: 9072988b0ba231cb46fb323fd326c7fe NeedsCompilation: no Title: DKFZ FACS example data Description: FACS example data for cell-based assays. This data is used in the examples and vignettes of the package prada. biocViews: ExperimentData, MicrotitrePlateAssayData Author: Florian Hahne Maintainer: Florian Hahne URL: http://www.dkfz.de/mga git_url: https://git.bioconductor.org/packages/facsDorit git_branch: RELEASE_3_8 git_last_commit: 69a2b6d git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/facsDorit_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: FANTOM3and4CAGE Version: 1.18.0 Depends: R (>= 2.15.0) License: GPL-3 MD5sum: c55a0fa84038a6e16773118479ae213c NeedsCompilation: no Title: CAGE data from FANTOM3 and FANTOM4 projects Description: CAGE (Cap Analysis Gene Expression) data from FANTOM3 and FANTOM4 projects produced by RIKEN Omics Science Center. biocViews: ExperimentData, Tissue Author: Vanja Haberle, Department of Biology, University of Bergen, Norway Maintainer: Vanja Haberle git_url: https://git.bioconductor.org/packages/FANTOM3and4CAGE git_branch: RELEASE_3_8 git_last_commit: 68f0ad5 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/FANTOM3and4CAGE_1.18.0.tar.gz vignettes: vignettes/FANTOM3and4CAGE/inst/doc/FANTOM3and4CAGE.pdf vignetteTitles: FANTOM3and4CAGE hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FANTOM3and4CAGE/inst/doc/FANTOM3and4CAGE.R Package: ffpeExampleData Version: 1.20.0 Depends: R (>= 2.10.0), lumi Suggests: genefilter, affy License: GPL (>2) MD5sum: 3e1855c53c4cef163383ef8921a86ab1 NeedsCompilation: no Title: Illumina DASL example microarray data Description: A subset of GSE17565 (April et al. 2009) containing 32 FFPE samples of Burkitts Lymphoma and Breast Adenocarcinoma, with a dilution series in technical duplicate. biocViews: Tissue, Genome, MicroarrayData, TissueMicroarrayData, GEO Author: Levi Waldron Maintainer: Levi Waldron git_url: https://git.bioconductor.org/packages/ffpeExampleData git_branch: RELEASE_3_8 git_last_commit: 56faaa6 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ffpeExampleData_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fibroEset Version: 1.24.0 Depends: Biobase (>= 2.5.5) License: LGPL MD5sum: 62d8b288008e726bd897b0a7296aade1 NeedsCompilation: no Title: exprSet for Karaman et al. (2003) fibroblasts data Description: exprSet for Karaman et al. (2003) human, bonobo and gorilla fibroblasts data biocViews: ExperimentData, Genome, Homo_sapiens_Data, MicroarrayData, ChipOnChipData Author: Sylvia Merk Maintainer: Sylvia Merk git_url: https://git.bioconductor.org/packages/fibroEset git_branch: RELEASE_3_8 git_last_commit: 4286c8f git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/fibroEset_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: FIs Version: 1.10.0 Depends: R (>= 3.3) License: GPL-3 MD5sum: b7e898f0a018f003f8268ed5b255049f NeedsCompilation: no Title: Human Functional Interactions (FIs) for splineTimeR package Description: Data set containing two complete lists of identified functional interaction partners in Human. Data are derived from Reactome and BioGRID databases. biocViews: PathwayInteractionDatabase, Homo_sapiens_Data Author: Agata Michna Maintainer: Herbert Braselmann git_url: https://git.bioconductor.org/packages/FIs git_branch: RELEASE_3_8 git_last_commit: 264cc2a git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/FIs_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fission Version: 1.2.0 Depends: R (>= 2.10), SummarizedExperiment Suggests: knitr License: LGPL MD5sum: 9576468d0dd81fb3edc7e7b550e0dc86 NeedsCompilation: no Title: RangedSummarizedExperiment for time course RNA-Seq of fission yeast in response to stress, by Leong et al., Nat Commun 2014. Description: This package provides a RangedSummarizedExperiment object of read counts in genes for a time course RNA-Seq experiment of fission yeast (Schizosaccharomyces pombe) in response to oxidative stress (1M sorbitol treatment) at 0, 15, 30, 60, 120 and 180 mins. The samples are further divided between a wild-type group and a group with deletion of atf21. The read count matrix was prepared and provided by the author of the study: Leong HS, Dawson K, Wirth C, Li Y, Connolly Y, Smith DL, Wilkinson CR, Miller CJ. "A global non-coding RNA system modulates fission yeast protein levels in response to stress". Nat Commun 2014 May 23;5:3947. PMID: 24853205. GEO: GSE56761. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData, GEO Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/fission git_branch: RELEASE_3_8 git_last_commit: f5befb8 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/fission_1.2.0.tar.gz vignettes: vignettes/fission/inst/doc/fission.html vignetteTitles: Fission yeast time course hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/fission/inst/doc/fission.R Package: Fletcher2013a Version: 1.18.0 Depends: R (>= 2.15), limma Imports: Biobase ,VennDiagram, gplots,grid License: GPL (>= 2) MD5sum: 8fc3c9e06927fa7a6508ea42fee23dd7 NeedsCompilation: no Title: Gene expression data from breast cancer cells under FGFR2 signalling perturbation Description: The package Fletcher2013a contains time-course gene expression data from MCF-7 cells treated under different experimental systems in order to perturb FGFR2 signalling. The data comes from Fletcher et al. (Nature Comms 4:2464, 2013) where further details about the background and the experimental design of the study can be found. biocViews: ExperimentData, ExpressionData, CancerData, BreastCancerData, MicroarrayData Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin Meyer. Maintainer: Mauro Castro URL: http://dx.doi.org/10.1038/ncomms3464 git_url: https://git.bioconductor.org/packages/Fletcher2013a git_branch: RELEASE_3_8 git_last_commit: 7512fd4 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/Fletcher2013a_1.18.0.tar.gz vignettes: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.pdf vignetteTitles: Main vignette:Fletcher2013a hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Fletcher2013a/inst/doc/Fletcher2013a.R dependsOnMe: Fletcher2013b Package: Fletcher2013b Version: 1.18.0 Depends: R (>= 2.15), Fletcher2013a, RTN (>= 1.1.2), RedeR (>= 1.8.1), igraph Imports: RColorBrewer License: GPL (>= 2) MD5sum: 02757b2d756e7d7fb48641ad9a81aaf4 NeedsCompilation: no Title: Master regulators of FGFR2 signalling and breast cancer risk Description: This package reproduces the systems biology analysis for the data in package Fletcher2013a using RTN. biocViews: ExperimentData, ChIPSeqData, CancerData, BreastCancerData, SNPData Author: Mauro Castro, Michael Fletcher, Florian Markowetz and Kerstin Meyer. Maintainer: Mauro Castro URL: http://dx.doi.org/10.1038/ncomms3464 git_url: https://git.bioconductor.org/packages/Fletcher2013b git_branch: RELEASE_3_8 git_last_commit: 56691d9 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/Fletcher2013b_1.18.0.tar.gz vignettes: vignettes/Fletcher2013b/inst/doc/Fletcher2013b.pdf vignetteTitles: Main vignette:Fletcher2013b hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Fletcher2013b/inst/doc/Fletcher2013b.R Package: flowFitExampleData Version: 1.18.0 Depends: R (>= 2.12.2), flowCore Imports: methods License: Artistic-2.0 MD5sum: 1ffa4e31d23b8df9f4df96504a893639 NeedsCompilation: no Title: Example data for the flowFit package Description: Two dataset that can be used to run examples from the flowFit vignette and examples biocViews: FlowCytometryData Author: davide Rambaldi Maintainer: Davide Rambaldi git_url: https://git.bioconductor.org/packages/flowFitExampleData git_branch: RELEASE_3_8 git_last_commit: 0912e05 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/flowFitExampleData_1.18.0.tar.gz vignettes: vignettes/flowFitExampleData/inst/doc/flowFitExampleData.pdf vignetteTitles: flowFitExampleData: example data for the beadarray package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/flowFitExampleData/inst/doc/flowFitExampleData.R Package: flowPloidyData Version: 1.8.0 Depends: R (>= 3.3.1) Suggests: knitr, rmarkdown, flowCore License: GPL-3 MD5sum: 86881aa99d32cc1ce20304591cb599ab NeedsCompilation: no Title: Example Flow Cytometry Data Description: A collection of raw flow cytometry data for use in vignettes for the flowPloidy package. biocViews: FlowCytometryData Author: Tyler Smith Maintainer: Tyler Smith VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/flowPloidyData git_branch: RELEASE_3_8 git_last_commit: 3e0ed9d git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/flowPloidyData_1.8.0.tar.gz vignettes: vignettes/flowPloidyData/inst/doc/flowPloidyData.html vignetteTitles: flowPloidy Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: flowQBData Version: 1.8.0 Depends: R (>= 3.2.0) Suggests: flowQB License: Artistic License 2.0 MD5sum: 4692d5e5b2c714b9b1d55636c65b90d4 NeedsCompilation: no Title: flowQB test and example data files Description: The flowQBData package provides data files used as examples and for testing of the software provided in the flowQB package. biocViews: ExperimentData, FlowCytometryData Author: Josef Spidlen, Wayne Moore, David Parks, Faysal El Khettabi, Ryan Brinkman Maintainer: Josef Spidlen git_url: https://git.bioconductor.org/packages/flowQBData git_branch: RELEASE_3_8 git_last_commit: acc432a git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/flowQBData_1.8.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: FlowSorted.Blood.450k Version: 1.20.0 Depends: R (>= 2.13.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: de53e97b7b4dd6b5930d22cef0cf7a64 NeedsCompilation: no Title: Illumina HumanMethylation data on sorted blood cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays, and an object depicting which CpGs on the array are associated with cell type. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Andrew E Jaffe Maintainer: Andrew E Jaffe git_url: https://git.bioconductor.org/packages/FlowSorted.Blood.450k git_branch: RELEASE_3_8 git_last_commit: ec6f767 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/FlowSorted.Blood.450k_1.20.0.tar.gz vignettes: vignettes/FlowSorted.Blood.450k/inst/doc/FlowSorted.Blood.450k.pdf vignetteTitles: FlowSorted Blood 450k Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.Blood.450k/inst/doc/FlowSorted.Blood.450k.R suggestsMe: FlowSorted.Blood.EPIC Package: FlowSorted.Blood.EPIC Version: 1.0.0 Depends: R (>= 3.5), minfi (>= 1.21.2), SummarizedExperiment, genefilter, quadprog, nlme, S4Vectors, graphics, stats, utils, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, ExperimentHub Suggests: knitr, rmarkdown, EpiDISH, FlowSorted.Blood.450k(>= 1.0.1), FlowSorted.CordBlood.450k, FlowSorted.CordBloodNorway.450k, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: GPL-3 MD5sum: 8d567155aab1d5b96ad468d0f0632acd NeedsCompilation: no Title: Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells Description: Raw data objects to be used for blood cell proportion estimation in minfi and similar packages. The FlowSorted.Blood.EPIC object is based in samples assayed by Brock Christensen and colleagues; for details see Salas et al. 2018. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, Genome, TissueMicroarrayData, MethylationArrayData Author: Lucas A. Salas [cre, aut], Devin C. Koestler [aut], Rondi A. Butler [ctb], Helen M. Hansen [ctb], John K. Wiencke [ctb], Karl T. Kelsey [ctb], Brock C. Christensen [ctb], Kasper Daniel Hansen [ctb] (author and maintainer of the original minfi estimateCellCounts and internal functions), Jean-Philippe Fortin [ctb] (contributor in the original minfi estimateCellCounts and internal functions), Shan V. Andrews [ctb] (contributor in the original minfi estimateCellCounts and internal functions), E. Andres Houseman [ctb] (author of the original quadratic programming function used for cell projection), Andrew E Jaffe [ctb] (author of the original estimateCellCounts and internal functions within minfi) Maintainer: Lucas A. Salas URL: https://github.com/immunomethylomics/FlowSorted.Blood.EPIC VignetteBuilder: knitr BugReports: https://github.com/immunomethylomics/FlowSorted.Blood.EPIC/issues. git_url: https://git.bioconductor.org/packages/FlowSorted.Blood.EPIC git_branch: RELEASE_3_8 git_last_commit: f4f54f3 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/FlowSorted.Blood.EPIC_1.0.0.tar.gz vignettes: vignettes/FlowSorted.Blood.EPIC/inst/doc/FlowSorted.Blood.EPIC.html vignetteTitles: FlowSorted.Blood.EPIC hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.Blood.EPIC/inst/doc/FlowSorted.Blood.EPIC.R Package: FlowSorted.CordBlood.450k Version: 1.10.0 Depends: R (>= 3.2.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: 5a049ecac95e4b77ea0d497838edb2e0 NeedsCompilation: no Title: Illumina 450k data on sorted cord blood cells Description: Raw data objects to be used for cord blood cell proportion estimation in minfi. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Shan V. Andrews [cre, aut], Kelly M. Bakulski [aut] Maintainer: Shan V. Andrews git_url: https://git.bioconductor.org/packages/FlowSorted.CordBlood.450k git_branch: RELEASE_3_8 git_last_commit: 6ca3f8d git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/FlowSorted.CordBlood.450k_1.10.0.tar.gz vignettes: vignettes/FlowSorted.CordBlood.450k/inst/doc/FlowSorted.CordBlood.450k.pdf vignetteTitles: Minfi Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: FlowSorted.Blood.EPIC Package: FlowSorted.CordBloodNorway.450k Version: 1.8.0 Depends: R (>= 3.2.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: f8a375e9ed900e593e944cbd95f13750 NeedsCompilation: no Title: Illumina HumanMethylation data on sorted cord blood cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays, for cell type composition estimation. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: kristina gervin [cre, aut], Kasper Daniel Hansen [aut] Maintainer: kristina gervin URL: https://bitbucket.com/kasperdanielhansen/Illumina_CordBlood git_url: https://git.bioconductor.org/packages/FlowSorted.CordBloodNorway.450k git_branch: RELEASE_3_8 git_last_commit: 0d8d46c git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/FlowSorted.CordBloodNorway.450k_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: FlowSorted.Blood.EPIC Package: FlowSorted.DLPFC.450k Version: 1.18.0 Depends: R (>= 2.13.0), minfi (>= 1.21.2) License: Artistic-2.0 MD5sum: de071e70f511a405aad3ee9b3196fd43 NeedsCompilation: no Title: Illumina HumanMethylation data on sorted frontal cortex cell populations Description: Raw data objects for the Illumina 450k DNA methylation microarrays. biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, TissueMicroarrayData, MethylationArrayData Author: Andrew E Jaffe, Zachary A. Kaminsky Maintainer: Andrew E Jaffe git_url: https://git.bioconductor.org/packages/FlowSorted.DLPFC.450k git_branch: RELEASE_3_8 git_last_commit: 800ad40 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/FlowSorted.DLPFC.450k_1.18.0.tar.gz vignettes: vignettes/FlowSorted.DLPFC.450k/inst/doc/FlowSorted.DLPFC.450k.pdf vignetteTitles: FlowSorted DLPFC 450k Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FlowSorted.DLPFC.450k/inst/doc/FlowSorted.DLPFC.450k.R Package: flowWorkspaceData Version: 2.18.0 License: GPL-2 MD5sum: 67cd786b29a27ccdbb1b1c423bfce42d NeedsCompilation: no Title: A data package containing two flowJo, one diva xml workspace and the associated fcs files as well as three GatingSets for testing the flowWorkspace, openCyto and CytoML packages. Description: The necessary external data to run the flowWorkspace and openCyto vignette is found in this package. biocViews: ExperimentData, FlowCytometryData Author: Greg Finak Maintainer: Mike Jiang git_url: https://git.bioconductor.org/packages/flowWorkspaceData git_branch: RELEASE_3_8 git_last_commit: 2ebc067 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/flowWorkspaceData_2.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: frmaExampleData Version: 1.18.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: d4faf0fddd05a0522bb832c1569b052d NeedsCompilation: no Title: Frma Example Data Description: Data files used by the examples in frma and frmaTools packages biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/frmaExampleData git_branch: RELEASE_3_8 git_last_commit: d764665 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/frmaExampleData_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: FunciSNP.data Version: 1.18.0 Depends: R (>= 2.14.0), IRanges Imports: rtracklayer License: GPL-3 MD5sum: d92989e8bb3e92138d3a597266fd0770 NeedsCompilation: no Title: Various data sets for use with the FunciSNP package Description: Data sets needed for FunciSNP to integrate information from GWAS, 1000genomes and chromatin feature, in order to identify functional SNP in coding or non-coding regions. biocViews: SNPData, Project1000genomes, ENCODE Author: Simon G. Coetzee and Houtan Noushmehr, PhD Maintainer: Simon G. Coetzee URL: http://coetzeeseq.usc.edu/publication/Coetzee_SG_et_al_2012/ git_url: https://git.bioconductor.org/packages/FunciSNP.data git_branch: RELEASE_3_8 git_last_commit: 4d90d85 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/FunciSNP.data_1.18.0.tar.gz vignettes: vignettes/FunciSNP.data/inst/doc/FunciSNP.data.pdf vignetteTitles: FunciSNP Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/FunciSNP.data/inst/doc/FunciSNP.data.R Package: furrowSeg Version: 1.10.0 Depends: R (>= 3.3), EBImage Imports: abind, dplyr, locfit, tiff Suggests: BiocStyle, ggplot2, knitr License: Artistic-2.0 MD5sum: dc60909e3fe7d7b517d4aaa5693fbe83 NeedsCompilation: no Title: Furrow Segmentation Description: Image feature data and analysis codes for the Guglielmi, Barry et al. paper describing the application of an optogenetics tools to disrupt Drosophila embryo furrowing. biocViews: ExperimentData, Drosophila_melanogaster_Data, Tissue, ReproducibleResearch Author: Joseph Barry Maintainer: Joseph Barry VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/furrowSeg git_branch: RELEASE_3_8 git_last_commit: d7772b0 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/furrowSeg_1.10.0.tar.gz vignettes: vignettes/furrowSeg/inst/doc/exampleFurrowSegmentation.pdf, vignettes/furrowSeg/inst/doc/genPaperFigures.pdf vignetteTitles: Supplementary Methods - Example furrow segmentation, Supplementary Methods - Automatic generation of paper figures hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/furrowSeg/inst/doc/exampleFurrowSegmentation.R, vignettes/furrowSeg/inst/doc/genPaperFigures.R Package: gageData Version: 2.20.0 Depends: R (>= 2.10) Suggests: gage, pathview, genefilter License: GPL (>=2.0) MD5sum: d483527aa3d7520e62154c90057f7d23 NeedsCompilation: no Title: Auxillary data for gage package Description: This is a supportive data package for the software package, gage. However, the data supplied here are also useful for gene set or pathway analysis or microarray data analysis in general. In this package, we provide two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and BMP6 (originally published as an demo dataset for GAGE, also registered as GSE13604 in GEO). This package also includes commonly used gene set data based on KEGG pathways and GO terms for major research species, including human, mouse, rat and budding yeast. Mapping data between common gene IDs for budding yeast are also included. biocViews: ExperimentData, StemCell, CancerData, BreastCancerData, MicroarrayData, GEO Author: Weijun Luo Maintainer: Weijun Luo git_url: https://git.bioconductor.org/packages/gageData git_branch: RELEASE_3_8 git_last_commit: 4734b57 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/gageData_2.20.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: gaschYHS Version: 1.20.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: c6348bdc5404d69a6c6e4726478d2e62 NeedsCompilation: no Title: ExpressionSet for response of yeast to heat shock and other environmental stresses Description: Data from PMID 11102521 biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data Author: Audrey Gasch and colleagues Maintainer: Vince Carey URL: http://genome-www.stanford.edu/yeast_stress/data/rawdata/complete_dataset.txt git_url: https://git.bioconductor.org/packages/gaschYHS git_branch: RELEASE_3_8 git_last_commit: 150e97c git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/gaschYHS_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gatingMLData Version: 2.22.0 Depends: R (>= 1.9.0) Suggests: flowUtils License: GPL MD5sum: ea5dc27900b34bcf1588ec22100f1d95 NeedsCompilation: no Title: Data and XML files for Gating-ML Test suite Description: Test data and XML files for testing compliance of the flowUtils/flowCore packages with Gating-ML (1.5 and 2.0) standards. biocViews: ExperimentData, FlowCytometryData Author: J. Spidlen, N. Gopalakrishnan Maintainer: J. Spidlen git_url: https://git.bioconductor.org/packages/gatingMLData git_branch: RELEASE_3_8 git_last_commit: 2319759 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/gatingMLData_2.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gcspikelite Version: 1.20.0 Depends: R (>= 2.5.0) License: LGPL MD5sum: d365d11462a9a1ed68634ff8e9e0cfa4 NeedsCompilation: no Title: Spike-in data for GC/MS data and methods within flagme Description: Spike-in data for GC/MS data and methods within flagme biocViews: MassSpectrometryData Author: Mark Robinson Maintainer: Mark Robinson git_url: https://git.bioconductor.org/packages/gcspikelite git_branch: RELEASE_3_8 git_last_commit: 1c7b3df git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/gcspikelite_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: geneLenDataBase Version: 1.18.0 Depends: R (>= 2.11.0) Imports: utils, rtracklayer, GenomicFeatures (>= 1.3.15) License: LGPL (>= 2) MD5sum: 6bb5df37b2b3472202006a767123ac34 NeedsCompilation: no Title: Lengths of mRNA transcripts for a number of genomes Description: Length of mRNA transcripts for a number of genomes and gene ID formats, largely based on UCSC table browser biocViews: ExperimentData, Genome Author: Matthew Young Maintainer: Nadia Davidson , Anthony Hawkins git_url: https://git.bioconductor.org/packages/geneLenDataBase git_branch: RELEASE_3_8 git_last_commit: 77db87e git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/geneLenDataBase_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: genomationData Version: 1.14.0 Suggests: knitr License: GPL-3 MD5sum: c0a8b50d7fbe4e4179d172ce02204bf6 NeedsCompilation: no Title: Experimental data for showing functionalities of the genomation package Description: The package contains Chip Seq, Methylation and Cage data, downloaded from Encode biocViews: ExperimentData, Genome, StemCell, SequencingData, ChIPSeqData, ChipOnChipData, ENCODE Author: Altuna Akalin, Vedran Franke Maintainer: Vedran Franke VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/genomationData git_branch: RELEASE_3_8 git_last_commit: 4b67025 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/genomationData_1.14.0.tar.gz vignettes: vignettes/genomationData/inst/doc/genomationData-knitr.pdf vignetteTitles: genomationData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/genomationData/inst/doc/genomationData-knitr.R Package: GeuvadisTranscriptExpr Version: 1.10.0 Depends: R (>= 3.3.0) Suggests: limma, rtracklayer, GenomicRanges, Rsamtools, VariantAnnotation, tools, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: e7df5c58da3c1e58245c8b0d12263735 NeedsCompilation: no Title: Data package with transcript expression and bi-allelic genotypes from the GEUVADIS project Description: Provides transcript expression and bi-allelic genotypes corresponding to the chromosome 19 for CEU individuals from the GEUVADIS project, Lappalainen et al. biocViews: Homo_sapiens_Data, SNPData, Genome, RNASeqData, SequencingData, ExpressionData Author: Malgorzata Nowicka [aut, cre] Maintainer: Malgorzata Nowicka VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GeuvadisTranscriptExpr git_branch: RELEASE_3_8 git_last_commit: b9df29f git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/GeuvadisTranscriptExpr_1.10.0.tar.gz vignettes: vignettes/GeuvadisTranscriptExpr/inst/doc/GeuvadisTranscriptExpr.pdf vignetteTitles: Preprocessing and preparation of transcript expression and genotypes from the GEUVADIS project for sQTL analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GeuvadisTranscriptExpr/inst/doc/GeuvadisTranscriptExpr.R Package: geuvPack Version: 1.14.0 Depends: R (>= 2.10), SummarizedExperiment License: Artistic-2.0 MD5sum: 0fddefe9a5285b6545e39af655ef2502 NeedsCompilation: no Title: summarized experiment with expression data from GEUVADIS Description: FPKM from GEUVADIS, annotated to gencode regions biocViews: ExperimentData, Genome, SequencingData, MicroarrayData, ArrayExpress Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/geuvPack git_branch: RELEASE_3_8 git_last_commit: 4622f51 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/geuvPack_1.14.