Package: ABAData
Version: 1.20.0
Depends: R (>= 3.2)
Suggests: BiocStyle, knitr, ABAEnrichment
License: GPL (>= 2)
MD5sum: 1c23aaa7753793a26351e7b711c557d6
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 <steffi_grote@eva.mpg.de>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/ABAData
git_branch: RELEASE_3_12
git_last_commit: c08a841
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ABAData_1.20.0.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
importsMe: ABAEnrichment
dependencyCount: 0
Package: adductData
Version: 1.6.0
Depends: R (>= 3.6)
Imports: ExperimentHub (>= 1.9.0), AnnotationHub (>= 2.13.10), stats
(>= 3.5.0), utils (>= 3.5.0), methods (>= 3.5.0), datasets (>=
3.5.0)
Suggests: knitr (>= 1.15.1), rmarkdown (>= 1.5)
License: Artistic-2.0
MD5sum: 52755259db6664171723160f293276c3
NeedsCompilation: no
Title: Data from untargeted MS of modifications to Cys34 of serum
albumin
Description: mzXML files from Grigoryan et al 2016 (Anal Chem).
biocViews: ExperimentData,MassSpectrometryData,ExperimentHub
Author: Josie Hayes
Maintainer: Josie Hayes <jlhayes1982@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/adductData
git_branch: RELEASE_3_12
git_last_commit: 24e2b4d
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/adductData_1.6.0.tar.gz
vignettes: vignettes/adductData/inst/doc/adductData.html
vignetteTitles: Raw mzXML data using Bioconductor's ExperimentHub
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/adductData/inst/doc/adductData.R
dependsOnMe: adductomicsR
dependencyCount: 78
Package: affycompData
Version: 1.28.0
Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp
License: GPL (>= 2)
MD5sum: bbdbb831ee2ee7ce27c18b8d21ebd8b9
NeedsCompilation: no
Title: affycomp data
Description: Data needed by the affycomp package.
biocViews: MicroarrayData
Author: Rafael A. Irizarry <rafa@jhu.edu> and Zhijin Wu
<zwu@stat.brown.edu> with contributions from Simon Cawley
<simon_cawley@affymetrix.com>
Maintainer: Harris Jaffee <hj@jhu.edu>
git_url: https://git.bioconductor.org/packages/affycompData
git_branch: RELEASE_3_12
git_last_commit: eb50fbf
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/affycompData_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: affycomp
dependencyCount: 8
Package: affydata
Version: 1.38.0
Depends: R (>= 2.4.0), affy (>= 1.23.4)
Imports: methods
Suggests: hgu95av2cdf, hgu133acdf
License: GPL (>= 2)
MD5sum: b5f6d846e3a2ae09dc0bb9a1f0638042
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 <laurent@cbs.dtu.dk>
Maintainer: Harris Jaffee <hj@jhu.edu>
git_url: https://git.bioconductor.org/packages/affydata
git_branch: RELEASE_3_12
git_last_commit: b5e843b
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/affydata_1.38.0.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
dependsOnMe: affyContam
suggestsMe: affy, affycoretools, affyPara, affyPLM, affyQCReport,
arrayMvout, ArrayTools, bgx, Biostrings, farms, gcrma, Harman,
mimager, puma, pvac, RefPlus, RPA, sscore, TurboNorm, vsn,
yaqcaffy, RobLoxBioC
dependencyCount: 13
Package: Affyhgu133A2Expr
Version: 1.26.0
Depends: R (>= 2.10)
License: GPL (>=2)
MD5sum: ca43dcb47b19557465d897757ce2c4f7
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 <zji4@jhu.edu>
git_url: https://git.bioconductor.org/packages/Affyhgu133A2Expr
git_branch: RELEASE_3_12
git_last_commit: 71b413a
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/Affyhgu133A2Expr_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: GSCA
dependencyCount: 0
Package: Affyhgu133aExpr
Version: 1.28.0
Depends: R (>= 2.10)
License: GPL (>=2)
MD5sum: 712c088b0c7408eddf018a63b19dc065
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 <zji4@jhu.edu>
git_url: https://git.bioconductor.org/packages/Affyhgu133aExpr
git_branch: RELEASE_3_12
git_last_commit: 44cf3f3
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/Affyhgu133aExpr_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: GSCA
dependencyCount: 0
Package: Affyhgu133Plus2Expr
Version: 1.24.0
Depends: R (>= 2.10)
License: GPL (>=2)
MD5sum: a42161b83a4559f8b87af6e90ceb2874
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 <zji4@jhu.edu>
git_url: https://git.bioconductor.org/packages/Affyhgu133Plus2Expr
git_branch: RELEASE_3_12
git_last_commit: 141936d
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/Affyhgu133Plus2Expr_1.24.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: GSCA
dependencyCount: 0
Package: AffymetrixDataTestFiles
Version: 0.28.0
Depends: R (>= 2.5.0)
License: LGPL-2.1
MD5sum: b4fdccca316dd7a98407c89f753e18d6
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 <hb@stat.berkeley.edu>
git_url: https://git.bioconductor.org/packages/AffymetrixDataTestFiles
git_branch: RELEASE_3_12
git_last_commit: 0af6083
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/AffymetrixDataTestFiles_0.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: affxparser, affyILM, aroma.affymetrix
dependencyCount: 0
Package: Affymoe4302Expr
Version: 1.28.0
Depends: R (>= 2.10)
License: GPL (>=2)
MD5sum: 0d497a43b9b9d78f0f6c697c28f4b42c
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 <zji4@jhu.edu>
git_url: https://git.bioconductor.org/packages/Affymoe4302Expr
git_branch: RELEASE_3_12
git_last_commit: bb74007
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/Affymoe4302Expr_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: GSCA
dependencyCount: 0
Package: airway
Version: 1.10.0
Depends: R (>= 3.5.0), SummarizedExperiment
Suggests: knitr, GEOquery
License: LGPL
MD5sum: 16f62759b25497b75645d3aab68ca9cd
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 <michaelisaiahlove@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/airway
git_branch: RELEASE_3_12
git_last_commit: dd99f8e
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/airway_1.10.0.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
dependsOnMe: rnaseqGene
importsMe: consensusDE
suggestsMe: apeglm, biobroom, BioCor, BiocSet, CeTF, DelayedArray,
DESeq2, EnhancedVolcano, EnrichmentBrowser, ideal, IHW, iSEEu,
OPWeight, pathwayPCA, pcaExplorer, progeny, runibic,
SummarizedExperiment, ToPASeq, TTMap, weitrix, IHWpaper,
RegParallel, seqgendiff
dependencyCount: 26
Package: ALL
Version: 1.32.0
Depends: R (>= 2.10), Biobase (>= 2.5.5)
Suggests: rpart
License: Artistic-2.0
MD5sum: a7181423086d1ea752a3e417ff1063c0
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 <rgentlem@gmail.com>
git_url: https://git.bioconductor.org/packages/ALL
git_branch: RELEASE_3_12
git_last_commit: 83327cf
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ALL_1.32.0.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
importsMe: ConsensusClusterPlus, dGAselID, scRNAtools
suggestsMe: a4, a4Base, a4Classif, a4Preproc, Biobase, BiocCaseStudies,
BioNet, Category, CellMapper, ChromHeatMap, clipper, eisa,
EnrichmentBrowser, esetVis, ExpressionView, genefilter,
GeneSelectMMD, GOstats, graphite, GSAR, GSEAlm, mdgsa,
MLInterfaces, npGSEA, pathRender, ReportingTools, rScudo,
SNAGEE, topGO, SNAGEEdata, MMDvariance, nlcv, SourceSet
dependencyCount: 7
Package: ALLMLL
Version: 1.30.0
Depends: R (>= 2.10), affy (>= 1.23.4)
License: GPL-2
MD5sum: 693726b515612095490f7526e650a45c
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 <bolstad@stat.berkeley.edu
Maintainer: B. M. Bolstad <bmb@bmbolstad.com>
git_url: https://git.bioconductor.org/packages/ALLMLL
git_branch: RELEASE_3_12
git_last_commit: 6a5347b
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ALLMLL_1.30.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: arrayQualityMetrics, pvac
dependencyCount: 13
Package: alpineData
Version: 1.16.0
Depends: ExperimentHub, GenomicAlignments
Imports: utils, AnnotationHub
Suggests: GenomicAlignments, knitr
License: GPL (>=2)
MD5sum: b8fb0e3c6e8cbe7b8b3415c8ad77302a
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 <michaelisaiahlove@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/alpineData
git_branch: RELEASE_3_12
git_last_commit: 379b61e
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/alpineData_1.16.0.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
suggestsMe: alpine
dependencyCount: 102
Package: AmpAffyExample
Version: 1.30.0
Depends: R (>= 2.4.0), affy (>= 1.23.4)
Suggests: hgu133acdf
License: LGPL (>= 2)
MD5sum: a140d828812d26cd8dd4ae56c5c650e5
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 <rafa@jhu.edu>
git_url: https://git.bioconductor.org/packages/AmpAffyExample
git_branch: RELEASE_3_12
git_last_commit: 272695e
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/AmpAffyExample_1.30.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: AffyRNADegradation
dependencyCount: 13
Package: AneuFinderData
Version: 1.18.0
Depends: R (>= 3.3)
License: file LICENSE
MD5sum: 4511db22b073f9f363f01f80f149a0c9
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 <aaron.taudt@gmail.com>
git_url: https://git.bioconductor.org/packages/AneuFinderData
git_branch: RELEASE_3_12
git_last_commit: 1bf1657
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/AneuFinderData_1.18.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
dependsOnMe: AneuFinder
dependencyCount: 0
Package: antiProfilesData
Version: 1.26.0
Depends: Biobase,
Suggests: frma, GEOquery, GEOmetadb
License: Artistic-2.0
MD5sum: 5081aa25de2620fe2b36889af6cbff6c
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 <hcorrada@gmail.com>
git_url: https://git.bioconductor.org/packages/antiProfilesData
git_branch: RELEASE_3_12
git_last_commit: 372e2ae
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/antiProfilesData_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: antiProfiles, epivizr, epivizrChart, messina
dependencyCount: 7
Package: aracne.networks
Version: 1.16.0
Depends: R (>= 3.3), viper
License: file LICENSE
MD5sum: ebb5c0e1389dbee4257a7c7152b7569b
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 <federico.giorgi@gmail.com>, Mariano
Alvarez <reef103@gmail.com>
git_url: https://git.bioconductor.org/packages/aracne.networks
git_branch: RELEASE_3_12
git_last_commit: 4b502d6
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/aracne.networks_1.16.0.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
dependencyCount: 22
Package: ARRmData
Version: 1.26.0
Depends: R (>= 3.0.0)
License: Artistic-2.0
MD5sum: 505a7b4638390d6852c2fe5154ff222d
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 <jfortin@jhsph.edu>
git_url: https://git.bioconductor.org/packages/ARRmData
git_branch: RELEASE_3_12
git_last_commit: e0e4c3f
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ARRmData_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: ARRmNormalization
dependencyCount: 0
Package: AshkenazimSonChr21
Version: 1.20.0
Suggests: knitr, VariantAnnotation
License: Artistic-2.0
MD5sum: 0bc7375e3ec8e03a8ded4204e3026a7f
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 <tomasz.stokowy@k2.uib.no>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/AshkenazimSonChr21
git_branch: RELEASE_3_12
git_last_commit: 66b710d
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/AshkenazimSonChr21_1.20.0.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
dependencyCount: 0
Package: ASICSdata
Version: 1.10.0
Depends: R (>= 3.5)
Suggests: knitr, rmarkdown, BiocStyle
License: GPL (>= 2)
MD5sum: b5ef1eab770a9884ab7c124c6358df67
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 <gaelle.lefort@inra.fr>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/ASICSdata
git_branch: RELEASE_3_12
git_last_commit: 7176761
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ASICSdata_1.10.0.tar.gz
vignettes: vignettes/ASICSdata/inst/doc/ASICSdata.html
vignetteTitles: ASICSdata
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: ASICS
dependencyCount: 0
Package: AssessORFData
Version: 1.8.0
Depends: R (>= 3.5.0)
Imports: DECIPHER, utils
Suggests: AssessORF, BiocStyle, knitr, rmarkdown
License: GPL-3
MD5sum: 292e80d30160a853bc7e4dbfae38f8e5
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 <dkorandl@alumni.cmu.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/AssessORFData
git_branch: RELEASE_3_12
git_last_commit: 8c560b1
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/AssessORFData_1.8.0.tar.gz
vignettes: vignettes/AssessORFData/inst/doc/AssessORFDataGuide.pdf
vignetteTitles: Using AssessORFData
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/AssessORFData/inst/doc/AssessORFDataGuide.R
suggestsMe: AssessORF
dependencyCount: 31
Package: bcellViper
Version: 1.26.0
Depends: R(>= 2.14.0), Biobase, methods
License: GPL (>=2)
MD5sum: 403524bec2d1d50787129570d3011366
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 <malvarez@c2b2.columbia.edu>
git_url: https://git.bioconductor.org/packages/bcellViper
git_branch: RELEASE_3_12
git_last_commit: f82cb21
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/bcellViper_1.26.0.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
importsMe: dorothea
suggestsMe: iterClust, pageRank, viper
dependencyCount: 7
Package: beadarrayExampleData
Version: 1.28.0
Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>=
2.0.0)
License: GPL-2
MD5sum: 5bda365319fbe079957deef1f35990fd
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 <Mark.Dunning@cancer.org.uk>
git_url: https://git.bioconductor.org/packages/beadarrayExampleData
git_branch: RELEASE_3_12
git_last_commit: a9d22f9
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/beadarrayExampleData_1.28.0.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
suggestsMe: beadarray, MiRaGE, beadarrayFilter, RobLoxBioC
dependencyCount: 76
Package: BeadArrayUseCases
Version: 1.28.0
Imports: beadarray (>= 2.3.18), limma, GEOquery
Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db,
illuminaHumanv2.db, illuminaHumanv3.db
License: GPL-2
MD5sum: 252c0c67c112d599ceaccc276ce3e087
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 <grimbough@gmail.com>
git_url: https://git.bioconductor.org/packages/BeadArrayUseCases
git_branch: RELEASE_3_12
git_last_commit: 5e935c0
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/BeadArrayUseCases_1.28.0.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
dependencyCount: 92
Package: benchmarkfdrData2019
Version: 1.4.0
Depends: R (>= 3.6.0), SummarizedExperiment, ExperimentHub
Imports: utils
Suggests: knitr, BiocStyle, testthat, SummarizedBenchmark, dplyr,
ggplot2, rlang
License: MIT + file LICENSE
MD5sum: 5b9ed222125247af1d761aa25d8707d2
NeedsCompilation: no
Title: Data and Benchmarking Results from Korthauer and Kimes et al.
(2019)
Description: Benchmarking results for experimental and simulated data
sets used in Korthauer and Kimes et al. (2019) to compare
methods for controlling the false discovery rate.
biocViews: SingleCellData, ExperimentData, RNASeqData, ExpressionData,
ExperimentData, ExperimentHub
Author: Stephanie Hicks [aut, cre]
(<https://orcid.org/0000-0002-7858-0231>), Keegan Korthauer
[aut] (<https://orcid.org/0000-0002-4565-1654>), Patrick Kimes
[aut] (<https://orcid.org/0000-0001-6819-9077>)
Maintainer: Stephanie Hicks <shicks19@jhu.edu>
VignetteBuilder: knitr
BugReports:
https://github.com/stephaniehicks/benchmarkfdrData2019/issues
git_url: https://git.bioconductor.org/packages/benchmarkfdrData2019
git_branch: RELEASE_3_12
git_last_commit: 98823f5
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/benchmarkfdrData2019_1.4.0.tar.gz
vignettes:
vignettes/benchmarkfdrData2019/inst/doc/benchmarkfdrData2019.html
vignetteTitles: Exploring and updating FDR benchmarking results
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/benchmarkfdrData2019/inst/doc/benchmarkfdrData2019.R
dependencyCount: 91
Package: beta7
Version: 1.28.0
Depends: R (>= 2.4.0), marray
License: LGPL
MD5sum: 45af6b943d1a76f65d347a7a8656253c
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 <jean@biostat.ucsf.edu>
Maintainer: Jean Yang <jean@biostat.ucsf.edu>
git_url: https://git.bioconductor.org/packages/beta7
git_branch: RELEASE_3_12
git_last_commit: e89f68c
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/beta7_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 7
Package: biotmleData
Version: 1.14.0
Depends: R (>= 3.0)
Suggests: Biobase, SummarizedExperiment
License: file LICENSE
MD5sum: 3c30d26ba76b9a2bc65e298988b627d8
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 <nhejazi@berkeley.edu>
git_url: https://git.bioconductor.org/packages/biotmleData
git_branch: RELEASE_3_12
git_last_commit: b524e5e
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/biotmleData_1.14.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
suggestsMe: biotmle
dependencyCount: 0
Package: biscuiteerData
Version: 1.4.0
Depends: R (>= 3.6.0), ExperimentHub
Imports: AnnotationHub, utils, curl
Suggests: knitr
License: GPL-3
MD5sum: be43f39062eb86983c1938d2b7f395b2
NeedsCompilation: no
Title: Data Package for Biscuiteer
Description: Contains default datasets used by the Bioconductor package
biscuiteer.