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: yriMulti suggestsMe: yriMulti Package: geuvStore2 Version: 1.12.0 Depends: BatchJobs, GenomicRanges Imports: methods, gQTLBase Suggests: Homo.sapiens, knitr (>= 1.7), rmarkdown License: Artistic-2.0 MD5sum: 4a979fce43756a969ef30510fc7edd7f NeedsCompilation: no Title: demonstrate storage discipline for eQTL enumerations, revised Description: demonstrate storage discipline for eQTL enumerations and analyses based on a selection of GEUVADIS results biocViews: ExperimentData, SequencingData, MicroarrayData Author: VJ Carey Maintainer: VJ Carey VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/geuvStore2 git_branch: RELEASE_3_8 git_last_commit: 489dcfd git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/geuvStore2_1.12.0.tar.gz vignettes: vignettes/geuvStore2/inst/doc/geuvStore2.pdf vignetteTitles: geuvStore: sharded storage for cis-association statistics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/geuvStore2/inst/doc/geuvStore2.R Package: GGdata Version: 1.20.0 Depends: R (>= 2.12.0), methods, Biobase (>= 2.5.5), GGBase, snpStats, illuminaHumanv1.db, AnnotationDbi Enhances: GGtools License: LGPL MD5sum: dffb9127f0d21be6e27478b178bf9d13 NeedsCompilation: no Title: all 90 hapmap CEU samples, 47K expression, 4mm SNP Description: data exemplars dealing with hapmap SNP reports, GWAS, etc. biocViews: ExperimentData, HapMap, Genome, SequencingData, MicroarrayData, SNPData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/GGdata git_branch: RELEASE_3_8 git_last_commit: 8febeb6 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/GGdata_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GIGSEAdata Version: 1.0.0 Depends: R (>= 3.5) Suggests: GIGSEA, knitr, rmarkdown License: LGPL-3 MD5sum: 9036142a6d2c9eecdfec8023c032aa7f NeedsCompilation: no Title: Gene set collections for the GIGSEA package Description: The gene set collection used for the GIGSEA package. biocViews: ExperimentData, Homo_sapiens_Data Author: Shijia Zhu Maintainer: Shijia Zhu VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GIGSEAdata git_branch: RELEASE_3_8 git_last_commit: f7157c7 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/GIGSEAdata_1.0.0.tar.gz vignettes: vignettes/GIGSEAdata/inst/doc/GIGSEAdata_tutorial.pdf vignetteTitles: GIGSEAdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GIGSEAdata/inst/doc/GIGSEAdata_tutorial.R Package: golubEsets Version: 1.24.0 Depends: R (>= 2.14.0), Biobase (>= 2.5.5) License: LGPL MD5sum: 0fe60bd861eca25969193aeadcd0bc59 NeedsCompilation: no Title: exprSets for golub leukemia data Description: representation of public golub data with some covariate data of provenance unknown to the maintainer at present; now employs ExpressionSet format biocViews: ExperimentData, Genome, CancerData, LeukemiaCancerData Author: Todd Golub Maintainer: Vince Carey git_url: https://git.bioconductor.org/packages/golubEsets git_branch: RELEASE_3_8 git_last_commit: 32c84ff git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/golubEsets_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: grndata Version: 1.14.0 Depends: R (>= 2.10) Suggests: RUnit, BiocGenerics, knitr License: GPL-3 MD5sum: aacdf027236c99022b11fdabb983bbe4 NeedsCompilation: no Title: Synthetic Expression Data for Gene Regulatory Network Inference Description: Simulated expression data for five large Gene Regulatory Networks from different simulators biocViews: ExperimentData, NetworkInference, GeneExpression, Microarray, GeneRegulation, Network Author: Pau Bellot, Catharina Olsen, Patrick E Meyer Maintainer: Pau Bellot VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/grndata git_branch: RELEASE_3_8 git_last_commit: fe91af0 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/grndata_1.14.0.tar.gz vignettes: vignettes/grndata/inst/doc/grndata.html vignetteTitles: GRNdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: GSBenchMark Version: 1.2.0 Depends: R (>= 2.13.1) License: GPL-2 MD5sum: 5fa1f183443b3841de7e075441d47c5d NeedsCompilation: no Title: Gene Set Benchmark Description: Benchmarks for Machine Learning Analysis of the Gene Sets. The package contains a list of pathways and gene expression data sets used in "Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)" (2010) by Eddy et al. biocViews: MicroarrayData Author: Bahman Afsari , Elana J. Fertig Maintainer: Bahman Afsari git_url: https://git.bioconductor.org/packages/GSBenchMark git_branch: RELEASE_3_8 git_last_commit: a58b6f0 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/GSBenchMark_1.2.0.tar.gz vignettes: vignettes/GSBenchMark/inst/doc/GSBenchMark.pdf vignetteTitles: Working with the GSBenchMark package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GSBenchMark/inst/doc/GSBenchMark.R Package: GSE62944 Version: 1.10.0 Depends: Biobase, GEOquery Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle License: Artistic-2.0 MD5sum: fecc45362eda757435ba7a0735c96b11 NeedsCompilation: no Title: GEO accession data GSE62944 as a SummarizedExperiment Description: TCGA processed RNA-Seq data for 9264 tumor and 741 normal samples across 24 cancer types and made them available as GEO accession [GSE62944](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944). GSE62944 data have been parsed into a SummarizedExperiment object available in ExperimentHub. biocViews: ExperimentData, Genome, DNASeqData, RNASeqData Author: Sonali Arora Maintainer: Bioconductor Package Maintainer URL: http://bioconductor.org/packages/release/bioc/html/GSE62944.html VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/GSE62944 git_branch: RELEASE_3_8 git_last_commit: c088a28 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/GSE62944_1.10.0.tar.gz vignettes: vignettes/GSE62944/inst/doc/GSE62944.html vignetteTitles: Raw TCGA data using Bioconductor's ExperimentHub hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/GSE62944/inst/doc/GSE62944.R Package: gskb Version: 1.14.0 Depends: R (>= 3.2.0) Suggests: PGSEA License: Artistic-2.0 MD5sum: d2053bb9fd322f0c71360f6721761443 NeedsCompilation: no Title: Gene Set data for pathway analysis in mouse Description: Gene Set Knowledgebase (GSKB) is a comprehensive knowledgebase for pathway analysis in mouse. Interpretation of high-throughput genomics data based on biological pathways constitutes a constant challenge, partly because of the lack of supporting pathway database. We created a functional genomics knowledgebase in mouse, which includes 33,261 pathways and gene sets compiled from 40 sources such as Gene Ontology, KEGG, GeneSetDB, PANTHER, microRNA and transcription factor target genes, etc. In addition, we also manually collected and curated 8,747 lists of differentially expressed genes from 2,526 published gene expression studies to enable the detection of similarity to previously reported gene expression signatures. These two types of data constitute a comprehensive Gene Set Knowledgebase (GSKB), which can be readily used by various pathway analysis software such as gene set enrichment analysis (GSEA). As a first step, we gathered annotation information from 40 existing databases for mouse-related gene sets. These gene sets are divided into 7 categories, namely, Gene Ontology, Curated pathways, Metabolic Pathways, Transcription Factor (TF) and microRNA target genes, location (cytogenetics band), and others. We used information in GeneSetDB for some of the databases. Detailed information on these 40 sources and the citations is available http://ge-lab.org/gskb/Table%201-sources.pdf . The gene lists from literature were retrieved manually from individual gene expression studies through a process similar to the one used to create AraPath, a similar resource for Arabidopsis[12]. As most expression studies upload raw data to repositories like GEO and ArrayExpress, we used the meta-data in these databases to search for publications. We scanned all datasets we can found and retrieved 4,313 potentially useful papers reporting gene expression studies in mouse. These papers were individually read by curators to identify lists of differentially expressed genes in various conditions. We compiled a total of 8,747 lists of differently expressed genes from 2,518 of papers. Each gene list was annotated with a unique name, brief description, and publication information, similar to the protocol used in MSigDB and Arapath. These gene lists constitute a large collection of published gene expression signatures that form a foundation for interpret new gene lists and expression profiles. More information about this data is available here http://ge-lab.org/gskb/. There is also a paper describing these data are currently in revision by Database: The Journal of Biological Databases and Curation. biocViews: ExperimentData, Mus_musculus Author: Valerie Bares, Xijin Ge Maintainer: Valerie Bares git_url: https://git.bioconductor.org/packages/gskb git_branch: RELEASE_3_8 git_last_commit: 354b384 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/gskb_1.14.0.tar.gz vignettes: vignettes/gskb/inst/doc/gskb.pdf vignetteTitles: gskb: mouse data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/gskb/inst/doc/gskb.R Package: GSVAdata Version: 1.18.0 Depends: R (>= 2.10), Biobase, GSEABase, hgu95a.db License: GPL (>= 2) MD5sum: 10c95ec0b4214f43609e0bfdfc860bc8 NeedsCompilation: no Title: Data employed in the vignette of the GSVA package Description: This package stores the data employed in the vignette of the GSVA package. These data belong to the following publications: Armstrong et al. Nat Genet 30:41-47, 2002; Cahoy et al. J Neurosci 28:264-278, 2008; Carrel and Willard, Nature, 434:400-404, 2005; Huang et al. PNAS, 104:9758-9763, 2007; Pickrell et al. Nature, 464:768-722, 2010; Skaletsky et al. Nature, 423:825-837; Verhaak et al. Cancer Cell 17:98-110, 2010 biocViews: ExperimentData, RNASeqData, Homo_sapiens_Data, CancerData, LeukemiaCancerData Author: Robert Castelo Maintainer: Robert Castelo git_url: https://git.bioconductor.org/packages/GSVAdata git_branch: RELEASE_3_8 git_last_commit: ca55088 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/GSVAdata_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GWASdata Version: 1.20.0 Depends: GWASTools License: Artistic-2.0 MD5sum: 6b7ab74910c712639fa896f6b19e2934 NeedsCompilation: no Title: Data used in the examples and vignettes of the GWASTools package Description: Selected Affymetrix and Illlumina SNP data for HapMap subjects. Data provided by the Center for Inherited Disease Research at Johns Hopkins University and the Broad Institute of MIT and Harvard University. biocViews: ExperimentData, MicroarrayData, SNPData, HapMap Author: Stephanie Gogarten Maintainer: Stephanie Gogarten , Adrienne Stilp git_url: https://git.bioconductor.org/packages/GWASdata git_branch: RELEASE_3_8 git_last_commit: d46ab17 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/GWASdata_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: h5vcData Version: 2.2.0 Suggests: h5vc License: GPL (>= 3) MD5sum: dafde62ac2fd221e41398ba6b3d6ccc2 NeedsCompilation: no Title: Example data for the h5vc package Description: This package contains the data used in the vignettes and examples of the 'h5vc' package biocViews: CancerData Author: Paul Theodor Pyl Maintainer: Paul Theodor Pyl git_url: https://git.bioconductor.org/packages/h5vcData git_branch: RELEASE_3_8 git_last_commit: 14677a9 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/h5vcData_2.2.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap100khind Version: 1.24.0 Suggests: oligo License: GPL MD5sum: 41f5b3455328c928df5b6ae2d81e7c8b NeedsCompilation: no Title: Sample data - Hapmap 100K HIND Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap100khind git_branch: RELEASE_3_8 git_last_commit: 9c0e5a4 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/hapmap100khind_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap100kxba Version: 1.24.0 Suggests: oligo License: GPL MD5sum: a1d77e1d940c42e5b253d8517a29f414 NeedsCompilation: no Title: Sample data - Hapmap 100K XBA Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap100kxba git_branch: RELEASE_3_8 git_last_commit: 33d3b9b git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/hapmap100kxba_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap500knsp Version: 1.24.0 Suggests: oligo License: GPL MD5sum: 6a1ab68e668feec8e7388dbbd4308252 NeedsCompilation: no Title: Sample data - Hapmap 500K NSP Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap500knsp git_branch: RELEASE_3_8 git_last_commit: f55c93a git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/hapmap500knsp_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmap500ksty Version: 1.24.0 Suggests: oligo License: GPL MD5sum: b33d5168b902765a63c25a6f2dae66af NeedsCompilation: no Title: Sample data - Hapmap 500K STY Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmap500ksty git_branch: RELEASE_3_8 git_last_commit: d67e8c2 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/hapmap500ksty_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmapsnp5 Version: 1.24.0 Suggests: oligo License: GPL MD5sum: 518ce21d478eb25e29ed81256154e6fe NeedsCompilation: no Title: Sample data - Hapmap SNP 5.0 Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, CancerData, SNPData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmapsnp5 git_branch: RELEASE_3_8 git_last_commit: 76e09ff git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/hapmapsnp5_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hapmapsnp6 Version: 1.24.0 Depends: R (>= 2.15) Suggests: oligo, oligoClasses License: GPL MD5sum: 2d6a0cd7f337c99834d143215d74e787 NeedsCompilation: no Title: Sample data - Hapmap SNP 6.0 Affymetrix Description: Sample dataset obtained from http://www.hapmap.org biocViews: ExperimentData, HapMap, SNPData Author: Hapmap Consortium Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/hapmapsnp6 git_branch: RELEASE_3_8 git_last_commit: c7e3bc2 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/hapmapsnp6_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: harbChIP Version: 1.20.0 Depends: R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5), Biostrings Imports: methods, stats License: Artistic-2.0 MD5sum: 2dedda8ec8b79f7cd73648090853a31a NeedsCompilation: no Title: Experimental Data Package: harbChIP Description: data from a yeast ChIP-chip experiment biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/harbChIP git_branch: RELEASE_3_8 git_last_commit: 26db266 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/harbChIP_1.20.0.tar.gz vignettes: vignettes/harbChIP/inst/doc/yeastUpstream.pdf vignetteTitles: upstream sequence management for yeast hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/harbChIP/inst/doc/yeastUpstream.R Package: HarmanData Version: 1.10.0 Depends: R (>= 3.2.3) Suggests: BiocGenerics, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 527bf6823b7a6135e7c04b0031c8c486 NeedsCompilation: no Title: Data for the Harman package Description: Datasets of accompany Harman, a PCA and constrained optimisation based technique. Contains three datasets: IMR90, Human lung fibroblast cells exposed to nitric oxide; NPM, an experiment to test skin penetration of metal oxide nanoparticles following topical application of sunscreens in non-pregnant mice; OLF; an experiment to gauge the response of human olfactory neurosphere-derived (hONS) cells to ZnO nanoparticles. biocViews: ExpressionData, MicroarrayData, ExperimentData, Homo_sapiens_Data, Mus_musculus_Data Author: Josh Bowden [aut], Jason Ross [aut, cre], Yalchin Oytam [aut] Maintainer: Jason Ross URL: http://www.bioinformatics.csiro.au/harman/ VignetteBuilder: knitr BugReports: https://github.com/JasonR055/Harman/issues git_url: https://git.bioconductor.org/packages/HarmanData git_branch: RELEASE_3_8 git_last_commit: c23b585 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/HarmanData_1.10.0.tar.gz vignettes: vignettes/HarmanData/inst/doc/HarmanData.html vignetteTitles: HarmanData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HarmanData/inst/doc/HarmanData.R Package: HarmonizedTCGAData Version: 1.4.0 Depends: R (>= 3.4.0) Imports: ExperimentHub Suggests: AnnotationHub, knitr, rmarkdown, igraph, survival, ANF, stats, testthat License: GPL-3 MD5sum: 064823184770359197455c835096eacb NeedsCompilation: no Title: Processed Harmonized TCGA Data of Five Selected Cancer Types Description: This package contains the processed harmonized TCGA data of five cancer types used in "Tianle Ma and Aidong Zhang, Integrate Multi-omic Data Using Affinity Network Fusion (ANF) for Cancer Patient Clustering". biocViews: CancerData, ReproducibleResearch Author: Tianle Ma Maintainer: Tianle Ma VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/HarmonizedTCGAData git_branch: RELEASE_3_8 git_last_commit: 1f74350 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/HarmonizedTCGAData_1.4.0.tar.gz vignettes: vignettes/HarmonizedTCGAData/inst/doc/HarmonizedTCGAData.html vignetteTitles: Patient Affinity Matrices Derived from Harmonized TCGA Dataset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HarmonizedTCGAData/inst/doc/HarmonizedTCGAData.R Package: HD2013SGI Version: 1.22.0 Depends: R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots, limma, vcd, LSD,EBImage Suggests: BiocStyle License: Artistic-2.0 MD5sum: e67f8f961700314d6ba0326dfebb0e3b NeedsCompilation: no Title: Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping Description: This package contains the experimental data and a complete executable transcript (vignette) of the analysis of the HCT116 genetic interaction matrix presented in the paper "Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping" by C. Laufer, B. Fischer, M. Billmann, W. Huber, M. Boutros; Nature Methods (2013) 10:427-31. doi: 10.1038/nmeth.2436. biocViews: ExperimentData, CancerData, ColonCancerData, MicrotitrePlateAssayData, CellCulture, Homo_sapiens_Data, HighThroughputImagingData Author: Bernd Fischer Maintainer: Bernd Fischer SystemRequirements: GNU make git_url: https://git.bioconductor.org/packages/HD2013SGI git_branch: RELEASE_3_8 git_last_commit: 26a64a8 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/HD2013SGI_1.22.0.tar.gz vignettes: vignettes/HD2013SGI/inst/doc/HD2013SGI.pdf vignetteTitles: HD2013SGI hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HD2013SGI/inst/doc/HD2013SGI.R Package: HDCytoData Version: 1.2.11 Depends: ExperimentHub, SummarizedExperiment, flowCore Imports: utils, methods Suggests: BiocStyle, knitr, rmarkdown, FlowSOM, Rtsne, ggplot2 License: MIT + file LICENSE MD5sum: fcf634ef68d6e28d9f54933320e6730d NeedsCompilation: no Title: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats Description: Data package containing a collection of high-dimensional cytometry benchmark datasets saved in SummarizedExperiment and flowSet Bioconductor object formats, including row and column metadata describing samples, cell populations (clusters), and protein markers. biocViews: ExperimentHub, ExperimentData, ExpressionData, FlowCytometryData, Homo_sapiens_Data, ImmunoOncologyData Author: Lukas M. Weber [aut, cre], Charlotte Soneson [aut] Maintainer: Lukas M. Weber URL: https://github.com/lmweber/HDCytoData VignetteBuilder: knitr BugReports: https://github.com/lmweber/HDCytoData/issues git_url: https://git.bioconductor.org/packages/HDCytoData git_branch: RELEASE_3_8 git_last_commit: b39e82e git_last_commit_date: 2019-01-30 Date/Publication: 2019-02-03 source.ver: src/contrib/HDCytoData_1.2.11.tar.gz vignettes: vignettes/HDCytoData/inst/doc/HDCytoData.html vignetteTitles: HDCytoData data package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/HDCytoData/inst/doc/HDCytoData.R Package: healthyFlowData Version: 1.20.0 Depends: R (>= 2.15.0), flowCore Imports: methods License: Artistic-2.0 MD5sum: b8581160bd5bfcc2d539dd7c15b6015b NeedsCompilation: no Title: Healthy dataset used by the flowMatch package Description: A healthy dataset with 20 flow cytometry samples used by the flowMatch package. biocViews: FlowCytometryData Author: Ariful Azad Maintainer: Ariful Azad git_url: https://git.bioconductor.org/packages/healthyFlowData git_branch: RELEASE_3_8 git_last_commit: 002bb2f git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/healthyFlowData_1.20.0.tar.gz vignettes: vignettes/healthyFlowData/inst/doc/healthyFlowData.pdf vignetteTitles: healthyFlowData: A healthy dataset with 20 flow cytometry samples used by the flowMatch package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/healthyFlowData/inst/doc/healthyFlowData.R Package: HEEBOdata Version: 1.20.0 License: LGPL MD5sum: 637405f7b381653f36c87414a2902907 NeedsCompilation: no Title: HEEBO set and HEEBO controls. Description: R objects describing the HEEBO oligo set. biocViews: ExperimentData Author: Agnes Paquet Maintainer: Agnes Paquet URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/ git_url: https://git.bioconductor.org/packages/HEEBOdata git_branch: RELEASE_3_8 git_last_commit: dbc8a8f git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/HEEBOdata_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: HelloRangesData Version: 1.8.0 Suggests: BiocStyle License: GPL (>= 2) MD5sum: 544429f8fe98d0ec98dd22061944d673 NeedsCompilation: no Title: Data for the HelloRanges tutorial vignette Description: Provides the data that were used in the bedtools tutorial by Aaron Quinlan (http://quinlanlab.org/tutorials/bedtools/bedtools.html). Includes a subset of the DnaseI hypersensitivity data from "Maurano et al. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA. Science. 2012. Vol. 337 no. 6099 pp. 1190-1195." The rest of the tracks were originally downloaded from the UCSC table browser. See the HelloRanges vignette for a port of the bedtools tutorial to R. biocViews: ExperimentData, SequencingData Author: Michael Lawrence Maintainer: Michael Lawrence git_url: https://git.bioconductor.org/packages/HelloRangesData git_branch: RELEASE_3_8 git_last_commit: 06dee33 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/HelloRangesData_1.8.0.tar.gz vignettes: vignettes/HelloRangesData/inst/doc/intro.pdf vignetteTitles: HelloRanges Example Data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HelloRangesData/inst/doc/intro.R Package: hgu133abarcodevecs Version: 1.20.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: b32e4538a860079a21da485ffc31fbb9 NeedsCompilation: no Title: hgu133a data for barcode Description: Data used by the barcode package for microarrays of type hgu133a. biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/hgu133abarcodevecs git_branch: RELEASE_3_8 git_last_commit: ede0ff9 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/hgu133abarcodevecs_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu133plus2barcodevecs Version: 1.20.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 638f4fcd029bb5b3d07a2c3b79ffa3f9 NeedsCompilation: no Title: hgu133plus2 data for barcode Description: Data used by the barcode package for microarrays of type hgu133plus2. biocViews: Homo_sapiens_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/hgu133plus2barcodevecs git_branch: RELEASE_3_8 git_last_commit: e72f8d1 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/hgu133plus2barcodevecs_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hgu133plus2CellScore Version: 1.2.0 Depends: R (>= 3.5.0) Imports: Biobase (>= 2.39.1) Suggests: knitr License: GPL-3 MD5sum: 354194eddcc3f67ac375b08422007602 NeedsCompilation: no Title: CellScore Standard Cell Types Expression Dataset [hgu133plus2] Description: The CellScore Standard Dataset contains expression data from a wide variety of human cells and tissues, which should be used as standard cell types in the calculation of the CellScore. All data was curated from public databases such as Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) or ArrayExpress (https://www.ebi.ac.uk/arrayexpress/). This standard dataset only contains data from the Affymetrix GeneChip Human Genome U133 Plus 2.0 microarrays. Samples were manually annotated using the database information or consulting the publications in which the datasets originated. The sample annotations are stored in the phenoData slot of the expressionSet object. Raw data (CEL files) were processed with the affy package to generate present/absent calls (mas5calls) and background-subtracted values, which were then normalized by the R-package yugene to yield the final expression values for the standard expression matrix. The annotation table for the microarray was retrieved from the BioC annotation package hgu133plus2. All data are stored in an expressionSet object. biocViews: ExpressionData, MicroarrayData, GEO, ExperimentData, Homo_sapiens_Data, Genome, ArrayExpress Author: Nancy Mah, Katerina Taskova Maintainer: Nancy Mah VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/hgu133plus2CellScore git_branch: RELEASE_3_8 git_last_commit: 052abce git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/hgu133plus2CellScore_1.2.0.tar.gz vignettes: vignettes/hgu133plus2CellScore/inst/doc/hgu133plus2Vignette.pdf vignetteTitles: R packages: hgu133plus2CellScore hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/hgu133plus2CellScore/inst/doc/hgu133plus2Vignette.R Package: hgu2beta7 Version: 1.22.0 Depends: R (>= 2.0.0) License: Artistic-2.0 MD5sum: 66fe43b6e1b602122964c9026dc9a660 NeedsCompilation: no Title: A data package containing annotation data for hgu2beta7 Description: Annotation data file for hgu2beta7 assembled using data from public data repositories biocViews: Genome Author: Chenwei Lin Maintainer: Bioconductor Package Maintainer git_url: https://git.bioconductor.org/packages/hgu2beta7 git_branch: RELEASE_3_8 git_last_commit: 49ae873 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/hgu2beta7_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: HiCDataHumanIMR90 Version: 1.2.0 Depends: R (>= 2.10) Suggests: HiTC License: GPL-3 MD5sum: cdf34ec2f78ce9a1482efbea622d81e0 NeedsCompilation: no Title: Human IMR90 Fibroblast HiC data from Dixon et al. 2012 Description: The HiC data from Human Fibroblast IMR90 cell line (HindIII restriction) was retrieved from the GEO website, accession number GSE35156 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35156). The raw reads were processed as explained in Dixon et al. (Nature 2012). biocViews: ExperimentData, Genome, Homo_sapiens_Data, GEO Author: Nicolas Servant Maintainer: Nicolas Servant git_url: https://git.bioconductor.org/packages/HiCDataHumanIMR90 git_branch: RELEASE_3_8 git_last_commit: 823e9ad git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/HiCDataHumanIMR90_1.2.0.tar.gz vignettes: vignettes/HiCDataHumanIMR90/inst/doc/HiC_Human_IMR90.pdf vignetteTitles: HiC Data Human Fibroblast Dixon et al. 2012 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HiCDataHumanIMR90/inst/doc/HiC_Human_IMR90.R Package: HiCDataLymphoblast Version: 1.18.0 Suggests: GOTHiC, ShortRead License: GPL-3 MD5sum: 55d001daefcf400a6f3474a4a6859c6e NeedsCompilation: no Title: Human lymphoblastoid HiC data from Lieberman-Aiden et al. 2009 Description: The HiC data from human lymphoblastoid cell line (HindIII restriction) was retrieved from the sequence read archive and two ends of the paired reads were aligned separately with bowtie. biocViews: ExperimentData, Homo_sapiens_Data Author: Borbala Mifsud Maintainer: Borbala Mifsud git_url: https://git.bioconductor.org/packages/HiCDataLymphoblast git_branch: RELEASE_3_8 git_last_commit: 0dd1d66 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/HiCDataLymphoblast_1.18.0.tar.gz vignettes: vignettes/HiCDataLymphoblast/inst/doc/package_vignettes.pdf vignetteTitles: package_vignettes.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HiCDataLymphoblast/inst/doc/package_vignettes.R Package: Hiiragi2013 Version: 1.18.0 Depends: R (>= 3.0.0), affy, Biobase, boot, clue, cluster, genefilter, geneplotter, gplots, gtools, KEGGREST, MASS, mouse4302.db, RColorBrewer, xtable Imports: grid, lattice, latticeExtra Suggests: ArrayExpress, BiocStyle License: Artistic-2.0 MD5sum: 0e1fdc481e61f2612f88120f4d7cbdff NeedsCompilation: no Title: Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages Description: This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881." biocViews: ExperimentData, MicroarrayData, qPCRData, ReproducibleResearch Author: Andrzej Oles, Wolfgang Huber Maintainer: Andrzej Oles git_url: https://git.bioconductor.org/packages/Hiiragi2013 git_branch: RELEASE_3_8 git_last_commit: cff201f git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/Hiiragi2013_1.18.0.tar.gz vignettes: vignettes/Hiiragi2013/inst/doc/Hiiragi2013.pdf vignetteTitles: Hiiragi2013 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Hiiragi2013/inst/doc/Hiiragi2013.R Package: HIVcDNAvantWout03 Version: 1.22.0 License: GPL (>= 2) MD5sum: e6bf73521bce0a019338afdbb9bbef30 NeedsCompilation: no Title: T cell line infections with HIV-1 LAI (BRU) Description: The expression levels of approximately 4600 cellular RNA transcripts were assessed in CD4+ T cell lines at different times after infection with HIV-1BRU using DNA microarrays. This data corresponds to the first block of a 12 block array image (001030_08_1.GEL) in the first data set (2000095918 A) in the first experiment (CEM LAI vs HI-LAI 24hr). There are two data sets, which are part of a dye-swap experiment with replicates, representing the Cy3 (green) absorption intensities for channel 1 (hiv1raw) and the Cy5 (red) absorption intensities for channel 2 (hiv2raw). biocViews: ExperimentData, MicroarrayData, TwoChannelData, HIVData Author: Dr. Angelique van't Wout, Department of Microbiology, University of Washington Maintainer: Chris Fraley URL: http://expression.microslu.washington.edu/expression/vantwoutjvi2002.html git_url: https://git.bioconductor.org/packages/HIVcDNAvantWout03 git_branch: RELEASE_3_8 git_last_commit: d9f257a git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/HIVcDNAvantWout03_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: HMP16SData Version: 1.2.1 Depends: R (>= 3.5.0), SummarizedExperiment Imports: AnnotationHub, assertthat, dplyr, ExperimentHub, kableExtra, knitr, magrittr, methods, readr, S4Vectors, tibble, utils Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, circlize, covr, cowplot, curatedMetagenomicData, dendextend, devtools, ggplot2, gridExtra, haven, phyloseq, rmarkdown, roxygen2, stats, testthat License: Artistic-2.0 MD5sum: 9284199ac9708f5f9d31f7f972844b28 NeedsCompilation: no Title: 16S rRNA Sequencing Data from the Human Microbiome Project Description: HMP16SData is a Bioconductor ExperimentData package of the Human Microbiome Project (HMP) 16S rRNA sequencing data for variable regions 1–3 and 3–5. Raw data files are provided in the package as downloaded from the HMP Data Analysis and Coordination Center. Processed data is provided as SummarizedExperiment class objects via ExperimentHub. biocViews: ExperimentData, Homo_sapiens_Data, MicrobiomeData, ReproducibleResearch, SequencingData Author: Lucas Schiffer , Rimsha Azhar , Marcel Ramos , Ludwig Geistlinger , Levi Waldron Maintainer: Lucas Schiffer URL: https://github.com/waldronlab/HMP16SData VignetteBuilder: knitr BugReports: https://github.com/waldronlab/HMP16SData/issues git_url: https://git.bioconductor.org/packages/HMP16SData git_branch: RELEASE_3_8 git_last_commit: d5ff5c5 git_last_commit_date: 2019-02-17 Date/Publication: 2019-02-19 source.ver: src/contrib/HMP16SData_1.2.1.tar.gz vignettes: vignettes/HMP16SData/inst/doc/HMP16SData.html vignetteTitles: HMP16SData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HMP16SData/inst/doc/HMP16SData.R Package: hmyriB36 Version: 1.18.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.5.5), GGBase Suggests: GGtools, illuminaHumanv1.db License: Artistic-2.0 MD5sum: b5674b509a47b85c82b4173b4a13e5f1 NeedsCompilation: no Title: YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes Description: YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes biocViews: ExperimentData, Genome, SNPData, HapMap Author: Vincent Carey Maintainer: Vincent Carey git_url: https://git.bioconductor.org/packages/hmyriB36 git_branch: RELEASE_3_8 git_last_commit: e9cd022 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/hmyriB36_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: HSMMSingleCell Version: 1.2.0 Depends: R (>= 2.10) License: Artistic-2.0 MD5sum: 13554a8eacb310fd9af3900ba9ce68b9 NeedsCompilation: no Title: Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM) Description: Skeletal myoblasts undergo a well-characterized sequence of morphological and transcriptional changes during differentiation. In this experiment, primary human skeletal muscle myoblasts (HSMM) were expanded under high mitogen conditions (GM) and then differentiated by switching to low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several hundred cells taken over a time-course of serum-induced differentiation. Between 49 and 77 cells were captured at each of four time points (0, 24, 48, 72 hours) following serum switch using the Fluidigm C1 microfluidic system. RNA from each cell was isolated and used to construct mRNA-Seq libraries, which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell. biocViews: ExperimentData, RNASeqData Author: Cole Trapnell Maintainer: Cole Trapnell git_url: https://git.bioconductor.org/packages/HSMMSingleCell git_branch: RELEASE_3_8 git_last_commit: 7518e5e git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/HSMMSingleCell_1.2.