biocViews: ExperimentHub, ExperimentData, Genome, Homo_sapiens_Data
Author: Tim Triche, Jr. [aut, cre], Wanding Zhou [aut], Ben Johnson
[aut], Jacob Morrison [aut], Lyong Heo [aut]
Maintainer: "Jacob Morrison" <jacob.morrison@vai.org>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/biscuiteerData
git_branch: RELEASE_3_12
git_last_commit: c83cdb2
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/biscuiteerData_1.4.0.tar.gz
vignettes: vignettes/biscuiteerData/inst/doc/biscuiteerData.html
vignetteTitles: Biscuiteer User Guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/biscuiteerData/inst/doc/biscuiteerData.R
dependsOnMe: biscuiteer
dependencyCount: 77
Package: bladderbatch
Version: 1.28.0
Depends: Biobase
License: Artistic-2.0
MD5sum: e1421ef1205eab02947a1dacd76b2b4c
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 <jleek@jhsph.edu>
Maintainer: Jeffrey T. Leek <jleek@jhsph.edu>
git_url: https://git.bioconductor.org/packages/bladderbatch
git_branch: RELEASE_3_12
git_last_commit: 5d604cb
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/bladderbatch_1.28.0.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
importsMe: RUVcorr
suggestsMe: Harman, singleCellTK, sva
dependencyCount: 7
Package: blimaTestingData
Version: 1.10.0
Depends: R(>= 3.0.0)
Suggests: blima, beadarray, illuminaHumanv4.db, BiocStyle
License: GPL-3
MD5sum: b1a62eb143707a3f3cbcd48c98d56f17
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 <kulvait@gmail.com>
URL: https://bitbucket.org/kulvait/blima
git_url: https://git.bioconductor.org/packages/blimaTestingData
git_branch: RELEASE_3_12
git_last_commit: ca61895
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/blimaTestingData_1.10.0.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
suggestsMe: blima
dependencyCount: 0
Package: BloodCancerMultiOmics2017
Version: 1.10.0
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, xtable
License: LGPL (>= 3)
MD5sum: f946cd2e702bbb48fcd3cfb37cdb3a5b
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 <dr.malgorzata.oles@gmail.com>
VignetteBuilder: knitr
git_url:
https://git.bioconductor.org/packages/BloodCancerMultiOmics2017
git_branch: RELEASE_3_12
git_last_commit: 46a123d
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/BloodCancerMultiOmics2017_1.10.0.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
dependencyCount: 148
Package: bodymapRat
Version: 1.6.0
Depends: R (>= 3.6.0), SummarizedExperiment, ExperimentHub
Imports: utils
Suggests: knitr, BiocStyle, testthat
License: CC BY 4.0
MD5sum: 60593e9c1b95d5e1363772f0b19d6fd7
NeedsCompilation: no
Title: Experimental dataset from the rat BodyMap project
Description: This package contains a SummarizedExperiment from the Yu
et al. (2013) paper that performed the rat BodyMap across 11
organs and 4 developmental stages. Raw FASTQ files were
downloaded and mapped using STAR. Data is available on
ExperimentHub as a data package.
biocViews: SequencingData, RNASeqData, ExpressionData, ExperimentData,
ExperimentHub
Author: Stephanie Hicks [aut, cre]
(<https://orcid.org/0000-0002-7858-0231>), Kwame Okrah [aut]
Maintainer: Stephanie Hicks <shicks19@jhu.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/bodymapRat
git_branch: RELEASE_3_12
git_last_commit: da33656
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/bodymapRat_1.6.0.tar.gz
vignettes: vignettes/bodymapRat/inst/doc/bodymapRat.html
vignetteTitles: The bodymapRat data user's guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/bodymapRat/inst/doc/bodymapRat.R
suggestsMe: qsmooth
dependencyCount: 91
Package: brainImageRdata
Version: 1.8.0
Depends: ExperimentHub
Suggests: knitr
License: CC BY-SA 4.0
MD5sum: b1766a59e137f48555c150930ca9cdd9
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 <slinker@salk.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/brainImageRdata
git_branch: RELEASE_3_12
git_last_commit: e4da301
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/brainImageRdata_1.8.0.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
dependencyCount: 77
Package: breakpointRdata
Version: 1.8.0
Depends: R (>= 3.5)
Suggests: knitr, BiocStyle,
License: file LICENSE
MD5sum: cb4298e2ea31f8d0c6e21a3475c2cd51
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 <david.porubsky@gmail.com>
URL: https://github.com/daewoooo/breakpointRdata
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/breakpointRdata
git_branch: RELEASE_3_12
git_last_commit: e9f0df6
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/breakpointRdata_1.8.0.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
dependsOnMe: breakpointR
dependencyCount: 0
Package: breastCancerMAINZ
Version: 1.28.0
Depends: R (>= 2.5.0)
Suggests: survcomp, genefu, Biobase
License: Artistic-2.0
MD5sum: 20c0c500638dabd893af58ac27bba29e
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 <mschroed@jimmy.harvard.edu>, Benjamin
Haibe-Kains <bhaibeka@jimmy.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
git_url: https://git.bioconductor.org/packages/breastCancerMAINZ
git_branch: RELEASE_3_12
git_last_commit: 57c2a87
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/breastCancerMAINZ_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: DART, genefu, MIGSA, MineICA, STROMA4
dependencyCount: 0
Package: breastCancerNKI
Version: 1.28.0
Depends: R (>= 2.5.0)
Suggests: survcomp, genefu, Biobase
License: Artistic-2.0
MD5sum: 79e9b0a0836ac359f05bd7814e4d1766
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 <mschroed@jimmy.harvard.edu>, Benjamin
Haibe-Kains <bhaibeka@jimmy.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
git_url: https://git.bioconductor.org/packages/breastCancerNKI
git_branch: RELEASE_3_12
git_last_commit: 3cc1834
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/breastCancerNKI_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: genefu, MIGSA, SigCheck, seventyGeneData
dependencyCount: 0
Package: breastCancerTRANSBIG
Version: 1.28.0
Depends: R (>= 2.5.0)
Suggests: survcomp, genefu, Biobase
License: Artistic-2.0
MD5sum: 6fef4acd3bf1902f220787195b83d933
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 <mschroed@jimmy.harvard.edu>, Benjamin
Haibe-Kains <bhaibeka@jimmy.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
git_url: https://git.bioconductor.org/packages/breastCancerTRANSBIG
git_branch: RELEASE_3_12
git_last_commit: e7de199
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/breastCancerTRANSBIG_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: genefu, GSgalgoR, MIGSA, MineICA
dependencyCount: 0
Package: breastCancerUNT
Version: 1.28.0
Depends: R (>= 2.5.0)
Suggests: survcomp, genefu, Biobase
License: Artistic-2.0
MD5sum: 8b34ec4f5eb0d0d285e6d4a4fc871de8
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 <mschroed@jimmy.harvard.edu>, Benjamin
Haibe-Kains <bhaibeka@jimmy.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
git_url: https://git.bioconductor.org/packages/breastCancerUNT
git_branch: RELEASE_3_12
git_last_commit: 59fb821
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/breastCancerUNT_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: genefu, MIGSA
dependencyCount: 0
Package: breastCancerUPP
Version: 1.28.0
Depends: R (>= 2.5.0)
Suggests: survcomp, genefu, Biobase
License: Artistic-2.0
MD5sum: f174af97676727b7948d59c4ca575aa4
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 <mschroed@jimmy.harvard.edu>, Benjamin
Haibe-Kains <bhaibeka@jimmy.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
git_url: https://git.bioconductor.org/packages/breastCancerUPP
git_branch: RELEASE_3_12
git_last_commit: 4d7fe07
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/breastCancerUPP_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: genefu, GSgalgoR, MIGSA, MineICA, safe
dependencyCount: 0
Package: breastCancerVDX
Version: 1.28.0
Depends: R (>= 2.5.0)
Suggests: survcomp, genefu, Biobase
License: Artistic-2.0
MD5sum: 21bdffe570070496f61e7c8df1b38252
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 <mschroed@jimmy.harvard.edu>, Benjamin
Haibe-Kains <bhaibeka@jimmy.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
git_url: https://git.bioconductor.org/packages/breastCancerVDX
git_branch: RELEASE_3_12
git_last_commit: dfce14e
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/breastCancerVDX_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: BAGS
suggestsMe: AIMS, DART, genefu, MIGSA, MineICA, ToPASeq
dependencyCount: 0
Package: brgedata
Version: 1.12.0
Depends: R (>= 3.4), Biobase
Imports: SummarizedExperiment
Suggests: minfi, MultiAssayExperiment, knitr, rexposome
License: MIT + file LICENSE
MD5sum: 4588d10ff9b8f5f4ceb3a6933d8d2c0f
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 <carlos.ruiz@isglobal.org>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/brgedata
git_branch: RELEASE_3_12
git_last_commit: 6bbaafe
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/brgedata_1.12.0.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
suggestsMe: MEAL, MultiDataSet, omicRexposome
dependencyCount: 26
Package: bronchialIL13
Version: 1.28.0
Depends: R(>= 2.10.0), affy (>= 1.23.4)
License: GPL-2
MD5sum: b40ff627317375f01f7bbf21de872de3
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 <stvjc@channing.harvard.edu>
Maintainer: Vince Carey <stvjc@channing.harvard.edu>
URL: http://www.biostat.harvard.edu/~carey
git_url: https://git.bioconductor.org/packages/bronchialIL13
git_branch: RELEASE_3_12
git_last_commit: b8d0db6
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/bronchialIL13_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 13
Package: bsseqData
Version: 0.28.0
Depends: R (>= 2.15), bsseq (>= 1.16.0)
License: Artistic-2.0
MD5sum: 180dede038973aa962c9c1ca417a3578
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 <khansen@jhsph.edu>
git_url: https://git.bioconductor.org/packages/bsseqData
git_branch: RELEASE_3_12
git_last_commit: e83176a
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/bsseqData_0.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: bsseq, methylSig
dependencyCount: 69
Package: cancerdata
Version: 1.28.0
Depends: R (>= 2.10.1), Biobase
License: GPL (>= 2)
MD5sum: e2f87bfb6144bd25332a3acd963bb86b
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 <danielkossi@hotmail.com>
git_url: https://git.bioconductor.org/packages/cancerdata
git_branch: RELEASE_3_12
git_last_commit: 0ac2fd4
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/cancerdata_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: cancerclass
dependencyCount: 7
Package: CardinalWorkflows
Version: 1.22.0
Depends: R (>= 2.10), Cardinal
Suggests: BiocStyle, knitr
License: Artistic-2.0
MD5sum: b361361e41a39a0a6d67a97dfccd233b
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 <k.bemis@northeastern.edu>
Maintainer: Kylie A. Bemis <k.bemis@northeastern.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/CardinalWorkflows
git_branch: RELEASE_3_12
git_last_commit: 0cef890
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/CardinalWorkflows_1.22.0.tar.gz
vignettes:
vignettes/CardinalWorkflows/inst/doc/MSI-classification.html,
vignettes/CardinalWorkflows/inst/doc/MSI-segmentation.html,
vignettes/CardinalWorkflows/inst/doc/MSI-testing.html
vignetteTitles: 2. Classification: Supervised analysis workflow, 1.
Segmentation: Unsupervised analysis workflow, 3. Class
comparision: Statistical testing workflow
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CardinalWorkflows/inst/doc/MSI-classification.R,
vignettes/CardinalWorkflows/inst/doc/MSI-segmentation.R,
vignettes/CardinalWorkflows/inst/doc/MSI-testing.R
dependencyCount: 65
Package: ccdata
Version: 1.16.0
Depends: R (>= 3.3)
License: MIT + file LICENSE
MD5sum: dc31208e5291fa4f81d1b9842bad042d
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 <alexvpickering@gmail.com>
git_url: https://git.bioconductor.org/packages/ccdata
git_branch: RELEASE_3_12
git_last_commit: 7cfa9c5
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ccdata_1.16.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
importsMe: ccmap
dependencyCount: 0
Package: CCl4
Version: 1.28.0
Depends: R (>= 2.6.0), Biobase (>= 2.5.5), limma
License: Artistic-2.0
MD5sum: c8049af9173fdd949e25ca81bb2d1c29
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 <audrey@ebi.ac.uk>
git_url: https://git.bioconductor.org/packages/CCl4
git_branch: RELEASE_3_12
git_last_commit: 452a2a5
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/CCl4_1.28.0.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
suggestsMe: arrayQualityMetrics, BiocCaseStudies
dependencyCount: 9
Package: ccTutorial
Version: 1.28.0
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: a36b66e1fad77bd562e41ee01483a119
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 <joern.toedling@curie.fr>
git_url: https://git.bioconductor.org/packages/ccTutorial
git_branch: RELEASE_3_12
git_last_commit: a39d3f2
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ccTutorial_1.28.0.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
dependencyCount: 81
Package: celarefData
Version: 1.8.0
Depends: R (>= 3.5.0)
Suggests: ExperimentHub, knitr, rmarkdown
License: GPL-3
MD5sum: 339c1fdafb03680b9ef8e3df52f7e7fb
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, ExperimentHub
Author: Sarah Williams [aut, cre]
Maintainer: Sarah Williams <sarah.williams1@monash.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/celarefData
git_branch: RELEASE_3_12
git_last_commit: 1b2e482
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/celarefData_1.8.0.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
dependencyCount: 0
Package: celldex
Version: 1.0.0
Depends: SummarizedExperiment
Imports: utils, ExperimentHub, AnnotationHub, AnnotationDbi, S4Vectors,
DelayedArray, DelayedMatrixStats
Suggests: testthat, knitr, rmarkdown, BiocStyle, DT
License: GPL-3
MD5sum: fcbf9341066a8ece3a934a925a6b47f8
NeedsCompilation: no
Title: Reference Index for Cell Types
Description: Provides a collection of reference expression datasets
with curated cell type labels, for use in procedures like
automated annotation of single-cell data or deconvolution of
bulk RNA-seq.
biocViews: ExperimentHub, ExperimentData, ExpressionData,
SequencingData, RNASeqData
Author: Dvir Aran [aut], Aaron Lun [aut, cre, cph], Daniel Bunis [aut],
Jared Andrews [aut], Friederike Dündar [aut]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
URL: https://github.com/LTLA/celldex
VignetteBuilder: knitr
BugReports: https://support.bioconductor.org/
git_url: https://git.bioconductor.org/packages/celldex
git_branch: RELEASE_3_12
git_last_commit: c398631
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/celldex_1.0.0.tar.gz
vignettes: vignettes/celldex/inst/doc/userguide.html
vignetteTitles: Cell type references
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/celldex/inst/doc/userguide.R
suggestsMe: ontoProc, SingleR, tidySingleCellExperiment
dependencyCount: 104
Package: CellMapperData
Version: 1.16.0
Depends: ExperimentHub, CellMapper
Suggests: BiocStyle
License: Artistic-2.0
MD5sum: 5c032fb20d4d96c52f622485848372b1
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 <bnelms.research@gmail.com>
git_url: https://git.bioconductor.org/packages/CellMapperData
git_branch: RELEASE_3_12
git_last_commit: d6d5b69
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/CellMapperData_1.16.0.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
suggestsMe: CellMapper
dependencyCount: 78
Package: ceu1kg
Version: 0.28.0
Depends: R (>= 2.12.0), GGBase (>= 3.9.0), GGtools, Biobase
Suggests: SNPlocs.Hsapiens.dbSNP.20101109
License: Artistic-2.0
MD5sum: a52f1dac8b569a939c9967d101b63049
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 <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/ceu1kg
git_branch: RELEASE_3_12
git_last_commit: baecf9f
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ceu1kg_0.28.0.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
dependencyCount: 164
Package: ceu1kgv
Version: 0.32.0
Depends: R (>= 3.0), GGBase
Imports: Biobase
License: Artistic-2.0
MD5sum: 06142b0a3776177b425b42c5c4a089fe
NeedsCompilation: no
Title: expression + genotype on 79 unrelated CEU individuals
Description: expression + genotype on 79 unrelated CEU individuals
biocViews: ArrayExpress
Author: VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/ceu1kgv
git_branch: RELEASE_3_12
git_last_commit: 99148cd
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ceu1kgv_0.32.0.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
dependencyCount: 60
Package: ceuhm3
Version: 0.28.0
Depends: R (>= 2.12.0), GGBase, Biobase
Imports: GGtools
License: Artistic-2.0
MD5sum: ee18605d8a8288b06d888fdfabb36838
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 <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/ceuhm3
git_branch: RELEASE_3_12
git_last_commit: 1b2abea
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ceuhm3_0.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 164
Package: cgdv17
Version: 0.28.0
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: 37f5ae3d4f5ff05dbecf18340991ad74
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 <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/cgdv17
git_branch: RELEASE_3_12
git_last_commit: 60af2c9
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/cgdv17_0.28.0.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
dependsOnMe: variants
dependencyCount: 90
Package: ChAMPdata
Version: 2.22.0
Depends: GenomicRanges (>= 1.22.4),BiocGenerics(>= 0.16.1),R (>= 3.3)
License: GPL-3
MD5sum: 3da92daf51d2d0079b5f68da32f8199b
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 <champ450k@gmail.com>
git_url: https://git.bioconductor.org/packages/ChAMPdata
git_branch: RELEASE_3_12
git_last_commit: eeedd4c
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ChAMPdata_2.22.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: ChAMP
dependencyCount: 17
Package: ChIC.data
Version: 1.10.0
Depends: R (>= 3.5)
Imports: caret (>= 6.0-78)
License: GPL-2
MD5sum: 88e93f1ec65b7f668f67f7452d7b3674
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 <carmen.livi@ifom.eu>
git_url: https://git.bioconductor.org/packages/ChIC.data
git_branch: RELEASE_3_12
git_last_commit: 1ceb1d5
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ChIC.data_1.10.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
importsMe: ChIC
dependencyCount: 72
Package: ChimpHumanBrainData
Version: 1.28.0
Depends: affy,qvalue,limma,hexbin,statmod
License: MIT
MD5sum: dc42f1fe38088b10e3065652f29cc516
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 <sdavis2@mail.nih.gov>
git_url: https://git.bioconductor.org/packages/ChimpHumanBrainData
git_branch: RELEASE_3_12
git_last_commit: e5fcb42
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ChimpHumanBrainData_1.28.0.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
dependencyCount: 56
Package: chipenrich.data
Version: 2.14.0
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: fec4b10f3d4395558fcfc7ad3624a533
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 <rcavalca@umich.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/chipenrich.data
git_branch: RELEASE_3_12
git_last_commit: 15d78e9
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/chipenrich.data_2.14.0.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
importsMe: chipenrich
dependencyCount: 68
Package: ChIPexoQualExample
Version: 1.14.0
Depends: R (>= 3.3)
License: GPL (>= 2)
MD5sum: 5b280808c6b8294eedad2b9d63dc21f7
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 <welch@stat.wisc.edu>
URL: http://www.github.com/keleslab/ChIPexoQualExample
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/ChIPexoQualExample
git_branch: RELEASE_3_12
git_last_commit: 8fc9b51
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ChIPexoQualExample_1.14.0.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
suggestsMe: ChIPexoQual
dependencyCount: 0
Package: chipseqDBData
Version: 1.6.0
Imports: AnnotationHub, ExperimentHub, Rsamtools, S4Vectors
Suggests: knitr, BiocStyle
License: CC BY 4.0
MD5sum: d2e9b600e63871f7e6de934928eeb909
NeedsCompilation: no
Title: Data for the chipseqDB Workflow
Description: Sorted and indexed BAM files for ChIP-seq libraries, for
use in the chipseqDB workflow. BAM indices are also included.
biocViews: SequencingData, ChIPSeqData, ExperimentHub
Author: Aaron Lun [aut, cre]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/chipseqDBData
git_branch: RELEASE_3_12
git_last_commit: ffdf891
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/chipseqDBData_1.6.0.tar.gz
vignettes: vignettes/chipseqDBData/inst/doc/chipseqDBData.html
vignetteTitles: File manifest and statistics
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/chipseqDBData/inst/doc/chipseqDBData.R
suggestsMe: chipseqDB, csawUsersGuide
dependencyCount: 94
Package: ChIPXpressData
Version: 1.28.0
Depends: bigmemory
License: GPL (>=2)
MD5sum: ba7ef6f12e2580e8e5d614275834cf85
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 <gewu@jhsph.edu>
git_url: https://git.bioconductor.org/packages/ChIPXpressData
git_branch: RELEASE_3_12
git_last_commit: 2c31561
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ChIPXpressData_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: ChIPXpress
dependencyCount: 6
Package: chromstaRData
Version: 1.16.0
Depends: R (>= 3.3)
License: GPL-3
MD5sum: a8695bc238dd3712c532f301bd19a824
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 <aaron.taudt@gmail.com>
git_url: https://git.bioconductor.org/packages/chromstaRData
git_branch: RELEASE_3_12
git_last_commit: de21cd8
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/chromstaRData_1.16.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: chromstaR
dependencyCount: 0
Package: CLL
Version: 1.30.0
Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5)
License: LGPL
MD5sum: e9732351c00670d6708201866f150119
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 <rgentlem@fhcrc.org>
git_url: https://git.bioconductor.org/packages/CLL
git_branch: RELEASE_3_12
git_last_commit: e2e2507
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/CLL_1.30.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: BiocCaseStudies
dependencyCount: 13
Package: CLLmethylation
Version: 1.10.0
Depends: R (>= 3.5.0)
Imports: SummarizedExperiment, ExperimentHub
Suggests: BiocStyle, ggplot2, knitr, rmarkdown
License: LGPL
MD5sum: a204c3eb034492961b1e3a4352f58b59
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 <dr.malgorzata.oles@gmail.com>, Andreas
Mock <andreas.mock@embl.de>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/CLLmethylation
git_branch: RELEASE_3_12
git_last_commit: 731aab4
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/CLLmethylation_1.10.0.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
dependencyCount: 91
Package: CluMSIDdata
Version: 1.6.0
Depends: R (>= 3.6)
License: MIT + file LICENSE
MD5sum: 1471f858ae85a021e8173acc74ad4d3f
NeedsCompilation: no
Title: Data for the CluMSID package
Description: This package contains various LC-MS/MS and GC-MS data that
is used in vignettes and examples in the CluMSID package.
biocViews: ExperimentData, MassSpectrometryData
Author: Tobias Depke [aut, cre]
Maintainer: Tobias Depke <tobias.depke@helmholtz-hzi.de>
git_url: https://git.bioconductor.org/packages/CluMSIDdata
git_branch: RELEASE_3_12
git_last_commit: df11685
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/CluMSIDdata_1.6.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
suggestsMe: CluMSID
dependencyCount: 0
Package: clustifyrdatahub
Version: 1.0.0
Depends: R (>= 4.0), ExperimentHub
Imports: utils
Suggests: clustifyr, Seurat, usethis, rmarkdown, knitr, tidyr,
BiocStyle
License: MIT + file LICENSE
MD5sum: fa00df701fefb222dce66346414395c8
NeedsCompilation: no
Title: External data sets for clustifyr in ExperimentHub
Description: References made from external single-cell mRNA sequencing
data sets, stored as average gene expression matrices. For use
with clustifyr <https://bioconductor.org/packages/clustifyr> to
assign cell type identities.
biocViews: SingleCellData, SequencingData, MicroarrayData,
ExperimentHub, RNASeqData, PackageTypeData, ExpressionData
Author: Rui Fu [aut, cre] (<https://orcid.org/0000-0001-8183-4549>),
Kent Riemondy [aut] (<https://orcid.org/0000-0003-0750-1273>),
RNA Bioscience Initiative [fnd], Austin Gillen [ctb]
(<https://orcid.org/0000-0003-2928-6308>), Jay Hesselberth
[ctb] (<https://orcid.org/0000-0002-6299-179X>), Sidhant
Puntambekar [ctb]
Maintainer: Rui Fu <raysinensis@gmail.com>
URL: https://rnabioco.github.io/clustifyrdatahub
VignetteBuilder: knitr
BugReports: https://github.com/rnabioco/clustifyrdatahub/issues
git_url: https://git.bioconductor.org/packages/clustifyrdatahub
git_branch: RELEASE_3_12
git_last_commit: cbd5308
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/clustifyrdatahub_1.0.0.tar.gz
vignettes: vignettes/clustifyrdatahub/inst/doc/clustifyrdatahub.html
vignetteTitles: clustifyrdatahub
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/clustifyrdatahub/inst/doc/clustifyrdatahub.R
dependencyCount: 77
Package: cMap2data
Version: 1.26.0
Depends: R (>= 2.10)
License: GPL-3
MD5sum: 3eee624936f9f324ef7a5f337a158734
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 <saezrodriguez@ebi.ac.uk>
git_url: https://git.bioconductor.org/packages/cMap2data
git_branch: RELEASE_3_12
git_last_commit: 8ac71dd
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/cMap2data_1.26.0.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
dependsOnMe: DrugVsDisease
dependencyCount: 0
Package: cnvGSAdata
Version: 1.26.0
Depends: R (>= 2.10), cnvGSA
License: LGPL
MD5sum: e3c8db1abea6b0ba8a43d98d462de475
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 <joseph.r.lugo@gmail.com>
Maintainer: Joseph Lugo <joseph.r.lugo@gmail.com>
git_url: https://git.bioconductor.org/packages/cnvGSAdata
git_branch: RELEASE_3_12
git_last_commit: b699546
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/cnvGSAdata_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: cnvGSA
dependencyCount: 26
Package: COHCAPanno
Version: 1.26.0
Depends: R (>= 2.10)
License: GPL-3
MD5sum: 298ff9d979750c2247bbbcb21fd9065f
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 <cwarden45@gmail.com>
git_url: https://git.bioconductor.org/packages/COHCAPanno
git_branch: RELEASE_3_12
git_last_commit: a896171
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/COHCAPanno_1.26.0.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
dependsOnMe: COHCAP
dependencyCount: 0
Package: colonCA
Version: 1.32.0
Depends: Biobase (>= 2.5.5)
License: LGPL
MD5sum: cd267cda8d61b65fb0df3d7c1aa0b734
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 <sylvia.merk@ukmuenster.de>
git_url: https://git.bioconductor.org/packages/colonCA
git_branch: RELEASE_3_12
git_last_commit: 001877f
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/colonCA_1.32.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: clustComp, copa
dependencyCount: 7
Package: CONFESSdata
Version: 1.18.0
Depends: R (>= 3.3)
License: GPL-2
MD5sum: dda8f172ecf21ba0b00e963d6231cb37
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 <dlow@imcb.a-star.edu.sg>
git_url: https://git.bioconductor.org/packages/CONFESSdata
git_branch: RELEASE_3_12
git_last_commit: 26bb1fc
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/CONFESSdata_1.18.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: CONFESS
dependencyCount: 0
Package: ConnectivityMap
Version: 1.26.0
Depends: R (>= 2.15.1)
Suggests: RUnit, BiocGenerics
License: GPL-3
MD5sum: 5c08dc220e174734ca74fd589aec189a
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<pshannon@systemsbiology.org>
git_url: https://git.bioconductor.org/packages/ConnectivityMap
git_branch: RELEASE_3_12
git_last_commit: a724faa
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ConnectivityMap_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: COPDSexualDimorphism.data
Version: 1.26.0
License: LGPL-2.1
MD5sum: 7247454744e4b193f56e990e2feb18ac
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 <fah@cs.stanford.edu>
git_url:
https://git.bioconductor.org/packages/COPDSexualDimorphism.data
git_branch: RELEASE_3_12
git_last_commit: c093858
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/COPDSexualDimorphism.data_1.26.0.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
dependencyCount: 0
Package: CopyhelpeR
Version: 1.22.0
Depends: R(>= 2.10)
Suggests: BiocStyle
License: GPL-2
MD5sum: fb29dbd790ca5fc2325534c31b0ed02f
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 <o.krijgsman@nki.nl>
git_url: https://git.bioconductor.org/packages/CopyhelpeR
git_branch: RELEASE_3_12
git_last_commit: 205e1ab
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/CopyhelpeR_1.22.0.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
importsMe: CopywriteR
dependencyCount: 0
Package: CopyNeutralIMA
Version: 1.8.0
Depends: R (>= 3.5.0)
Imports: ExperimentHub,Rdpack (>= 0.8)
Suggests: BiocStyle,knitr,rmarkdown,minfi,conumee,minfiData
License: Artistic-2.0
MD5sum: 71821baad71fd44f7ae150de964cb906
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 <xavier.pastor@compbio-dev.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/CopyNeutralIMA
git_branch: RELEASE_3_12
git_last_commit: 2f77b25
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/CopyNeutralIMA_1.8.0.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
dependencyCount: 79
Package: COSMIC.67
Version: 1.26.0
Depends: R (>= 3.0.2)
Imports: GenomicRanges, SummarizedExperiment, VariantAnnotation
Suggests: testthat, BiocStyle, knitr
License: GPL-3
MD5sum: fffff2f348c0206f432ddcb35ad2ba19
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 <jg-bioc@gmx.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/COSMIC.67
git_branch: RELEASE_3_12
git_last_commit: ae9f5cb
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/COSMIC.67_1.26.0.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
importsMe: appreci8R
dependencyCount: 90
Package: CRCL18
Version: 1.10.0
Depends: R (>= 3.0), Biobase
License: GPL-2
MD5sum: 331bd8ee85f2e873748545e4a992ec6d
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 <claudio.isella@ircc.it>
git_url: https://git.bioconductor.org/packages/CRCL18
git_branch: RELEASE_3_12
git_last_commit: 401b60e
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/CRCL18_1.10.0.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
dependencyCount: 7
Package: curatedAdipoArray
Version: 1.2.0
Depends: R (>= 4.0)
Suggests: knitr, rmarkdown, ExperimentHub, SummarizedExperiment
License: GPL-3 + file LICENSE
MD5sum: 81026f9ca27d857e8fe4831d9c63859b
NeedsCompilation: no
Title: A Curated Microarrays Dataset of MDI-induced Differentiated
Adipocytes (3T3-L1) Under Genetic and Pharmacological
Perturbations
Description: A curated dataset of Microarrays samples. The samples are
MDI- induced pre-adipocytes (3T3-L1) at different time
points/stage of differentiation under different types of
genetic (knockdown/overexpression) and pharmacological (drug
treatment) perturbations. The package documents the data
collection and processing. In addition to the documentation,
the package contains the scripts that was used to generated the
data.
biocViews: ExperimentData, ExperimentHub, GEO, MicroarrayData
Author: Mahmoud Ahmed [aut, cre]
(<https://orcid.org/0000-0002-4377-6541>)
Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy@students.kasralainy.edu.eg>
URL: https://github.com/MahShaaban/curatedAdipoArray
VignetteBuilder: knitr
BugReports: https://github.com/MahShaaban/curatedAdipoArray/issues
git_url: https://git.bioconductor.org/packages/curatedAdipoArray
git_branch: RELEASE_3_12
git_last_commit: 1c38c92
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/curatedAdipoArray_1.2.0.tar.gz
vignettes: vignettes/curatedAdipoArray/inst/doc/curatedAdipoArray.html
vignetteTitles: Using curatedAdipoArray
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/curatedAdipoArray/inst/doc/curatedAdipoArray.R
dependencyCount: 0
Package: curatedAdipoChIP
Version: 1.6.0
Depends: R (>= 3.6), SummarizedExperiment, ExperimentHub
Suggests: knitr, rmarkdown, GenomicFeatures, ChIPseeker, AnnotationDbi,
S4Vectors, DESeq2, fastqcr, devtools, testthat, readr, dplyr,
tidyr, ggplot2
License: GPL-3
MD5sum: 9bd98da195821d9c0a53c0e3f5acae60
NeedsCompilation: no
Title: A Curated ChIP-Seq Dataset of MDI-induced Differentiated
Adipocytes (3T3-L1)
Description: A curated dataset of publicly available ChIP-sequencing of
transcription factors, chromatin remodelers and histone
modifications in the 3T3-L1 pre-adipocyte cell line. The
package document the data collection, pre-processing and
processing of the data. In addition to the documentation, the
package contains the scripts that was used to generated the
data.
biocViews: ExperimentData, ExperimentHub, GEO, ChIPSeqData,
SequencingData
Author: Mahmoud Ahmed [aut, cre]
(<https://orcid.org/0000-0002-4377-6541>)
Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy@students.kasralainy.edu.eg>
URL: https://github.com/MahShaaban/curatedAdipoChIP
VignetteBuilder: knitr
BugReports: https://github.com/MahShaaban/curatedAdipoChIP/issues
git_url: https://git.bioconductor.org/packages/curatedAdipoChIP
git_branch: RELEASE_3_12
git_last_commit: 8d022c7
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/curatedAdipoChIP_1.6.0.tar.gz
vignettes: vignettes/curatedAdipoChIP/inst/doc/curatedAdipoChIP.html
vignetteTitles: Using curatedAdipoChIP
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/curatedAdipoChIP/inst/doc/curatedAdipoChIP.R
dependencyCount: 91
Package: curatedAdipoRNA
Version: 1.6.0
Depends: R (>= 3.6), SummarizedExperiment
Suggests: knitr, rmarkdown, DESeq2, fastqcr, devtools, testthat, readr,
dplyr, tidyr, ggplot2, S4Vectors
License: GPL-3
MD5sum: 443349a9adfb56bfea59313f48586108
NeedsCompilation: no
Title: A Curated RNA-Seq Dataset of MDI-induced Differentiated
Adipocytes (3T3-L1)
Description: A curated dataset of RNA-Seq samples. The samples are
MDI-induced pre-phagocytes (3T3-L1) at different time
points/stage of differentiation. The package document the data
collection, pre-processing and processing. In addition to the
documentation, the package contains the scripts that was used
to generated the data.