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: HumanAffyData Version: 1.8.0 Depends: ExperimentHub, Biobase, R (>= 3.3) Suggests: BiocStyle License: Artistic-2.0 MD5sum: dfe3425fce62815fdd066bd003bfb4d5 NeedsCompilation: no Title: GEO accession GSE64985 and ArrayExpress accession E-MTAB-62 as ExpressionSet objects Description: Re-analysis of human gene expression data generated on the Affymetrix HG_U133PlusV2 (EH176) and Affymetrix HG_U133A (EH177) platforms. The original data were normalized using robust multiarray averaging (RMA) to obtain an integrated gene expression atlas across diverse biological sample types and conditions. The entire compendia comprisee 9395 arrays for EH176 and 5372 arrays for EH177. biocViews: ExperimentData, GEO, ArrayExpress, Homo_sapiens_Data, MicroarrayData, ExpressionData Author: Brad Nelms Maintainer: Brad Nelms git_url: https://git.bioconductor.org/packages/HumanAffyData git_branch: RELEASE_3_8 git_last_commit: 7e022ca git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/HumanAffyData_1.8.0.tar.gz vignettes: vignettes/HumanAffyData/inst/doc/HumanAffyData.pdf vignetteTitles: Intro to the HumanAffyData package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/HumanAffyData/inst/doc/HumanAffyData.R Package: humanStemCell Version: 0.22.0 Depends: Biobase (>= 2.5.5), hgu133plus2.db License: Artistic-2.0 MD5sum: 9c51c8672331f6416b56f0224b5e7494 NeedsCompilation: no Title: Human Stem Cells time course experiment Description: Affymetrix time course experiment on human stem cells (two time points: undifferentiated and differentiated). biocViews: ExperimentData, Homo_sapiens_Data Author: R. Gentleman, N. Le Meur, M. Tewari Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/humanStemCell git_branch: RELEASE_3_8 git_last_commit: 3ea4155 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/humanStemCell_0.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: IHWpaper Version: 1.10.0 Depends: R (>= 3.3), IHW Imports: Rcpp, stats, splines, methods, utils, DESeq2, SummarizedExperiment, fdrtool, genefilter, qvalue, Biobase, BiocGenerics, BiocParallel, dplyr, grid, ggplot2, cowplot LinkingTo: Rcpp Suggests: testthat, RColorBrewer, wesanderson, scales, gridExtra, BiocStyle, knitr, rmarkdown, airway, pasilla, DESeq, locfdr, tidyr, ggbio, latex2exp License: Artistic-2.0 MD5sum: 941b62cdbd35bd8c0327712b47963bf2 NeedsCompilation: yes Title: Reproduce figures in IHW paper Description: This package conveniently wraps all functions needed to reproduce the figures in the IHW paper (https://www.nature.com/articles/nmeth.3885) and the latest arXiv preprint available under http://arxiv.org/abs/1701.05179. Thus it is a companion package to the Bioconductor IHW package. biocViews: ReproducibleResearch, ExperimentData, RNASeqData, ExpressionData Author: Nikos Ignatiadis [aut, cre] Maintainer: Nikos Ignatiadis VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/IHWpaper git_branch: RELEASE_3_8 git_last_commit: 2547942 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/IHWpaper_1.10.0.tar.gz vignettes: vignettes/IHWpaper/inst/doc/BH-explanation.html, vignettes/IHWpaper/inst/doc/explaining_tdr.html, vignettes/IHWpaper/inst/doc/grenander_vs_ecdf.html, vignettes/IHWpaper/inst/doc/hqtl_IHW_BY.html, vignettes/IHWpaper/inst/doc/IHW_bonferroni_simulations.html, vignettes/IHWpaper/inst/doc/IHW_censoring_storey_simulations.html, vignettes/IHWpaper/inst/doc/real_data_examples_single_curve.html, vignettes/IHWpaper/inst/doc/real_data_examples.html, vignettes/IHWpaper/inst/doc/simulations_vignette.html, vignettes/IHWpaper/inst/doc/stratified_histograms.html, vignettes/IHWpaper/inst/doc/tdr_pvalue_rejection_thresholds.html, vignettes/IHWpaper/inst/doc/weights_vs_filtering.html vignetteTitles: "Various: BH explanation / visualization", "NMeth paper: Explaining tdr", "Various: Grenander Estimator as applied to IHW (vs ECDF)", "Stats paper: hQTL analysis with IHW-Benjamini-Yekutieli", "NMeth paper: IHW-Bonferroni simulations", "Stats paper: IHW-censoring & Storey simulations", "Various: Real data examples: 1-fold weight function", "NMeth paper: Real data examples", "NMeth paper: Simulation Figures", "NMeth paper: Stratified Histograms", "Various: tdr and pvalue rejection regions", "Various: Weights vs Independent Filtering" hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/IHWpaper/inst/doc/BH-explanation.R, vignettes/IHWpaper/inst/doc/explaining_tdr.R, vignettes/IHWpaper/inst/doc/grenander_vs_ecdf.R, vignettes/IHWpaper/inst/doc/hqtl_IHW_BY.R, vignettes/IHWpaper/inst/doc/IHW_bonferroni_simulations.R, vignettes/IHWpaper/inst/doc/IHW_censoring_storey_simulations.R, vignettes/IHWpaper/inst/doc/real_data_examples_single_curve.R, vignettes/IHWpaper/inst/doc/real_data_examples.R, vignettes/IHWpaper/inst/doc/simulations_vignette.R, vignettes/IHWpaper/inst/doc/stratified_histograms.R, vignettes/IHWpaper/inst/doc/tdr_pvalue_rejection_thresholds.R, vignettes/IHWpaper/inst/doc/weights_vs_filtering.R Package: Illumina450ProbeVariants.db Version: 1.18.0 Depends: R (>= 3.0.1) License: GPL-3 MD5sum: f1a96cc966c6de6c687ad024efdc6551 NeedsCompilation: no Title: Annotation Package combining variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes Description: Includes details on variants for each probe on the 450k bead chip for each of the four populations (Asian, American, African and European) biocViews: Homo_sapiens_Data, CancerData, ChipOnChipData, SNPData Author: Lee Butcher Maintainer: Tiffany Morris git_url: https://git.bioconductor.org/packages/Illumina450ProbeVariants.db git_branch: RELEASE_3_8 git_last_commit: e2bd4ce git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/Illumina450ProbeVariants.db_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: IlluminaDataTestFiles Version: 1.20.0 License: Artistic-2.0 MD5sum: 4038cc1acc8bcd01c8b18d1de6ff1ffd NeedsCompilation: no Title: Illumina microarray files (IDAT) for testing Description: Example data for Illumina microarray output files, for testing purposes biocViews: MicroarrayData Author: Kasper Daniel Hansen, Mike L. Smith Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/IlluminaDataTestFiles git_branch: RELEASE_3_8 git_last_commit: e452608 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/IlluminaDataTestFiles_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: iontreeData Version: 1.18.0 License: GPL-2 MD5sum: 212d5af9852edd8e2d0505ba6f208185 NeedsCompilation: no Title: Data provided to show the usage of functions in iontree package Description: Raw MS2, MS3 scans from direct infusion mass spectrometry (DIMS) and a demo ion tree database 'mzDB' derived from the DIMS data are included. The demo database is used to show the functionalities provided by the 'iontree' package, not for the purpose of compound identification by any means. biocViews: ExperimentData, MassSpectrometryData Author: Mingshu Cao Maintainer: Mingshu Cao PackageStatus: Deprecated git_url: https://git.bioconductor.org/packages/iontreeData git_branch: RELEASE_3_8 git_last_commit: 677fbef git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/iontreeData_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ITALICSData Version: 2.20.0 Depends: R (>= 2.0.0) License: GPL MD5sum: a6efafe837fc28cafd205d8acfc3a94a NeedsCompilation: no Title: ITALICSData Description: Data needed to use the ITALICS package biocViews: ExperimentData, HapMap Author: Guillem Rigaill Maintainer: Guillem Rigaill URL: http://bioinfo.curie.fr git_url: https://git.bioconductor.org/packages/ITALICSData git_branch: RELEASE_3_8 git_last_commit: 3216223 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ITALICSData_2.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Iyer517 Version: 1.24.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: db3def2128ea25dabad86019961b2126 NeedsCompilation: no Title: exprSets for Iyer, Eisen et all 1999 Science paper Description: representation of public Iyer data from http://genome-www.stanford.edu/serum/clusters.html biocViews: ExperimentData Author: Vishy Iyer Maintainer: Vince Carey git_url: https://git.bioconductor.org/packages/Iyer517 git_branch: RELEASE_3_8 git_last_commit: 7730e98 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/Iyer517_1.24.0.tar.gz vignettes: vignettes/Iyer517/inst/doc/Iyer517.pdf vignetteTitles: Iyer517 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Iyer517/inst/doc/Iyer517.R Package: JASPAR2014 Version: 1.18.0 Depends: R (>= 3.0.1), methods, Biostrings (>= 2.29.19) License: GPL-2 MD5sum: 4b68fc946528a33446e29411731e9097 NeedsCompilation: no Title: Data package for JASPAR Description: Data package for JASPAR 2014. To search this databases, please use the package TFBSTools. biocViews: ExperimentData, SequencingData Author: Ge Tan Maintainer: Ge Tan URL: http://jaspar.genereg.net/ git_url: https://git.bioconductor.org/packages/JASPAR2014 git_branch: RELEASE_3_8 git_last_commit: 2fb8952 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/JASPAR2014_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: JASPAR2016 Version: 1.10.0 Depends: R (>= 3.2.2), methods License: GPL-2 MD5sum: 3dc95f750e4a98dfb227a4c3de6ce501 NeedsCompilation: no Title: Data package for JASPAR 2016 Description: Data package for JASPAR 2016. To search this databases, please use the package TFBSTools (>= 1.8.1). biocViews: ExperimentData, MotifAnnotation, GeneRegulation Author: Ge Tan Maintainer: Ge Tan URL: http://jaspar.genereg.net/ git_url: https://git.bioconductor.org/packages/JASPAR2016 git_branch: RELEASE_3_8 git_last_commit: c013681 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/JASPAR2016_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: JctSeqData Version: 1.12.0 Depends: R (>= 3.3) Suggests: knitr, BiocStyle, DESeq2, DEXSeq, edgeR, JunctionSeq License: file LICENSE MD5sum: 76da9f6116c1a71cbb2244c7dd5c32a2 NeedsCompilation: no Title: Example Junction Count data for use with JunctionSeq Description: Junction count data from an example dataset taken from a subset of the RNA-seq reads from six samples. Data was subsampled and modified to provide edge cases for testing and to reduce file sizes. biocViews: Rattus_norvegicus_Data, ExperimentData, Genome, RNASeqData, RepositoryData, GEO Author: Stephen Hartley [aut, cre] (PhD) Maintainer: Stephen Hartley URL: http://hartleys.github.io/JunctionSeq/ VignetteBuilder: knitr BugReports: http://github.com/hartleys/JunctionSeq/issues git_url: https://git.bioconductor.org/packages/JctSeqData git_branch: RELEASE_3_8 git_last_commit: 929bab0 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/JctSeqData_1.12.0.tar.gz vignettes: vignettes/JctSeqData/inst/doc/JunctionSeqExampleData.pdf vignetteTitles: Example Walkthrough hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Package: KEGGandMetacoreDzPathwaysGEO Version: 1.2.0 Depends: R (>= 2.15.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: da545248fec755e65427c118cd8d518d NeedsCompilation: no Title: Disease Datasets from GEO Description: This is a collection of 18 data sets for which the phenotype is a disease with a corresponding pathway in either KEGG or metacore database.This collection of datasets were used as gold standard in comparing gene set analysis methods. biocViews: ExperimentData, GEO Author: Gaurav Bhatti Maintainer: Gaurav Bhatti git_url: https://git.bioconductor.org/packages/KEGGandMetacoreDzPathwaysGEO git_branch: RELEASE_3_8 git_last_commit: 6fe913f git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/KEGGandMetacoreDzPathwaysGEO_1.2.0.tar.gz vignettes: vignettes/KEGGandMetacoreDzPathwaysGEO/inst/doc/KEGGandMetacoreDzPathwaysGEO.pdf vignetteTitles: KEGGandMetacoreDzPathwaysGEO Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/KEGGandMetacoreDzPathwaysGEO/inst/doc/KEGGandMetacoreDzPathwaysGEO.R Package: KEGGdzPathwaysGEO Version: 1.20.0 Depends: R (>= 2.13.0) Imports: Biobase, BiocGenerics License: GPL-2 MD5sum: 773a71a68a75a39fc631776efb73e7dc NeedsCompilation: no Title: KEGG Disease Datasets from GEO Description: This is a collection of 24 data sets for which the phenotype is a disease with a corresponding pathway in the KEGG database.This collection of datasets were used as gold standard in comparing gene set analysis methods by the PADOG package. biocViews: MicroarrayData, GEO, ExperimentData Author: Gaurav Bhatti, Adi L. Tarca Maintainer: Gaurav Bhatti git_url: https://git.bioconductor.org/packages/KEGGdzPathwaysGEO git_branch: RELEASE_3_8 git_last_commit: 6f0083c git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/KEGGdzPathwaysGEO_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: kidpack Version: 1.24.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5) License: GPL-2 MD5sum: 322beb70d039afe48c7107df1a498bc4 NeedsCompilation: no Title: DKFZ kidney package Description: kidney microarray data biocViews: ExperimentData, CancerData, KidneyCancerData, MicroarrayData, ArrayExpress Author: Wolfgang Huber Maintainer: Wolfgang Huber URL: http://www.dkfz.de/mga git_url: https://git.bioconductor.org/packages/kidpack git_branch: RELEASE_3_8 git_last_commit: 35fa277 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/kidpack_1.24.0.tar.gz vignettes: vignettes/kidpack/inst/doc/kidpack.pdf vignetteTitles: kidpack - overview over the DKFZ kidney data package hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/kidpack/inst/doc/kidpack.R Package: KOdata Version: 1.8.0 Depends: R (>= 3.3.0) License: MIT + file LICENSE MD5sum: e5ea569cc1a24a77599835327a104962 NeedsCompilation: no Title: LINCS Knock-Out Data Package Description: Contains consensus genomic signatures (CGS) for experimental cell-line specific gene knock-outs as well as baseline gene expression data for a subset of experimental cell-lines. Intended for use with package KEGGlincs. biocViews: ExpressionData, CancerData, Homo_sapiens_Data Author: Shana White Maintainer: Shana White git_url: https://git.bioconductor.org/packages/KOdata git_branch: RELEASE_3_8 git_last_commit: b1b756c git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/KOdata_1.8.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Package: leeBamViews Version: 1.18.0 Depends: R (>= 2.15.0), Biobase, Rsamtools (>= 0.1.50), BSgenome Imports: GenomicRanges, GenomicAlignments, methods Suggests: GenomeGraphs, biomaRt, org.Sc.sgd.db, edgeR Enhances: multicore License: Artistic 2.0 MD5sum: 0ef787cb317db2a29797f2b72a513c60 NeedsCompilation: no Title: leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009 Description: data from PMID 19096707; prototype for managing multiple NGS samples biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData, SNPData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/leeBamViews git_branch: RELEASE_3_8 git_last_commit: ce04f72 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/leeBamViews_1.18.0.tar.gz vignettes: vignettes/leeBamViews/inst/doc/leeViews.pdf vignetteTitles: managing multiple NGS samples with bamViews hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/leeBamViews/inst/doc/leeViews.R Package: leukemiasEset Version: 1.18.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 266d9f40a851b36ce15025356ed08a72 NeedsCompilation: no Title: Leukemia's microarray gene expression data (expressionSet). Description: Expressionset containing gene expresion data from 60 bone marrow samples of patients with one of the four main types of leukemia (ALL, AML, CLL, CML) or non-leukemia. biocViews: Tissue, Genome, Homo_sapiens_Data, CancerData, LeukemiaCancerData, MicroarrayData, ChipOnChipData, TissueMicroarrayData, GEO Author: Sara Aibar, Celia Fontanillo and Javier De Las Rivas. Bioinformatics and Functional Genomics Group. Cancer Research Center (CiC-IBMCC, CSIC/USAL). Salamanca. Spain. Maintainer: Sara Aibar git_url: https://git.bioconductor.org/packages/leukemiasEset git_branch: RELEASE_3_8 git_last_commit: fec03e3 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/leukemiasEset_1.18.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: LiebermanAidenHiC2009 Version: 0.20.0 Depends: KernSmooth, IRanges License: LGPL MD5sum: 94eef9564f0209911a15142129efd9d0 NeedsCompilation: no Title: Selected data from the HiC paper of E. Lieberman-Aiden et al. in Science (2009) Description: This package provides data that were presented in the article "Comprehensive mapping of long-range interactions reveals folding principles of the human genome", Science 2009 Oct 9;326(5950):289-93. PMID: 19815776 biocViews: ExperimentData, Genome, SequencingData, DNASeqData, ChIPSeqData, miRNAData, SmallRNAData, ChipOnChipData, GEO, NCI, ENCODE Author: Wolfgang Huber, Felix Klein Maintainer: Felix Klein git_url: https://git.bioconductor.org/packages/LiebermanAidenHiC2009 git_branch: RELEASE_3_8 git_last_commit: 0c4ea54 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/LiebermanAidenHiC2009_0.20.0.tar.gz vignettes: vignettes/LiebermanAidenHiC2009/inst/doc/LiebermanAidenHiC2009.pdf vignetteTitles: Exploration of HiC data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/LiebermanAidenHiC2009/inst/doc/LiebermanAidenHiC2009.R Package: ListerEtAlBSseq Version: 1.14.0 Depends: R (>= 3.1.1), methylPipe Suggests: BSgenome.Hsapiens.UCSC.hg18 License: Artistic 2.0 MD5sum: c36fbf6d20c087f6591c9c39174878cb NeedsCompilation: no Title: BS-seq data of H1 and IMR90 cell line excerpted from Lister et al. 2009 Description: Base resolution bisulfite sequencing data of Human DNA methylomes biocViews: ExperimentData, Homo_sapiens_Data, SequencingData Author: Kamal Kishore Maintainer: Kamal Kishore git_url: https://git.bioconductor.org/packages/ListerEtAlBSseq git_branch: RELEASE_3_8 git_last_commit: 380e84e git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ListerEtAlBSseq_1.14.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: lumiBarnes Version: 1.22.0 Depends: R (>= 2.0), Biobase (>= 2.5.5), lumi (>= 1.1.0) License: LGPL MD5sum: 1bd89b6adf74489e3e5a23434809ebac NeedsCompilation: no Title: Barnes Benchmark Illumina Tissues Titration Data Description: The Barnes benchmark dataset can be used to evaluate the algorithms for Illumina microarrays. It measured a titration series of two human tissues, blood and placenta, and includes six samples with the titration ratio of blood and placenta as 100:0, 95:5, 75:25, 50:50, 25:75 and 0:100. The samples were hybridized on HumanRef-8 BeadChip (Illumina, Inc) in duplicate. The data is loaded as an LumiBatch Object (see documents in the lumi package). biocViews: ExperimentData, Tissue, MicroarrayData, ChipOnChipData Author: Pan Du Maintainer: Pan Du git_url: https://git.bioconductor.org/packages/lumiBarnes git_branch: RELEASE_3_8 git_last_commit: 0e2cd7a git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/lumiBarnes_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: LungCancerACvsSCCGEO Version: 1.18.0 Depends: R (>= 2.15.0) License: GPL-2 MD5sum: de4f81552f2a5f3484bd43cb1e089c76 NeedsCompilation: no Title: A lung cancer dataset that can be used with maPredictDSC package for developing outcome prediction models from Affymetrix CEL files. Description: This package contains 30 Affymetrix CEL files for 7 Adenocarcinoma (AC) and 8 Squamous cell carcinoma (SCC) lung cancer samples taken at random from 3 GEO datasets (GSE10245, GSE18842 and GSE2109) and other 15 samples from a dataset produced by the organizers of the IMPROVER Diagnostic Signature Challenge available from GEO (GSE43580). biocViews: CancerData, LungCancerData, MicroarrayData, GEO Author: Adi Laurentiu Tarca Maintainer: Adi Laurentiu Tarca URL: http://bioinformaticsprb.med.wayne.edu/ git_url: https://git.bioconductor.org/packages/LungCancerACvsSCCGEO git_branch: RELEASE_3_8 git_last_commit: 4be4cf2 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/LungCancerACvsSCCGEO_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: LungCancerLines Version: 0.20.0 Imports: Rsamtools License: Artistic-2.0 MD5sum: 05943d693a693d21d910d70e7fa2e6b3 NeedsCompilation: no Title: Reads from Two Lung Cancer Cell Lines Description: Reads from an RNA-seq experiment between two lung cancer cell lines: H1993 (met) and H2073 (primary). The reads are stored as Fastq files and are meant for use with the TP53Genome object in the gmapR package. biocViews: ExperimentData, Genome, CancerData, LungCancerData, RNASeqData Author: Cory Barr, Michael Lawrence Maintainer: Cory Barr git_url: https://git.bioconductor.org/packages/LungCancerLines git_branch: RELEASE_3_8 git_last_commit: 7ebb242 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/LungCancerLines_0.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: lungExpression Version: 0.20.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: ddf0673ccf961ceb1875ac92d104f512 NeedsCompilation: no Title: ExpressionSets for Parmigiani et al., 2004 Clinical Cancer Research paper Description: Data from three large lung cancer studies provided as ExpressionSets biocViews: ExperimentData, CancerData, LungCancerData Author: Robert Scharpf , Simens Zhong , Giovanni Parmigiani Maintainer: Robert Scharpf git_url: https://git.bioconductor.org/packages/lungExpression git_branch: RELEASE_3_8 git_last_commit: 5d13839 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/lungExpression_0.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: lydata Version: 1.8.0 License: MIT + file LICENSE MD5sum: d64eba72812c41d245f9972c33d71226 NeedsCompilation: no Title: Example Dataset for crossmeta Package Description: Raw data downloaded from GEO for the compound LY294002. Raw data is from multiple platforms from Affymetrix and Illumina. This data is used to illustrate the cross-platform meta-analysis of microarray data using the crossmeta package. biocViews: ExperimentData, MicroarrayData Author: Alex Pickering Maintainer: Alex Pickering git_url: https://git.bioconductor.org/packages/lydata git_branch: RELEASE_3_8 git_last_commit: 4d0a374 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/lydata_1.8.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Package: M3DExampleData Version: 1.8.0 Depends: R (>= 3.3) License: GPL (>=2) MD5sum: 13f405ac3714731aff20afbab68db3f6 NeedsCompilation: no Title: M3Drop Example Data Description: Example data for M3Drop package. biocViews: Mus_musculus_Data, RNASeqData, ExpressionData, GEO, Tissue, ExperimentData Author: Tallulah Andrews Maintainer: Tallulah Andrews git_url: https://git.bioconductor.org/packages/M3DExampleData git_branch: RELEASE_3_8 git_last_commit: 5d7204d git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/M3DExampleData_1.8.0.tar.gz hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mammaPrintData Version: 1.18.0 Depends: R (>= 2.13.0) Suggests: Biobase, gdata, limma License: Artistic-2.0 MD5sum: 8bf8e8805b3af4953469a353d305c74c NeedsCompilation: no Title: RGLists from the Glas and Buyse breast cancer studies Description: Gene expression data for the two breast cancer cohorts published by Glas and Buyse in 2006. This cohorts were used to implement and validate the mammaPrint breast cancer test. biocViews: ExperimentData, ExpressionData, CancerData, BreastCancerData, MicroarrayData, TwoChannelData Author: Luigi Marchionni Maintainer: Luigi Marchionni URL: http://luigimarchionni.org/breastTSP.html git_url: https://git.bioconductor.org/packages/mammaPrintData git_branch: RELEASE_3_8 git_last_commit: 6a10dab git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/mammaPrintData_1.18.0.tar.gz vignettes: vignettes/mammaPrintData/inst/doc/mammaPrintData.pdf vignetteTitles: Working with the mammaPrintData package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mammaPrintData/inst/doc/mammaPrintData.R Package: mAPKLData Version: 1.14.0 Depends: R (>= 3.2.0) Suggests: Biobase License: Artistic-2.0 MD5sum: 6d044355ab9473e4e724918a054df95c NeedsCompilation: no Title: Gene expression data for testing of the package mAPKL. Description: Gene expression data from a breast cancer study published by Turashvili et al. in 2007, provided as an eSet. biocViews: ExperimentData, ExpressionData, Cancer, Breast Author: Argiris Sakellariou Maintainer: Argiris Sakellariou git_url: https://git.bioconductor.org/packages/mAPKLData git_branch: RELEASE_3_8 git_last_commit: 3fd033e git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/mAPKLData_1.14.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: maqcExpression4plex Version: 1.26.0 Suggests: oligo, pdInfoBuilder License: GPL MD5sum: 3ce8a0a849ae354153897db598f86fab NeedsCompilation: no Title: Sample Expression Data - MAQC / HG18 - NimbleGen Description: Data from human (HG18) 4plex NimbleGen array. It has 24k genes with 3 60mer probes per gene. biocViews: ExperimentData, CancerData Author: NimbleGen Systems Maintainer: Benilton Carvalho git_url: https://git.bioconductor.org/packages/maqcExpression4plex git_branch: RELEASE_3_8 git_last_commit: 4ad0773 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/maqcExpression4plex_1.26.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MAQCsubset Version: 1.20.0 Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), lumi, methods Suggests: genefilter, codelink License: Artistic-2.0 MD5sum: e8b9ec1c5c7aec22ebe396f03e5088ad NeedsCompilation: no Title: Experimental Data Package: MAQCsubset Description: Data Package automatically created on Sun Nov 19 15:59:29 2006. biocViews: ExperimentData, MicroarrayData, GEO Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/MAQCsubset git_branch: RELEASE_3_8 git_last_commit: e17125a git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/MAQCsubset_1.20.0.tar.gz vignettes: vignettes/MAQCsubset/inst/doc/maqcNotes.pdf vignetteTitles: MAQC notes hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MAQCsubset/inst/doc/maqcNotes.R Package: MAQCsubsetAFX Version: 1.20.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 9463855db7431adda8bd920b13a090b2 NeedsCompilation: no Title: MAQC data subset for the Affymetrix platform Description: MAQC data subset for the Affymetrix platform biocViews: ExperimentData, Genome, Homo_sapiens_Data, MicroarrayData Author: Laurent Gatto Maintainer: Laurent Gatto git_url: https://git.bioconductor.org/packages/MAQCsubsetAFX git_branch: RELEASE_3_8 git_last_commit: 2cb5aae git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/MAQCsubsetAFX_1.20.0.tar.gz vignettes: vignettes/MAQCsubsetAFX/inst/doc/MAQCsubsetAFX.pdf vignetteTitles: MAQCsubsetAFX: MAQC data subset for the Affymetrix platform hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MAQCsubsetAFX/inst/doc/MAQCsubsetAFX.R Package: MAQCsubsetILM Version: 1.20.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), lumi License: Artistic-2.0 MD5sum: 92c3de4c8a84a1ef6f3ef994f9a627f3 NeedsCompilation: no Title: MAQC data subset for the Illumina platform Description: MAQC data subset for the Illumina platform biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData Author: Laurent Gatto Maintainer: Laurent Gatto git_url: https://git.bioconductor.org/packages/MAQCsubsetILM git_branch: RELEASE_3_8 git_last_commit: 62c8c3f git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/MAQCsubsetILM_1.20.0.tar.gz vignettes: vignettes/MAQCsubsetILM/inst/doc/MAQCsubsetILM.pdf vignetteTitles: MAQCsubsetILM: MAQC data subset for the Illumina platform hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MAQCsubsetILM/inst/doc/MAQCsubsetILM.R Package: mCSEAdata Version: 1.2.0 Depends: R (>= 3.5) Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 45eb34bc0dcb1414abbd892e3d4f70ec NeedsCompilation: no Title: Data package for mCSEA package Description: Data objects necessary to some mCSEA package functions. There are also example data objects to illustrate mCSEA package functionality. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData, ExperimentData Author: Jordi Martorell Marugán Maintainer: Jordi Martorell Marugán VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mCSEAdata git_branch: RELEASE_3_8 git_last_commit: fbc1734 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/mCSEAdata_1.2.0.tar.gz vignettes: vignettes/mCSEAdata/inst/doc/mCSEAdata.pdf vignetteTitles: Data for mCSEA package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mCSEAdata/inst/doc/mCSEAdata.R Package: mcsurvdata Version: 1.0.0 Depends: R (>= 3.5), ExperimentHub Imports: AnnotationHub, Biobase Suggests: knitr License: GPL (>=2) MD5sum: b58022a7e2590ccf7b3a38d4587d7f50 NeedsCompilation: no Title: Meta cohort survival data Description: This package stores two merged expressionSet objects that contain the gene expression profile and clinical information of -a- six breast cancer cohorts and -b- four colorectal cancer cohorts. Breast cancer data are employed in the vignette of the hrunbiased package for survival analysis of gene signatures. biocViews: ExperimentData, Homo_sapiens_Data, GEO, MicroarrayData Author: Adria Caballe Mestres [aut, cre], Antoni Berenguer Llergo [aut], Camille Stephan-Otto Attolini [aut] Maintainer: Adria Caballe Mestres URL: https://github.com/adricaba/mcsurvdata VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mcsurvdata git_branch: RELEASE_3_8 git_last_commit: c5060d3 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/mcsurvdata_1.0.0.tar.gz vignettes: vignettes/mcsurvdata/inst/doc/mcsurvdata.html vignetteTitles: analysis vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mcsurvdata/inst/doc/mcsurvdata.R Package: MEDIPSData Version: 1.18.0 Depends: R (>= 2.15.0) License: GPL (>= 2) MD5sum: 80c0076eae9f53aeda545a4e2716ab69 NeedsCompilation: no Title: Example data for MEDIPS and QSEA packages Description: Example data for MEDIPS and QSEA packages, consisting of chromosome 22 MeDIP and control/Input sample data. Additionally, the package contains MeDIP seq data from 3 NSCLC samples and adjacent normal tissue (chr 20-22). All data has been aligned to human genome hg19. biocViews: ExperimentData, Genome, SequencingData Author: Lukas Chavez Maintainer: Lukas Chavez git_url: https://git.bioconductor.org/packages/MEDIPSData git_branch: RELEASE_3_8 git_last_commit: 16ed8d3 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/MEDIPSData_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MEEBOdata Version: 1.20.0 License: LGPL MD5sum: 6f406364f10353a1a634a4d726c66a22 NeedsCompilation: no Title: MEEBO set and MEEBO controls. Description: R objects describing the MEEBO set. biocViews: ExperimentData Author: Agnes Paquet Maintainer: Agnes Paquet URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/ git_url: https://git.bioconductor.org/packages/MEEBOdata git_branch: RELEASE_3_8 git_last_commit: 74c1cca git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/MEEBOdata_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MetaGxBreast Version: 1.2.0 Depends: Biobase, stats, lattice, impute, AnnotationHub, ExperimentHub, R (>= 3.5.0) Suggests: testthat, xtable License: Artistic-2.0 MD5sum: 1157831dd3b4e2b789b5833c1586b7a6 NeedsCompilation: no Title: Transcriptomic Breast Cancer Datasets Description: A collection of Breast Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium. biocViews: ExpressionData, CancerData, Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData, ExperimentData, BreastCancerData Author: Michael Zon , Deena M.A. Gendoo , Benjamin Haibe-Kains Maintainer: Michael Zon git_url: https://git.bioconductor.org/packages/MetaGxBreast git_branch: RELEASE_3_8 git_last_commit: 1a7e9f5 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/MetaGxBreast_1.2.0.tar.gz vignettes: vignettes/MetaGxBreast/inst/doc/MetaGxBreast.pdf vignetteTitles: MetaGxBreast: a package for breast cancer gene expression analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MetaGxBreast/inst/doc/MetaGxBreast.R Package: MetaGxOvarian Version: 1.2.0 Depends: Biobase, stats, lattice, impute, AnnotationHub, ExperimentHub, R (>= 3.5.0) Suggests: testthat, xtable License: Artistic-2.0 MD5sum: fc131f6eb1d2c6317560da14ff12c06d NeedsCompilation: no Title: Transcriptomic Ovarian Cancer Datasets Description: A collection of Ovarian Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium. biocViews: Microarray, Software, GeneExpression, OneChannel, GeneSetEnrichment, GeneSignaling, Pathways, Preprocessing, Survival Author: Michael Zon , Deena M.A. Gendoo , Benjamin Haibe-Kains Maintainer: Michael Zon git_url: https://git.bioconductor.org/packages/MetaGxOvarian git_branch: RELEASE_3_8 git_last_commit: 5a5e3db git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/MetaGxOvarian_1.2.0.tar.gz vignettes: vignettes/MetaGxOvarian/inst/doc/MetaGxOvarian.pdf vignetteTitles: MetaGxOvarian: a package for ovarian cancer gene expression analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MetaGxOvarian/inst/doc/MetaGxOvarian.R Package: MetaGxPancreas Version: 1.2.0 Depends: Biobase, stats, lattice, impute, AnnotationHub, ExperimentHub, R (>= 3.5.0) Suggests: testthat, xtable License: Artistic-2.0 MD5sum: 974a7f5e6f82070585bdc35cc843ccea NeedsCompilation: no Title: Transcriptomic Pancreatic Cancer Datasets Description: A collection of pancreatic Cancer transcriptomic datasets that are part of the MetaGxData package compendium. biocViews: ExpressionData, CancerData, Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData, ExperimentData Author: Michael Zon , Vandana Sandhu , Benjamin Haibe-Kains Maintainer: Michael Zon git_url: https://git.bioconductor.org/packages/MetaGxPancreas git_branch: RELEASE_3_8 git_last_commit: 4706bd4 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/MetaGxPancreas_1.2.0.tar.gz vignettes: vignettes/MetaGxPancreas/inst/doc/MetaGxPancreas.pdf vignetteTitles: MetaGxPancreas: a package for pancreas cancer gene expression analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MetaGxPancreas/inst/doc/MetaGxPancreas.R Package: metaMSdata Version: 1.18.0 License: GPL (>= 2) MD5sum: c2755dd8852d556ae98deb6d06d355af NeedsCompilation: no Title: Example CDF data for the metaMS package Description: Example CDF data for the metaMS package biocViews: ExperimentData, MassSpectrometryData Author: Ron Wehrens [aut, cre], Pietro Franceschi [aut], Georg Weingart [ctb] Maintainer: Ron Wehrens git_url: https://git.bioconductor.org/packages/metaMSdata git_branch: RELEASE_3_8 git_last_commit: ffdc2ad git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/metaMSdata_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MethylAidData Version: 1.14.0 Depends: MethylAid, R (>= 3.2) Suggests: BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC License: GPL (>= 2) MD5sum: b7445efd87e21834a9a35e92bae6bbad NeedsCompilation: no Title: MethylAid-summarized data for 2800 Illumina 450k array samples and 2620 EPIC array samples Description: A data package containing summarized Illumina 450k array data on 2800 samples and summarized EPIC data for 2620 samples. The data can be use as a background data set in the interactive application. biocViews: ExperimentData, TechnologyData, MicroarrayData, MethylationArrayData Author: Davy Cats, Tyler J. Gorrie-Stone, Bastiaan T. Heijmans, John W. Holloway, BIOS Consortium, Maarten van Iterson, Faisal I. Rezwam, Leonard Schalkwyk Maintainer: M. van Iterson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MethylAidData git_branch: RELEASE_3_8 git_last_commit: 06d3ca2 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/MethylAidData_1.14.0.tar.gz vignettes: vignettes/MethylAidData/inst/doc/MethylAidData.pdf vignetteTitles: MethylAid-summarized data on 2800 Illumina 450k array samples hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MethylAidData/inst/doc/MethylAidData.R Package: methyvimData Version: 1.4.0 Depends: R (>= 3.4.0), minfi Suggests: Biobase, BiocStyle, SummarizedExperiment, knitr, rmarkdown License: file LICENSE MD5sum: 2d04580044269f4e9f1f904aed11ff6f NeedsCompilation: no Title: Example experimental data for use with the methyvim package Description: Contains a reduced set of simulated data inspired by data produced by the Infinium EPIC BeadChip assays by Illumina. The example data set is made available to highlight many of the key procedures that are available within the core functions of the methyvim package. biocViews: Clustering, DNAMethylation, DifferentialMethylation, MethylationArray, MethylSeq Author: Nima Hejazi [aut, cre] Maintainer: Nima Hejazi VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/methyvimData git_branch: RELEASE_3_8 git_last_commit: 46154fa git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/methyvimData_1.4.0.tar.gz vignettes: vignettes/methyvimData/inst/doc/data_methyvim.html vignetteTitles: Anatomy of the `methyvimData` package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/methyvimData/inst/doc/data_methyvim.R Package: microRNAome Version: 1.4.0 Depends: R (>= 3.4), SummarizedExperiment Suggests: BiocGenerics, RUnit License: GPL (>= 2) MD5sum: bae32fb7fe64c2d23b0ac8d5d5574a1a NeedsCompilation: no Title: SummarizedExperiment for the microRNAome project Description: This package provides a SummarizedExperiment object of read counts for microRNAs across tissues, cell-types, and cancer cell-lines. The read count matrix was prepared and provided by the author of the study: Towards the human cellular microRNAome. biocViews: ExperimentData, CellCulture, CancerData, SequencingData, RNASeqData, miRNAData Author: Matthew N. McCall , Marc K. Halushka Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/microRNAome git_branch: RELEASE_3_8 git_last_commit: 20fd431 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/microRNAome_1.4.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: MIGSAdata Version: 1.6.0 Depends: R (>= 3.4) Suggests: BiocGenerics License: GPL (>= 2) MD5sum: a9d6b8af543c349a1955dc93934b487b NeedsCompilation: no Title: MIGSA vignette data Description: MIGSA vignette data. The MIGSAdata package provides several data objects needed by MIGSA package to correctly generate its vignette, and follow it step by step. biocViews: ExperimentData, RepositoryData, ReproducibleResearch, CancerData, BreastCancerData, MicroarrayData Author: Juan C. Rodriguez, Cristobal Fresno, Andrea S. Llera and Elmer A. Fernandez Maintainer: Juan C. Rodriguez URL: http://www.bdmg.com.ar/ git_url: https://git.bioconductor.org/packages/MIGSAdata git_branch: RELEASE_3_8 git_last_commit: 2fccd05 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/MIGSAdata_1.6.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: minfiData Version: 0.28.0 Depends: R (>= 3.3.0), minfi (>= 1.21.2), IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 License: Artistic-2.0 MD5sum: 40cafa6a33fdc318ced42d538a27b98d NeedsCompilation: no Title: Example data for the Illumina Methylation 450k array Description: Data from 6 samples across 2 groups from 450k methylation arrays. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData Author: Kasper Daniel Hansen, Martin Aryee, Winston Timp Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/minfiData git_branch: RELEASE_3_8 git_last_commit: 95739f6 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/minfiData_0.28.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MethylAidData Package: minfiDataEPIC Version: 1.8.0 Depends: R (>= 3.3), minfi (>= 1.21.2), IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: Artistic-2.0 MD5sum: 92cb1d44c458f6d61d7893e7288a1589 NeedsCompilation: no Title: Example data for the Illumina Methylation EPIC array Description: Data from 3 technical replicates of the cell line GM12878 from the EPIC methylation array. biocViews: Homo_sapiens_Data, MethylationArrayData, MicroarrayData Author: Jean-Philippe Fortin, Kasper Daniel Hansen Maintainer: Kasper Daniel Hansen git_url: https://git.bioconductor.org/packages/minfiDataEPIC git_branch: RELEASE_3_8 git_last_commit: b307406 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/minfiDataEPIC_1.8.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MethylAidData Package: minionSummaryData Version: 1.12.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 4e3db62e383ae1e28af148fadaf23a40 NeedsCompilation: no Title: Summarised MinION sequencing data published by Ashton et al. 2015 Description: Summarised MinION sequencing data for Salmonella Typhi published by Ashton et al. in 2015. Three replicate runs are each provided as Fast5Summary objects. biocViews: ExperimentData, SequencingData Author: Mike Smith [aut, cre] Maintainer: Mike Smith VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/minionSummaryData git_branch: RELEASE_3_8 git_last_commit: 6154fdf git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/minionSummaryData_1.12.0.tar.gz vignettes: vignettes/minionSummaryData/inst/doc/creating-Styphi-Dataset.html vignetteTitles: Creating example MinION summary dataset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/minionSummaryData/inst/doc/creating-Styphi-Dataset.R Package: miRcompData Version: 1.12.0 Depends: R (>= 3.2), Imports: utils License: GPL-3 | file LICENSE MD5sum: 2b86aeb9ff05f956dbaa0f7dd132cbc4 NeedsCompilation: no Title: Data used in the miRcomp package Description: Raw amplification data from a large microRNA mixture / dilution study. These data are used by the miRcomp package to assess the performance of methods that estimate expression from the amplification curves. biocViews: ExperimentData, ExpressionData, qPCRData, Homo_sapiens_Data Author: Matthew N. McCall Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/miRcompData git_branch: RELEASE_3_8 git_last_commit: a911a98 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/miRcompData_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Package: miRNATarget Version: 1.20.0 Depends: R (>= 2.10), Biobase License: GPL MD5sum: ccb859ec474b6235e9d5deb41c955dda NeedsCompilation: no Title: gene target tabale of miRNA for human/mouse used for MiRaGE package Description: gene target tabale of miRNA for human/mouse used for MiRaGE package biocViews: ExperimentData, Homo_sapiens_Data Author: Y-h. Taguchi Maintainer: Y-h. Taguchi git_url: https://git.bioconductor.org/packages/miRNATarget git_branch: RELEASE_3_8 git_last_commit: 38c949c git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/miRNATarget_1.20.0.tar.gz vignettes: vignettes/miRNATarget/inst/doc/miRNATarget.pdf vignetteTitles: miRNATargetTutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/miRNATarget/inst/doc/miRNATarget.R Package: mitoODEdata Version: 1.18.0 Depends: R (>= 2.14.0) License: LGPL MD5sum: 2b4cf1081b1509c750a63a16a9ec3fc9 NeedsCompilation: no Title: Experimental data associated to the paper "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay" (submitted). Description: This package contains the experimental data (assay annotation, siRNA annotation, time-lapse cell counts) associated to the paper "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay" (submitted). The data ultimately come from the Mitocheck assay reported in "Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes" (Neumann, Walter et al, Nature 2010). biocViews: ExperimentData, Genome Author: Gregoire Pau Maintainer: Gregoire Pau SystemRequirements: git_url: https://git.bioconductor.org/packages/mitoODEdata git_branch: RELEASE_3_8 git_last_commit: befbad0 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/mitoODEdata_1.18.0.tar.gz vignettes: vignettes/mitoODEdata/inst/doc/mitoODEdata-introduction.pdf vignetteTitles: Mitoode data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mitoODEdata/inst/doc/mitoODEdata-introduction.R Package: MMDiffBamSubset Version: 1.18.0 Suggests: MMDiff2 License: LGPL MD5sum: 28e6a879bd736040d44de460c7e582aa NeedsCompilation: no Title: Example ChIP-Seq data for the MMDiff package Description: Subset of BAM files, including WT_2.bam, Null_2.bam, Resc_2.bam, Input.bam from the "Cfp1" experiment (see Clouaire et al., Genes Dev. 2012). Data is available under ArrayExpress accession numbers E-ERAD-79. Additionally, corresponding subset of peaks called by MACS biocViews: ExperimentData, Genome, StemCell, Mus_musculus_Data, DNASeqData, ChIPSeqData, ArrayExpress Author: Gabriele Schweikert Maintainer: Gabriele Schweikert git_url: https://git.bioconductor.org/packages/MMDiffBamSubset git_branch: RELEASE_3_8 git_last_commit: f086162 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/MMDiffBamSubset_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mosaicsExample Version: 1.20.0 Depends: R (>= 2.11.1) License: GPL (>= 2) MD5sum: 5f16c9ddafc0db17641a7c8dde96a62b NeedsCompilation: no Title: Example data for the mosaics package, which implements MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data for transcription factor binding and histone modification Description: Data for the mosaics package, consisting of (1) chromosome 22 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding and H3K4me3 modification in MCF7 cell line from ENCODE database (HG19) and (2) 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, Rene Welch, Sunduz Keles Maintainer: Dongjun Chung URL: http://groups.google.com/group/mosaics_user_group git_url: https://git.bioconductor.org/packages/mosaicsExample git_branch: RELEASE_3_8 git_last_commit: 99594fc git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/mosaicsExample_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mouse4302barcodevecs Version: 1.20.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 01aade84e4b3b235cfe37e825c8fe171 NeedsCompilation: no Title: mouse4302 data for barcode Description: Data used by the barcode package for microarrays of type mouse4302. biocViews: Mus_musculus_Data, MicroarrayData Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall git_url: https://git.bioconductor.org/packages/mouse4302barcodevecs git_branch: RELEASE_3_8 git_last_commit: e557b32 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/mouse4302barcodevecs_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MSBdata Version: 1.0.0 License: LGPL MD5sum: 6062b5f8703a14ba744ca00891f547e9 NeedsCompilation: no Title: Data sets for the book 'Modern Statistics for Biology' Description: Data sets for the book 'Modern Statistics for Modern Biology', S.P. Holmes and W. Huber biocViews: ExperimentData, ReproducibleResearch Author: Wolfgang Huber, Andrzej Oles, Mike Smith Maintainer: Wolfgang Huber PackageStatus: Deprecated git_url: https://git.bioconductor.org/packages/MSBdata git_branch: RELEASE_3_8 git_last_commit: 3a4a328 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/MSBdata_1.0.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: msd16s Version: 1.2.0 Depends: R (>= 2.10), Biobase, metagenomeSeq, License: Artistic-2.0 MD5sum: 1c717466a3154de3717810a24aa2620f NeedsCompilation: no Title: Healthy and moderate to severe diarrhea 16S expression data Description: Gut 16S sequencing expression data from 992 healthy and moderate-to-severe diarrhetic samples used in 'Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition'. biocViews: ExperimentData, SequencingData, MicrobiomeData Author: Joseph N. Paulson, Hector Corrada Bravo, Mihai Pop Maintainer: Joseph N. Paulson URL: http://www.cbcb.umd.edu/research/projects/GEMS-pathogen-discovery git_url: https://git.bioconductor.org/packages/msd16s git_branch: RELEASE_3_8 git_last_commit: 37c0d59 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/msd16s_1.2.0.tar.gz vignettes: vignettes/msd16s/inst/doc/msd16s.pdf vignetteTitles: msd16s hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/msd16s/inst/doc/msd16s.R Package: msdata Version: 0.22.0 Depends: R (>= 2.10) Suggests: xcms, mzR, MSnbase License: GPL (>= 2) MD5sum: a0a63e124df97fca391c7ae458439dad NeedsCompilation: no Title: Various Mass Spectrometry raw data example files Description: Ion Trap positive ionization mode data in mzData file format. Subset from 500-850 m/z and 1190-1310 seconds, incl. MS2 and MS3, intensity threshold 100.000. Extracts from FTICR Apex III, m/z 400-450. Subset of UPLC - Bruker micrOTOFq data, both mzData, mzML and mz5. LC-MSMS and MRM files from proteomics experiments. PSI mzIdentML example files for various search engines. biocViews: ExperimentData, MassSpectrometryData Author: Steffen Neumann , Laurent Gatto with contriutions from Johannes Rainer Maintainer: Steffen Neumann , Laurent Gatto git_url: https://git.bioconductor.org/packages/msdata git_branch: RELEASE_3_8 git_last_commit: 7970a22 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/msdata_0.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics Package: MSMB Version: 1.0.2 Depends: R (>= 2.10) Suggests: knitr, BiocStyle License: LGPL MD5sum: d4b84584eb62a67297dc48130d679ffa NeedsCompilation: no Title: Data sets for the book 'Modern Statistics for Biology' Description: Data sets for the book 'Modern Statistics for Modern Biology', S.P. Holmes and W. Huber. biocViews: ExperimentData, ReproducibleResearch Author: Wolfgang Huber, Andrzej Oles, Mike Smith Maintainer: Wolfgang Huber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MSMB git_branch: RELEASE_3_8 git_last_commit: fb2de2e git_last_commit_date: 2018-12-19 Date/Publication: 2018-12-20 source.ver: src/contrib/MSMB_1.0.2.tar.gz vignettes: vignettes/MSMB/inst/doc/MSMB.pdf vignetteTitles: Modern Statistics for Modern Biology hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MSMB/inst/doc/MSMB.R Package: msPurityData Version: 1.10.0 Suggests: knitr License: GPL (>= 2) MD5sum: 4425b2e32df130a6cdd51cf1647ed17a NeedsCompilation: no Title: Fragmentation spectral libraries and data to test the msPurity package Description: Fragmentation spectral libraries and data to test the msPurity package biocViews: ExperimentData, MassSpectrometryData Author: Thomas N. Lawson Maintainer: Thomas N. Lawson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/msPurityData git_branch: RELEASE_3_8 git_last_commit: fb93041 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/msPurityData_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: msqc1 Version: 1.10.0 Depends: R (>= 3.2), lattice, stats, utils Suggests: BiocStyle, knitr, testthat, specL License: GPL MD5sum: 9c2ac1fa46c8e7b1baa7e503c5c8d3b3 NeedsCompilation: no Title: Sigma mix MSQC1 data Description: The data set contains an eight technical replicate data set and a three replicate dilution series of the MS Qual/Quant QC Mix standard sample (Sigma-Aldrich, Buchs, Switzerland) measured on five different mass spec platforms at the Functional Genomics Center Zurich. biocViews: ExperimentData, MassSpectrometryData, ReproducibleResearch Author: Tobias Kockmann, Christian Trachsel, Christian Panse Maintainer: Christian Panse URL: https://panoramaweb.org/labkey/MSQC1.url, http://fgcz-bfabric.uzh.ch/bfabric/project.html?projectId=1959 VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/msqc1 git_branch: RELEASE_3_8 git_last_commit: 93049fe git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/msqc1_1.10.0.tar.gz vignettes: vignettes/msqc1/inst/doc/poster.pdf, vignettes/msqc1/inst/doc/chromatography.html, vignettes/msqc1/inst/doc/msqc1.html vignetteTitles: ASMS 2016 poster (in portrait) abstract ID number: 282492, LC Observations - Retention Time Stability, Introducing msqc1 - A Mass Spec Data set for Targeted Proteomics Performance Evaluation hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/msqc1/inst/doc/chromatography.R, vignettes/msqc1/inst/doc/msqc1.R, vignettes/msqc1/inst/doc/poster.R Package: MSstatsBioData Version: 1.4.0 Depends: R (>= 3.4) Suggests: BiocStyle, knitr, MSstats License: Artistic-2.0 MD5sum: d6b9978157012351f0fea33b1c678296 NeedsCompilation: no Title: Datasets of published biological studies with DDA or SRM experiments Description: Provides the peak intensity data for detecting differentially abundant proteins in seven published biological investigations. biocViews: ExperimentData, MassSpectrometryData, Proteome Author: Meena Choi Maintainer: Meena Choi VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/MSstatsBioData git_branch: RELEASE_3_8 git_last_commit: ae30d7b git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/MSstatsBioData_1.4.0.tar.gz vignettes: vignettes/MSstatsBioData/inst/doc/MSstatsBioData.html vignetteTitles: MSstatsBioData: Datasets of published biological studies with DDA or SRM experiments hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MSstatsBioData/inst/doc/MSstatsBioData.R Package: mtbls2 Version: 1.12.0 Depends: R (>= 2.10) Suggests: xcms (>= 3.0.0), CAMERA, Risa (>= 1.0.0), knitr, Heatplus, pcaMethods, sp License: CC0 MD5sum: d5fee1a7b0b6c8511edb2f540f59997d NeedsCompilation: no Title: MetaboLights MTBLS2: Comparative LC/MS-based profiling of silver nitrate-treated Arabidopsis thaliana leaves of wild-type and cyp79B2 cyp79B3 double knockout plants. Böttcher et al. (2004) Description: Indole-3-acetaldoxime (IAOx) represents an early intermediate of the biosynthesis of a variety of indolic secondary metabolites including the phytoanticipin indol-3-ylmethyl glucosinolate and the phytoalexin camalexin (3-thiazol-2'-yl-indole). Arabidopsis thaliana cyp79B2 cyp79B3 double knockout plants are completely impaired in the conversion of tryptophan to indole-3-acetaldoxime and do not accumulate IAOx-derived metabolites any longer. Consequently, comparative analysis of wild-type and cyp79B2 cyp79B3 plant lines has the potential to explore the complete range of IAOx-derived indolic secondary metabolites. biocViews: MassSpectrometryData, RepositoryData Author: Steffen Neumann Maintainer: Steffen Neumann URL: http://www.ebi.ac.uk/metabolights/MTBLS2, https://github.com/sneumann/mtbls2 VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/mtbls2 git_branch: RELEASE_3_8 git_last_commit: d77ffe0 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/mtbls2_1.12.0.tar.gz vignettes: vignettes/mtbls2/inst/doc/MTBLS2-xcms3.html, vignettes/mtbls2/inst/doc/MTBLS2.html vignetteTitles: MTBLS2 Processing and Analysis with xcms,, CAMERA and export to MetaboLights, MTBLS2 Processing and Analysis with xcms,, CAMERA and export to MetaboLights hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/mtbls2/inst/doc/MTBLS2-xcms3.R, vignettes/mtbls2/inst/doc/MTBLS2.R Package: MTseekerData Version: 1.0.0 Depends: R (>= 3.5) Imports: utils, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, VariantAnnotation, Homo.sapiens, MTseeker Suggests: gmapR, xml2, rtracklayer License: Artistic-2.0 MD5sum: f5271cbb8d617a4fb35b794def24e72a NeedsCompilation: no Title: Supporting Data for the MTseeker Package Description: Provides examples for the MTseeker package vignette. biocViews: ExperimentData, Genome Author: Tim Triche, Jr; Noor Sohail; Ben Johnson Maintainer: Tim Triche, Jr. git_url: https://git.bioconductor.org/packages/MTseekerData git_branch: RELEASE_3_8 git_last_commit: a1eba5b git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/MTseekerData_1.0.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: MUGAExampleData Version: 1.2.0 Depends: R (>= 2.10.0) License: GPL-3 MD5sum: 66132942d0d409057570d914ec435e39 NeedsCompilation: no Title: Example {M}ouse {U}niversal {G}enotyping {A}rray data for genome reconstruction and quantitative trait locus mapping. Description: This package contains example data for the MUGA array that is used by the R package DOQTL. biocViews: ExperimentData, Mus_musculus_Data Author: Daniel Gatti Maintainer: Daniel Gatti git_url: https://git.bioconductor.org/packages/MUGAExampleData git_branch: RELEASE_3_8 git_last_commit: 4ddcb75 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/MUGAExampleData_1.2.0.tar.gz vignettes: vignettes/MUGAExampleData/inst/doc/MUGAExampleData.pdf vignetteTitles: User Manual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/MUGAExampleData/inst/doc/MUGAExampleData.R Package: Mulder2012 Version: 0.22.0 Depends: R (>= 2.14), org.Hs.eg.db, KEGG.db Imports: igraph, HTSanalyzeR, PANR, RedeR, pvclust, MASS Suggests: snow License: Artistic-2.0 MD5sum: 4c3890e75f415c4978187fb416586b1b NeedsCompilation: no Title: Predicting functional networks and modules of chromatin factors controlling adult stem cell fate from RNA interference screens Description: This package provides functions to reproduce results and figures in Mulder K. et. al. published in Nature Cell Biology 2012 and Wang X. et. al. published in PLoS Computational Biology 2012. biocViews: StemCell, CancerData Author: Xin Wang , Florian Markowetz Maintainer: Xin Wang git_url: https://git.bioconductor.org/packages/Mulder2012 git_branch: RELEASE_3_8 git_last_commit: f7d95c7 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/Mulder2012_0.22.0.tar.gz vignettes: vignettes/Mulder2012/inst/doc/Mulder2012-Vignette.pdf vignetteTitles: Main vignette:Posterior association network and enriched functional gene modules inferred from rich phenotypes of gene perturbations hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Mulder2012/inst/doc/Mulder2012-Vignette.R Package: mvoutData Version: 1.18.0 Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4), lumi License: Artistic-2.0 MD5sum: 8927221feca30eeac834f6b88ab2d83b NeedsCompilation: no Title: affy and illumina raw data for assessing outlier detector performance Description: affy and illumina raw data for assessing outlier detector performance biocViews: ExperimentData, MicroarrayData Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/mvoutData git_branch: RELEASE_3_8 git_last_commit: be64511 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/mvoutData_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: NCIgraphData Version: 1.18.0 Depends: R (>= 2.10.0) Suggests: Rgraphviz License: GPL-3 MD5sum: fc2723da5d02c9f6baa7d05054f912a1 NeedsCompilation: no Title: Data for the NCIgraph software package Description: Provides pathways from the NCI Pathways Database as R graph objects biocViews: NCI Author: Laurent Jacob Maintainer: Laurent Jacob git_url: https://git.bioconductor.org/packages/NCIgraphData git_branch: RELEASE_3_8 git_last_commit: 30138d6 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/NCIgraphData_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Neve2006 Version: 0.20.0 Depends: R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0), hgu133a.db, annotate License: Artistic-2.0 MD5sum: b20d24255cdccb1d06f070bc60879d28 NeedsCompilation: no Title: expression and CGH data on breast cancer cell lines Description: Experimental organization of combined expression and CGH data biocViews: ExperimentData, CancerData, BreastCancerData Author: M. Neve et al. in Gray Lab at LBL Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/Neve2006 git_branch: RELEASE_3_8 git_last_commit: 95e2a3e git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/Neve2006_0.20.0.tar.gz vignettes: vignettes/Neve2006/inst/doc/neve06notes.pdf vignetteTitles: Neve 2006: combined CGH and expression data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Neve2006/inst/doc/neve06notes.R Package: NGScopyData Version: 1.2.0 License: GPL (>=2) MD5sum: 5a873e124972f000b294486fd2512c12 NeedsCompilation: no Title: Subset of BAM files of human tumor and pooled normal sequencing data (Zhao et al. 2014) for the NGScopy package Description: Subset of BAM files of human lung tumor and pooled normal samples by targeted panel sequencing. [Zhao et al 2014. Targeted Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using the University of North Carolina (UNC) Sequencing Assay Captures Most Previously Described Genetic Aberrations in NSCLC. In preparation.] Each sample is a 10 percent random subsample drawn from the original sequencing data. The pooled normal sample has been rescaled accroding to the total number of normal samples in the "pool". Here provided is the subsampled data on chr6 (hg19). biocViews: ExperimentData, CancerData, LungCancerData, SequencingData Author: Xiaobei Zhao [aut, cre, cph] Maintainer: Xiaobei Zhao URL: http://www.bioconductor.org/packages/release/data/experiment/html/NGScopyData.html git_url: https://git.bioconductor.org/packages/NGScopyData git_branch: RELEASE_3_8 git_last_commit: 5a9d5de git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/NGScopyData_1.2.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: OMICsPCAdata Version: 1.0.0 Depends: R (>= 3.5.0), MultiAssayExperiment Suggests: knitr, kableExtra, rmarkdown License: GPL-3 MD5sum: aec265a048e822143e27ad37dbde1c38 NeedsCompilation: no Title: Supporting data for package OMICsPCA Description: Supporting data for package OMICsPCA biocViews: RepositoryData, TechnologyData, ChIPSeqData, SequencingData, ExpressionData, ENCODE Author: Author: Subhadeep Das Maintainer: Subhadeep Das VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/OMICsPCAdata git_branch: RELEASE_3_8 git_last_commit: 2c66b84 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/OMICsPCAdata_1.0.0.tar.gz vignettes: vignettes/OMICsPCAdata/inst/doc/vignettes.html vignetteTitles: OMICsPCAdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/OMICsPCAdata/inst/doc/vignettes.R Package: OnassisJavaLibs Version: 1.4.2 Depends: R (>= 3.4) Imports: rJava Suggests: BiocStyle, rmarkdown, knitr License: GPL-2 MD5sum: 06e52b38a80a47e6b340cc0365e47554 NeedsCompilation: no Title: OnassisJavaLibs, java libraries to run conceptmapper and semantic similarity Description: A package that contains java libraries to call conceptmapper and compute semnatic similarity from R biocViews: ExperimentData Author: Eugenia Galeota Maintainer: Eugenia Galeota SystemRequirements: Java (>= 1.8) VignetteBuilder: rmarkdown, knitr git_url: https://git.bioconductor.org/packages/OnassisJavaLibs git_branch: RELEASE_3_8 git_last_commit: b0f159f git_last_commit_date: 2018-11-22 Date/Publication: 2018-11-25 source.ver: src/contrib/OnassisJavaLibs_1.4.2.tar.gz vignettes: vignettes/OnassisJavaLibs/inst/doc/OnassisJavaLibs.html vignetteTitles: OnassisJavaLibs: Java Libraries to support Onassis,, Ontology Annotation and Semantic Similarity software hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/OnassisJavaLibs/inst/doc/OnassisJavaLibs.R Package: parathyroidSE Version: 1.20.0 Depends: SummarizedExperiment, R (>= 2.10) Suggests: Rsamtools, GenomicAlignments, GEOquery, SRAdb, GenomicFeatures, BiocStyle License: LGPL MD5sum: 3a64ecf796315fd4b7b86173612b586e NeedsCompilation: no Title: RangedSummarizedExperiment for RNA-Seq of primary cultures of parathyroid tumors by Haglund et al., J Clin Endocrinol Metab 2012. Description: This package provides RangedSummarizedExperiment objects of read counts in genes and exonic parts for paired-end RNA-Seq data from experiments on primary cultures of parathyroid tumors. The data were presented in the article "Evidence of a Functional Estrogen Receptor in Parathyroid Adenomas" by Haglund F, Ma R, Huss M, Sulaiman L, Lu M, Nilsson IL, Hoog A, Juhlin CC, Hartman J, Larsson C, J Clin Endocrinol Metab. jc.2012-2484, Epub 2012 Sep 28, PMID: 23024189. The sequencing was performed on tumor cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control). One control sample was omitted by the paper authors due to low quality. The package vignette describes the creation of the object from raw sequencing data provided by NCBI Gene Expression Omnibus under accession number GSE37211. The gene and exon features are the GRCh37 Ensembl annotations. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love git_url: https://git.bioconductor.org/packages/parathyroidSE git_branch: RELEASE_3_8 git_last_commit: 77b31a9 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/parathyroidSE_1.20.0.tar.gz vignettes: vignettes/parathyroidSE/inst/doc/parathyroidSE.pdf vignetteTitles: parathyroidGenesSE hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/parathyroidSE/inst/doc/parathyroidSE.R Package: pasilla Version: 1.10.0 Depends: R (>= 3.3.0) Suggests: DEXSeq, rmarkdown, BiocStyle, knitr License: LGPL MD5sum: 88ad1534662b8442e6d7a61cd0bb40dc NeedsCompilation: no Title: Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011. Description: This package provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in the article "Conservation of an RNA regulatory map between Drosophila and mammals" by Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR, Genome Res. 2011 Feb;21(2):193-202, Epub 2010 Oct 4, PMID: 20921232. The experiment studied the effect of RNAi knockdown of Pasilla, the Drosophila melanogaster ortholog of mammalian NOVA1 and NOVA2, on the transcriptome. The package vignette describes how the data provided here were derived from the RNA-Seq read sequence data that are provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. biocViews: ExperimentData, Genome, Drosophila_melanogaster_Data, RNASeqData Author: Wolfgang Huber, Alejandro Reyes Maintainer: Alejandro Reyes VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/pasilla git_branch: RELEASE_3_8 git_last_commit: d1cc142 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/pasilla_1.10.0.tar.gz vignettes: vignettes/pasilla/inst/doc/create_objects.html vignetteTitles: "Data preprocessing and creation of the data objects pasillaGenes and pasillaExons" hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pasilla/inst/doc/create_objects.R suggestsMe: IHWpaper, pasillaBamSubset Package: pasillaBamSubset Version: 0.20.0 Suggests: pasilla License: LGPL MD5sum: a418f3d054320e023b3c533c5df9a20a NeedsCompilation: no Title: Subset of BAM files from "Pasilla" experiment Description: Subset of BAM files untreated1.bam (single-end reads) and untreated3.bam (paired-end reads) from "Pasilla" experiment (Pasilla knock-down by Brooks et al., Genome Research 2011). See the vignette in the pasilla data package for how BAM files untreated1.bam and untreated3.bam were obtained from the RNA-Seq read sequence data that is provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. Also contains the DNA sequence for fly chromosome 4 to which the reads can be mapped. biocViews: ExperimentData, Genome, DNASeqData, RNASeqData Author: Hervé Pagès Maintainer: Hervé Pagès git_url: https://git.bioconductor.org/packages/pasillaBamSubset git_branch: RELEASE_3_8 git_last_commit: eb18bd0 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/pasillaBamSubset_0.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: PasillaTranscriptExpr Version: 1.10.0 Depends: R (>= 3.3.0) Suggests: rtracklayer, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: dd8a68bb858f26a8a675895b7aaf4467 NeedsCompilation: no Title: Data package with transcript expression obtained with kallisto from pasilla knock-down RNA-Seq data from Brooks et al. Description: Provides kallisto workflow and transcript expression of RNA-Seq data from Brooks et al. biocViews: Drosophila_melanogaster_Data, Genome, RNASeqData, ExperimentData, SequencingData, ExpressionData, GEO Author: Malgorzata Nowicka [aut, cre] Maintainer: Malgorzata Nowicka VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/PasillaTranscriptExpr git_branch: RELEASE_3_8 git_last_commit: 450561c git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/PasillaTranscriptExpr_1.10.0.tar.gz vignettes: vignettes/PasillaTranscriptExpr/inst/doc/PasillaTranscriptExpr.pdf vignetteTitles: Generation of transcript counts from pasilla dataset with kallisto hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/PasillaTranscriptExpr/inst/doc/PasillaTranscriptExpr.R Package: PathNetData Version: 1.18.0 Depends: R (>= 1.14.0) License: GPL-3 MD5sum: baad9f77b8914d21f84963e3b19f67ed NeedsCompilation: no Title: Experimental data for the PathNet package Description: This package contains the data employed in the vignette of the PathNet package. These data belong to the following publication: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J., Source Code for Biology and Medicine 2012 Sep 24;7(1):10. biocViews: ExperimentData, PathwayInteractionDatabase Author: Bhaskar Dutta , Anders Wallqvist , and Jaques Reifman Maintainer: Jason B. Smith git_url: https://git.bioconductor.org/packages/PathNetData git_branch: RELEASE_3_8 git_last_commit: 9294179 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/PathNetData_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pathprintGEOData Version: 1.12.0 Depends: R (>= 3.4) Suggests: pathprint, SummarizedExperiment License: GPL MD5sum: ad2f10bec6bb16df90e3e9ad1e193563 NeedsCompilation: no Title: Pathway fingerprint vectors representing a subsection of arrays from the GEO data repository Description: Pathway Fingerprint vectors that have been pre-calculated for ~390,000 publicly available arrays from the GEO corpus, spanning 6 species and 31 platforms. All data are accompanied by their associated metadata. biocViews: ExperimentData, ExpressionData, MicroarrayData, GEO, Homo_sapiens_Data, Mus_musculus_Data, Drosophila_melanogaster_Data, Rattus_norvegicus_Data, Caenorhabditis_elegans_Data, Danio_rerio_Data,Genome, SequencingData, OneChannelData, TwoChannelData,PathwayInteractionDatabase Author: Gabriel Altschuler, Sokratis Kariotis Maintainer: Sokratis Kariotis git_url: https://git.bioconductor.org/packages/pathprintGEOData git_branch: RELEASE_3_8 git_last_commit: 1e60f61 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/pathprintGEOData_1.12.0.tar.gz vignettes: vignettes/pathprintGEOData/inst/doc/usingPathprintGEOData.pdf vignetteTitles: pathprintGEOData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pathprintGEOData/inst/doc/usingPathprintGEOData.R Package: pcaGoPromoter.Hs.hg19 Version: 1.18.0 License: GPL (>= 2) MD5sum: 4cc30df25e7ebdcfda9a818e51a58a5d NeedsCompilation: no Title: pcaGoPromoter.Hs.hg19 is a data package used by pcaGoPromoter Description: Contains the data for transciption factors analysis of organism Homo Sapiens with package pcaGoPromoter biocViews: Homo_sapiens_Data Author: Morten Hansen Maintainer: Morten Hansen git_url: https://git.bioconductor.org/packages/pcaGoPromoter.Hs.hg19 git_branch: RELEASE_3_8 git_last_commit: 8cd86a9 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/pcaGoPromoter.Hs.hg19_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Mm.mm9 Version: 1.18.0 License: GPL (>= 2) MD5sum: 33379deaeaa464ca75ad1b86a737c8dd NeedsCompilation: no Title: pcaGoPromoter.Mm.mm9 is a data package used by pcaGoPromoter Description: Contains the data for transciption factors analysis of organism Mus musculus with package pcaGoPromoter biocViews: Mus_musculus_Data Author: Morten Hansen, Maintainer: Morten Hansen git_url: https://git.bioconductor.org/packages/pcaGoPromoter.Mm.mm9 git_branch: RELEASE_3_8 git_last_commit: c120679 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/pcaGoPromoter.Mm.mm9_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter.Rn.rn4 Version: 1.18.0 License: GPL (>= 2) MD5sum: 8d3ddf814343009ddddecc7082f971c5 NeedsCompilation: no Title: pcaGoPromoter.Rn.rn4 is a data package used by pcaGoPromoter Description: Contains the data for transciption factors analysis of organism Rattus norvegicus with package pcaGoPromoter biocViews: Rattus_norvegicus_Data Author: Morten Hansen Maintainer: Morten Hansen, git_url: https://git.bioconductor.org/packages/pcaGoPromoter.Rn.rn4 git_branch: RELEASE_3_8 git_last_commit: 31aaec8 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/pcaGoPromoter.Rn.rn4_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: PCHiCdata Version: 1.10.0 Depends: R (>= 3.2), Chicago Suggests: testthat, BiocStyle, knitr License: Artistic-2.0 MD5sum: 8e3da1443273ed288b35b8fd0cdf1d1d NeedsCompilation: no Title: Promoter Capture Hi-C data Description: Subsets of Promoter Capture Hi-C data conveniently packaged for Chicago users. Data includes interactions detected for chromosomes 20 and 21 in GM12878 cells and for chromosomes 18 and 19 in mESC. biocViews: ExperimentData, SequencingData, Homo_sapiens_Data, Mus_musculus_Data, StemCell Author: Paula Freire-Pritchett, Jonathan Cairns, Steven Wingett, Mikhail Spivakov Maintainer: Paula Freire-Pritchett VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/PCHiCdata git_branch: RELEASE_3_8 git_last_commit: 504d427 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/PCHiCdata_1.10.0.tar.gz vignettes: vignettes/PCHiCdata/inst/doc/PCHiCdata.html vignetteTitles: PCHiCdata Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/PCHiCdata/inst/doc/PCHiCdata.R Package: pcxnData Version: 2.4.0 Depends: R (>= 3.4) Suggests: pcxn License: MIT + file LICENSE MD5sum: b5c348c5e4f36193ef30afef989fdc49 NeedsCompilation: no Title: Correlation coefficients and p values between pre-defined pathway/gene sets Description: PCxN database contains correlation coefficients and p values between pre-defined gene sets within MSigDB H hallmark gene sets, MSigDB C2 CP (Canonical pathways), MSigDB C5 GO BP gene sets and Pathprint respectively, as well as adjusted pathway correlations to account for the shared genes between pathway pairs. biocViews: ExperimentData, ExpressionData, MicroarrayData, GEO, Homo_sapiens_Data, OneChannelData, PathwayInteractionDatabase Author: Sokratis Kariotis, Yered Pita-Juarez, Wenbin Wei, Winston Hide Maintainer: Sokratis Kariotis git_url: https://git.bioconductor.org/packages/pcxnData git_branch: RELEASE_3_8 git_last_commit: dd5d5df git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/pcxnData_2.4.0.tar.gz vignettes: vignettes/pcxnData/inst/doc/usingpcxnData.pdf vignetteTitles: pcxnData hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/pcxnData/inst/doc/usingpcxnData.R Package: pd.atdschip.tiling Version: 0.20.0 Depends: R (>= 2.14.0), methods, RSQLite (>= 0.10.0), oligoClasses (>= 1.15.58), oligo (>= 1.17.3), DBI Imports: Biostrings (>= 2.21.11), IRanges (>= 1.11.31), S4Vectors License: Artistic-2.0 MD5sum: 4e8b33dcee82491454fb2954983fab60 NeedsCompilation: no Title: Platform Design Info for Affymetrix Atdschip_tiling Description: Platform Design Info for Affymetrix Atdschip_tiling biocViews: Arabidopsis_thaliana_Data, MicroarrayData, SNPData Author: Kristof De Beuf Maintainer: Kristof De Beuf git_url: https://git.bioconductor.org/packages/pd.atdschip.tiling git_branch: RELEASE_3_8 git_last_commit: a2cd1a6 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/pd.atdschip.tiling_0.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pepDat Version: 1.2.0 Depends: R(>= 3.0.0) Imports: GenomicRanges Suggests: knitr License: Artistic-2.0 MD5sum: 6348dfe04bb83e78df150d7f67fb3e03 NeedsCompilation: no Title: Peptide microarray data package Description: Provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV. biocViews: MicroarrayData Author: Renan Sauteraud, Raphael Gottardo Maintainer: Renan Sauteraud VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/pepDat git_branch: RELEASE_3_8 git_last_commit: 810813d git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/pepDat_1.2.0.tar.gz vignettes: vignettes/pepDat/inst/doc/pepDat.pdf vignetteTitles: The pepDat users guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pepDat/inst/doc/pepDat.R Package: PepsNMRData Version: 1.0.0 Depends: R (>= 3.5) Suggests: knitr, markdown, rmarkdown, BiocStyle License: GPL-2 | file LICENSE MD5sum: ef7f2931dab1c82cb13f7b1af8bfd91f NeedsCompilation: no Title: Datasets for the PepsNMR package Description: This package contains all the datasets used in the PepsNMR package. biocViews: ExperimentData, OrganismData, Homo_sapiens_Data Author: Manon Martin [aut, cre], Bernadette Govaerts [aut, ths], Pascal de Tullio [dtc] Maintainer: Manon Martin BugReports: https://github.com/ManonMartin/PepsNMRData/issues git_url: https://git.bioconductor.org/packages/PepsNMRData git_branch: RELEASE_3_8 git_last_commit: d54d847 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/PepsNMRData_1.0.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Package: plasFIA Version: 1.10.0 Depends: proFIA License: LGPL MD5sum: 9eecc8e69adc6fae52eb4eac6d18de51 NeedsCompilation: no Title: FIA-HRMS plasma dataset Description: Positive Ionization FIA-HRMS data of human plasma spiked with a pool of 40 compounds acquired in FIA-HRMS mode on an orbitrap fusion. plasFIA also include the result of the processing by the proFIA package with adapted parameters for an Orbitrap Fusion. biocViews: ExperimentData, MassSpectrometryData Author: Alexis Delabriere, Etienne Thevenot, Ulli Hohenester and Christophe Junot. Maintainer: Alexis Delabriere git_url: https://git.bioconductor.org/packages/plasFIA git_branch: RELEASE_3_8 git_last_commit: bedc6c2 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/plasFIA_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ppiData Version: 0.20.0 Depends: graph Imports: AnnotationDbi Suggests: org.Sc.sgd.db, ppiStats License: Artistic-2.0 MD5sum: eff4cead7fba4a8443cb3c3426391bb0 NeedsCompilation: no Title: A package that contains the bait to prey directed graphs for protein-protein interactions. Description: This package contains the directed graphs for protein interaction data as derived from Y2H and APMS as well as the code used to obtain the y2h data from IntAct Repository. biocViews: ExperimentData Author: Tony Chiang Maintainer: Bioconductor Package Maintainer git_url: https://git.bioconductor.org/packages/ppiData git_branch: RELEASE_3_8 git_last_commit: cdf5387 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ppiData_0.20.0.tar.gz vignettes: vignettes/ppiData/inst/doc/ppiData.pdf vignetteTitles: Using the package ppiStats hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/ppiData/inst/doc/ppiData.R Package: prebsdata Version: 1.18.0 Depends: R (>= 2.14.0) License: Artistic-2.0 MD5sum: ddb000d474c089466ab15aa67b44cdfa NeedsCompilation: no Title: Data for 'prebs' package Description: This package contains data required to run examples in 'prebs' package. The data files include: 1) Small sample bam files for demonstration purposes 2) Probe sequence mappings for Custom CDF (taken from http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp) 3) Probe sequence mappings for manufacturer's CDF (manually created using bowtie) biocViews: ExperimentData, SequencingData, RNASeqData Author: Karolis Uziela and Antti Honkela Maintainer: Karolis Uziela git_url: https://git.bioconductor.org/packages/prebsdata git_branch: RELEASE_3_8 git_last_commit: b6a1d62 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/prebsdata_1.18.0.tar.gz vignettes: vignettes/prebsdata/inst/doc/prebsdata.pdf vignetteTitles: prebsdata User Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: PREDAsampledata Version: 0.22.0 Depends: R (>= 2.10.0), methods, PREDA, Biobase, affy, annotate Suggests: hgu133plus2.db, hgu133plus2cdf License: Artistic-2.0 MD5sum: f8850b39d6ecfc64fe4cc26f6e305751 NeedsCompilation: no Title: expression and copy number data on clear cell renal carcinoma samples Description: Sample data for PREDA package. (annotations objects synchronized with GeneAnnot custom CDFs version 2.2.0) biocViews: ExperimentData, Tissue, CancerData, KidneyCancerData, MicroarrayData, TissueMicroarrayData, ArrayExpress Author: I. Cifola et al. in Cristina Battaglia Lab, University of Milan Maintainer: Francesco Ferrari git_url: https://git.bioconductor.org/packages/PREDAsampledata git_branch: RELEASE_3_8 git_last_commit: 493a070 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/PREDAsampledata_0.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ProData Version: 1.20.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5) License: GPL MD5sum: 3c3b90d81fe5c686b86ea33d8d4c15e8 NeedsCompilation: no Title: SELDI-TOF data of Breast cancer samples Description: A data package of SELDI-TOF protein mass spectrometry data of 167 breast cancer and normal samples. biocViews: ExperimentData, CancerData, BreastCancerData, MassSpectrometryData, NCI Author: Xiaochun Li Maintainer: Xiaochun Li git_url: https://git.bioconductor.org/packages/ProData git_branch: RELEASE_3_8 git_last_commit: 56ff8e8 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/ProData_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pRolocdata Version: 1.20.0 Depends: R (>= 2.15), MSnbase Imports: Biobase, utils Suggests: pRoloc (>= 1.13.8), testthat License: GPL-2 MD5sum: a251f615e1307eb3129875b823c2ed22 NeedsCompilation: no Title: Data accompanying the pRoloc package Description: Mass-spectrometry based spatial proteomics data sets and protein complex separation data. Also contains the time course expression experiment from Mulvey et al. 2015. biocViews: ExperimentData, Homo_sapiens_Data, MassSpectrometryData, Arabidopsis_thaliana_Data, Drosophila_melanogaster_Data, Mus_musculus_Data, StemCell, Proteome Author: Laurent Gatto, Olive M. Crook and Lisa M. Breckels Maintainer: Laurent Gatto URL: https://github.com/lgatto/pRolocdata BugReports: https://github.com/lgatto/pRolocdata/issues git_url: https://git.bioconductor.org/packages/pRolocdata git_branch: RELEASE_3_8 git_last_commit: 229fec9 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/pRolocdata_1.20.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics Package: prostateCancerCamcap Version: 1.10.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: bd8f6f0d10eaeebeb45ec56d911ee8d3 NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Ross-Adams (2015) Prostate Cancer dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerCamcap git_branch: RELEASE_3_8 git_last_commit: c5bc660 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/prostateCancerCamcap_1.10.0.tar.gz vignettes: vignettes/prostateCancerCamcap/inst/doc/prostateCancerCamcap.pdf vignetteTitles: prostateCancerCamcap hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/prostateCancerCamcap/inst/doc/prostateCancerCamcap.R Package: prostateCancerGrasso Version: 1.10.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: 91b4dadaaa9d775625c625dc7763b6bd NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Grasso (2012) Prostate Cancer dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerGrasso git_branch: RELEASE_3_8 git_last_commit: 94ef38f git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/prostateCancerGrasso_1.10.0.tar.gz vignettes: vignettes/prostateCancerGrasso/inst/doc/prostateCancerGrasso.pdf vignetteTitles: prostateCancerGrasso hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/prostateCancerGrasso/inst/doc/prostateCancerGrasso.R Package: prostateCancerStockholm Version: 1.10.0 Depends: Biobase , R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: e76e4cf258025b14950fa035662b7be5 NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Stockholm dataset biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerStockholm git_branch: RELEASE_3_8 git_last_commit: 75e090e git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/prostateCancerStockholm_1.10.0.tar.gz vignettes: vignettes/prostateCancerStockholm/inst/doc/prostateCancerStockholm.pdf vignetteTitles: prostateCancerStockholm hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/prostateCancerStockholm/inst/doc/prostateCancerStockholm.R Package: prostateCancerTaylor Version: 1.10.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery, org.Hs.eg.db License: Artistic-2.0 MD5sum: 17217ff2d4cfaa8ff50b4fb5b1da2bf1 NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Taylor et al (2010) dataset. biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerTaylor git_branch: RELEASE_3_8 git_last_commit: 61ebd1a git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/prostateCancerTaylor_1.10.0.tar.gz vignettes: vignettes/prostateCancerTaylor/inst/doc/prostateCancerTaylor.pdf vignetteTitles: prostateCancerTaylor hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/prostateCancerTaylor/inst/doc/prostateCancerTaylor.R Package: prostateCancerVarambally Version: 1.10.0 Depends: Biobase, R (>= 3.3) Suggests: GEOquery License: Artistic-2.0 MD5sum: c35f1f99121183a4332dbbc56a3de36b NeedsCompilation: no Title: Prostate Cancer Data Description: A Bioconductor data package for the Varambally dataset biocViews: ExperimentData, ExpressionData,GEO, MicroarrayData, CancerData, ProstateCancerData Author: Mark Dunning Maintainer: Mark Dunning git_url: https://git.bioconductor.org/packages/prostateCancerVarambally git_branch: RELEASE_3_8 git_last_commit: da2b00f git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/prostateCancerVarambally_1.10.0.tar.gz vignettes: vignettes/prostateCancerVarambally/inst/doc/prostateCancerVarambally.pdf vignetteTitles: prostateCancerVarambally hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/prostateCancerVarambally/inst/doc/prostateCancerVarambally.R Package: PtH2O2lipids Version: 1.8.0 Depends: R (>= 3.3), xcms, CAMERA, LOBSTAHS, methods, utils Suggests: gplots, RColorBrewer, cluster, vegan, clustsig License: MIT + file LICENSE MD5sum: 4e581e8fef911bd546261ddc9c4f7cb7 NeedsCompilation: no Title: P. tricornutum HPLC-ESI-MS Lipid Data from van Creveld et al. (2015) Description: Annotated HPLC-ESI-MS lipid data in positive ionization mode from an experiment in which cultures of the marine diatom Phaeodactylum tricornutum were treated with various concentrations of hydrogen peroxide (H2O2) to induce oxidative stress. The experiment is described in Graff van Creveld, et al., 2015, "Early perturbation in mitochondria redox homeostasis in response to environmental stress predicts cell fate in diatoms," ISME Journal 9:385-395. PtH2O2lipids consists of two objects: A CAMERA xsAnnotate object (ptH2O2lipids$xsAnnotate) and LOBSTAHS LOBSet object (ptH2O2lipids$xsAnnotate$LOBSet). The LOBSet includes putative compound assignments from the default LOBSTAHS database. Isomer annotation is recorded in three other LOBSet slots. biocViews: ReproducibleResearch, CellCulture, MassSpectrometryData, Phaeodactylum_tricornutum_data Author: Shiri Graff van Creveld [aut], Shilo Rosenwasser [aut], Daniella Schatz [aut], Ilan Koren [aut], Assaf Vardi [aut], James Collins [cre] Maintainer: James Collins URL: http://dx.doi.org/10.1038/ismej.2014.136, https://github.com/vanmooylipidomics/PtH2O2lipids, http://www.whoi.edu/page.do?pid=133616&tid=282&cid=192529 BugReports: https://github.com/vanmooylipidomics/PtH2O2lipids/issues/new git_url: https://git.bioconductor.org/packages/PtH2O2lipids git_branch: RELEASE_3_8 git_last_commit: 21c8d05 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/PtH2O2lipids_1.8.