biocViews: ExperimentData, GEO, RNASeqData, SequencingData
Author: Mahmoud Ahmed [aut, cre]
(<https://orcid.org/0000-0002-4377-6541>)
Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy@students.kasralainy.edu.eg>
URL: https://github.com/MahShaaban/curatedAdipoRNA
VignetteBuilder: knitr
BugReports: https://github.com/MahShaaban/curatedAdipoRNA/issues
git_url: https://git.bioconductor.org/packages/curatedAdipoRNA
git_branch: RELEASE_3_12
git_last_commit: 0f10b2d
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/curatedAdipoRNA_1.6.0.tar.gz
vignettes:
vignettes/curatedAdipoRNA/inst/doc/curatedadiporna_vignette.html
vignetteTitles: Using curatedAdipoRNA
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/curatedAdipoRNA/inst/doc/curatedadiporna_vignette.R
dependencyCount: 26
Package: curatedBladderData
Version: 1.26.0
Depends: R (>= 2.10.0), affy
Suggests: BiocStyle, survival, xtable, sva, genefilter, logging
License: Artistic-2.0
MD5sum: 41e26d27e586d73abca624091e1012cc
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 <markus@jimmy.harvard.edu>
URL: https://github.com/lima1/curatedBladderData
git_url: https://git.bioconductor.org/packages/curatedBladderData
git_branch: RELEASE_3_12
git_last_commit: 10c26cc
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/curatedBladderData_1.26.0.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
suggestsMe: covEB
dependencyCount: 13
Package: curatedBreastData
Version: 2.18.0
Depends: R (>= 3.0.0), XML, ggplot2, impute, Biobase, BiocStyle
Imports: methods, stats
License: GPL (>= 2)
MD5sum: a7d4a16107607aac279cf9408454189a
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 <katie.planey@gmail.com>
git_url: https://git.bioconductor.org/packages/curatedBreastData
git_branch: RELEASE_3_12
git_last_commit: 464335b
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/curatedBreastData_2.18.0.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
dependencyCount: 61
Package: curatedCRCData
Version: 2.22.0
Depends: R (>= 2.10.0), nlme
Imports: BiocGenerics
Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable,
futile.logger, BiocStyle
License: Artistic-2.0
MD5sum: a6979b1f911ecb7321e2ccdac26962cb
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 <princyparsana@jhu.edu>
URL: https://bitbucket.org/biobakery/curatedcrcdata
git_url: https://git.bioconductor.org/packages/curatedCRCData
git_branch: RELEASE_3_12
git_last_commit: fe88edd
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/curatedCRCData_2.22.0.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
dependencyCount: 10
Package: curatedMetagenomicData
Version: 1.20.0
Depends: R (>= 4.0.0), AnnotationHub (>= 2.9.0), Biobase (>= 2.37.0),
dplyr (>= 0.5.0), ExperimentHub (>= 1.3.0)
Imports: magrittr, methods, S4Vectors, tidyr, utils
Suggests: ape, covr, BiocCheck, BiocManager, BiocParallel, BiocStyle,
devtools, ggplot2, knitr, metagenomeSeq, phyloseq, readr,
RISmed, rmarkdown, roxygen2, testthat
License: Artistic-2.0
MD5sum: 2d9208076ddeb06ee8c52e46521f6fb7
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 <schiffer.lucas@gmail.com>, Edoardo Pasolli
<edoardo.pasolli@unitn.it>, Levi Waldron
<lwaldron.research@gmail.com>, Faizan Malik
<faizankmalik2012@yahoo.com>, Nicola Segata
<nicola.segata@unitn.it>, Valerie Obenchain
<Valerie.Obenchain@roswellpark.org>, Morgan Martin
<martin.morgan@roswellpark.org>
Maintainer: Lucas Schiffer <schiffer.lucas@gmail.com>
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_12
git_last_commit: 0af9806
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/curatedMetagenomicData_1.20.0.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: lefser, metavizr, MMUPHin, HMP16SData
dependencyCount: 79
Package: curatedOvarianData
Version: 1.28.0
Depends: R (>= 2.10.0), affy
Imports: BiocGenerics
Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable,
futile.logger, BiocStyle
License: Artistic-2.0
MD5sum: a85ad4d6258a7a78a000c185e7b17e3d
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 <lwaldron.research@gmail.com>
URL: http://bcb.dfci.harvard.edu/ovariancancer
git_url: https://git.bioconductor.org/packages/curatedOvarianData
git_branch: RELEASE_3_12
git_last_commit: 27fa1d5
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/curatedOvarianData_1.28.0.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
suggestsMe: doppelgangR, simulatorZ
dependencyCount: 13
Package: curatedTCGAData
Version: 1.12.1
Depends: R (>= 3.5.0), MultiAssayExperiment
Imports: AnnotationHub, ExperimentHub, HDF5Array, methods, S4Vectors,
stats, SummarizedExperiment, utils
Suggests: BiocStyle, knitr, RaggedExperiment, readr, rmarkdown,
TCGAutils, testthat
License: Artistic-2.0
MD5sum: 31afbe438f83a01613291454d930d0d5
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) as MultiAssayExperiment objects.
MultiAssayExperiment integrates multiple assays (e.g., RNA-seq,
copy number, mutation, microRNA, protein, and others) with
clinical / pathological data. It also links assay barcodes with
patient identifiers, enabling harmonized subsetting of rows
(features) and columns (patients / samples) across the entire
multi-'omics experiment.
biocViews: Homo_sapiens_Data, ReproducibleResearch, CancerData,
ExperimentHub
Author: Marcel Ramos [aut, cre], Levi Waldron [ctb], Lucas Schiffer
[ctb], Ludwig Geistlinger [ctb], Valerie Obenchain [ctb],
Martin Morgan [ctb]
Maintainer: Marcel Ramos <marcel.ramos@roswellpark.org>
VignetteBuilder: knitr
BugReports: https://github.com/waldronlab/curatedTCGAData/issues
git_url: https://git.bioconductor.org/packages/curatedTCGAData
git_branch: RELEASE_3_12
git_last_commit: 967b951
git_last_commit_date: 2021-04-23
Date/Publication: 2021-04-26
source.ver: src/contrib/curatedTCGAData_1.12.1.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
importsMe: AMARETTO, BiocOncoTK
suggestsMe: CNVRanger, deco, glmSparseNet, netDx, TCGAutils
dependencyCount: 98
Package: DAPARdata
Version: 1.20.1
Depends: R (>= 4.0.3)
Imports: utils, knitr, MSnbase
Suggests: DAPAR, Prostar
License: GPL-2
MD5sum: f91728791d6d45d5e50eca764af4a499
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 <samuel.wieczorek@cea.fr>
URL: http://www.prostar-proteomics.org/
BugReports: https://github.com/samWieczorek/DAPARdata/issues
git_url: https://git.bioconductor.org/packages/DAPARdata
git_branch: RELEASE_3_12
git_last_commit: 65d3947
git_last_commit_date: 2020-11-16
Date/Publication: 2020-11-16
source.ver: src/contrib/DAPARdata_1.20.1.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: 1.30.0
Depends: R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db
License: LGPL
MD5sum: 020cdac17c49a10583970d2c4ef2c238
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 <huber@ebi.ac.uk>, Joern Toedling
<toedling@ebi.ac.uk>
Maintainer: Wolfgang Huber <huber@ebi.ac.uk>
URL: http://www.ebi.ac.uk/huber
git_url: https://git.bioconductor.org/packages/davidTiling
git_branch: RELEASE_3_12
git_last_commit: d086898
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/davidTiling_1.30.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 81
Package: depmap
Version: 1.4.0
Depends: R (>= 3.6), methods, dplyr
Imports: utils, ExperimentHub, AnnotationHub
Suggests: knitr, rmarkdown, BiocStyle, viridis, gridExtra, ggplot2,
readr, tibble, stringr, tidyr
License: Artistic-2.0
MD5sum: acf3810b6d2120cdee9354ac32418f64
NeedsCompilation: no
Title: Cancer Dependency Map Data Package
Description: The depmap package is a data package that accesses datsets
from the Broad Institute DepMap cancer dependency study using
ExperimentHub. Datasets from the most current release are
available, including RNAI and CRISPR-Cas9 gene knockout screens
quantifying the genetic dependency for select cancer cell
lines. Additional datasets are also available pertaining to the
log copy number of genes for select cell lines, protein
expression of cell lines as measured by reverse phase protein
lysate microarray (RPPA), 'Transcript Per Million' (TPM) data,
as well as supplementary datasets which contain metadata and
mutation calls for the other datasets found in the current
release. The 19Q3 release adds the drug_dependency dataset,
that contains cancer cell line dependency data with respect to
drug and drug-candidate compounds. The 20Q2 release adds the
proteomic dataset that contains quantitative profiling of
proteins via mass spectrometry. This package will be updated on
a quarterly basis to incorporate the latest Broad Institute
DepMap Public cancer dependency datasets. All data made
available in this package was generated by the Broad Institute
DepMap for research purposes and not intended for clinical use.
This data is distributed under the Creative Commons license
(Attribution 4.0 International (CC BY 4.0)).
biocViews: ExperimentHub, ExperimentData, ReproducibleResearch,
RepositoryData, AssayDomainData, CopyNumberVariationData,
DiseaseModel, CancerData, BreastCancerData, ColonCancerData,
KidneyCancerData, LeukemiaCancerData, LungCancerData,
OvarianCancerData, ProstateCancerData, OrganismData,
Homo_sapiens_Data, PackageTypeData, SpecimenSource,
CellCulture, Genome, Proteome, StemCell, Tissue
Author: Laurent Gatto [cre, aut], Theo Killian [aut]
Maintainer: Laurent Gatto <laurent.gatto@uclouvain.be>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/depmap
git_branch: RELEASE_3_12
git_last_commit: 8f31da1
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/depmap_1.4.0.tar.gz
vignettes: vignettes/depmap/inst/doc/depmap.html,
vignettes/depmap/inst/doc/using_depmap.html
vignetteTitles: depmap, depmap use cases
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/depmap/inst/doc/depmap.R,
vignettes/depmap/inst/doc/using_depmap.R
dependencyCount: 77
Package: derfinderData
Version: 2.8.1
Depends: R(>= 3.1.1)
Suggests: sessioninfo, knitr (>= 1.6), RefManageR, rmarkdown (>=
0.3.3), BiocStyle
License: Artistic-2.0
MD5sum: f869a002a5f352d038887b03e85e6ece
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]
(<https://orcid.org/0000-0003-2140-308X>), Andrew Jaffe [aut]
(<https://orcid.org/0000-0001-6886-1454>), Jeffrey Leek [aut,
ths] (<https://orcid.org/0000-0002-2873-2671>)
Maintainer: Leonardo Collado-Torres <lcolladotor@gmail.com>
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_12
git_last_commit: 4f572dd
git_last_commit_date: 2020-12-17
Date/Publication: 2020-12-21
source.ver: src/contrib/derfinderData_2.8.1.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
suggestsMe: derfinder, derfinderPlot
dependencyCount: 0
Package: DeSousa2013
Version: 1.26.0
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: de6791649f9c7eb0ee52e07ac94081d1
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 <Xin.Wang@cruk.cam.ac.uk>
Maintainer: Xin Wang <Xin.Wang@cruk.cam.ac.uk>
git_url: https://git.bioconductor.org/packages/DeSousa2013
git_branch: RELEASE_3_12
git_last_commit: 46e8cec
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/DeSousa2013_1.26.0.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
dependencyCount: 135
Package: diffloopdata
Version: 1.18.0
Suggests: knitr, rmarkdown
License: MIT + file LICENSE
MD5sum: c4846251bd0310376e6e2bd684230f34
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 <caleblareau@g.harvard.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/diffloopdata
git_branch: RELEASE_3_12
git_last_commit: 02b0f89
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/diffloopdata_1.18.0.tar.gz
vignettes: vignettes/diffloopdata/inst/doc/diffloopdata.html
vignetteTitles: diffloopdata
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
suggestsMe: diffloop
dependencyCount: 0
Package: diggitdata
Version: 1.22.0
Depends: R(>= 2.14.0), Biobase, methods
Imports: viper
License: GPL (>=2)
MD5sum: 76cecf55162d30e82871e14710f3cfa7
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 <reef103@gmail.com>
git_url: https://git.bioconductor.org/packages/diggitdata
git_branch: RELEASE_3_12
git_last_commit: d913c35
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/diggitdata_1.22.0.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
suggestsMe: diggit
dependencyCount: 22
Package: DLBCL
Version: 1.30.0
Depends: R(>= 2.11.0), Biobase
License: GPL (>=2)
MD5sum: 07852b15eed41ac0e616691d984b3eaa
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
<marcus.dittrich@biocentrum.uni-wuerzburg.de>
URL: http://bionet.bioapps.biozentrum.uni-wuerzburg.de/
git_url: https://git.bioconductor.org/packages/DLBCL
git_branch: RELEASE_3_12
git_last_commit: b7a34f3
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/DLBCL_1.30.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: BioNet
dependencyCount: 7
Package: DmelSGI
Version: 1.22.1
Depends: R (>= 3.0)
Imports: grid, TSP, limma, rhdf5, knitr, abind, gplots, igraph,
grDevices, graphics, stats
Suggests: BiocStyle, EBImage, RColorBrewer, RNAinteractMAPK,
RSVGTipsDevice, cgdsr, hwriter, xtable, beeswarm
License: Artistic-2.0
MD5sum: 9a0cfcec3136b07bf23d1b10a89dea36
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 [aut], Wolfgang Huber [ctb], Mike Smith [cre]
Maintainer: Mike Smith <mike.smith@embl.de>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/DmelSGI
git_branch: RELEASE_3_12
git_last_commit: 32f1478
git_last_commit_date: 2020-12-17
Date/Publication: 2020-12-21
source.ver: src/contrib/DmelSGI_1.22.1.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
dependencyCount: 36
Package: DMRcatedata
Version: 2.8.2
Depends: R (>= 3.6), ExperimentHub
Imports: GenomicFeatures, Gviz, readxl, plyr, rtracklayer,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Suggests: knitr
License: GPL-3
MD5sum: 2749d251c87be574964588508b110ab5
NeedsCompilation: no
Title: Data Package for DMRcate
Description: This package contains 9 data objects supporting
functionality and examples of the Bioconductor package DMRcate.
biocViews: ExperimentHub, ExperimentData, SNPData, Homo_sapiens_Data,
Mus_musculus_Data, SequencingData, MicroarrayData, Genome
Author: Tim Peters
Maintainer: Tim Peters <t.peters@garvan.org.au>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/DMRcatedata
git_branch: RELEASE_3_12
git_last_commit: 65779e8
git_last_commit_date: 2021-02-08
Date/Publication: 2021-02-11
source.ver: src/contrib/DMRcatedata_2.8.2.tar.gz
vignettes: vignettes/DMRcatedata/inst/doc/DMRcatedata.pdf
vignetteTitles: The DMRcate package user's guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DMRcatedata/inst/doc/DMRcatedata.R
dependencyCount: 195
Package: DonaPLLP2013
Version: 1.28.0
Depends: EBImage, parallel
License: Artistic-2.0
MD5sum: a712142d0ef20154b977ac84881d4761
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 <joseph.barry@embl.de>
git_url: https://git.bioconductor.org/packages/DonaPLLP2013
git_branch: RELEASE_3_12
git_last_commit: da3f5ed
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/DonaPLLP2013_1.28.0.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
dependencyCount: 25
Package: dorothea
Version: 1.2.2
Depends: R (>= 4.0)
Imports: dplyr, magrittr, bcellViper, viper
Suggests: Biobase, BiocStyle, knitr, pheatmap, pkgdown, rmarkdown,
Seurat, SingleCellExperiment, SummarizedExperiment, testthat
(>= 2.1.0), tibble, tidyr, utils
License: GPL-3 + file LICENSE
MD5sum: 3b1e90fe8e55a5579ba83fb59933f856
NeedsCompilation: no
Title: Collection Of Human And Mouse TF Regulons
Description: This package contains human and mouse TF regulons. The
human regulons were curated and collected from different types
of evidence such as literature curated resources, ChIP-seq
peaks, TF binding site motifs and interactions inferred
directly from gene expression. The mouse regulons were
constructed by mapping the human gene symbols to their
orthologs in mice. Those regulons can be coupled with any
statistical method that aims to analyse gene sets to infer TF
activity from gene expression data. Preferably the statistical
method viper is used.
biocViews: ExperimentData, Homo_sapiens_Data, Mus_musculus_Data
Author: Christian H. Holland [cre, aut]
(<https://orcid.org/0000-0002-3060-5786>), Luz Garcia-Alonso
[aut], Alberto Valdeolivas [ctb], Minoo Ashtiani [ctb], Attila
Gabor [ctb]
Maintainer: Christian H. Holland <cholland2408@gmail.com>
URL: https://saezlab.github.io/dorothea/,
https://github.com/saezlab/dorothea
VignetteBuilder: knitr
BugReports: https://github.com/saezlab/dorothea/issues
git_url: https://git.bioconductor.org/packages/dorothea
git_branch: RELEASE_3_12
git_last_commit: 88a7812
git_last_commit_date: 2021-04-18
Date/Publication: 2021-04-19
source.ver: src/contrib/dorothea_1.2.2.tar.gz
vignettes: vignettes/dorothea/inst/doc/bulk_vignette.html,
vignettes/dorothea/inst/doc/single_cell_vignette.html
vignetteTitles: TF activity inference from bulk transcriptomic data
with DoRothEA as regulon resource., TF activity inference from
scRNA-seq data with DoRothEA as regulon resource.
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/dorothea/inst/doc/bulk_vignette.R,
vignettes/dorothea/inst/doc/single_cell_vignette.R
suggestsMe: MethReg
dependencyCount: 41
Package: DREAM4
Version: 1.26.0
Depends: R (>= 2.15.1), SummarizedExperiment
Suggests: RUnit, networkBMA
License: GPL
MD5sum: 7c586716529100136738a81ff4091df1
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 <pshannon@systemsbiology.org>
git_url: https://git.bioconductor.org/packages/DREAM4
git_branch: RELEASE_3_12
git_last_commit: 6ae07c0
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/DREAM4_1.26.0.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
dependencyCount: 26
Package: dressCheck
Version: 0.28.0
Depends: R (>= 2.10.1), methods, Biobase (>= 2.5.5)
Suggests: survival, chron
License: Artistic-2.0
MD5sum: a97ead2bc0d2455642ce4649245e2f2b
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 <stvjc@channing.harvard.edu>
Maintainer: Vincent Carey <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/dressCheck
git_branch: RELEASE_3_12
git_last_commit: 1551865
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/dressCheck_0.28.0.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
dependencyCount: 7
Package: DropletTestFiles
Version: 1.0.0
Imports: utils, ExperimentHub, AnnotationHub, S4Vectors
Suggests: BiocStyle, knitr, rmarkdown, testthat, DropletUtils
License: GPL-3
MD5sum: 1ece96b688674c1001b7adb4dd816433
NeedsCompilation: no
Title: Test Files for Single-Cell Droplet Utilities
Description: Assorted files generated from droplet-based single-cell
protocols, to be used for testing functions in DropletUtils.