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Package: pumadata Version: 2.18.0 Depends: R (>= 3.2.0), affy (>= 1.46.0), Biobase (>= 2.5.5),puma ,oligo(>= 1.32.0) License: LGPL MD5sum: ec6c6ebbaa066139f26af9e175936484 NeedsCompilation: no Title: Various data sets for use with the puma package Description: This is a simple data package including various data sets derived from the estrogen data for use with the puma (Propagating Uncertainty in Microarray Analysis) package. biocViews: ExperimentData, MicroarrayData, SNPData Author: Richard Pearson Maintainer: Richard Pearson URL: http://umber.sbs.man.ac.uk/resources/puma git_url: https://git.bioconductor.org/packages/pumadata git_branch: RELEASE_3_8 git_last_commit: 1bbdf0d git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/pumadata_2.18.0.tar.gz vignettes: vignettes/pumadata/inst/doc/pumadata.pdf vignetteTitles: pumadata User Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/pumadata/inst/doc/pumadata.R Package: PWMEnrich.Dmelanogaster.background Version: 4.16.0 Depends: methods, PWMEnrich License: GPL-3 MD5sum: 265967f539c3da744389a1fb5a3f112a NeedsCompilation: no Title: D. melanogaster background for PWMEnrich Description: PWMEnrich pre-compiled background objects for Drosophila melanogaster and MotifDb D. melanogaster motifs. biocViews: Drosophila_melanogaster_Data Author: Robert Stojnic Maintainer: Robert Stojnic git_url: https://git.bioconductor.org/packages/PWMEnrich.Dmelanogaster.background git_branch: RELEASE_3_8 git_last_commit: b236e0b git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/PWMEnrich.Dmelanogaster.background_4.16.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: PWMEnrich.Hsapiens.background Version: 4.16.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: bffb6a95c2c744fe3a430bbb758dc8e0 NeedsCompilation: no Title: H. sapiens background for PWMEnrich Description: PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs. biocViews: Homo_sapiens_Data, CGHData Author: Robert Stojnic Maintainer: Robert Stojnic git_url: https://git.bioconductor.org/packages/PWMEnrich.Hsapiens.background git_branch: RELEASE_3_8 git_last_commit: f4f4078 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/PWMEnrich.Hsapiens.background_4.16.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: PWMEnrich.Mmusculus.background Version: 4.16.0 Depends: R (>= 2.10), methods, PWMEnrich License: GPL-3 MD5sum: a26cdb4eb465daba22b3e13e4db1a86b NeedsCompilation: no Title: M. musculus background for PWMEnrich Description: PWMEnrich pre-compiled background objects for M.musculus (mouse) and MotifDb M. musculus motifs. biocViews: Mus_musculus_Data Author: Robert Stojnic Maintainer: Robert Stojnic git_url: https://git.bioconductor.org/packages/PWMEnrich.Mmusculus.background git_branch: RELEASE_3_8 git_last_commit: 49246e4 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/PWMEnrich.Mmusculus.background_4.16.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: QDNAseq.hg19 Version: 1.12.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: 5644d966c2331d01df686107f85f0899 NeedsCompilation: no Title: QDNAseq bin annotation for hg19 Description: This package provides QDNAseq bin annotations for the human genome build hg19. biocViews: ExperimentData, OrganismData, Homo_sapiens_Data Author: Daoud Sie [aut, cre] Maintainer: Daoud Sie URL: https://github.com/tgac-vumc/QDNAseq.hg19 BugReports: https://github.com/tgac-vumc/QDNAseq.hg19/issues git_url: https://git.bioconductor.org/packages/QDNAseq.hg19 git_branch: RELEASE_3_8 git_last_commit: 44c7e7b git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/QDNAseq.hg19_1.12.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: QDNAseq.mm10 Version: 1.12.0 Depends: R (>= 3.2.1), QDNAseq License: GPL MD5sum: 3557bc3a5f5820eb17d7a643730ed314 NeedsCompilation: no Title: Bin annotation mm10 Description: This package provides QDNAseq bin annotations for the mouse genome build mm10. biocViews: ExperimentData, OrganismData, Mus_musculus_Data Author: Daoud Sie [aut, cre] Maintainer: Daoud Sie URL: https://github.com/tgac-vumc/QDNAseq.mm10 BugReports: https://github.com/tgac-vumc/QDNAseq.mm10/issues git_url: https://git.bioconductor.org/packages/QDNAseq.mm10 git_branch: RELEASE_3_8 git_last_commit: 8618bab git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/QDNAseq.mm10_1.12.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: qPLEXdata Version: 1.0.1 Depends: R (>= 3.5), qPLEXanalyzer Imports: utils, knitr, MSnbase, dplyr License: GPL-2 MD5sum: 27c05de065b8225c34d8a99ac7ce1992 NeedsCompilation: no Title: Data accompanying qPLEXanalyzer package Description: qPLEX-RIME and Full proteome TMT mass spectrometry datasets. biocViews: ExperimentData, MassSpectrometryData, Proteome Author: Kamal Kishore Developer [aut, cre] Maintainer: Kamal Kishore Developer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/qPLEXdata git_branch: RELEASE_3_8 git_last_commit: a1f5cf9 git_last_commit_date: 2018-11-16 Date/Publication: 2018-11-18 source.ver: src/contrib/qPLEXdata_1.0.1.tar.gz vignettes: vignettes/qPLEXdata/inst/doc/qPLEXdata.pdf vignetteTitles: qPLEXdata hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/qPLEXdata/inst/doc/qPLEXdata.R Package: QUBICdata Version: 1.10.0 Depends: R (>= 3.1) Suggests: knitr, rmarkdown License: Unlimited | file LICENSE MD5sum: 66ed9092477ac1c0ddf2b367d55682e1 NeedsCompilation: no Title: Data employed in the vignette of the QUBIC package Description: The data employed in the vignette of the QUBIC package. These data belong to Many Microbe Microarrays Database and STRING v10. biocViews: Escherichia_coli_Data, OrganismData, ExperimentData Author: Yu Zhang [aut, cre], Qin Ma [aut] Maintainer: Yu Zhang URL: http://github.com/zy26/QUBICdata VignetteBuilder: knitr BugReports: http://github.com/zy26/QUBICdata/issues git_url: https://git.bioconductor.org/packages/QUBICdata git_branch: RELEASE_3_8 git_last_commit: a2a8188 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/QUBICdata_1.10.0.tar.gz vignettes: vignettes/QUBICdata/inst/doc/qubic_data_vignette.pdf vignetteTitles: QUBIC Data Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/QUBICdata/inst/doc/qubic_data_vignette.R Package: rcellminerData Version: 2.4.0 Depends: R (>= 3.1.1), Biobase Suggests: knitr, testthat, BiocStyle, rcellminer License: LGPL-3 + file LICENSE MD5sum: 7259b2817b463847c17e2d6f1d85fe04 NeedsCompilation: no Title: rcellminerData: Molecular Profiles and Drug Response for the NCI-60 Cell Lines Description: The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data. biocViews: CancerData, CopyNumberVariationData, ExpressionData, SNPData, NCI, MicroarrayData, miRNAData Author: Augustin Luna, Vinodh Rajapakse, Fabricio Sousa Maintainer: Augustin Luna , Vinodh Rajapakse , Fathi Elloumi VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/rcellminerData git_branch: RELEASE_3_8 git_last_commit: b61fe9e git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/rcellminerData_2.4.0.tar.gz vignettes: vignettes/rcellminerData/inst/doc/rcellminerDataUsage.html vignetteTitles: Accessing CellMiner Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/rcellminerData/inst/doc/rcellminerDataUsage.R Package: RcisTarget.hg19.motifDBs.cisbpOnly.500bp Version: 1.2.0 Depends: R (>= 3.3) Imports: data.table License: GPL-3 MD5sum: a43b2fd762e2ea0d13283c4c7fa5221c NeedsCompilation: no Title: RcisTarget motif databases for human (hg19) - Subset of 4.6k motifs Description: RcisTarget databases: Gene-based motif rankings and annotation to transcription factors. This package contains a subset of 4.6k motifs (cisbp motifs), scored only within 500bp upstream and the TSS. See RcisTarget tutorial to download the full databases, containing 20k motifs and search space up to 10kbp around the TSS. biocViews: Homo_sapiens_Data Author: Sara Aibar, Gert Hulselmans, Stein Aerts. Laboratory of Computational Biology, KU Leuven Center for Human Genetics. Leuven, Belgium. Maintainer: Sara Aibar URL: http://scenic.aertslab.org git_url: https://git.bioconductor.org/packages/RcisTarget.hg19.motifDBs.cisbpOnly.500bp git_branch: RELEASE_3_8 git_last_commit: 36c81c9 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.2.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: RegParallel Version: 1.0.0 Depends: R (>= 3.5.0), doParallel, foreach, parallel, iterators, data.table, stringr, survival, arm, MASS, stats, utils, methods Suggests: RUnit, BiocGenerics, knitr, DESeq2, airway, magrittr, Biobase, GEOquery, biomaRt, survminer License: GPL-3 MD5sum: dbfebc547b8aaf83e060210498e8492a NeedsCompilation: no Title: Standard regression functions in R enabled for parallel processing over large data-frames Description: In many analyses, a large amount of variables have to be tested independently against the trait/endpoint of interest, and also adjusted for covariates and confounding factors at the same time. The major bottleneck in these is the amount of time that it takes to complete these analyses. With RegParallel, a large number of tests can be performed simultaneously. On a 12-core system, 144 variables can be tested simultaneously, with 1000s of variables processed in a matter of seconds via 'nested' parallel processing. Works for logistic regression, linear regression, conditional logistic regression, Cox proportional hazards and survival models, Bayesian logistic regression, and negative binomial regression. biocViews: DiseaseModel Author: Kevin Blighe Maintainer: Kevin Blighe URL: https://github.com/kevinblighe/RegParallel VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RegParallel git_branch: RELEASE_3_8 git_last_commit: 5178d6f git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RegParallel_1.0.0.tar.gz vignettes: vignettes/RegParallel/inst/doc/RegParallel.html vignetteTitles: Standard regression functions in R enabled for parallel processing over large data-frames hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RegParallel/inst/doc/RegParallel.R Package: restfulSEData Version: 1.4.0 Depends: R (>= 3.4), SummarizedExperiment, ExperimentHub Imports: utils, methods Suggests: knitr License: Artistic-2.0 MD5sum: a4008a223e2c5417f8f164fb3b2d3752 NeedsCompilation: no Title: Example metadata for the "restfulSE" R package Description: Metadata RangedSummarizedExperiment shell for use with restfulSE. biocViews: ExperimentData, Mus_musculus_Data, Homo_sapiens_Data, ExpressionData, SequencingData Author: Vincent Carey [aut], Shweta Gopaulakrishnan [cre, aut] Maintainer: Bioconductor Package Maintainer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/restfulSEData git_branch: RELEASE_3_8 git_last_commit: 3759a2b git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/restfulSEData_1.4.0.tar.gz vignettes: vignettes/restfulSEData/inst/doc/restfulSEData.pdf vignetteTitles: restfulSEData -- SummarizedExperiment shells for remote assay data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/restfulSEData/inst/doc/restfulSEData.R Package: RforProteomics Version: 1.20.0 Depends: MSnbase (>= 2.5.3) Imports: R.utils, shiny, biocViews, BiocManager Suggests: AnnotationDbi, rpx, DT, knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, isobar, MALDIquant (>= 1.12), MALDIquantForeign, readBrukerFlexData, rTANDEM, synapter, synapterdata, IPPD, Rdisop, OrgMassSpecR, SummarizedExperiment, BRAIN, rols, hpar, GO.db, org.Hs.eg.db, e1071, biomaRt, RColorBrewer, ggplot2, reshape2, xtable, lattice, mzID, pRoloc, pRolocdata, MSGFplus, MSGFgui, MSnID, msmsTests, msmsEDA, DEP, corrplot, beanplot, Heatplus, gplots, VennDiagram, protViz, genefilter, plotly, gridExtra, dplyr, lubridate Enhances: cleaver License: Artistic-2.0 MD5sum: c2df3edec11e6ebf57e0c7b7c19c3e14 NeedsCompilation: no Title: Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication Description: This package contains code to illustrate the 'Using R and Bioconductor for proteomics data analysis' and 'Visualisation of proteomics data using R and Bioconductor' manuscripts. The vignettes describe the code and data needed to reproduce the examples and figures described in the paper and functionality for proteomics visualisation. It also contain various function to discover R software for mass spectrometry and proteomics. biocViews: ExperimentData, MassSpectrometryData, ReproducibleResearch Author: Laurent Gatto [aut, cre], Thomas Lin Pedersen [ctb], Sebastian Gibb [ctb], Vlad Petyuk [ctb] Maintainer: Laurent Gatto URL: http://lgatto.github.com/RforProteomics/ VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RforProteomics git_branch: RELEASE_3_8 git_last_commit: e4de488 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RforProteomics_1.20.0.tar.gz vignettes: vignettes/RforProteomics/inst/doc/RforProteomics.html, vignettes/RforProteomics/inst/doc/RProtVis.html vignetteTitles: Using R for proteomics data analysis, Visualisation of proteomics data using R and Bioconductor hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RforProteomics/inst/doc/RforProteomics.R, vignettes/RforProteomics/inst/doc/RProtVis.R Package: RGMQLlib Version: 1.2.0 Depends: R(>= 3.4.2) Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 71eae8b46e7104c9733252c6162002f6 NeedsCompilation: no Title: RGMQLlib, java libraries to run GMQL scala API Description: A package that contains scala libraries to call GMQL from R used by RGMQL package. It contains a scalable data management engine written in Scala programming language. biocViews: ExperimentData,RepositoryData Author: Simone Pallotta, Marco Masseroli Maintainer: Simone Pallotta URL: http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/ VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RGMQLlib git_branch: RELEASE_3_8 git_last_commit: 3186f94 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RGMQLlib_1.2.0.tar.gz vignettes: vignettes/RGMQLlib/inst/doc/RGMQLlib.pdf vignetteTitles: RGMQLlib: scala Libraries to support GMQL hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: rheumaticConditionWOLLBOLD Version: 1.20.0 Depends: R (>= 2.10.0) Suggests: genefilter, Biobase, hgu133plus2.db License: Artistic-2.0 MD5sum: 8e65dd2904480c3e37fa19cec75c15c9 NeedsCompilation: no Title: Normalized gene expression dataset published by Wollbold et al. [2009] (WOLLBOLD). Description: Normalized gene expression data from rheumatic diseases from study published by Wollbold et al. in 2009, provided as an eSet. biocViews: ExperimentData, Tissue, MicroarrayData, MultiChannelData, ChipOnChipData, TissueMicroarrayData, GEO, ArrayExpress Author: Alejandro Quiroz-Zarate, John Quackenbush Maintainer: Alejandro Quiroz-Zarate URL: http://compbio.dfci.harvard.edu/ git_url: https://git.bioconductor.org/packages/rheumaticConditionWOLLBOLD git_branch: RELEASE_3_8 git_last_commit: 46a06c3 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/rheumaticConditionWOLLBOLD_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RIPSeekerData Version: 1.18.0 Depends: RIPSeeker License: GPL-2 MD5sum: f81b8966e307327aeba0796f80f0e97a NeedsCompilation: no Title: test data for RIPSeeker Description: The RIP-seq data in BAM format are the test data for the package RIPSeeker. The data correspond to two RIP-seq experiments, namely PRC2 and CCNT1. Raw data from NCBI Gene Expression Omnibus under accession numbers GSE17064 for PRC2 and in-house for CCNT1. biocViews: ExperimentData, Genome, StemCell, SequencingData, RIPSeqData, GEO Author: Yue Li Maintainer: Alejandro Reyes git_url: https://git.bioconductor.org/packages/RIPSeekerData git_branch: RELEASE_3_8 git_last_commit: 0687394 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RIPSeekerData_1.18.0.tar.gz vignettes: vignettes/RIPSeekerData/inst/doc/RIPSeekerData.pdf vignetteTitles: RIP-seq datasets for testing RIPSeeker package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RIPSeekerData/inst/doc/RIPSeekerData.R Package: RITANdata Version: 1.6.0 Depends: R (>= 3.4) License: file LICENSE MD5sum: 2cf6bf4546fd2e53d870202ba8b33ad3 NeedsCompilation: no Title: This package contains the annotation and network data sets Description: Data such as is contained in these two R data files in this package are required for the RITAN package. Users may use their own or additional resources in conjunction with RITANdata. See the RITAN vignettes for more information. biocViews: AnnotationData, Homo_sapiens Author: Michael Zimmermann Maintainer: Michael Zimmermann VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RITANdata git_branch: RELEASE_3_8 git_last_commit: 091e0e2 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RITANdata_1.6.0.tar.gz vignettes: vignettes/RITANdata/inst/doc/RITANdata.html vignetteTitles: Vignette Title hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/RITANdata/inst/doc/RITANdata.R Package: RMassBankData Version: 1.20.0 Suggests: RMassBank License: Artistic-2.0 MD5sum: 46d74376c499336ed7d6f2abbad99b73 NeedsCompilation: no Title: Test dataset for RMassBank Description: Example spectra, example compound list(s) and an example annotation list for a narcotics dataset; required to test RMassBank. The package is described in the man page for RMassBankData. Includes new XCMS test data. biocViews: ExperimentData, MassSpectrometryData Author: Michael Stravs, Emma Schymanski, Steffen Neumann Maintainer: Michael Stravs, Emma Schymanski git_url: https://git.bioconductor.org/packages/RMassBankData git_branch: RELEASE_3_8 git_last_commit: a84b8b2 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RMassBankData_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RNAinteractMAPK Version: 1.20.0 Depends: R (>= 2.12.0), methods, fields, sparseLDA, RNAinteract Imports: grid, gdata, MASS, genefilter Suggests: qvalue, lattice License: Artistic-2.0 MD5sum: 06d12d93a9a99709c6b5946fa4932486 NeedsCompilation: no Title: Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi Description: This package includes all data used in the paper -Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi- by Horn, Sandmann, Fischer et al.., Nat. Methods, 2011. The package vignette shows the R code to reproduce all figures in the paper. biocViews: ExperimentData, MicrotitrePlateAssayData, Drosophila_melanogaster_Data, CellCulture Author: Bernd Fischer Maintainer: Bernd Fischer git_url: https://git.bioconductor.org/packages/RNAinteractMAPK git_branch: RELEASE_3_8 git_last_commit: f093191 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RNAinteractMAPK_1.20.0.tar.gz vignettes: vignettes/RNAinteractMAPK/inst/doc/RNAinteractMAPK.pdf vignetteTitles: RNAinteractMAPK hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RNAinteractMAPK/inst/doc/RNAinteractMAPK.R suggestsMe: DmelSGI Package: RNAseqData.HNRNPC.bam.chr14 Version: 0.20.0 Suggests: GenomicAlignments, BiocManager License: LGPL MD5sum: 936faad52a796dfc487f2d104bfb91bd NeedsCompilation: no Title: Aligned reads from RNAseq experiment: Transcription profiling by high throughput sequencing of HNRNPC knockdown and control HeLa cells Description: The package contains 8 BAM files, 1 per sequencing run. Each BAM file was obtained by (1) aligning the reads (paired-end) to the full hg19 genome with TopHat2, and then (2) subsetting to keep only alignments on chr14. See accession number E-MTAB-1147 in the ArrayExpress database for details about the experiment, including links to the published study (by Zarnack et al., 2012) and to the FASTQ files. biocViews: ExperimentData, Genome, Homo_sapiens_Data, SequencingData, GEO, NCI, RNASeqData, ArrayExpress Author: Hervé Pagès Maintainer: Hervé Pagès URL: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1147/ git_url: https://git.bioconductor.org/packages/RNAseqData.HNRNPC.bam.chr14 git_branch: RELEASE_3_8 git_last_commit: 1ce421e git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RNAseqData.HNRNPC.bam.chr14_0.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RNASeqRData Version: 1.0.0 Depends: R (>= 3.5.0) Suggests: png, grid License: Artistic-2.0 MD5sum: aac4f4cb75fd142b66b9e954ac2652e3 NeedsCompilation: no Title: RNASeqRData: sample data for RNASeqR software package demonstration Description: RNASeqRData is a helper experiment package for vignette demonstration purpose in RNASeqR software package. biocViews: ExperimentData, Saccharomyces_cerevisiae_Data Author: Kuan-Hao Chao Maintainer: Kuan-Hao Chao git_url: https://git.bioconductor.org/packages/RNASeqRData git_branch: RELEASE_3_8 git_last_commit: 34b47cc git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RNASeqRData_1.0.0.tar.gz vignettes: vignettes/RNASeqRData/inst/doc/RNASeqRData.html vignetteTitles: RNASeqRData.html hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RnaSeqSampleSizeData Version: 1.14.0 Depends: edgeR,R (>= 2.10) Suggests: BiocStyle, knitr License: GPL (>= 2) MD5sum: faba578ad3a43e5fb8a72961dc17eef6 NeedsCompilation: no Title: RnaSeqSampleSizeData Description: RnaSeqSampleSizeData package provides the read counts and dispersion distribution from real RNA-seq experiments. It can be used by RnaSeqSampleSize package to estimate sample size and power for RNA-seq experiment design. biocViews: ExperimentData, CancerData, RNASeqData Author: Shilin Zhao, Chung-I Li, Yan Guo, Quanhu Sheng, Yu Shyr Maintainer: Shilin Zhao VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/RnaSeqSampleSizeData git_branch: RELEASE_3_8 git_last_commit: c4b619a git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RnaSeqSampleSizeData_1.14.0.tar.gz vignettes: vignettes/RnaSeqSampleSizeData/inst/doc/RnaSeqSampleSizeData.pdf vignetteTitles: RnaSeqSampleSizeData: Read counts and dispersion distribution from real data for sample size estimation of RNA-seq experiments hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RnaSeqSampleSizeData/inst/doc/RnaSeqSampleSizeData.R Package: RnBeads.hg19 Version: 1.14.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 4fc451cec743ae5482c90aa230bfbc05 NeedsCompilation: no Title: RnBeads.hg19 Description: Automatically generated RnBeads annotation package for the assembly hg19. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.hg19 git_branch: RELEASE_3_8 git_last_commit: 000e4a4 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RnBeads.hg19_1.14.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: RnBeads.hg38 Version: 1.14.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 184f7387ab19409cbb5eee2cbe0da8df NeedsCompilation: no Title: RnBeads.hg38 Description: Automatically generated RnBeads annotation package for the assembly hg38. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.hg38 git_branch: RELEASE_3_8 git_last_commit: 6eb5463 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RnBeads.hg38_1.14.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: RnBeads.mm10 Version: 1.14.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 94634f0b5fcea83c3c35545a7f097251 NeedsCompilation: no Title: RnBeads.mm10 Description: Automatically generated RnBeads annotation package for the assembly mm10. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.mm10 git_branch: RELEASE_3_8 git_last_commit: 33cb648 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RnBeads.mm10_1.14.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: RnBeads.mm9 Version: 1.14.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: 613c050b649b8ac4f8de05aff0df51ad NeedsCompilation: no Title: RnBeads.mm9 Description: Automatically generated RnBeads annotation package for the assembly mm9. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.mm9 git_branch: RELEASE_3_8 git_last_commit: 92b7c3b git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RnBeads.mm9_1.14.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: RnBeads.rn5 Version: 1.14.0 Depends: R (>= 3.0.0), GenomicRanges Suggests: RnBeads License: GPL-3 MD5sum: f3a037e9bd35824a15ceaededed22b6d NeedsCompilation: no Title: RnBeads.rn5 Description: Automatically generated RnBeads annotation package for the assembly rn5. Author: RnBeadsAnnotationCreator Maintainer: RnBeadsAnnotationCreator git_url: https://git.bioconductor.org/packages/RnBeads.rn5 git_branch: RELEASE_3_8 git_last_commit: 3f8d9aa git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RnBeads.rn5_1.14.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: RRBSdata Version: 1.2.0 Depends: R (>= 3.1.0), BiSeq (>= 1.9.2) License: LGPL-3 MD5sum: 0b5b0c9b0b5dba4129cc67482eb24e58 NeedsCompilation: no Title: An RRBS data set with 12 samples and 10,000 simulated DMRs Description: RRBS data set comprising 12 samples with simulated differentially methylated regions (DMRs). biocViews: ExperimentData, CancerData, SequencingData, CpGIslandData Author: Katja Hebestreit, Hans-Ulrich Klein Maintainer: Katja Hebestreit git_url: https://git.bioconductor.org/packages/RRBSdata git_branch: RELEASE_3_8 git_last_commit: 213db1b git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RRBSdata_1.2.0.tar.gz vignettes: vignettes/RRBSdata/inst/doc/RRBSdata.pdf vignetteTitles: An RRBS data set with 12 samples and 10,,000 simulated DMRs. hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RRBSdata/inst/doc/RRBSdata.R Package: rRDPData Version: 1.2.0 Depends: rRDP License: GPL-2 MD5sum: 92bc7797510726832537d8aafdcb220d NeedsCompilation: no Title: Database for the Default RDP Classifier Description: Database used by the default RDP Classifier biocViews: SequencingData, MicrobiomeData Author: Michael Hahsler, Anurag Nagar Maintainer: Michael Hahsler SystemRequirements: Java git_url: https://git.bioconductor.org/packages/rRDPData git_branch: RELEASE_3_8 git_last_commit: d436675 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/rRDPData_1.2.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RTCGA.clinical Version: 20151101.12.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 8b41502e323b7992553be6850c754c40 NeedsCompilation: no Title: Clinical datasets from The Cancer Genome Atlas Project Description: Package provides clinical datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Clinical data format is explained here https://wiki.nci.nih.gov/display/TCGA/Clinical+Data+Overview. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.clinical git_branch: RELEASE_3_8 git_last_commit: 5083a09 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RTCGA.clinical_20151101.12.0.tar.gz vignettes: vignettes/RTCGA.clinical/inst/doc/downloading_clinical_datasets.html vignetteTitles: Using RTCGA to download clinical data as included in RTCGA.clinical hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.clinical/inst/doc/downloading_clinical_datasets.R Package: RTCGA.CNV Version: 1.10.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 136f7ff44b65e7a2034e913694fbec9a NeedsCompilation: no Title: CNV (Copy-number variation) datasets from The Cancer Genome Atlas Project Description: Package provides CNV (based on Merge snp) datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Retrieving +Data+Using+the+Data+Matrix. Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Przemyslaw Biecek Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.CNV git_branch: RELEASE_3_8 git_last_commit: d268b11 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RTCGA.CNV_1.10.0.tar.gz vignettes: vignettes/RTCGA.CNV/inst/doc/downloading_cnv_datasets.html, vignettes/RTCGA.CNV/inst/doc/frequency_of_cnv_for_mdm3.html vignetteTitles: Using RTCGA to download CNV data as included in RTCGA.CNV, Using RTCGA to estimate ratio of MDM2 duplications hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.CNV/inst/doc/downloading_cnv_datasets.R, vignettes/RTCGA.CNV/inst/doc/frequency_of_cnv_for_mdm3.R Package: RTCGA.methylation Version: 1.10.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 769045e7855bdfbafdb6477a419b72fc NeedsCompilation: no Title: Methylation datasets from The Cancer Genome Atlas Project Description: Package provides methylation (humanmethylation27) datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/DNA+methylation Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Marcin Kosinski [aut, cre], Witold Chodor [aut] Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.methylation git_branch: RELEASE_3_8 git_last_commit: 2e72951 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RTCGA.methylation_1.10.0.tar.gz vignettes: vignettes/RTCGA.methylation/inst/doc/downloading_methylation_datasets.html vignetteTitles: Using RTCGA to download methylation data as included in RTCGA.methylation hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.methylation/inst/doc/downloading_methylation_datasets.R Package: RTCGA.miRNASeq Version: 1.10.