Primarily intended for storing files that directly come out of
processing pipelines like 10X Genomics' CellRanger software,
prior to the formation of a SingleCellExperiment object. Unlike
other packages, this is not designed to provide objects that
are immediately ready for analysis.
biocViews: ExperimentHub, ExperimentData, ExpressionData,
SequencingData, RNASeqData, SingleCellData
Author: Aaron Lun [ctb, cre]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/DropletTestFiles
git_branch: RELEASE_3_12
git_last_commit: 47f2429
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/DropletTestFiles_1.0.0.tar.gz
vignettes: vignettes/DropletTestFiles/inst/doc/motivation.html
vignetteTitles: Test files for droplet-based single-cell utilities
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DropletTestFiles/inst/doc/motivation.R
suggestsMe: DropletUtils
dependencyCount: 77
Package: DrugVsDiseasedata
Version: 1.26.0
Depends: R (>= 2.10)
License: GPL-3
MD5sum: 8171e917de9d7c39412b4cd440204237
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 <saezrodriguez@ebi.ac.uk>
git_url: https://git.bioconductor.org/packages/DrugVsDiseasedata
git_branch: RELEASE_3_12
git_last_commit: 343ffe5
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/DrugVsDiseasedata_1.26.0.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
dependsOnMe: DrugVsDisease
dependencyCount: 0
Package: dsQTL
Version: 0.28.0
Depends: R (>= 2.15.0), utils, Biobase, SummarizedExperiment, GGBase
(>= 3.31.1)
Suggests: GGtools, rtracklayer
License: Artistic-2.0
MD5sum: fbfe32fb1a198d0d3b2af1d521b83828
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 <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/dsQTL
git_branch: RELEASE_3_12
git_last_commit: 7026e53
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/dsQTL_0.28.0.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
dependencyCount: 60
Package: DuoClustering2018
Version: 1.8.0
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: 6b5e862d99d00d4af5238bc26bf4de6e
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 <angelo.duo@icloud.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/DuoClustering2018
git_branch: RELEASE_3_12
git_last_commit: 6cdb6ba
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/DuoClustering2018_1.8.0.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
suggestsMe: corral, scry
dependencyCount: 104
Package: DvDdata
Version: 1.26.0
Depends: R (>= 2.10)
License: GPL-3
MD5sum: a2c804758996296c68585304ba76ea26
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 <saezrodriguez@ebi.ac.uk>
git_url: https://git.bioconductor.org/packages/DvDdata
git_branch: RELEASE_3_12
git_last_commit: 11bae02
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/DvDdata_1.26.0.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
dependencyCount: 0
Package: dyebiasexamples
Version: 1.30.0
Depends: R (>= 1.4.1), marray, GEOquery
Suggests: dyebias, convert, Biobase
License: GPL-3
MD5sum: 9c09e15dec9d1ef74135df21905a20a3
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 <plijnzaad@gmail.com>
URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad
git_url: https://git.bioconductor.org/packages/dyebiasexamples
git_branch: RELEASE_3_12
git_last_commit: bd3863c
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/dyebiasexamples_1.30.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
suggestsMe: dyebias
dependencyCount: 44
Package: EatonEtAlChIPseq
Version: 0.28.0
Depends: GenomicRanges (>= 1.5.42), ShortRead, rtracklayer
License: Artistic 2.0
MD5sum: 9ed0412eab89b316b17c190c6d2c167c
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 <paboyoun@fhcrc.org>
Maintainer: Patrick Aboyoun <paboyoun@fhcrc.org>
git_url: https://git.bioconductor.org/packages/EatonEtAlChIPseq
git_branch: RELEASE_3_12
git_last_commit: 2fdb80c
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/EatonEtAlChIPseq_0.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 46
Package: ecoliLeucine
Version: 1.30.0
Depends: R (>= 1.9.0), affy (>= 1.23.4), ecolicdf
License: GPL (>= 2)
MD5sum: da5ba90ef198c3bf7f4b5f1090e37cdb
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 <lgautier@gmail.com>
git_url: https://git.bioconductor.org/packages/ecoliLeucine
git_branch: RELEASE_3_12
git_last_commit: 17c3f26
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ecoliLeucine_1.30.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: ecolitk
dependencyCount: 33
Package: EGSEAdata
Version: 1.18.0
Depends: R (>= 3.4)
Suggests: EGSEA
License: file LICENSE
MD5sum: 0f3e2631bed49e54122484c3fb141790
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 <m.hamdoosh@gmail.com>
git_url: https://git.bioconductor.org/packages/EGSEAdata
git_branch: RELEASE_3_12
git_last_commit: dee7183
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/EGSEAdata_1.18.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
importsMe: EGSEA
dependencyCount: 0
Package: ELMER.data
Version: 2.14.0
Depends: R (>= 3.5.0)
Imports: GenomicRanges
Suggests: BiocStyle, knitr, dplyr, devtools, DT
License: GPL-3
MD5sum: 731029db8af9f972705aac37cf4a30de
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 - Human_genes__GRCh37_p13 -
Human_genes__GRCh38_p12 - Human_genes__GRCh37_p13__tss -
Human_genes__GRCh38_p12__tss
biocViews: AssayDomainData, TechnologyData, OrganismData
Author: Tiago Chedraoui Silva, Lijing Yao Simon Coetzee, Benjamin P.
Berman
Maintainer: Tiago Chedraoui Silva <tiagochst@usp.br>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/ELMER.data
git_branch: RELEASE_3_12
git_last_commit: f9d6121
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ELMER.data_2.14.0.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
dependsOnMe: ELMER
dependencyCount: 17
Package: estrogen
Version: 1.36.0
Suggests: affy, hgu95av2, hgu95av2cdf, vsn, knitr
License: LGPL
MD5sum: 2d2db0089775e2269a83d091e43f8e69
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 <wolfgang.huber@embl.de>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/estrogen
git_branch: RELEASE_3_12
git_last_commit: bc62605
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/estrogen_1.36.0.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
suggestsMe: AffyExpress, categoryCompare
dependencyCount: 0
Package: etec16s
Version: 1.18.0
Depends: R (>= 3.3), Biobase, metagenomeSeq(>= 1.12.0)
License: Artistic-2.0
MD5sum: b21ca05bc6c54f26c97d6253524906c4
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 <jpaulson@jimmy.harvard.edu>
git_url: https://git.bioconductor.org/packages/etec16s
git_branch: RELEASE_3_12
git_last_commit: 5c229f4
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/etec16s_1.18.0.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
suggestsMe: metavizr
dependencyCount: 29
Package: faahKO
Version: 1.30.0
Depends: R (>= 2.10), xcms (>= 3.4.0)
License: LGPL
MD5sum: 79b9f4f1ee9df24f65b0c9437b273f85
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 <csmith@scripps.edu>
Maintainer: Steffen Neumann <sneumann@ipb-halle.de>
URL: http://dx.doi.org/10.1021/bi0480335
git_url: https://git.bioconductor.org/packages/faahKO
git_branch: RELEASE_3_12
git_last_commit: 08e8a3d
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/faahKO_1.30.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
importsMe: cosmiq
suggestsMe: CAMERA, IPO, MAIT, peakPantheR, Risa, xcms
dependencyCount: 92
Package: fabiaData
Version: 1.28.0
Depends: R (>= 2.10.0), Biobase
Imports: utils
Suggests: fabia
License: LGPL (>= 2.1)
MD5sum: ca293edfe8825ec23d92e687e6aaa7c3
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 <hochreit@bioinf.jku.at>
Maintainer: Sepp Hochreiter <hochreit@bioinf.jku.at>
URL: http://www.bioinf.jku.at/software/fabia/fabia.html
git_url: https://git.bioconductor.org/packages/fabiaData
git_branch: RELEASE_3_12
git_last_commit: 303b9fa
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/fabiaData_1.28.0.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
dependencyCount: 7
Package: facsDorit
Version: 1.32.0
Depends: R (>= 1.9.1), prada (>= 1.0.5)
License: GPL-2
MD5sum: 47ebdabaa1996948fc860b0ec7746549
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 <f.hahne@dfkz-heidelberg.de>
Maintainer: Florian Hahne <f.hahne@dfkz-heidelberg.de>
URL: http://www.dkfz.de/mga
git_url: https://git.bioconductor.org/packages/facsDorit
git_branch: RELEASE_3_12
git_last_commit: b2236cc
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/facsDorit_1.32.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 1
Package: FANTOM3and4CAGE
Version: 1.26.0
Depends: R (>= 2.15.0)
License: GPL-3
MD5sum: 391989302c9e5c4648880e437621846a
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 <vanja.haberle@bio.uib.no>
Maintainer: Vanja Haberle <vanja.haberle@bio.uib.no>
git_url: https://git.bioconductor.org/packages/FANTOM3and4CAGE
git_branch: RELEASE_3_12
git_last_commit: 5d4f3b9
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/FANTOM3and4CAGE_1.26.0.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
suggestsMe: CAGEr
dependencyCount: 0
Package: ffpeExampleData
Version: 1.28.0
Depends: R (>= 2.10.0), lumi
Suggests: genefilter, affy
License: GPL (>2)
MD5sum: 358082994186101e379ebd587203fd02
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 <lwaldron@hsph.harvard.edu>
git_url: https://git.bioconductor.org/packages/ffpeExampleData
git_branch: RELEASE_3_12
git_last_commit: 6c21a7b
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ffpeExampleData_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: ffpe
dependencyCount: 151
Package: fibroEset
Version: 1.32.0
Depends: Biobase (>= 2.5.5)
License: LGPL
MD5sum: 8904c2a4b2860cfb07e0aa68f8958344
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 <merk@ibe.med.uni-muenchen.de>
git_url: https://git.bioconductor.org/packages/fibroEset
git_branch: RELEASE_3_12
git_last_commit: 63d4a9b
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/fibroEset_1.32.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: biocGraph, clusterStab, geneplotter
dependencyCount: 7
Package: FieldEffectCrc
Version: 1.0.0
Depends: utils
Imports: BiocStyle, RUnit, SummarizedExperiment, ExperimentHub (>=
0.99.6), AnnotationHub, DESeq2
Suggests: knitr, rmarkdown, BiocGenerics, sva, BiocManager
License: Artistic-2.0
MD5sum: 0839850a87335d4073f74c6281bf3b91
NeedsCompilation: no
Title: Tumor, tumor-adjacent normal, and healthy colorectal
transcriptomes as SummarizedExperiment objects
Description: Processed RNA-seq data for 1,139 human primary colorectal
tissue samples across three phenotypes, including tumor, normal
adjacent-to-tumor, and healthy, available as Synapse ID
syn22237139 on synapse.org. Data have been parsed into
SummarizedExperiment objects available via ExperimentHub to
facilitate reproducibility and extension of results from
Dampier et al. (PMCID: PMC7386360, PMID: 32764205).
biocViews: ExperimentData, ReproducibleResearch, Tissue,
Homo_sapiens_Data, ColonCancerData, RNASeqData, ExpressionData,
ExperimentHub, SequencingData
Author: Christopher Dampier [aut, cre]
(<https://orcid.org/0000-0003-3099-6462>), Bioconductor Package
Maintainer [ctb]
Maintainer: Christopher Dampier <chd5n@virginia.edu>
URL:
http://bioconductor.org/packages/release/bioc/html/FieldEffectCrc.html
VignetteBuilder: knitr
BugReports: https://github.com/Bioconductor/FieldEffectCrc/
git_url: https://git.bioconductor.org/packages/FieldEffectCrc
git_branch: RELEASE_3_12
git_last_commit: 5d85803
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/FieldEffectCrc_1.0.0.tar.gz
vignettes: vignettes/FieldEffectCrc/inst/doc/FieldEffectCrc.html
vignetteTitles: SummarizedExperiments of colorectal transcriptomes
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/FieldEffectCrc/inst/doc/FieldEffectCrc.R
dependencyCount: 132
Package: FIs
Version: 1.18.0
Depends: R (>= 3.3)
License: GPL-3
MD5sum: 4ee01349e2693325aeb5d791c0477c8e
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 <hbraselmann@online.de>, Martin
Selmansberger <martin.selmansberger@helmholtz-muenchen.de>
git_url: https://git.bioconductor.org/packages/FIs
git_branch: RELEASE_3_12
git_last_commit: 3ec7700
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/FIs_1.18.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: splineTimeR
dependencyCount: 0
Package: fission
Version: 1.10.0
Depends: R (>= 2.10), SummarizedExperiment
Suggests: knitr
License: LGPL
MD5sum: f7cfcd0f5b86b9ed1028c9719e451271
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 <michaelisaiahlove@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/fission
git_branch: RELEASE_3_12
git_last_commit: ce9c694
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/fission_1.10.0.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
dependsOnMe: ROCpAI, rnaseqGene
dependencyCount: 26
Package: Fletcher2013a
Version: 1.26.0
Depends: R (>= 2.15), limma
Imports: Biobase ,VennDiagram, gplots,grid
License: GPL (>= 2)
MD5sum: db06990ebb49a4761bd8d77760c825a4
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 <mauro.a.castro@gmail.com>
URL: http://dx.doi.org/10.1038/ncomms3464
git_url: https://git.bioconductor.org/packages/Fletcher2013a
git_branch: RELEASE_3_12
git_last_commit: dfcc5cf
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/Fletcher2013a_1.26.0.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
dependencyCount: 20
Package: Fletcher2013b
Version: 1.26.0
Depends: R (>= 2.15), Fletcher2013a, RTN (>= 1.1.2), RedeR (>= 1.8.1),
igraph
Imports: RColorBrewer
License: GPL (>= 2)
MD5sum: 5c265a7b8870cc699a2bf2dee3d08621
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 <mauro.a.castro@gmail.com>
URL: http://dx.doi.org/10.1038/ncomms3464
git_url: https://git.bioconductor.org/packages/Fletcher2013b
git_branch: RELEASE_3_12
git_last_commit: 99bb143
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/Fletcher2013b_1.26.0.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
suggestsMe: geneplast, RTNsurvival
dependencyCount: 133
Package: flowFitExampleData
Version: 1.26.0
Depends: R (>= 2.12.2), flowCore
Imports: methods
License: Artistic-2.0
MD5sum: f84c6a4199827c4f31921d363c24e383
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 <davide.rambaldi@gmail.com>
PackageStatus: Deprecated
git_url: https://git.bioconductor.org/packages/flowFitExampleData
git_branch: RELEASE_3_12
git_last_commit: dd51ba5
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/flowFitExampleData_1.26.0.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
dependencyCount: 19
Package: flowPloidyData
Version: 1.16.0
Suggests: knitr, rmarkdown, flowCore
License: GPL-3
MD5sum: 65ae27ef08ec3633dbe2f25ab5574adc
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 <tyler@plantarum.ca>
Maintainer: Tyler Smith <tyler@plantarum.ca>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/flowPloidyData
git_branch: RELEASE_3_12
git_last_commit: f1cc4d8
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/flowPloidyData_1.16.0.tar.gz
vignettes: vignettes/flowPloidyData/inst/doc/flowPloidyData.html
vignetteTitles: flowPloidy Data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: flowPloidy
dependencyCount: 0
Package: FlowSorted.Blood.450k
Version: 1.28.0
Depends: R (>= 2.13.0), minfi (>= 1.21.2)
License: Artistic-2.0
MD5sum: d2e60244abf62d37defcd2a8d00956ba
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 <andrew.jaffe@libd.org>
git_url: https://git.bioconductor.org/packages/FlowSorted.Blood.450k
git_branch: RELEASE_3_12
git_last_commit: e784ed9
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/FlowSorted.Blood.450k_1.28.0.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
dependsOnMe: methylCC, methylationArrayAnalysis
suggestsMe: mCSEA, minfi, sesame, FlowSorted.Blood.EPIC
dependencyCount: 130
Package: FlowSorted.Blood.EPIC
Version: 1.8.0
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.CordBloodCombined.450k,
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: 9105fa404dee763cb23fefe5ef0626c8
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 <lucas.a.salas.diaz@dartmouth.edu>
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_12
git_last_commit: ffc8bf0
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/FlowSorted.Blood.EPIC_1.8.0.tar.gz
vignettes:
vignettes/FlowSorted.Blood.EPIC/inst/doc/FlowSorted.Blood.EPIC.html
vignetteTitles: FlowSorted.Blood.EPIC
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hasNEWS: TRUE
hasINSTALL: FALSE
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Rfiles:
vignettes/FlowSorted.Blood.EPIC/inst/doc/FlowSorted.Blood.EPIC.R
dependsOnMe: FlowSorted.CordBloodCombined.450k
dependencyCount: 153
Package: FlowSorted.CordBlood.450k
Version: 1.18.0
Depends: R (>= 3.2.0), minfi (>= 1.21.2)
License: Artistic-2.0
MD5sum: 53bad1f7dc311b5a652a9920b5fd1247
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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 <sandre17@jhu.edu>
git_url:
https://git.bioconductor.org/packages/FlowSorted.CordBlood.450k
git_branch: RELEASE_3_12
git_last_commit: edd3525
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/FlowSorted.CordBlood.450k_1.18.0.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
dependencyCount: 130
Package: FlowSorted.CordBloodCombined.450k
Version: 1.6.0
Depends: R (>= 3.6), minfi (>= 1.21.2), SummarizedExperiment,
IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1),
IlluminaHumanMethylationEPICanno.ilm10b4.hg19, ExperimentHub(>=
1.9.1), FlowSorted.Blood.EPIC, utils
Suggests: knitr, rmarkdown, testthat,
IlluminaHumanMethylation450kmanifest(>= 0.2.0),
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
License: GPL-3
MD5sum: 00526756acad9a09c7cd4d5a7411415a
NeedsCompilation: no
Title: Illumina 450k/EPIC data on FACS and MACS umbilical blood cells
Description: Raw data objects to be used for umbilical cord blood cell
proportion estimation in minfi and similar packages. The
FlowSorted.CordBloodCombined.450k object is based in samples
assayed by Bakulski et al, Gervin et al., de Goede et al., and
Lin et al.
biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData,
Genome, TissueMicroarrayData, MethylationArrayData,
ExperimentHub
Author: Lucas A. Salas [cre, aut], Kristina Gervin [aut], Meaghan C.