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 245f55ab458f95ce93485c2e108a7a81 NeedsCompilation: no Title: miRNASeq datasets from The Cancer Genome Atlas Project Description: Package provides miRNASeq datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/miRNASeq#miRNASeq-DataOverview Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.miRNASeq git_branch: RELEASE_3_8 git_last_commit: 4e9934c git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RTCGA.miRNASeq_1.10.0.tar.gz vignettes: vignettes/RTCGA.miRNASeq/inst/doc/downloading_miRNASeq_datasets.html vignetteTitles: Using RTCGA to download miRNASeq data as included in RTCGA.miRNASeq hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.miRNASeq/inst/doc/downloading_miRNASeq_datasets.R Package: RTCGA.mRNA Version: 1.10.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 7b8d58ede359d36512a5c838c23f0ce2 NeedsCompilation: no Title: mRNA datasets from The Cancer Genome Atlas Project Description: Package provides mRNA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Gene+expression+data Data from 2015-11-01 snapshot. biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.mRNA git_branch: RELEASE_3_8 git_last_commit: 13ee53c git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RTCGA.mRNA_1.10.0.tar.gz vignettes: vignettes/RTCGA.mRNA/inst/doc/downloading_mRNA_datasets.html vignetteTitles: Using RTCGA to download mRNA data as included in RTCGA.mRNA hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.mRNA/inst/doc/downloading_mRNA_datasets.R Package: RTCGA.mutations Version: 20151101.12.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 742f2540bf6458f5b74a670666c5510a NeedsCompilation: no Title: Mutations datasets from The Cancer Genome Atlas Project Description: Package provides mutations datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Mutations data format is explained here https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+(MAF)+Specification. There is extra one column with patients' barcodes. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.mutations git_branch: RELEASE_3_8 git_last_commit: b5537a1 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RTCGA.mutations_20151101.12.0.tar.gz vignettes: vignettes/RTCGA.mutations/inst/doc/downloading_mutations_datasets.html vignetteTitles: Using RTCGA to download mutations data as included in RTCGA.mutations hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.mutations/inst/doc/downloading_mutations_datasets.R Package: RTCGA.PANCAN12 Version: 1.10.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 182d4b50b5b54b364dcec350ee225320 NeedsCompilation: no Title: PanCan 12 from Genome Cancer Browser Description: Package provides clinical, expression, cnv and mutation data from Genome Cancer Browser. biocViews: AnnotationData Author: Przemyslaw Biecek Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.PANCAN12 git_branch: RELEASE_3_8 git_last_commit: ab9a03e git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RTCGA.PANCAN12_1.10.0.tar.gz vignettes: vignettes/RTCGA.PANCAN12/inst/doc/pancan12.html vignetteTitles: Using RTCGA.PANCAN12 to compare time to death hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.PANCAN12/inst/doc/pancan12.R Package: RTCGA.rnaseq Version: 20151101.12.0 Depends: R (>= 3.2.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: bf1eb3e02b137d9ded0089bd3a2c4f38 NeedsCompilation: no Title: Rna-seq datasets from The Cancer Genome Atlas Project Description: Package provides rna-seq datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Rna-seq data format is explained here https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2. Data source is illumina hiseq Level 3 RSEM normalized expression data. Data from 2015-11-01 snapshot. biocViews: Annotation Data Author: Marcin Kosinski Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.rnaseq git_branch: RELEASE_3_8 git_last_commit: 68e13a7 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RTCGA.rnaseq_20151101.12.0.tar.gz vignettes: vignettes/RTCGA.rnaseq/inst/doc/downloading_rnaseq_datasets.html vignetteTitles: Using RTCGA to download RNAseq data as included in RTCGA.rnaseq hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.rnaseq/inst/doc/downloading_rnaseq_datasets.R Package: RTCGA.RPPA Version: 1.10.0 Depends: R (>= 3.3.0), RTCGA Suggests: knitr License: GPL-2 MD5sum: 22570706e120890e3bc21225a910409b NeedsCompilation: no Title: RPPA datasets from The Cancer Genome Atlas Project Description: Package provides RPPA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Protein+Array +Data+Format+Specification?src=search biocViews: AnnotationData Author: Witold Chodor Maintainer: Marcin Kosinski VignetteBuilder: knitr BugReports: https://github.com/RTCGA/RTCGA/issues git_url: https://git.bioconductor.org/packages/RTCGA.RPPA git_branch: RELEASE_3_8 git_last_commit: f072a7e git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RTCGA.RPPA_1.10.0.tar.gz vignettes: vignettes/RTCGA.RPPA/inst/doc/downloading_RPPA_datasets.html vignetteTitles: Using RTCGA to download RPPA data as included in RTCGA.RPPA hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RTCGA.RPPA/inst/doc/downloading_RPPA_datasets.R Package: RUVnormalizeData Version: 1.2.0 Depends: R (>= 2.10.0), Biobase License: GPL-3 MD5sum: 8c3859b5bf555e74be9d480d3ba9539b NeedsCompilation: no Title: Gender data for the RUVnormalize package Description: Microarray gene expression data from the study of Vawter et al., 2004. biocViews: MicroarrayData Author: Laurent Jacob Maintainer: Laurent Jacob git_url: https://git.bioconductor.org/packages/RUVnormalizeData git_branch: RELEASE_3_8 git_last_commit: 26bb6a4 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/RUVnormalizeData_1.2.0.tar.gz vignettes: vignettes/RUVnormalizeData/inst/doc/RUVnormalizeData.pdf vignetteTitles: RUVnormalizeData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/RUVnormalizeData/inst/doc/RUVnormalizeData.R Package: sampleClassifierData Version: 1.6.0 Depends: R (>= 3.4), SummarizedExperiment Suggests: BiocStyle License: Artistic-2.0 MD5sum: 82f2071bfa8b19d3909760e813dfa760 NeedsCompilation: no Title: Pre-processed data for use with the sampleClassifier package Description: This package contains two microarray and two RNA-seq datasets that have been preprocessed for use with the sampleClassifier package. The RNA-seq data are derived from Fagerberg et al. (2014) and the Illumina Body Map 2.0 data. The microarray data are derived from Roth et al. (2006) and Ge et al. (2005). biocViews: ExperimentData, ExpressionData, MicroarrayData, SequencingData, RNASeqData, ArrayExpress Author: Khadija El Amrani Maintainer: Khadija El Amrani git_url: https://git.bioconductor.org/packages/sampleClassifierData git_branch: RELEASE_3_8 git_last_commit: 1ca7a04 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/sampleClassifierData_1.6.0.tar.gz vignettes: vignettes/sampleClassifierData/inst/doc/sampleClassifierData.pdf vignetteTitles: sampleClassifierData Introduction hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/sampleClassifierData/inst/doc/sampleClassifierData.R Package: SCLCBam Version: 1.14.0 Depends: R(>= 2.10) Suggests: BiocStyle License: GPL-2 MD5sum: c9a6578784fd79568802485be95841f5 NeedsCompilation: no Title: Sequence data from chromosome 4 of a small-cell lung tumor Description: Whole-exome sequencing data from a murine small-cell lung tumor; only contains data of chromosome 4. biocViews: SequencingData, LungCancerData Author: Thomas Kuilman Maintainer: Oscar Krijgsman git_url: https://git.bioconductor.org/packages/SCLCBam git_branch: RELEASE_3_8 git_last_commit: f164edc git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/SCLCBam_1.14.0.tar.gz vignettes: vignettes/SCLCBam/inst/doc/SCLCBam.pdf vignetteTitles: SCLCBam hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SCLCBam/inst/doc/SCLCBam.R Package: scRNAseq Version: 1.8.0 Depends: R (>= 3.3), SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown License: CC0 MD5sum: fe0e002e82591d592eefbf687d46dc56 NeedsCompilation: no Title: A Collection of Public Single-Cell RNA-Seq Datasets Description: Gene-level read counts of three public scRNA-seq datasets. See vignette for details. biocViews: ExperimentData, ExpressionData, SequencingData, RNASeqData Author: Davide Risso [aut, cre, cph], Michael Cole [aut] Maintainer: Davide Risso VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/scRNAseq git_branch: RELEASE_3_8 git_last_commit: f901eb5 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/scRNAseq_1.8.0.tar.gz vignettes: vignettes/scRNAseq/inst/doc/scRNAseq.html vignetteTitles: scRNAseq hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/scRNAseq/inst/doc/scRNAseq.R Package: seq2pathway.data Version: 1.14.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: ca93e7796ded3a3f92e56f3539a39291 NeedsCompilation: no Title: data set for R package seq2pathway Description: Supporting data for the seq2patheway package. Includes modified gene sets from MsigDB and org.Hs.eg.db; gene locus definitions from GENCODE project. biocViews: ExperimentData Author: Bin Wang Maintainer: Xinan Holly Yang git_url: https://git.bioconductor.org/packages/seq2pathway.data git_branch: RELEASE_3_8 git_last_commit: 452f905 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/seq2pathway.data_1.14.0.tar.gz vignettes: vignettes/seq2pathway.data/inst/doc/seq2pathway.data.pdf vignetteTitles: An R data package for sequence hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: seqc Version: 1.16.0 Depends: R (>= 2.10) Imports: utils, Biobase License: GPL-3 MD5sum: 376dcb3255c528683e1c4be13ee3c5c5 NeedsCompilation: no Title: RNA-seq data generated from SEQC (MAQC-III) study Description: The SEQC/MAQC-III Consortium has produced benchmark RNA-seq data for the assessment of RNA sequencing technologies and data analysis methods (Nat Biotechnol, 2014). Billions of sequence reads have been generated from ten different sequencing sites. This package contains the summarized read count data for ~2000 sequencing libraries. It also includes all the exon-exon junctions discovered from the study. TaqMan RT-PCR data for ~1000 genes and ERCC spike-in sequence data are included in this package as well. biocViews: ExperimentData, RNASeqData, qPCRData, SequencingData Author: Yang Liao and Wei Shi with contributions from Gordon K Smyth and Steve Lianoglou. Maintainer: Yang Liao and Wei Shi URL: http://bioconductor.org/packages/release/data/experiment/html/seqc.html git_url: https://git.bioconductor.org/packages/seqc git_branch: RELEASE_3_8 git_last_commit: 104acf8 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/seqc_1.16.0.tar.gz vignettes: vignettes/seqc/inst/doc/seqc.pdf vignetteTitles: SEQC Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/seqc/inst/doc/seqc.R Package: seqCNA.annot Version: 1.18.0 Depends: R (>= 2.10) License: GPL-3 MD5sum: a83620fb92adae77c4f61769854844a6 NeedsCompilation: no Title: Annotation for the copy number analysis of deep sequencing cancer data with seqCNA Description: Provides annotation on GC content, mappability and genomic features for various genomes biocViews: Genome, CopyNumberVariationData Author: David Mosen-Ansorena Maintainer: David Mosen-Ansorena git_url: https://git.bioconductor.org/packages/seqCNA.annot git_branch: RELEASE_3_8 git_last_commit: 4455fbb git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/seqCNA.annot_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: serumStimulation Version: 1.18.0 Depends: R (>= 2.10) License: GPL (>= 2) MD5sum: 702b8e053465a52491f19961654f3dc0 NeedsCompilation: no Title: serumStimulation is a data package which is used by examples in package pcaGoPromoter Description: Contains 13 micro array data results from a serum stimulation experiment biocViews: ExperimentData, MicroarrayData Author: Morten Hansen Maintainer: Morten Hansen, git_url: https://git.bioconductor.org/packages/serumStimulation git_branch: RELEASE_3_8 git_last_commit: 7bec851 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/serumStimulation_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: sesameData Version: 1.0.0 Depends: R (>= 3.5), ExperimentHub, AnnotationHub Imports: utils, curl Suggests: GenomicRanges, BiocGenerics, sesame, testthat, knitr License: Artistic-2.0 MD5sum: dc24068fe6bdc6ef7e62c89c38b8d949 NeedsCompilation: no Title: Supporting Data for SeSAMe Package Description: Provides supporting annotation and test data for SeSAMe package. biocViews: ExperimentData, MicroarrayData, Genome Author: Wanding Zhou [aut, cre], Hui Shen [aut], Timothy Triche [ctb] Maintainer: Wanding Zhou VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/sesameData git_branch: RELEASE_3_8 git_last_commit: 559ff17 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/sesameData_1.0.0.tar.gz vignettes: vignettes/sesameData/inst/doc/sesameData.html vignetteTitles: sesameData User Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/sesameData/inst/doc/sesameData.R Package: seventyGeneData Version: 1.18.0 Depends: R (>= 2.13.0) Suggests: Biobase, gdata, limma, breastCancerNKI License: Artistic-2.0 MD5sum: f5232714137c1bb3d94e058b651ab041 NeedsCompilation: no Title: ExpressionSets from the van't Veer and Van de Vijver breast cancer studies Description: Gene expression data for the two breast cancer cohorts published by van't Veer and Van de Vijver in 2002 biocViews: ExperimentData, CancerData, BreastCancerData, MicroarrayData Author: Luigi Marchionni Maintainer: Luigi Marchionni URL: http://luigimarchionni.org/breastTSP.html git_url: https://git.bioconductor.org/packages/seventyGeneData git_branch: RELEASE_3_8 git_last_commit: 2333119 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/seventyGeneData_1.18.0.tar.gz vignettes: vignettes/seventyGeneData/inst/doc/seventyGeneData.pdf vignetteTitles: Working with the seventyGeneData package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/seventyGeneData/inst/doc/seventyGeneData.R Package: shinyMethylData Version: 1.2.0 Depends: R (>= 3.0.0) License: Artistic-2.0 MD5sum: c7cfcef8e0c7dff18eb34609812ea3b4 NeedsCompilation: no Title: Example dataset of input data for shinyMethyl Description: Extracted data from 369 TCGA Head and Neck Cancer DNA methylation samples. The extracted data serve as an example dataset for the package shinyMethyl. Original samples are from 450k methylation arrays, and were obtained from The Cancer Genome Atlas (TCGA). 310 samples are from tumor, 50 are matched normals and 9 are technical replicates of a control cell line. biocViews: Genome, CancerData Author: Jean-Philippe Fortin [cre, aut], Kasper Daniel Hansen [aut] Maintainer: Jean-Philippe Fortin git_url: https://git.bioconductor.org/packages/shinyMethylData git_branch: RELEASE_3_8 git_last_commit: 805b182 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/shinyMethylData_1.2.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: simpIntLists Version: 1.18.0 License: GPL (>= 2) MD5sum: 9276ea6e949af976d59fe3317bb0e208 NeedsCompilation: no Title: The package contains BioGRID interactions for various organisms in a simple format Description: The package contains BioGRID interactions for arabidopsis(thale cress), c.elegans, fruit fly, human, mouse, yeast( budding yeast ) and S.pombe (fission yeast) . Entrez ids, official names and unique ids can be used to find proteins. The format of interactions are lists. For each gene/protein, there is an entry in the list with "name" containing name of the gene/protein and "interactors" containing the list of genes/proteins interacting with it. biocViews: ExperimentData, Arabidopsis_thaliana_Data Author: Kircicegi Korkmaz, Volkan Atalay, Rengul Cetin-Atalay Maintainer: Kircicegi Korkmaz git_url: https://git.bioconductor.org/packages/simpIntLists git_branch: RELEASE_3_8 git_last_commit: 8ea13e3 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/simpIntLists_1.18.0.tar.gz vignettes: vignettes/simpIntLists/inst/doc/simpIntLists.pdf vignetteTitles: simpIntLists hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/simpIntLists/inst/doc/simpIntLists.R Package: Single.mTEC.Transcriptomes Version: 1.10.0 Suggests: DESeq2, GenomicRanges, GenomicFeatures, genefilter, statmod, gdata, RColorBrewer, ggplot2, gplots, cluster, clue, grid, gridExtra, ggbio, Gviz, geneplotter, matrixStats, pheatmap, BiocStyle, knitr License: LGPL MD5sum: b56327144804cf3af178a5750b028707 NeedsCompilation: no Title: Single Cell Transcriptome Data and Analysis of Mouse mTEC cells Description: This data package contains the code used to analyse the single-cell RNA-seq and the bulk ATAC-seq data from the manuscript titled: Single-cell transcriptome analysis reveals coordinated ectopic-gene expression patterns in medullary thymic epithelial cells. This paper was published in Nature Immunology 16,933-941(2015). The data objects provided in this package has been pre-processed: the raw data files can be downloaded from ArrayExpress under the accession identifiers E-MTAB-3346 and E-MTAB-3624. The vignette of this data package provides a documented and reproducible workflow that includes the code that was used to generate each statistic and figure from the manuscript. biocViews: ExperimentData Author: Alejandro Reyes Maintainer: Alejandro Reyes VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/Single.mTEC.Transcriptomes git_branch: RELEASE_3_8 git_last_commit: 113b090 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/Single.mTEC.Transcriptomes_1.10.0.tar.gz vignettes: vignettes/Single.mTEC.Transcriptomes/inst/doc/mTECs.pdf vignetteTitles: Analysis of single cell mTEC data. hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/Single.mTEC.Transcriptomes/inst/doc/mTECs.R Package: SNAData Version: 1.28.0 Depends: R (>= 2.4.0), graph Suggests: Rgraphviz License: LGPL MD5sum: f7bb6899038f7adb395147bf50e203c2 NeedsCompilation: no Title: Social Networks Analysis Data Examples Description: Data from Wasserman & Faust (1999) "Social Network Analysis" biocViews: ExperimentData Author: Denise Scholtens Maintainer: Denise Scholtens git_url: https://git.bioconductor.org/packages/SNAData git_branch: RELEASE_3_8 git_last_commit: c874d02 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/SNAData_1.28.0.tar.gz vignettes: vignettes/SNAData/inst/doc/SNAData.pdf vignetteTitles: SNAData hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SNAData/inst/doc/SNAData.R Package: SNAGEEdata Version: 1.18.0 Depends: R (>= 2.6.0) Suggests: ALL, hgu95av2.db, SNAGEE License: Artistic-2.0 MD5sum: 4b880530c37c0d088386211817f6f07b NeedsCompilation: no Title: SNAGEE data Description: SNAGEE data - gene list and correlation matrix biocViews: MicroarrayData Author: David Venet Maintainer: David Venet URL: http://fleming.ulb.ac.be/SNAGEE git_url: https://git.bioconductor.org/packages/SNAGEEdata git_branch: RELEASE_3_8 git_last_commit: a317e70 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/SNAGEEdata_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SNPhoodData Version: 1.12.0 Depends: R (>= 3.2) Suggests: BiocStyle,knitr,rmarkdown License: LGPL (>= 3) MD5sum: 5036868e32ed51fd9ffa32bfeb992051 NeedsCompilation: no Title: Additional and more complex example data for the SNPhood package Description: This companion package for SNPhood provides some example datasets of a larger size than allowed for the SNPhood package. They include full and real-world examples for performing analyses with the SNPhood package. biocViews: ExperimentData Author: Christian Arnold, Judith Zaugg Maintainer: Christian Arnold VignetteBuilder: knitr BugReports: christian.arnold@embl.de git_url: https://git.bioconductor.org/packages/SNPhoodData git_branch: RELEASE_3_8 git_last_commit: b72d66f git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/SNPhoodData_1.12.0.tar.gz vignettes: vignettes/SNPhoodData/inst/doc/SNPhoodData.html vignetteTitles: The *SNPhoodData* package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: SomatiCAData Version: 1.20.0 Depends: R (>= 2.14) License: Artistic-2.0 MD5sum: 1b0e5b1b155926d58365e3c7daf478a1 NeedsCompilation: no Title: An example cancer whole genome sequencing data for the SomatiCA package Description: An example cancer whole genome sequencing data for the SomatiCA package biocViews: ExperimentData, Genome, CancerData, SequencingData Author: Mengjie Chen Maintainer: Mengjie Chen git_url: https://git.bioconductor.org/packages/SomatiCAData git_branch: RELEASE_3_8 git_last_commit: e4757b5 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/SomatiCAData_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SomaticCancerAlterations Version: 1.18.0 Depends: R (>= 3.0.0) Imports: GenomicRanges, exomeCopy, stringr, IRanges, S4Vectors Suggests: testthat, ggbio, ggplot2, knitr License: GPL-3 MD5sum: 75e6cde71f730fa57516677022042573 NeedsCompilation: no Title: Somatic Cancer Alterations Description: Collection of somatic cancer alteration datasets biocViews: ExperimentData, Genome, CancerData, Project1000genomes, NCI Author: Julian Gehring (EMBL Heidelberg) Maintainer: Julian Gehring VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/SomaticCancerAlterations git_branch: RELEASE_3_8 git_last_commit: 5835b1e git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/SomaticCancerAlterations_1.18.0.tar.gz vignettes: vignettes/SomaticCancerAlterations/inst/doc/SomaticCancerAlterations-html.html vignetteTitles: SomaticCancerAlterations - HTML hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SomaticCancerAlterations/inst/doc/SomaticCancerAlterations-html.R Package: SpikeIn Version: 1.24.0 Depends: R (>= 1.6), affy (>= 1.23.4) License: Artistic-2.0 MD5sum: c9e1bcb003e2a9789fd4f48e5c98430a NeedsCompilation: no Title: Affymetrix Spike-In Experiment Data Description: Contains the HGU133 and HGU95 spikein experiment data. biocViews: ExperimentData, MicroarrayData Author: Rafael Irizarry Maintainer: Rafael A. Irizarry git_url: https://git.bioconductor.org/packages/SpikeIn git_branch: RELEASE_3_8 git_last_commit: b0d9fd6 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/SpikeIn_1.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SpikeInSubset Version: 1.22.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5), affy (>= 1.23.4) License: LGPL MD5sum: adc9c4e0f5abe8c9b0c789a3698e5f5a NeedsCompilation: no Title: Part of Affymetrix's Spike-In Experiment Data Description: Includes probe-level and expression data for the HGU133 and HGU95 spike-in experiments biocViews: ExperimentData, MicroarrayData Author: Rafael Irizarry and Zhijin Wu Maintainer: Rafael A. Irizarry git_url: https://git.bioconductor.org/packages/SpikeInSubset git_branch: RELEASE_3_8 git_last_commit: ced9561 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/SpikeInSubset_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: stemHypoxia Version: 1.18.0 Depends: R (>= 2.14.1) License: GPL (>=2) MD5sum: 1fb8f0225f86414a4c7870ce3c2969bd NeedsCompilation: no Title: Differentiation of Human Embryonic Stem Cells under Hypoxia gene expression dataset by Prado-Lopez et al. (2010) Description: Expression profiling using microarray technology to prove if 'Hypoxia Promotes Efficient Differentiation of Human Embryonic Stem Cells to Functional Endothelium' by Prado-Lopez et al. (2010) Stem Cells 28:407-418. Full data available at Gene Expression Omnibus series GSE37761. biocViews: ExperimentData, Tissue, StemCell, Homo_sapiens_Data, CancerData, MicroarrayData, TissueMicroarrayData, GEO Author: Cristobal Fresno and Elmer A. Fernandez Maintainer: Cristobal Fresno URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37761, http://onlinelibrary.wiley.com/doi/10.1002/stem.295/abstract git_url: https://git.bioconductor.org/packages/stemHypoxia git_branch: RELEASE_3_8 git_last_commit: 30c9c81 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/stemHypoxia_1.18.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: stjudem Version: 1.22.0 Depends: R (>= 2.10), utils License: LGPL (>= 2) MD5sum: 73c7d2523afdebc972054b62080d37c7 NeedsCompilation: no Title: Microarray Data from Yeoh et al. in MACAT format Description: This is a microarray data set on acute lymphoblastic leukemia, published in 2002 (Yeoh et al.Cancer Cell 2002). The experiments were conducted in the St.Jude Children's Research Hospital, Memphis, Tenessee, USA. The raw data was preprocessed by variance stabilizing normalization (Huber et al.) on probe and subsequent summarization of probe expression values into probe set expression values using median polish. biocViews: ExperimentData, CancerData, LeukemiaCancerData, MicroarrayData, ChipOnChipData Author: Benjamin Georgi, Matthias Heinig, Sebastian Schmeier, Joern Toedling Maintainer: Joern Toedling git_url: https://git.bioconductor.org/packages/stjudem git_branch: RELEASE_3_8 git_last_commit: d7f70a5 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/stjudem_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SVM2CRMdata Version: 1.14.0 Depends: R(>= 3.2.0) License: LGPL (>= 2) MD5sum: 67239ac74ee3b881f2070be62472e43b NeedsCompilation: no Title: An example dataset for use with the SVM2CRM package Description: An example dataset for use with the SVM2CRM package. biocViews: ExperimentData, ChIPSeq, HistoneModification, Preprocessing, DataImport Author: Guidantonio Malagoli Tagliazucchi Maintainer: Guidantonio Malagoli Tagliazucchi git_url: https://git.bioconductor.org/packages/SVM2CRMdata git_branch: RELEASE_3_8 git_last_commit: b2e4b82 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/SVM2CRMdata_1.14.0.tar.gz vignettes: vignettes/SVM2CRMdata/inst/doc/SVM2CRMdata.pdf vignetteTitles: The \Rpackage{SVM2CRMdata} Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/SVM2CRMdata/inst/doc/SVM2CRMdata.R Package: synapterdata Version: 1.20.0 Depends: R (>= 2.10), synapter (>= 1.99.2) Imports: utils License: GPL-2 MD5sum: a13fa15f1bcbfa6495cce58c3d439a0e NeedsCompilation: no Title: Data accompanying the synapter package Description: Data independant acquisition of UPS1 protein mix in an E. coli background obtained on a Waters Synapt G2 instrument. biocViews: ExperimentData, MassSpectrometryData Author: Laurent Gatto, Sebastian Gibb and Pavel V. Shliaha Maintainer: Laurent Gatto git_url: https://git.bioconductor.org/packages/synapterdata git_branch: RELEASE_3_8 git_last_commit: 5b25b44 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/synapterdata_1.20.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RforProteomics Package: systemPipeRdata Version: 1.10.0 Depends: methods Imports: BiocGenerics Suggests: RUnit, BiocStyle, knitr, rmarkdown, systemPipeR License: Artistic-2.0 MD5sum: ba76fafb811f95cbaba27ef3953e55b3 NeedsCompilation: no Title: systemPipeRdata: NGS workflow templates and sample data Description: systemPipeRdata is a helper package to generate with a single command NGS workflow templates that are intended to be used by its parent package systemPipeR. The latter is an environment for building end-to-end analysis pipelines with automated report generation for next generation sequence (NGS) applications such as RNA-Seq, RIBO-Seq, ChIP-Seq, VAR-Seq and many others. Detailed examples for using systemPipeRdata are given in systemPipeR's overview vignette. biocViews: Genetics, Infrastructure, DataImport, Sequencing, RNASeq, ChIPSeq, MethylSeq, SNP, GeneExpression, Coverage, GeneSetEnrichment, Alignment, QualityControl Author: Thomas Girke Maintainer: Thomas Girke URL: https://github.com/tgirke/systemPipeRdata VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/systemPipeRdata git_branch: RELEASE_3_8 git_last_commit: 83e154f git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/systemPipeRdata_1.10.0.tar.gz vignettes: vignettes/systemPipeRdata/inst/doc/systemPipeRdata.html vignetteTitles: Overview Vignette hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/systemPipeRdata/inst/doc/systemPipeRdata.R Package: TabulaMurisData Version: 1.0.0 Depends: R (>= 3.5) Imports: ExperimentHub, utils Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran, scater, iSEE, testthat License: MIT + file LICENSE MD5sum: 1b4f8f16754586ce5866ac90de5ac0a4 NeedsCompilation: no Title: 10x And SmartSeq2 Data From The Tabula Muris Consortium Description: Access to processed 10x (droplet) and SmartSeq2 (on FACS-sorted cells) single-cell RNA-seq data from the Tabula Muris consortium (http://tabula-muris.ds.czbiohub.org/). biocViews: SingleCellData, ExperimentData, RNASeqData Author: Charlotte Soneson Maintainer: Charlotte Soneson VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TabulaMurisData git_branch: RELEASE_3_8 git_last_commit: 2b24bfe git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/TabulaMurisData_1.0.0.tar.gz vignettes: vignettes/TabulaMurisData/inst/doc/TabulaMurisData.html vignetteTitles: Tabula Muris data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Rfiles: vignettes/TabulaMurisData/inst/doc/TabulaMurisData.R Package: TargetScoreData Version: 1.18.0 Suggests: TargetScore, gplots License: GPL-2 MD5sum: fd759e7712396b9f33e3ad26502a7762 NeedsCompilation: no Title: TargetScoreData Description: Precompiled and processed miRNA-overexpression fold-changes from 84 Gene Expression Omnibus (GEO) series corresponding to 6 platforms, 77 human cells or tissues, and 113 distinct miRNAs. Accompanied with the data, we also included in this package the sequence feature scores from TargetScanHuman 6.1 including the context+ score and the probabilities of conserved targeting for each miRNA-mRNA interaction. Thus, the user can use these static sequence-based scores together with user-supplied tissue/cell-specific fold-change due to miRNA overexpression to predict miRNA targets using the package TargetScore (download separately) biocViews: ExperimentData, RNASeqData, miRNAData Author: Yue Li Maintainer: Yue Li git_url: https://git.bioconductor.org/packages/TargetScoreData git_branch: RELEASE_3_8 git_last_commit: cf86542 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/TargetScoreData_1.18.0.tar.gz vignettes: vignettes/TargetScoreData/inst/doc/TargetScoreData.pdf vignetteTitles: Processed human microRNA-overexpression data from GEO,, and sequence information from TargetScan,, and targetScore from TargetScore hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TargetScoreData/inst/doc/TargetScoreData.R Package: TargetSearchData Version: 1.20.0 License: GPL (>= 2) MD5sum: f22282a97204579a09ebe055434811b6 NeedsCompilation: no Title: Example GC-MS data for TargetSearch Package Description: This package provides example GC-MS data for TargetSearch Package. biocViews: ExperimentData, Escherichia_coli_Data Author: Alvaro Cuadros-Inostroza, Henning Redestig, Matt Hannah Maintainer: Alvaro Cuadros-Inostroza git_url: https://git.bioconductor.org/packages/TargetSearchData git_branch: RELEASE_3_8 git_last_commit: 04aacc0 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/TargetSearchData_1.20.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: TBX20BamSubset Version: 1.18.0 Depends: Rsamtools (>= 1.9.8) Imports: xtable License: LGPL MD5sum: 6b04fa46c1d81b4965a59ac7a3cbde37 NeedsCompilation: no Title: Subset of BAM files from the "TBX20" experiment Description: Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. A subset of the RNA-Seq data. biocViews: ExperimentData, SequencingData, RNASeqData Author: D. Bindreither Maintainer: D. Bindreither git_url: https://git.bioconductor.org/packages/TBX20BamSubset git_branch: RELEASE_3_8 git_last_commit: e2ed285 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/TBX20BamSubset_1.18.0.tar.gz vignettes: vignettes/TBX20BamSubset/inst/doc/TBX20BamSubset.pdf vignetteTitles: TBX20 RNA-Seq data subset hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TBX20BamSubset/inst/doc/TBX20BamSubset.R Package: TCGAbiolinksGUI.data Version: 1.2.0 Depends: R (>= 3.5.0) Suggests: BiocStyle, knitr, readr, readxl, dplyr, caret, randomForest, doMC, e1071, DT License: GPL-3 MD5sum: b3eeb50a569df22c6434bd7ff06fa460 NeedsCompilation: no Title: Data for the TCGAbiolinksGUI package Description: Supporting data for the TCGAbiolinksGUI package. It includes the following objects: glioma.gcimp.model, glioma.idhwt.model glioma.idhmut.model,glioma.idh.mode, probes2rm, maf.tumor,GDCdisease. biocViews: AssayDomainData, TechnologyData, OrganismData Author: Tiago Chedraoui Silva Maintainer: Tiago Chedraoui Silva URL: https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data VignetteBuilder: knitr BugReports: https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data/issues git_url: https://git.bioconductor.org/packages/TCGAbiolinksGUI.data git_branch: RELEASE_3_8 git_last_commit: c6fa401 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/TCGAbiolinksGUI.data_1.2.0.tar.gz vignettes: vignettes/TCGAbiolinksGUI.data/inst/doc/vignettes.html vignetteTitles: Supporting data for the TCGAbiolinksGUI package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TCGAbiolinksGUI.data/inst/doc/vignettes.R Package: TCGAcrcmiRNA Version: 1.2.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 75d707e6d1c7feb9d4dfd5d6e62f9c3a NeedsCompilation: no Title: TCGA CRC 450 miRNA dataset Description: colorectal cancer miRNA profile provided by TCGA biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/TCGAcrcmiRNA git_branch: RELEASE_3_8 git_last_commit: 6b56475 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/TCGAcrcmiRNA_1.2.0.tar.gz vignettes: vignettes/TCGAcrcmiRNA/inst/doc/TcgaCrcVignette.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TCGAcrcmiRNA/inst/doc/TcgaCrcVignette.R Package: TCGAcrcmRNA Version: 1.2.0 Depends: R (>= 3.0), Biobase License: GPL-2 MD5sum: 4d499e122eee3f40019b944889a63fe4 NeedsCompilation: no Title: TCGA CRC 450 mRNA dataset Description: colorectal cancer mRNA profile provided by TCGA biocViews: ExperimentData, CancerData Author: Claudio Isella Maintainer: Claudio Isella git_url: https://git.bioconductor.org/packages/TCGAcrcmRNA git_branch: RELEASE_3_8 git_last_commit: 3cbd939 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/TCGAcrcmRNA_1.2.0.tar.gz vignettes: vignettes/TCGAcrcmRNA/inst/doc/TcgaCrcVignette.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TCGAcrcmRNA/inst/doc/TcgaCrcVignette.R Package: TCGAMethylation450k Version: 1.18.0 License: GPL-2 MD5sum: 71ce8ebbc5ddcf78fe3c6995ee2c64f5 NeedsCompilation: no Title: The Cancer Genome Atlas Illumina 450k methylation example data Description: The Cancer Genome Atlas (TCGA) is applying genomics technologies to over 20 different types of cancer. This package contains a small set of 450k array data in idat format. biocViews: Genome, CancerData, MethylationArrayData Author: Sean Davis Maintainer: Sean Davis git_url: https://git.bioconductor.org/packages/TCGAMethylation450k git_branch: RELEASE_3_8 git_last_commit: 99c7542 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/TCGAMethylation450k_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: tcgaWGBSData.hg19 Version: 1.0.0 Depends: R (>= 3.5.0), ExperimentHub Imports: bsseq, knitr License: GPL-2 MD5sum: e614d37504300366b89e08aae9d82902 NeedsCompilation: no Title: Data Description: Data package for WGBS Data in TCGA. Data is stored as SummarizedExperiment Format. See vignette on how to extract the data and perform differential methylation analysis. biocViews: Genome, SequencingData, ExperimentData, Homo_sapiens_Data, CancerData Author: Divy Kangeyan Maintainer: Divy Kangeyan VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tcgaWGBSData.hg19 git_branch: RELEASE_3_8 git_last_commit: 3ac4253 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/tcgaWGBSData.hg19_1.0.0.tar.gz vignettes: vignettes/tcgaWGBSData.hg19/inst/doc/tcgaWGBSData.hg19.html vignetteTitles: Vignette Title hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tcgaWGBSData.hg19/inst/doc/tcgaWGBSData.hg19.R Package: TCGAWorkflowData Version: 1.6.0 Depends: R (>= 3.4.0) Imports: SummarizedExperiment Suggests: knitr, rmarkdown, pander, testthat License: GPL-3 MD5sum: 3c147bc7cf5ba811e359f12db8e7b42a NeedsCompilation: no Title: Data for TCGA Workflow Description: This experimental data package contains 11 data sets necessary to follow the "TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages". biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData, CancerData Author: Tiago Chedraoui Silva Maintainer: Tiago Chedraoui Silva URL: https://f1000research.com/articles/5-1542/v2 VignetteBuilder: knitr BugReports: https://github.com/BioinformaticsFMRP/TCGAWorkflow/issues git_url: https://git.bioconductor.org/packages/TCGAWorkflowData git_branch: RELEASE_3_8 git_last_commit: 7a8154d git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/TCGAWorkflowData_1.6.0.tar.gz vignettes: vignettes/TCGAWorkflowData/inst/doc/TCGAWorkflowData.html vignetteTitles: 'Example data for TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages' hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TCGAWorkflowData/inst/doc/TCGAWorkflowData.R Package: TENxBrainData Version: 1.2.0 Depends: SingleCellExperiment, HDF5Array Imports: AnnotationHub (>= 2.9.22), ExperimentHub Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel, data.table License: CC BY 4.0 MD5sum: 8f4e0317f3db09ed897fc30484e48115 NeedsCompilation: no Title: Data from the 10X 1.3 Million Brain Cell Study Description: Single-cell RNA-seq data for 1.3 million brain cells from E18 mice, generated by 10X Genomics. biocViews: SequencingData, RNASeqData, ExpressionData, SingleCellData Author: Aaron Lun [aut], Martin Morgan [aut], Bioconductor Package Maintainer [cre] Maintainer: Bioconductor Package Maintainer VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TENxBrainData git_branch: RELEASE_3_8 git_last_commit: d9c1e61 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/TENxBrainData_1.2.0.tar.gz vignettes: vignettes/TENxBrainData/inst/doc/TENxBrainData.html vignetteTitles: Exploring the 1.3 million brain cell scRNA-seq data from 10X Genomics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TENxBrainData/inst/doc/TENxBrainData.R Package: TENxPBMCData Version: 1.0.0 Depends: SingleCellExperiment, HDF5Array Imports: AnnotationHub, ExperimentHub Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel License: CC BY 4.0 MD5sum: 51a0e7d6a73413d7275fe368de4471bf NeedsCompilation: no Title: PBMC data from 10X Genomics Description: Single-cell RNA-seq data for on PBMC cells, generated by 10X Genomics. biocViews: SequencingData, RNASeqData, ExpressionData, SingleCellData Author: Kasper D. Hansen [aut], Davide Risso [aut], Stephanie Hicks [aut, cre] Maintainer: Stephanie Hicks VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TENxPBMCData git_branch: RELEASE_3_8 git_last_commit: 6df96d9 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/TENxPBMCData_1.0.0.tar.gz vignettes: vignettes/TENxPBMCData/inst/doc/TENxPBMCData.html vignetteTitles: Obtaining scRNA-seq data on PBMCs from 10X Genomics hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TENxPBMCData/inst/doc/TENxPBMCData.R Package: TimerQuant Version: 1.12.0 Depends: shiny Imports: ggplot2, grid, gridExtra, deSolve, dplyr, locfit Suggests: BiocStyle, reshape2, knitr, shinyBS License: Artistic-2.0 MD5sum: 6b6d3bd75b7a51740ede49802179a8e3 NeedsCompilation: no Title: Timer Quantification Description: Supplementary Data package for tandem timer methods paper by Barry et al. (2015) including TimerQuant shiny applications. biocViews: ExperimentData, Danio_rerio_Data, HighThroughputImagingData, Tissue Author: Joseph Barry Maintainer: Joseph Barry VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/TimerQuant git_branch: RELEASE_3_8 git_last_commit: 0c52872 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/TimerQuant_1.12.0.tar.gz vignettes: vignettes/TimerQuant/inst/doc/genPaperFigures.pdf, vignettes/TimerQuant/inst/doc/mathematicalDerivations.pdf vignetteTitles: Supplementary Methods - automatic generation of paper figures, Supplementary Methods - mathematical derivations hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/TimerQuant/inst/doc/genPaperFigures.R, vignettes/TimerQuant/inst/doc/mathematicalDerivations.R Package: tinesath1cdf Version: 1.20.0 License: Artistic-2.0 MD5sum: 95e256c032576c0eb2eb21d479ae5e68 NeedsCompilation: no Title: tinesath1cdf Description: A package containing an environment represeting the newcdf/tinesATH1.cdf.cdf file. biocViews: Arabidopsis_thaliana_Data, ChipOnChipData Author: Tine Casneuf Maintainer: Tine Casneuf git_url: https://git.bioconductor.org/packages/tinesath1cdf git_branch: RELEASE_3_8 git_last_commit: 8860be7 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/tinesath1cdf_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: XhybCasneuf Package: tinesath1probe Version: 1.20.0 Depends: R (>= 1.6), AnnotationDbi (>= 1.11.9) License: LGPL MD5sum: 8c43dc2ede1e42e22779059c5a6925f0 NeedsCompilation: no Title: Probe sequence data for microarrays of type tinesath1 Description: This package was automatically created by package matchprobes version 1.4.0. The probe sequence data was obtained from http://www.affymetrix.com. biocViews: Arabidopsis_thaliana_Data, SequencingData, MicroarrayData Author: The Bioconductor Project www.bioconductor.org Maintainer: Tine Casneuf git_url: https://git.bioconductor.org/packages/tinesath1probe git_branch: RELEASE_3_8 git_last_commit: 12b7e7c git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/tinesath1probe_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: tissueTreg Version: 1.2.0 Depends: R (>= 3.5) Suggests: BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq, SummarizedExperiment License: GPL (>= 2) MD5sum: 36f57ef9bb4affda62e679798e2fca58 NeedsCompilation: no Title: TWGBS and RNA-seq data from tissue T regulatory cells from mice Description: The package provides ready to use epigenomes (obtained from TWGBS) and transcriptomes (RNA-seq) from various tissues as obtained in the study (Delacher and Imbusch 2017, PMID: 28783152). Regulatory T cells (Treg cells) perform two distinct functions: they maintain self-tolerance, and they support organ homeostasis by differentiating into specialized tissue Treg cells. The underlying dataset characterises the epigenetic and transcriptomic modifications for specialized tissue Treg cells. biocViews: ExperimentData, Tissue, Mus_musculus_Data, SequencingData, RNASeqData Author: Charles Imbusch [aut, cre], Michael Delacher [aut], Markus Feuerer [aut], Benedikt Brors [aut] Maintainer: Charles Imbusch URL: https://github.com/cimbusch/tissueTreg VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tissueTreg git_branch: RELEASE_3_8 git_last_commit: 9599840 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/tissueTreg_1.2.0.tar.gz vignettes: vignettes/tissueTreg/inst/doc/tissueTreg.html vignetteTitles: tissueTreg hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tissueTreg/inst/doc/tissueTreg.R Package: tofsimsData Version: 1.10.0 Depends: R (>= 3.2.0) Suggests: knitr, rmarkdown, tools License: GPL-3 MD5sum: 545622a01ba2067b1cf805f07367a83a NeedsCompilation: no Title: Import, process and analysis of ToF-SIMS imaging data Description: This packages contains data to be used with the 'tofsims' package. biocViews: ExperimentData, MassSpectrometry, ImagingMassSpectrometry, DataImport Author: Lorenz Gerber, Viet Mai Hoang Maintainer: Lorenz Gerber VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tofsimsData git_branch: RELEASE_3_8 git_last_commit: 2a3a13a git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/tofsimsData_1.10.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: topdownrdata Version: 1.4.0 Depends: topdownr License: GPL (>= 3) MD5sum: 2e25621bd796b78859795b7f5158a289 NeedsCompilation: no Title: Example Files for the topdownr R Package Description: Example data for the topdownr package generated on a Thermo Orbitrap Fusion Lumos MS device. biocViews: ExperimentData, MassSpectrometryData Author: Sebastian Gibb [aut, cre], Pavel Shliaha [aut], Ole Nørregaard Jensen [aut] Maintainer: Sebastian Gibb URL: https://github.com/sgibb/topdownrdata/ BugReports: https://github.com/sgibb/topdownrdata/issues/ git_url: https://git.bioconductor.org/packages/topdownrdata git_branch: RELEASE_3_8 git_last_commit: b12807c git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/topdownrdata_1.4.0.tar.gz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: tweeDEseqCountData Version: 1.20.0 Depends: Biobase, R (>= 2.10) License: GPL (>=2) MD5sum: aaea601e98d23f6e80db25f3eabe68c3 NeedsCompilation: no Title: RNA-seq count data employed in the vignette of the tweeDEseq package Description: RNA-seq count data from Pickrell et al. (2010) employed to illustrate the use of the Poisson-Tweedie family of distributions with the tweeDEseq package. biocViews: Genome, Homo_sapiens_Data, RNASeqData Author: Juan R Gonzalez and Mikel Esnaola (with contributions from Robert Castelo ) Maintainer: Juan R Gonzalez URL: http://www.creal.cat/jrgonzalez/software.htm git_url: https://git.bioconductor.org/packages/tweeDEseqCountData git_branch: RELEASE_3_8 git_last_commit: a5ceedc git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/tweeDEseqCountData_1.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: tximportData Version: 1.10.0 Suggests: knitr License: GPL (>= 2) MD5sum: 54178cc67ba022548272a2474fcecaac NeedsCompilation: no Title: tximportData Description: This package provides the output of running various transcript abundance quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project. The quantifiers were Cufflinks, RSEM, kallisto, Salmon and Sailfish. For details on version numbers, sample information, and details on calls, see the package vignette. biocViews: ExperimentData, SequencingData, RNASeqData Author: Michael Love Maintainer: Michael Love VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/tximportData git_branch: RELEASE_3_8 git_last_commit: 0270c84 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/tximportData_1.10.0.tar.gz vignettes: vignettes/tximportData/inst/doc/tximportData.html vignetteTitles: Sample output files for tximport hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/tximportData/inst/doc/tximportData.R Package: VariantToolsData Version: 1.6.0 Depends: R (>= 2.10), VariantAnnotation (>= 1.7.35) Imports: BiocGenerics, GenomicRanges Suggests: VariantTools (>= 1.3.4), gmapR (>= 1.3.3), BiocStyle License: Artistic-2.0 MD5sum: 6d1a1707b091b0d4beeb7f2cf0f9fb7f NeedsCompilation: no Title: Data for the VariantTools tutorial Description: Data from the sequencing of a 50/50 mixture of HapMap trio samples NA12878 (CEU) and NA19240 (YRI), subset to the TP53 region. biocViews: ExperimentData, SequencingData, HapMap, SNPData Author: Michael Lawrence Maintainer: Michael Lawrence git_url: https://git.bioconductor.org/packages/VariantToolsData git_branch: RELEASE_3_8 git_last_commit: 7ca3118 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/VariantToolsData_1.6.0.tar.gz vignettes: vignettes/VariantToolsData/inst/doc/intro.pdf vignetteTitles: VariantTools Example Data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/VariantToolsData/inst/doc/intro.R Package: vulcandata Version: 1.4.0 Imports: utils License: LGPL-3 MD5sum: 65a1dc1a4c75edacf512fe57434790e2 NeedsCompilation: no Title: VirtUaL ChIP-Seq data Analysis using Networks, dummy dataset Description: This package provides a dummy regulatory network and ChIP-Seq dataset for running examples in the vulcan package biocViews: ExperimentData, Homo_sapiens_Data, CancerData, ChIPSeqData Author: Federico M. Giorgi, Andrew N. Holding, Florian Markowetz Maintainer: Federico M. Giorgi git_url: https://git.bioconductor.org/packages/vulcandata git_branch: RELEASE_3_8 git_last_commit: 09a2ee8 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/vulcandata_1.4.0.tar.gz vignettes: vignettes/vulcandata/inst/doc/vulcandata.pdf vignetteTitles: Vulcan: VirtUaL ChIP-Seq Analysis through Networks,, dummy datasets hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/vulcandata/inst/doc/vulcandata.R Package: waveTilingData Version: 1.18.0 Depends: R (>= 2.14.0) License: GPL (>= 2) MD5sum: 4fe1e828f7c998a4d3c9621886e5c5f1 NeedsCompilation: no Title: waveTiling Example Data Description: Experiment and Annotation Data files used by the examples / vignette in the waveTiling package biocViews: ExperimentData, Arabidopsis_thaliana_Data, MicroarrayData Author: Kristof De Beuf Maintainer: Kristof De Beuf git_url: https://git.bioconductor.org/packages/waveTilingData git_branch: RELEASE_3_8 git_last_commit: 72046c7 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/waveTilingData_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: WES.1KG.WUGSC Version: 1.14.0 License: GPL-2 MD5sum: d1013abff0fe02136aab55a3354529ee NeedsCompilation: no Title: Whole Exome Sequencing (WES) of chromosome 22 401st to 500th exon from the 1000 Genomes (1KG) Project by the Washington University Genome Sequencing Center (WUGSC). Description: The assembled .bam files of whole exome sequencing data from the 1000 Genomes Project. 46 samples sequenced by the Washington University Genome Sequencing Center are included. biocViews: ExperimentData, Project1000genomes, SequencingData, DNASeqData, Homo_sapiens_Data Author: Yuchao Jiang, Nancy R. Zhang Maintainer: Yuchao Jiang git_url: https://git.bioconductor.org/packages/WES.1KG.WUGSC git_branch: RELEASE_3_8 git_last_commit: bc41077 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/WES.1KG.WUGSC_1.14.0.tar.gz vignettes: vignettes/WES.1KG.WUGSC/inst/doc/WES.1KG.WUGSC_vignettes.pdf vignetteTitles: Using CODEX hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: XhybCasneuf Version: 1.20.0 Depends: R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf , RColorBrewer , methods, grid License: Artistic-2.0 MD5sum: e31cf97fb07e30678b32d6db51a6cea5 NeedsCompilation: no Title: EBI/PSB cross-hybridisation study package Description: Cross-hybridisation study on the ATH1 Affymetrix GeneChip biocViews: ExperimentData, Tissue, MicroarrayData, TissueMicroarrayData Author: Tineke Casneuf Maintainer: Tineke Casneuf git_url: https://git.bioconductor.org/packages/XhybCasneuf git_branch: RELEASE_3_8 git_last_commit: 8d2283d git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/XhybCasneuf_1.20.0.tar.gz vignettes: vignettes/XhybCasneuf/inst/doc/Xhyb.pdf vignetteTitles: Xhyb hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/XhybCasneuf/inst/doc/Xhyb.R Package: yeastCC Version: 1.22.0 Depends: Biobase (>= 2.5.5) License: Artistic-2.0 MD5sum: 5b31b8fadb3318846770cdd2f6b620a1 NeedsCompilation: no Title: Spellman et al. (1998) and Pramila/Breeden (2006) yeast cell cycle microarray data Description: ExpressionSet for Spellman et al. (1998) yeast cell cycle microarray experiment biocViews: ExperimentData, CellCulture, Saccharomyces_cerevisiae_Data, CancerData, MicroarrayData, OneChannelData, GEO Author: Sandrine Dudoit Maintainer: Sandrine Dudoit git_url: https://git.bioconductor.org/packages/yeastCC git_branch: RELEASE_3_8 git_last_commit: 9527a28 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/yeastCC_1.22.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastExpData Version: 0.28.0 Depends: R (>= 2.4), graph (>= 1.9.26) Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db License: GPL MD5sum: ab56e8741e012db8ce829bb43673cb35 NeedsCompilation: no Title: Yeast Experimental Data Description: A collection of different sets of experimental data from yeast. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data Author: R. Gentleman Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/yeastExpData git_branch: RELEASE_3_8 git_last_commit: d4cf68a git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/yeastExpData_0.28.0.tar.gz vignettes: vignettes/yeastExpData/inst/doc/yeastExample.pdf vignetteTitles: Yeast PPI Example hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/yeastExpData/inst/doc/yeastExample.R Package: yeastGSData Version: 0.20.0 License: Artistic-2.0 MD5sum: 16b3bf8e7fbdcabb099a801c9076f5e8 NeedsCompilation: no Title: Yeast Gold Standard Data Description: A collection of so-called gold (and other) standard data sets biocViews: ExperimentData, Saccharomyces_cerevisiae_Data Author: R. Gentleman Maintainer: R. Gentleman git_url: https://git.bioconductor.org/packages/yeastGSData git_branch: RELEASE_3_8 git_last_commit: 20cb55a git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/yeastGSData_0.20.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastNagalakshmi Version: 1.18.0 License: Artistic-2.0 MD5sum: c3f3493454c6d90bb79f06fa54021ee1 NeedsCompilation: no Title: Yeast genome RNA sequencing data based on Nagalakshmi et. al. Description: The yeast genome data was retrieved from the sequence read archive, aligned with bwa, and converted to BAM format with samtools. biocViews: ExperimentData, Genome, Saccharomyces_cerevisiae_Data, SequencingData, BiocViews, ChIPSeqData Author: Martin Morgan Maintainer: Bioconductor Package Maintainer git_url: https://git.bioconductor.org/packages/yeastNagalakshmi git_branch: RELEASE_3_8 git_last_commit: ec03944 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/yeastNagalakshmi_1.18.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yeastRNASeq Version: 0.20.0 Depends: R (>= 2.4) Suggests: Biobase, ShortRead, IRanges License: GPL MD5sum: a642a1c83917e78e156bc3841e609f7b NeedsCompilation: no Title: Yeast RNA-Seq Experimental Data from Lee et al. 2008 Description: A selection of RNA-Seq data from a yeast transcriptome experiment. biocViews: ExperimentData, Saccharomyces_cerevisiae_Data, SequencingData, RNASeqData Author: James H. Bullard and Kasper D. Hansen Maintainer: J. Bullard git_url: https://git.bioconductor.org/packages/yeastRNASeq git_branch: RELEASE_3_8 git_last_commit: 7e1af05 git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/yeastRNASeq_0.20.0.tar.gz vignettes: vignettes/yeastRNASeq/inst/doc/yeastRNASeq.pdf vignetteTitles: An overview of yeastRNASeq hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/yeastRNASeq/inst/doc/yeastRNASeq.R Package: yri1kgv Version: 0.24.0 Depends: GGBase Imports: Biobase License: Artistic-2.0 MD5sum: 6b8aff46adfa18440787125c32b2eac5 NeedsCompilation: no Title: expression + genotype on 79 unrelated YRI individuals Description: expression + genotype on 79 unrelated YRI individuals biocViews: ArrayExpress Author: VJ Carey Maintainer: VJ Carey git_url: https://git.bioconductor.org/packages/yri1kgv git_branch: RELEASE_3_8 git_last_commit: 7d2bfae git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/yri1kgv_0.24.0.tar.gz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: yriMulti Version: 0.12.0 Depends: Homo.sapiens, geuvPack, MultiAssayExperiment (>= 1.3.14) Imports: GenomicFiles (>= 1.13.6), VariantAnnotation (>= 1.23.1), gQTLBase, SummarizedExperiment, GenomicRanges, dsQTL, GenomeInfoDb Suggests: erma, BiocStyle, knitr, rmarkdown, gQTLstats (>= 1.9.2), doParallel, geuvPack, knitcitations, bibtex License: Artistic-2.0 MD5sum: a5ac85ebbea7b116ab9a5200658fbab6 NeedsCompilation: no Title: support for expression, methylation, DHS, VCF for YRI Description: expression, methylation, DHS for YRI Author: VJ Carey Maintainer: VJ Carey VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/yriMulti git_branch: RELEASE_3_8 git_last_commit: fa104ef git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/yriMulti_0.12.0.tar.gz vignettes: vignettes/yriMulti/inst/doc/yriMulti.pdf vignetteTitles: yriMulti -- HapMap YRI population,, multiassay interfaces hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/yriMulti/inst/doc/yriMulti.R Package: zebrafishRNASeq Version: 1.2.0 Depends: R (>= 2.10) Suggests: BiocStyle, knitr License: GPL MD5sum: f29dab65186b6775efb0a5e5eaeae5e0 NeedsCompilation: no Title: Zebrafish RNA-Seq Experimental Data from Ferreira et al. (2014) Description: Gene-level read counts from RNA-Seq for gallein-treated and control zebrafish. biocViews: ExperimentData, Danio_rerio_Data, RNASeqData Author: Davide Risso Maintainer: Davide Risso VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/zebrafishRNASeq git_branch: RELEASE_3_8 git_last_commit: 05aa6ac git_last_commit_date: 2018-10-30 Date/Publication: 2018-11-01 source.ver: src/contrib/zebrafishRNASeq_1.2.0.tar.gz vignettes: vignettes/zebrafishRNASeq/inst/doc/preprocessing.pdf vignetteTitles: Pre-Processing for the Zebrafish RNA-Seq Gene-Level Counts hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Rfiles: vignettes/zebrafishRNASeq/inst/doc/preprocessing.R Package: PGPC Version: 1.10.0 Depends: R (>= 3.0), EBImage, imageHTS, SearchTrees, limma, RColorBrewer, gplots, splots, ggplot2, geneplotter, ChemmineR, reshape2, plyr Suggests: BiocStyle, knitr License: Artistic-2.0 NeedsCompilation: no Title: Experimental data and analysis of the chemical-genetic interaction screen in isogenic HCT116 cell lines Description: This package contains the experimental data and a vignette guiding through the analysis of a chemical-genenetic interaction screen in isogenic HCT116 cell lines. The code can be executed to generate all results and figures for the manuscript "A chemical-genetic interaction map of small molecules using high-throughput imaging in cancer cells" accepted for publicaton at Molecular Systems Biology. Data availability: Complementary views on this dataset are available through different repositories. The image data files are available from the BioStudies database at the European Bioinformatics Institute (EMBL-EBI) under the accession S-BSMS-PGPC1 (http://wwwdev.ebi.ac.uk/biostudies/studies/S-BSMS-PGPC1) An interactive front-end for exploration of the images is provided by the IDR database http://dx.doi.org/10.17867/10000101. The authors are hosting an interactive webpage to browse images and interaction profiles at http://dedomena.embl.de/PGPC. biocViews: CancerData, ColonCancerData, ExperimentData Author: Felix Klein Maintainer: Felix Klein VignetteBuilder: knitr git_url: https://git.bioconductor.org/packages/PGPC git_branch: RELEASE_3_8 git_last_commit: c358381 git_last_commit_date: 2018-10-30 Date/Publication: 2019-04-14