Jones [aut], Kelly M. Bakulski [ctb], Devin C. Koestler [ctb],
John K. Wiencke [ctb], Karl T. Kelsey [ctb], Robert Lyle [ctb],
Brock C. Christensen [ctb], Janine Felix [ctb]
Maintainer: Lucas A. Salas <lucas.a.salas.diaz@dartmouth.edu>
URL:
https://github.com/immunomethylomics/FlowSorted.CordBloodCombined.450k
VignetteBuilder: knitr
BugReports:
https://github.com/immunomethylomics/FlowSorted.CordBloodCombined.450k/issues.
git_url:
https://git.bioconductor.org/packages/FlowSorted.CordBloodCombined.450k
git_branch: RELEASE_3_12
git_last_commit: 6b7dc43
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/FlowSorted.CordBloodCombined.450k_1.6.0.tar.gz
vignettes:
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Rfiles:
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dependencyCount: 155
Package: FlowSorted.CordBloodNorway.450k
Version: 1.16.0
Depends: R (>= 3.2.0), minfi (>= 1.21.2)
License: Artistic-2.0
MD5sum: 7fa6b88f0996ddbd3ba2b59bf7d713da
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 <kristina.gervin@medisin.uio.no>
URL: https://bitbucket.com/kasperdanielhansen/Illumina_CordBlood
git_url:
https://git.bioconductor.org/packages/FlowSorted.CordBloodNorway.450k
git_branch: RELEASE_3_12
git_last_commit: 00dc1f1
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/FlowSorted.CordBloodNorway.450k_1.16.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: sesame, FlowSorted.Blood.EPIC
dependencyCount: 130
Package: FlowSorted.DLPFC.450k
Version: 1.26.0
Depends: R (>= 2.13.0), minfi (>= 1.21.2)
License: Artistic-2.0
MD5sum: a2d4c816e10735c38c9301ae1fd99024
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 <andrew.jaffe@libd.org>
git_url: https://git.bioconductor.org/packages/FlowSorted.DLPFC.450k
git_branch: RELEASE_3_12
git_last_commit: 7cdd758
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/FlowSorted.DLPFC.450k_1.26.0.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
dependencyCount: 130
Package: flowWorkspaceData
Version: 3.2.0
License: GPL-2
MD5sum: cc6c73d1be535a7ff684560b18691d18
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 <wjiang2@fhcrc.org>
git_url: https://git.bioconductor.org/packages/flowWorkspaceData
git_branch: RELEASE_3_12
git_last_commit: 1722110
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/flowWorkspaceData_3.2.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: COMPASS, CytoML, flowClust, flowCore, flowWorkspace,
ggcyto, openCyto
dependencyCount: 0
Package: frmaExampleData
Version: 1.26.0
Depends: R (>= 2.10.0)
License: GPL (>= 2)
MD5sum: fa9b975e279a2c6dcee3b77f7a623ed9
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 <mmccall@jhsph.edu>
Maintainer: Matthew N. McCall <mmccall@jhsph.edu>
git_url: https://git.bioconductor.org/packages/frmaExampleData
git_branch: RELEASE_3_12
git_last_commit: 319cc8b
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/frmaExampleData_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: frma, frmaTools
dependencyCount: 0
Package: furrowSeg
Version: 1.18.0
Depends: R (>= 3.3), EBImage
Imports: abind, dplyr, locfit, tiff
Suggests: BiocStyle, ggplot2, knitr
License: Artistic-2.0
MD5sum: 908a1933c02e1b4c0976366fb71a2657
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 <joseph.barry@embl.de>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/furrowSeg
git_branch: RELEASE_3_12
git_last_commit: 772b9de
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/furrowSeg_1.18.0.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,
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dependencyCount: 42
Package: gageData
Version: 2.28.0
Depends: R (>= 2.10)
Suggests: gage, pathview, genefilter
License: GPL (>=2.0)
MD5sum: 9b35f4982ee08e306f85da97748094f3
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 <luo_weijun@yahoo.com>
git_url: https://git.bioconductor.org/packages/gageData
git_branch: RELEASE_3_12
git_last_commit: 364cde7
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/gageData_2.28.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: gage
dependencyCount: 0
Package: gaschYHS
Version: 1.28.0
Depends: R (>= 2.14.0), Biobase (>= 2.5.5)
License: Artistic-2.0
MD5sum: f5d6cb2475a29d034c2e8c2b960a908c
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 <stvjc@channing.harvard.edu>
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_12
git_last_commit: ee18d6a
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/gaschYHS_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
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dependencyCount: 7
Package: gatingMLData
Version: 2.30.0
Depends: R (>= 1.9.0)
Suggests: flowUtils
License: GPL
MD5sum: c59b4ff5a1101584c69d6793b80b256e
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 <jspidlen@bccrc.ca>
git_url: https://git.bioconductor.org/packages/gatingMLData
git_branch: RELEASE_3_12
git_last_commit: 6f9614e
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/gatingMLData_2.30.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: flowUtils
dependencyCount: 0
Package: gcspikelite
Version: 1.28.0
Depends: R (>= 2.5.0)
License: LGPL
MD5sum: ed0730bb47a0fc586c8169f55523b261
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 <mrobinson@wehi.edu.au>
Maintainer: Mark Robinson <mrobinson@wehi.edu.au>
git_url: https://git.bioconductor.org/packages/gcspikelite
git_branch: RELEASE_3_12
git_last_commit: 8ac5bc6
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/gcspikelite_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: flagme
dependencyCount: 0
Package: geneLenDataBase
Version: 1.26.0
Depends: R (>= 2.11.0)
Imports: utils, rtracklayer, GenomicFeatures (>= 1.3.15)
License: LGPL (>= 2)
MD5sum: 789e5613f0ed33e31fd475154322e25f
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: Matthew Young <my4@sanger.ac.uk>, Nadia Davidson
<nadia.davidson@mcri.edu.au>
git_url: https://git.bioconductor.org/packages/geneLenDataBase
git_branch: RELEASE_3_12
git_last_commit: 2724715
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/geneLenDataBase_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: goseq
importsMe: SMITE
dependencyCount: 88
Package: genomationData
Version: 1.22.0
Suggests: knitr
License: GPL-3
MD5sum: 9ed5ae9ce1c67be0d933d10e6b6ad7f2
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 <vedran.franke@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/genomationData
git_branch: RELEASE_3_12
git_last_commit: e1d4810
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/genomationData_1.22.0.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
suggestsMe: genomation
dependencyCount: 0
Package: GeuvadisTranscriptExpr
Version: 1.18.0
Depends: R (>= 3.3.0)
Suggests: limma, rtracklayer, GenomicRanges, Rsamtools,
VariantAnnotation, tools, BiocStyle, knitr, testthat
License: GPL (>= 3)
MD5sum: d07a57af5638d89a643169cd8755ecf0
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 <gosia.nowicka@uzh.ch>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/GeuvadisTranscriptExpr
git_branch: RELEASE_3_12
git_last_commit: 21a70c6
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/GeuvadisTranscriptExpr_1.18.0.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:
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suggestsMe: DRIMSeq
dependencyCount: 0
Package: geuvPack
Version: 1.22.0
Depends: R (>= 2.10), SummarizedExperiment
License: Artistic-2.0
MD5sum: 9038fcfaa7b4ea265043b050ee096c3e
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 <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
PackageStatus: Deprecated
git_url: https://git.bioconductor.org/packages/geuvPack
git_branch: RELEASE_3_12
git_last_commit: c24735f
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/geuvPack_1.22.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: yriMulti
suggestsMe: gQTLBase, gQTLstats, yriMulti
dependencyCount: 26
Package: geuvStore2
Version: 1.19.0
Depends: BatchJobs, GenomicRanges
Imports: methods, gQTLBase
Suggests: Homo.sapiens, knitr (>= 1.7), rmarkdown
License: Artistic-2.0
MD5sum: 2ace13e6f654dceeeed0bc902218de48
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 <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/geuvStore2
git_branch: master
git_last_commit: 4630bcf
git_last_commit_date: 2020-04-27
Date/Publication: 2020-04-30
source.ver: src/contrib/geuvStore2_1.19.0.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
suggestsMe: gQTLBase, gQTLstats
dependencyCount: 108
Package: GGdata
Version: 1.28.0
Depends: R (>= 2.12.0), methods, Biobase (>= 2.5.5), GGBase, snpStats,
illuminaHumanv1.db, AnnotationDbi
Enhances: GGtools
License: LGPL
MD5sum: 9239aa844a4a5856a2c2387c221080f2
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 <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
PackageStatus: Deprecated
git_url: https://git.bioconductor.org/packages/GGdata
git_branch: RELEASE_3_12
git_last_commit: c3d63d9
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/GGdata_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: eQTL
suggestsMe: crlmm, GGtools
dependencyCount: 62
Package: GIGSEAdata
Version: 1.8.0
Depends: R (>= 3.5)
Suggests: GIGSEA, knitr, rmarkdown
License: LGPL-3
MD5sum: 6b43dae5cef85628ef86ebd96619c016
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 <shijia.zhu@mssm.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/GIGSEAdata
git_branch: RELEASE_3_12
git_last_commit: ca487c4
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/GIGSEAdata_1.8.0.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
dependencyCount: 0
Package: golubEsets
Version: 1.32.0
Depends: R (>= 2.14.0), Biobase (>= 2.5.5)
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MD5sum: 66c2f633c545a1965990fd7ababfb895
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 <golub@wi.mit.edu>
Maintainer: Vince Carey <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/golubEsets
git_branch: RELEASE_3_12
git_last_commit: 1745916
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/golubEsets_1.32.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: adSplit, Biobase, biosigner, GlobalAncova, globaltest,
idiogram, MLInterfaces, pvca, RDRToolbox, twilight, rknn
dependencyCount: 7
Package: gpaExample
Version: 1.2.0
Depends: R (>= 4.0.0)
License: GPL (>= 2)
MD5sum: 6ff1aa08699bf83b1d88bbe5908494f9
NeedsCompilation: no
Title: Example data for the GPA package (Genetic analysis incorporating
Pleiotropy and Annotation)
Description: Example data for the GPA package, consisting of the
p-values of 1,219,805 SNPs for five psychiatric disorder GWAS
from the psychiatric GWAS consortium (PGC), with the annotation
data using genes preferentially expressed in the central
nervous system (CNS).
biocViews: ExperimentData, Homo_sapiens_Data, SNPData
Author: Dongjun Chung, Carter Allen
Maintainer: Dongjun Chung <dongjun.chung@gmail.com>
URL: http://dongjunchung.github.io/GPA/
git_url: https://git.bioconductor.org/packages/gpaExample
git_branch: RELEASE_3_12
git_last_commit: 96a535e
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/gpaExample_1.2.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: GPA
dependencyCount: 0
Package: grndata
Version: 1.22.0
Depends: R (>= 2.10)
Suggests: RUnit, BiocGenerics, knitr
License: GPL-3
MD5sum: 6a5f370e2c824477b216ef9ffa584121
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 <pau.bellot@upc.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/grndata
git_branch: RELEASE_3_12
git_last_commit: 29acc96
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/grndata_1.22.0.tar.gz
vignettes: vignettes/grndata/inst/doc/grndata.html
vignetteTitles: GRNdata
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: GSBenchMark
Version: 1.10.0
Depends: R (>= 2.13.1)
License: GPL-2
MD5sum: 04dcb99485ebff382e0eeddc413bf105
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 <bahman@jhu.edu>, Elana J. Fertig
<ejfertig@jhmi.edu>
Maintainer: Bahman Afsari <bahman@jhu.edu>
git_url: https://git.bioconductor.org/packages/GSBenchMark
git_branch: RELEASE_3_12
git_last_commit: c532dc3
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/GSBenchMark_1.10.0.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
suggestsMe: GSReg
dependencyCount: 0
Package: GSE62944
Version: 1.18.0
Depends: Biobase, GEOquery
Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle
License: Artistic-2.0
MD5sum: baaa6cf7c3a975a4016bdb1759490957
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
<maintainer@bioconductor.org>
URL: http://bioconductor.org/packages/release/bioc/html/GSE62944.html
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/GSE62944
git_branch: RELEASE_3_12
git_last_commit: 9d577f4
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/GSE62944_1.18.0.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
dependencyCount: 43
Package: gskb
Version: 1.22.0
Depends: R (>= 3.2.0)
Suggests: PGSEA
License: Artistic-2.0
MD5sum: fb695e1ed9f8cba8467751048f385ceb
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 <valerie.bares@sdstate.edu>
git_url: https://git.bioconductor.org/packages/gskb
git_branch: RELEASE_3_12
git_last_commit: b9c0097
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/gskb_1.22.0.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
dependencyCount: 0
Package: GSVAdata
Version: 1.26.0
Depends: R (>= 2.10), Biobase, GSEABase, hgu95a.db
License: GPL (>= 2)
MD5sum: 157b93098a0771a5550ca042c6da00ed
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 <robert.castelo@upf.edu>
Maintainer: Robert Castelo <robert.castelo@upf.edu>
git_url: https://git.bioconductor.org/packages/GSVAdata
git_branch: RELEASE_3_12
git_last_commit: 189f22e
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/GSVAdata_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
importsMe: singleCellTK, RVA
suggestsMe: GSAR, GSVA
dependencyCount: 42
Package: GWASdata
Version: 1.28.0
Depends: GWASTools
License: Artistic-2.0
MD5sum: cd1491b4eb1ad786e3b18b94ea3f24c8
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 <sdmorris@u.washington.edu>, Adrienne
Stilp <amstilp@u.washington.edu>
git_url: https://git.bioconductor.org/packages/GWASdata
git_branch: RELEASE_3_12
git_last_commit: 3989318
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/GWASdata_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: GENESIS, GWASTools
dependencyCount: 69
Package: h5vcData
Version: 2.10.0
Suggests: h5vc
License: GPL (>= 3)
MD5sum: dfca68c2d5ee8c8f166cef2bff832e47
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 <pyl@embl.de>
git_url: https://git.bioconductor.org/packages/h5vcData
git_branch: RELEASE_3_12
git_last_commit: d6eb85a
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/h5vcData_2.10.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
importsMe: h5vc
suggestsMe: HDF5Array, Rariant
dependencyCount: 0
Package: hapmap100khind
Version: 1.32.0
Suggests: oligo
License: GPL
MD5sum: 0ab398d99116dd6832dbf56d3a7f76b7
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 <Benilton.Carvalho@cancer.org.uk>
git_url: https://git.bioconductor.org/packages/hapmap100khind
git_branch: RELEASE_3_12
git_last_commit: dc1968d
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/hapmap100khind_1.32.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: hapmap100kxba
Version: 1.32.0
Suggests: oligo
License: GPL
MD5sum: f7b98d38a58342bcb18e77bece6b073a
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 <Benilton.Carvalho@cancer.org.uk>
git_url: https://git.bioconductor.org/packages/hapmap100kxba
git_branch: RELEASE_3_12
git_last_commit: 12e7208
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/hapmap100kxba_1.32.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: oligo
dependencyCount: 0
Package: hapmap500knsp
Version: 1.32.0
Suggests: oligo
License: GPL
MD5sum: 588ebf9ce5514ac872e150a5f6dd617c
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 <Benilton.Carvalho@cancer.org.uk>
git_url: https://git.bioconductor.org/packages/hapmap500knsp
git_branch: RELEASE_3_12
git_last_commit: 4d99b4c
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/hapmap500knsp_1.32.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: hapmap500ksty
Version: 1.32.0
Suggests: oligo
License: GPL
MD5sum: 803cc8d481cc44920d3fc729a56c29b5
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 <Benilton.Carvalho@cancer.org.uk>
git_url: https://git.bioconductor.org/packages/hapmap500ksty
git_branch: RELEASE_3_12
git_last_commit: 5d2f1ff
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/hapmap500ksty_1.32.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: hapmapsnp5
Version: 1.32.0
Suggests: oligo
License: GPL
MD5sum: e0430312a90a36f0509c98a9056adb31
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 <Benilton.Carvalho@cancer.org.uk>
git_url: https://git.bioconductor.org/packages/hapmapsnp5
git_branch: RELEASE_3_12
git_last_commit: e9007d4
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/hapmapsnp5_1.32.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: oligoClasses
dependencyCount: 0
Package: hapmapsnp6
Version: 1.32.0
Depends: R (>= 2.15)
Suggests: oligo, oligoClasses
License: GPL
MD5sum: 11f85eea7363a487738610586e622ecf
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 <Benilton.Carvalho@cancer.org.uk>
git_url: https://git.bioconductor.org/packages/hapmapsnp6
git_branch: RELEASE_3_12
git_last_commit: 4d80cd5
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/hapmapsnp6_1.32.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: crlmm, oligoClasses
dependencyCount: 0
Package: harbChIP
Version: 1.28.0
Depends: R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5),
Biostrings
Imports: methods, stats
License: Artistic-2.0
MD5sum: 652671ee0af64c10801b632aca8eee42
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 <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/harbChIP
git_branch: RELEASE_3_12
git_last_commit: 413ca21
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/harbChIP_1.28.0.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
dependencyCount: 16
Package: HarmanData
Version: 1.18.0
Depends: R (>= 3.2.3)
Suggests: BiocGenerics, BiocStyle, knitr, rmarkdown
License: GPL-3
MD5sum: 53b21f1bf6c29d31a1621dc63be5adee
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 <jason.ross@csiro.au>
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_12
git_last_commit: 1f1b6bd
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/HarmanData_1.18.0.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
suggestsMe: Harman
dependencyCount: 0
Package: HarmonizedTCGAData
Version: 1.12.0
Depends: R (>= 3.4.0)
Imports: ExperimentHub
Suggests: AnnotationHub, knitr, rmarkdown, igraph, survival, ANF,
stats, testthat
License: GPL-3
MD5sum: b68539f8e4298cfec21d84f29269d0c4
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 <tianlema@buffalo.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/HarmonizedTCGAData
git_branch: RELEASE_3_12
git_last_commit: 88f70a3
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/HarmonizedTCGAData_1.12.0.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
dependencyCount: 77
Package: HCAData
Version: 1.6.0
Depends: R (>= 3.6), SingleCellExperiment
Imports: ExperimentHub, AnnotationHub, HDF5Array, utils
Suggests: knitr, rmarkdown, BiocStyle, scran (>= 1.11.4), BiocSingular,
scater, scuttle, Rtsne, igraph, iSEE, testthat
License: MIT + file LICENSE
MD5sum: a5d900fef0e4bea286d2d765f03c5908
NeedsCompilation: no
Title: Accessing The Datasets Of The Human Cell Atlas in R/Bioconductor
Description: This package allows a direct access to the dataset
generated by the Human Cell Atlas project for further
processing in R and Bioconductor, in the comfortable format of
SingleCellExperiment objects (available in other formats here:
http://preview.data.humancellatlas.org/).
biocViews: RNASeqData, SingleCellData, ExperimentData, ExpressionData,
ExperimentHub
Author: Federico Marini [aut, cre]
(<https://orcid.org/0000-0003-3252-7758>)
Maintainer: Federico Marini <marinif@uni-mainz.de>
URL: https://github.com/federicomarini/HCAData
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/HCAData
git_branch: RELEASE_3_12
git_last_commit: 37094ca
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/HCAData_1.6.0.tar.gz
vignettes: vignettes/HCAData/inst/doc/hcadata.html
vignetteTitles: Accessing the Human Cell Atlas datasets
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/HCAData/inst/doc/hcadata.R
dependencyCount: 96
Package: HD2013SGI
Version: 1.30.0
Depends: R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots,
limma, vcd, LSD,EBImage
Suggests: BiocStyle
License: Artistic-2.0
MD5sum: 586411d5b3526cba04977b060e6f26d4
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 <b.fischer@dkfz.de>
SystemRequirements: GNU make
git_url: https://git.bioconductor.org/packages/HD2013SGI
git_branch: RELEASE_3_12
git_last_commit: 119ea3a
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/HD2013SGI_1.30.0.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
dependencyCount: 69
Package: HDCytoData
Version: 1.10.0
Depends: ExperimentHub, SummarizedExperiment, flowCore
Imports: utils, methods
Suggests: BiocStyle, knitr, rmarkdown, Rtsne, umap, ggplot2, FlowSOM,
mclust, diffcyt
License: MIT + file LICENSE
MD5sum: 522b735486293bf2517e1b684b7526ea
NeedsCompilation: no
Title: Collection of high-dimensional cytometry benchmark datasets in
Bioconductor object formats
Description: Data package containing a set of publicly available
high-dimensional cytometry benchmark datasets, formatted into
SummarizedExperiment and flowSet Bioconductor object formats,
including all required metadata. Row metadata includes sample
IDs, group IDs, patient IDs, reference cell population or
cluster labels (where available), and labels identifying
'spiked in' cells (where available). Column metadata includes
channel names, protein marker names, and protein marker classes
(cell type or cell state).
biocViews: ExperimentHub, ExperimentData, ExpressionData,
FlowCytometryData, SingleCellData, Homo_sapiens_Data,
ImmunoOncologyData
Author: Lukas M. Weber [aut, cre], Charlotte Soneson [aut]
Maintainer: Lukas M. Weber <lukas.weber.edu@gmail.com>
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_12
git_last_commit: bc12c72
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/HDCytoData_1.10.0.tar.gz
vignettes: vignettes/HDCytoData/inst/doc/Contribution_guidelines.html,
vignettes/HDCytoData/inst/doc/Examples_and_use_cases.html,
vignettes/HDCytoData/inst/doc/HDCytoData_package.html
vignetteTitles: 3. Contribution guidelines, 2. Examples and use cases,
1. HDCytoData package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/HDCytoData/inst/doc/Contribution_guidelines.R,
vignettes/HDCytoData/inst/doc/Examples_and_use_cases.R,
vignettes/HDCytoData/inst/doc/HDCytoData_package.R
dependsOnMe: cytofWorkflow
suggestsMe: diffcyt
dependencyCount: 98
Package: healthyFlowData
Version: 1.28.0
Depends: R (>= 2.15.0), flowCore
Imports: methods
License: Artistic-2.0
MD5sum: 79038935238c2ead511362971872c265
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 <aazad@purdue.edu>
git_url: https://git.bioconductor.org/packages/healthyFlowData
git_branch: RELEASE_3_12
git_last_commit: 6fbfb52
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/healthyFlowData_1.28.0.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
suggestsMe: flowMatch
dependencyCount: 19
Package: HEEBOdata
Version: 1.28.0
License: LGPL
MD5sum: 583bbe64e660308f14490fabf12ab408
NeedsCompilation: no
Title: HEEBO set and HEEBO controls.
Description: R objects describing the HEEBO oligo set.
biocViews: ExperimentData
Author: Agnes Paquet
Maintainer: Agnes Paquet <apaquet@medsfgh.ucsf.edu>
URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/
git_url: https://git.bioconductor.org/packages/HEEBOdata
git_branch: RELEASE_3_12
git_last_commit: 8c7fa51
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/HEEBOdata_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: arrayQuality
dependencyCount: 0
Package: HelloRangesData
Version: 1.16.0
Suggests: BiocStyle
License: GPL (>= 2)
MD5sum: 71a2163d60ece098698e7d3d81364bef
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 <michafla@gene.com>
git_url: https://git.bioconductor.org/packages/HelloRangesData
git_branch: RELEASE_3_12
git_last_commit: 56bb56b
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/HelloRangesData_1.16.0.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
suggestsMe: HelloRanges, plyranges
dependencyCount: 0
Package: hgu133abarcodevecs
Version: 1.28.0
Depends: R (>= 2.10.0)
License: GPL (>= 2)
MD5sum: 820ce265759752b2ab31cabb1d03408a
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 <mmccall@jhsph.edu>, Rafael A. Irizarry
<rafa@jhu.edu>
Maintainer: Matthew N. McCall <mmccall@jhsph.edu>
git_url: https://git.bioconductor.org/packages/hgu133abarcodevecs
git_branch: RELEASE_3_12
git_last_commit: 9bbca38
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/hgu133abarcodevecs_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: hgu133plus2barcodevecs
Version: 1.28.0
Depends: R (>= 2.10.0)
License: GPL (>= 2)
MD5sum: fe94ce7b665890693dd9bb2aa9d7aa6a
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 <mmccall@jhsph.edu>, Rafael A. Irizarry
<rafa@jhu.edu>
Maintainer: Matthew N. McCall <mmccall@jhsph.edu>
git_url: https://git.bioconductor.org/packages/hgu133plus2barcodevecs
git_branch: RELEASE_3_12
git_last_commit: 1cdf74e
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/hgu133plus2barcodevecs_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: hgu133plus2CellScore
Version: 1.10.0
Depends: R (>= 3.5.0)
Imports: Biobase (>= 2.39.1)
Suggests: knitr
License: GPL-3
MD5sum: c408d29a5ffa009519acf74fa97a746a
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 <nancy.l.mah@googlemail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/hgu133plus2CellScore
git_branch: RELEASE_3_12
git_last_commit: 8d8ce81
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/hgu133plus2CellScore_1.10.0.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
suggestsMe: CellScore
dependencyCount: 7
Package: hgu2beta7
Version: 1.30.0
Depends: R (>= 2.0.0)
License: Artistic-2.0
MD5sum: c28d584be6b16b136982e999ac3936a5
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
<maintainer@bioconductor.org>
git_url: https://git.bioconductor.org/packages/hgu2beta7
git_branch: RELEASE_3_12
git_last_commit: 72cec45
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/hgu2beta7_1.30.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: HiCDataHumanIMR90
Version: 1.10.0
Depends: R (>= 2.10)
Suggests: HiTC
License: GPL-3
MD5sum: 0b7a7227889105ee709e2dc0d5a09016
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 <Nicolas.Servant@curie.fr>
git_url: https://git.bioconductor.org/packages/HiCDataHumanIMR90
git_branch: RELEASE_3_12
git_last_commit: c14938a
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/HiCDataHumanIMR90_1.10.0.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
suggestsMe: HiTC
dependencyCount: 0
Package: HiCDataLymphoblast
Version: 1.26.0
Suggests: ShortRead
License: GPL-3
MD5sum: 09b2af74a0e55d9be7b56af34c0e3714
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 <b.mifsud@qmul.ac.uk>
git_url: https://git.bioconductor.org/packages/HiCDataLymphoblast
git_branch: RELEASE_3_12
git_last_commit: b52f792
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/HiCDataLymphoblast_1.26.0.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
suggestsMe: GOTHiC
dependencyCount: 0
Package: HighlyReplicatedRNASeq
Version: 1.2.0
Depends: SummarizedExperiment, ExperimentHub
Imports: S4Vectors
Suggests: BiocStyle, BiocFileCache, knitr, rmarkdown
License: MIT + file LICENSE
MD5sum: 963bfa9341ba5ac9aae0d5c183fe2b52
NeedsCompilation: no
Title: Collection of Bulk RNA-Seq Experiments With Many Replicates
Description: Gene-level count matrix data for bulk RNA-seq dataset with
many replicates. The data are provided as easy to use
SummarizedExperiment objects. The source data that is made
accessible through this package comes from
https://github.com/bartongroup/profDGE48.
biocViews: ExperimentHub, ExperimentData, ExpressionData,
SequencingData, RNASeqData
Author: Constantin Ahlmann-Eltze [aut, cre]
(<https://orcid.org/0000-0002-3762-068X>)
Maintainer: Constantin Ahlmann-Eltze <artjom31415@googlemail.com>
URL: https://github.com/const-ae/HighlyReplicatedRNASeq
VignetteBuilder: knitr
BugReports: https://github.com/const-ae/HighlyReplicatedRNASeq/issues
git_url: https://git.bioconductor.org/packages/HighlyReplicatedRNASeq
git_branch: RELEASE_3_12
git_last_commit: 8de508b
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/HighlyReplicatedRNASeq_1.2.0.tar.gz
vignettes:
vignettes/HighlyReplicatedRNASeq/inst/doc/HighlyReplicatedRNASeq.html
vignetteTitles: Exploring the 86 bulk RNA-seq samples from the Schurch
et al. (2016) study
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles:
vignettes/HighlyReplicatedRNASeq/inst/doc/HighlyReplicatedRNASeq.R
dependencyCount: 91
Package: Hiiragi2013
Version: 1.26.0
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: 9967bfd582d79ce18e4ecdd84fba2bb3
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 <andrzej.oles@embl.de>
git_url: https://git.bioconductor.org/packages/Hiiragi2013
git_branch: RELEASE_3_12
git_last_commit: a962879
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/Hiiragi2013_1.26.0.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
dependencyCount: 70
Package: HIVcDNAvantWout03
Version: 1.30.0
License: GPL (>= 2)
MD5sum: 8c942d197ca060dacca8a6770dc8e023
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 <fraley@stat.washington.edu>
URL:
http://expression.microslu.washington.edu/expression/vantwoutjvi2002.html
git_url: https://git.bioconductor.org/packages/HIVcDNAvantWout03
git_branch: RELEASE_3_12
git_last_commit: a5ec5d8
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/HIVcDNAvantWout03_1.30.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: HMP16SData
Version: 1.10.0
Depends: R (>= 4.0.0), SummarizedExperiment
Imports: AnnotationHub, assertthat, dplyr, ExperimentHub, kableExtra,
knitr, magrittr, methods, readr, S4Vectors, stringr, 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: 8c013975de58a3833513e7756d747ac2
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, ExperimentHub, Homo_sapiens_Data,
MicrobiomeData, ReproducibleResearch, SequencingData
Author: Lucas Schiffer <schiffer.lucas@gmail.com>, Rimsha Azhar
<rimsha_azhar@hotmail.com>, Marcel Ramos
<marcel.ramos@roswellpark.org>, Ludwig Geistlinger
<ludwig.geistlinger@sph.cuny.edu>, Levi Waldron
<lwaldron.research@gmail.com>
Maintainer: Lucas Schiffer <schiffer.lucas@gmail.com>
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_12
git_last_commit: c37993e
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/HMP16SData_1.10.0.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
dependencyCount: 123
Package: HMP2Data
Version: 1.4.0
Depends: R (>= 3.6.0)
Imports: AnnotationHub, assertthat, dplyr, ExperimentHub, kableExtra,
knitr, magrittr, methods, readr, S4Vectors,
SummarizedExperiment, phyloseq, MultiAssayExperiment,
data.table
Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, cowplot,
devtools, ggplot2, gridExtra, haven, rmarkdown, roxygen2,
stats, testthat, tibble, UpSetR
License: Artistic-2.0
MD5sum: c264c2f8f4ae972dca65c1dc169f827a
NeedsCompilation: no
Title: 16s rRNA sequencing data from the Human Microbiome Project 2
Description: HMP2Data is a Bioconductor package of the Human Microbiome
Project 2 (HMP2) 16S rRNA sequencing data. Processed data is
provided as phyloseq, SummarizedExperiment, and
MultiAssayExperiment class objects. Individual matrices and
data.frames used for building these S4 class objects are also
provided in the package.
biocViews: ExperimentData, Homo_sapiens_Data, MicrobiomeData,
ReproducibleResearch, SequencingData
Author: John Stansfield <stansfieldjc@vcu.edu>, Ekaterina Smirnova
<ekaterina.smirnova@vcuhealth.org>, Ni Zhao <nzhao10@jhu.edu>,
Jennifer Fettweis <jennifer.fettweis@vcuhealth.org>, Levi
Waldron <levi.waldron@sph.cuny.edu>, Mikhail Dozmorov
<mikhail.dozmorov@vcuhealth.org>
Maintainer: John Stansfield <stansfieldjc@vcu.edu>, Ekaterina Smirnova
<ekaterina.smirnova@vcuhealth.org>
URL: https://github.com/jstansfield0/HMP2Data
VignetteBuilder: knitr
BugReports: https://github.com/jstansfield0/HMP2Data/issues
git_url: https://git.bioconductor.org/packages/HMP2Data
git_branch: RELEASE_3_12
git_last_commit: b9ed5eb
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/HMP2Data_1.4.0.tar.gz
vignettes: vignettes/HMP2Data/inst/doc/hmp2data.html
vignetteTitles: HMP2Data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/HMP2Data/inst/doc/hmp2data.R
dependencyCount: 156
Package: hmyriB36
Version: 1.26.0
Depends: R (>= 2.13.0), methods, Biobase (>= 2.5.5), GGBase
Suggests: GGtools, illuminaHumanv1.db
License: Artistic-2.0
MD5sum: 299c4cc1c567d4e22dd574ba84dbae48
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 <stvjc@channing.harvard.edu>
Maintainer: Vincent Carey <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/hmyriB36
git_branch: RELEASE_3_12
git_last_commit: 6a9b11e
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/hmyriB36_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 60
Package: HSMMSingleCell
Version: 1.10.0
Depends: R (>= 2.10)
License: Artistic-2.0
MD5sum: 216744f2773a0c0cc7b11a1e27619055
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 <cole@broadinstitute.org>
git_url: https://git.bioconductor.org/packages/HSMMSingleCell
git_branch: RELEASE_3_12
git_last_commit: e872b6b
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/HSMMSingleCell_1.10.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
importsMe: ctgGEM, monocle
suggestsMe: cellTree
dependencyCount: 0
Package: HumanAffyData
Version: 1.16.0
Depends: ExperimentHub, Biobase, R (>= 3.3)
Suggests: BiocStyle
License: Artistic-2.0
MD5sum: 684682dd1a2ef50adf237d3869b682a6
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 <bnelms.research@gmail.com>
git_url: https://git.bioconductor.org/packages/HumanAffyData
git_branch: RELEASE_3_12
git_last_commit: 93e2c3c
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/HumanAffyData_1.16.0.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
suggestsMe: CellMapper
dependencyCount: 77
Package: humanStemCell
Version: 0.30.0
Depends: Biobase (>= 2.5.5), hgu133plus2.db
License: Artistic-2.0
MD5sum: cc6ab0bf3f1afc723ac82ab5f928fe09
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 <rgentlem@fhcrc.org>
git_url: https://git.bioconductor.org/packages/humanStemCell
git_branch: RELEASE_3_12
git_last_commit: 29e0718
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/humanStemCell_0.30.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: MiRaGE, rtracklayer
dependencyCount: 28
Package: IHWpaper
Version: 1.18.0
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: cd9648189ae94a6dac79695bbc29483a
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 <nikos.ignatiadis01@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/IHWpaper
git_branch: RELEASE_3_12
git_last_commit: 8bdf566
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/IHWpaper_1.18.0.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/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", "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/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
dependencyCount: 104
Package: Illumina450ProbeVariants.db
Version: 1.26.0
Depends: R (>= 3.0.1)
License: GPL-3
MD5sum: c9df1737e02bed11c152d3f5e89c3db4
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 <tiffany.morris@ucl.ac.uk>
git_url:
https://git.bioconductor.org/packages/Illumina450ProbeVariants.db
git_branch: RELEASE_3_12
git_last_commit: fffe603
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/Illumina450ProbeVariants.db_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: IlluminaDataTestFiles
Version: 1.28.0
License: Artistic-2.0
MD5sum: 28569835232e68198dec50650f437dfa
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 <khansen@jhsph.edu>
git_url: https://git.bioconductor.org/packages/IlluminaDataTestFiles
git_branch: RELEASE_3_12
git_last_commit: 55e39d8
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/IlluminaDataTestFiles_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: illuminaio
dependencyCount: 0
Package: ITALICSData
Version: 2.28.0
Depends: R (>= 2.0.0)
License: GPL
MD5sum: 230ef6bf192cffe58db43e808181b46c
NeedsCompilation: no
Title: ITALICSData
Description: Data needed to use the ITALICS package
biocViews: ExperimentData, HapMap
Author: Guillem Rigaill
Maintainer: Guillem Rigaill <italics@curie.fr>
URL: http://bioinfo.curie.fr
git_url: https://git.bioconductor.org/packages/ITALICSData
git_branch: RELEASE_3_12
git_last_commit: 9ec1919
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ITALICSData_2.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: ITALICS
dependencyCount: 0
Package: Iyer517
Version: 1.32.0
Depends: Biobase (>= 2.5.5)
License: Artistic-2.0
MD5sum: 51d87a8341cb9c69243aa156ba0ad39e
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 <vishy@cmgm.stanford.edu>
Maintainer: Vince Carey <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/Iyer517
git_branch: RELEASE_3_12
git_last_commit: cdc6191
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/Iyer517_1.32.0.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
dependencyCount: 7
Package: JASPAR2014
Version: 1.26.0
Depends: R (>= 3.0.1), methods, Biostrings (>= 2.29.19)
License: GPL-2
MD5sum: 04bec9056564f8ace769c30b929d475c
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 <ge.tan09@imperial.ac.uk>
Maintainer: Ge Tan <ge.tan09@imperial.ac.uk>
URL: http://jaspar.genereg.net/
git_url: https://git.bioconductor.org/packages/JASPAR2014
git_branch: RELEASE_3_12
git_last_commit: 90d06a2
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/JASPAR2014_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: MatrixRider, TFBSTools
dependencyCount: 15
Package: JASPAR2016
Version: 1.18.0
Depends: R (>= 3.2.2), methods
License: GPL-2
MD5sum: 1f255af7e1fd7e5f87cd11d48b1279dc
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 <ge.tan09@imperial.ac.uk>
Maintainer: Ge Tan <ge.tan09@imperial.ac.uk>
URL: http://jaspar.genereg.net/
git_url: https://git.bioconductor.org/packages/JASPAR2016
git_branch: RELEASE_3_12
git_last_commit: 5334d72
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/JASPAR2016_1.18.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: chromVAR, TFBSTools, CAGEWorkflow
dependencyCount: 1
Package: JctSeqData
Version: 1.20.0
Depends: R (>= 3.3)
Suggests: knitr, BiocStyle, DESeq2, DEXSeq, edgeR, JunctionSeq
License: file LICENSE
MD5sum: dcf4c571e87ec6f9df7f949bb7f77d35
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 <JunctionSeq-contact@list.nih.gov>
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_12
git_last_commit: b5ac061
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/JctSeqData_1.20.0.tar.gz
vignettes: vignettes/JctSeqData/inst/doc/JunctionSeqExampleData.pdf
vignetteTitles: Example Walkthrough
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
dependencyCount: 0
Package: KEGGandMetacoreDzPathwaysGEO
Version: 1.10.0
Depends: R (>= 2.15.0)
Imports: Biobase, BiocGenerics
License: GPL-2
MD5sum: 6e9b54de535554f7c7c769e526ffa779
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 <gbhatti@med.wayne.edu>
git_url:
https://git.bioconductor.org/packages/KEGGandMetacoreDzPathwaysGEO
git_branch: RELEASE_3_12
git_last_commit: af35edc
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/KEGGandMetacoreDzPathwaysGEO_1.10.0.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
importsMe: GSEABenchmarkeR
dependencyCount: 7
Package: KEGGdzPathwaysGEO
Version: 1.28.0
Depends: R (>= 2.13.0)
Imports: Biobase, BiocGenerics
License: GPL-2
MD5sum: 77aa90c670c3ca5d46d6e2ead3580268
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 <gbhatti@med.wayne.edu>
git_url: https://git.bioconductor.org/packages/KEGGdzPathwaysGEO
git_branch: RELEASE_3_12
git_last_commit: 28546ca
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/KEGGdzPathwaysGEO_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: PADOG
importsMe: GSEABenchmarkeR
dependencyCount: 7
Package: kidpack
Version: 1.32.0
Depends: R (>= 2.6.0), Biobase (>= 2.5.5)
License: GPL-2
MD5sum: 09e1c525df259e35f78bdf691a987a2b
NeedsCompilation: no
Title: DKFZ kidney package
Description: kidney microarray data
biocViews: ExperimentData, CancerData, KidneyCancerData,
MicroarrayData, ArrayExpress
Author: Wolfgang Huber <huber@ebi.ac.uk>
Maintainer: Wolfgang Huber <huber@ebi.ac.uk>
URL: http://www.dkfz.de/mga
git_url: https://git.bioconductor.org/packages/kidpack
git_branch: RELEASE_3_12
git_last_commit: d6074d5
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/kidpack_1.32.0.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
dependencyCount: 7
Package: KOdata
Version: 1.16.0
Depends: R (>= 3.3.0)
License: MIT + file LICENSE
MD5sum: 5d1c07ed4acf32ba0899aec0aa2be9cb
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 <vandersm@mail.uc.edu>
git_url: https://git.bioconductor.org/packages/KOdata
git_branch: RELEASE_3_12
git_last_commit: dbf7a3d
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/KOdata_1.16.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
dependsOnMe: KEGGlincs
dependencyCount: 0
Package: leeBamViews
Version: 1.26.0
Depends: R (>= 2.15.0), Biobase, Rsamtools (>= 0.1.50), BSgenome
Imports: GenomicRanges, GenomicAlignments, methods, S4Vectors,
parallel, IRanges
Suggests: biomaRt, org.Sc.sgd.db, edgeR
License: Artistic 2.0
MD5sum: 01010069b76c4784842b27dbda169adf
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 <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/leeBamViews
git_branch: RELEASE_3_12
git_last_commit: e8f0e19
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/leeBamViews_1.26.0.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
suggestsMe: EDASeq
dependencyCount: 41
Package: leukemiasEset
Version: 1.26.0
Depends: R (>= 2.10.1), Biobase (>= 2.5.5)
License: GPL (>= 2)
MD5sum: f9018f85f407e29c30409596f6e5797f
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 <saibar@usal.es>
git_url: https://git.bioconductor.org/packages/leukemiasEset
git_branch: RELEASE_3_12
git_last_commit: 2f260f7
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/leukemiasEset_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: geNetClassifier, mCSEA, multiclassPairs
dependencyCount: 7
Package: LiebermanAidenHiC2009
Version: 0.28.0
Depends: KernSmooth, IRanges
License: LGPL
MD5sum: 2ec616658f92b93df6b438223e2c22f3
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 <fklein@embl.de>
git_url: https://git.bioconductor.org/packages/LiebermanAidenHiC2009
git_branch: RELEASE_3_12
git_last_commit: 78285a4
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/LiebermanAidenHiC2009_0.28.0.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
dependencyCount: 10
Package: ListerEtAlBSseq
Version: 1.22.0
Depends: R (>= 3.1.1), methylPipe
Suggests: BSgenome.Hsapiens.UCSC.hg18
License: Artistic 2.0
MD5sum: 9c9f16800c12a49e9113c3df3ac54375
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 <kamal.fartiyal84@gmail.com>
Maintainer: Kamal Kishore <kamal.fartiyal84@gmail.com>
git_url: https://git.bioconductor.org/packages/ListerEtAlBSseq
git_branch: RELEASE_3_12
git_last_commit: 91cb664
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ListerEtAlBSseq_1.22.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 145
Package: lumiBarnes
Version: 1.30.0
Depends: R (>= 2.0), Biobase (>= 2.5.5), lumi (>= 1.1.0)
License: LGPL
MD5sum: a8149ecc6362cb36b1a8e8b1ba89faaa
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 <dupan@northwestern.edu>
git_url: https://git.bioconductor.org/packages/lumiBarnes
git_branch: RELEASE_3_12
git_last_commit: d2d3571
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/lumiBarnes_1.30.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: arrayMvout, lumi
dependencyCount: 151
Package: LungCancerACvsSCCGEO
Version: 1.26.0
Depends: R (>= 2.15.0)
License: GPL-2
MD5sum: 560c2e1111179119384c321a3dfbdca9
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 <atarca@med.wayne.edu>
Maintainer: Adi Laurentiu Tarca <atarca@med.wayne.edu>
URL: http://bioinformaticsprb.med.wayne.edu/
git_url: https://git.bioconductor.org/packages/LungCancerACvsSCCGEO
git_branch: RELEASE_3_12
git_last_commit: 0bfc3ac
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/LungCancerACvsSCCGEO_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: LungCancerLines
Version: 0.28.0
Imports: Rsamtools
License: Artistic-2.0
MD5sum: 0de328eb92537fed4220d7f6fc4b1f3c
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 <barr.cory@gene.com>
git_url: https://git.bioconductor.org/packages/LungCancerLines
git_branch: RELEASE_3_12
git_last_commit: cd224d9
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/LungCancerLines_0.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: gmapR, HTSeqGenie, VariantTools
dependencyCount: 29
Package: lungExpression
Version: 0.28.0
Depends: R (>= 2.4.0), Biobase (>= 2.5.5)
License: GPL (>= 2)
MD5sum: 0e1d7fc7f5eff698d3802bbed86f1a35
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 <rscharpf@jhsph.edu>, Simens Zhong
<zhong@mts.jhu.edu>, Giovanni Parmigiani <gp@jhu.edu>
Maintainer: Robert Scharpf <rscharpf@jhsph.edu>
git_url: https://git.bioconductor.org/packages/lungExpression
git_branch: RELEASE_3_12
git_last_commit: 3c5334d
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/lungExpression_0.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: globaltest
dependencyCount: 7
Package: lydata
Version: 1.16.0
License: MIT + file LICENSE
MD5sum: ecbed576f18fc74f0fb4ccb17fb4a1ea
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 <alexvpickering@gmail.com>
git_url: https://git.bioconductor.org/packages/lydata
git_branch: RELEASE_3_12
git_last_commit: 1a232ae
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/lydata_1.16.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
suggestsMe: ccmap, crossmeta
dependencyCount: 0
Package: M3DExampleData
Version: 1.16.0
Depends: R (>= 3.3)
License: GPL (>=2)
MD5sum: e9dc468595bb9005f391c7ed92090e26
NeedsCompilation: no
Title: M3Drop Example Data
Description: Example data for M3Drop package.
biocViews: Mus_musculus_Data, RNASeqData, ExpressionData, GEO, Tissue,
ExperimentData
Author: Tallulah Andrews <tallulandrews@gmail.com>
Maintainer: Tallulah Andrews <tallulandrews@gmail.com>
git_url: https://git.bioconductor.org/packages/M3DExampleData
git_branch: RELEASE_3_12
git_last_commit: 6f0dcd8
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/M3DExampleData_1.16.0.tar.gz
hasREADME: TRUE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: celda, M3Drop
dependencyCount: 0
Package: macrophage
Version: 1.6.0
Depends: R (>= 3.5.0)
Suggests: knitr
License: GPL (>= 2)
MD5sum: 749f419e5c6ef325bb6f742af9e02fa4
NeedsCompilation: no
Title: Human macrophage immune response
Description: This package provides the output of running Salmon on a
set of 24 RNA-seq samples from Alasoo, et al. "Shared genetic
effects on chromatin and gene expression indicate a role for
enhancer priming in immune response", published in Nature
Genetics, January 2018. For details on version numbers and how
the samples were processed see the package vignette.
biocViews: ExperimentData, SequencingData, RNASeqData
Author: Michael Love
Maintainer: Michael Love <michaelisaiahlove@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/macrophage
git_branch: RELEASE_3_12
git_last_commit: 770b471
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/macrophage_1.6.0.tar.gz
vignettes: vignettes/macrophage/inst/doc/macrophage.html
vignetteTitles: Salmon quantifications for human macrophage immune
response experiment
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/macrophage/inst/doc/macrophage.R
suggestsMe: fishpond, GeneTonic, fluentGenomics
dependencyCount: 0
Package: mammaPrintData
Version: 1.26.0
Depends: R (>= 2.13.0)
Suggests: Biobase, gdata, limma
License: Artistic-2.0
MD5sum: 3da2eda420dea0af88854d580e43ea56
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 <marchion@jhu.edu>
Maintainer: Luigi Marchionni <marchion@jhu.edu>
URL: http://luigimarchionni.org/breastTSP.html
git_url: https://git.bioconductor.org/packages/mammaPrintData
git_branch: RELEASE_3_12
git_last_commit: 835ea9d
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/mammaPrintData_1.26.0.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
dependencyCount: 0
Package: mAPKLData
Version: 1.22.0
Depends: R (>= 3.2.0)
Suggests: Biobase
License: Artistic-2.0
MD5sum: fae437ec8d2ef7f1752cd2f8b8a3a0c9
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 <a.sakellariou@gonkhosp.gr>
git_url: https://git.bioconductor.org/packages/mAPKLData
git_branch: RELEASE_3_12
git_last_commit: d71db97
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/mAPKLData_1.22.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: mAPKL
dependencyCount: 0
Package: maqcExpression4plex
Version: 1.34.0
Suggests: oligo, pdInfoBuilder
License: GPL
MD5sum: 27afa66e5943a7e91b05572fd07aaafa
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 <Benilton.Carvalho@cancer.org.uk>
git_url: https://git.bioconductor.org/packages/maqcExpression4plex
git_branch: RELEASE_3_12
git_last_commit: 8be1875
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/maqcExpression4plex_1.34.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: oligo
dependencyCount: 0
Package: MAQCsubset
Version: 1.28.0
Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), lumi,
methods
Suggests: genefilter, codelink
License: Artistic-2.0
MD5sum: ad0c877da467036705cecfa4ea055805
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 <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/MAQCsubset
git_branch: RELEASE_3_12
git_last_commit: 87827b5
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/MAQCsubset_1.28.0.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
suggestsMe: arrayMvout
dependencyCount: 151
Package: MAQCsubsetAFX
Version: 1.28.0
Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5)
License: Artistic-2.0
MD5sum: aead14b87a16b6b7ebd6a6c718f1e3ca
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 <lg390@cam.ac.uk>
git_url: https://git.bioconductor.org/packages/MAQCsubsetAFX
git_branch: RELEASE_3_12
git_last_commit: fee1a3d
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/MAQCsubsetAFX_1.28.0.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
suggestsMe: qcmetrics, yaqcaffy
dependencyCount: 13
Package: MAQCsubsetILM
Version: 1.28.0
Depends: R (>= 2.10), Biobase (>= 2.5.5), lumi
License: Artistic-2.0
MD5sum: ad9a3d88df5fcb0990f0ea2cb8f03d58
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 <lg390@cam.ac.uk>
git_url: https://git.bioconductor.org/packages/MAQCsubsetILM
git_branch: RELEASE_3_12
git_last_commit: fb4a3d8
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/MAQCsubsetILM_1.28.0.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
dependencyCount: 151
Package: mCSEAdata
Version: 1.10.1
Depends: R (>= 3.5)
Suggests: BiocStyle, knitr, rmarkdown
License: GPL-2
MD5sum: 755233b7db7210f225e63f9358a011e6
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 <jmartorellm@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/mCSEAdata
git_branch: RELEASE_3_12
git_last_commit: 25099f6
git_last_commit_date: 2020-12-09
Date/Publication: 2020-12-10
source.ver: src/contrib/mCSEAdata_1.10.1.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
dependsOnMe: mCSEA
dependencyCount: 0
Package: mcsurvdata
Version: 1.8.0
Depends: R (>= 3.5), ExperimentHub
Imports: AnnotationHub, Biobase
Suggests: knitr
License: GPL (>=2)
MD5sum: 737e83fe1c9a1ad9a2e47747d04b64c4
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 <adria.caballe@irbbarcelona.org>
URL: https://github.com/adricaba/mcsurvdata
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/mcsurvdata
git_branch: RELEASE_3_12
git_last_commit: a143a94
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/mcsurvdata_1.8.0.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
dependencyCount: 77
Package: MEDIPSData
Version: 1.26.0
Depends: R (>= 2.15.0)
License: GPL (>= 2)
MD5sum: 93de288633bb0d94c381d4d4fc960c7a
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 <lchavez@liai.org>
git_url: https://git.bioconductor.org/packages/MEDIPSData
git_branch: RELEASE_3_12
git_last_commit: 11ae33d
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/MEDIPSData_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: MEDIPS, qsea
dependencyCount: 0
Package: MEEBOdata
Version: 1.28.0
License: LGPL
MD5sum: c2ce1628a9d24cbec64a61756333643c
NeedsCompilation: no
Title: MEEBO set and MEEBO controls.
Description: R objects describing the MEEBO set.
biocViews: ExperimentData
Author: Agnes Paquet
Maintainer: Agnes Paquet <apaquet@medsfgh.ucsf.edu>
URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/
git_url: https://git.bioconductor.org/packages/MEEBOdata
git_branch: RELEASE_3_12
git_last_commit: a0bca3b
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/MEEBOdata_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: arrayQuality
dependencyCount: 0
Package: MetaGxBreast
Version: 1.10.1
Depends: R (>= 3.6.0), Biobase, AnnotationHub, ExperimentHub
Imports: stats, lattice, impute, SummarizedExperiment
Suggests: testthat, xtable, tinytex
License: Apache License (>= 2)
MD5sum: b2f597f3abfade9d0fcc58dbcac0ceac
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, ExperimentHub, CancerData,
Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData,
ExperimentData
Author: Michael Zon [aut], Deena M.A. Gendoo [aut], Christopher Eeles
[ctb], Benjamin Haibe-Kains [aut, cre]
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
git_url: https://git.bioconductor.org/packages/MetaGxBreast
git_branch: RELEASE_3_12
git_last_commit: b3b15a6
git_last_commit_date: 2021-04-23
Date/Publication: 2021-04-26
source.ver: src/contrib/MetaGxBreast_1.10.1.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
dependencyCount: 92
Package: MetaGxOvarian
Version: 1.10.0
Depends: Biobase, stats, lattice, impute, AnnotationHub, ExperimentHub,
SummarizedExperiment, R (>= 3.6.0)
Suggests: testthat, xtable
License: Artistic-2.0
MD5sum: f70f0daf06d6bdd45b499ddabb6dc22d
NeedsCompilation: no
Title: Transcriptomic Ovarian Cancer Datasets
Description: A collection of Ovarian Cancer Transcriptomic Datasets
that are part of the MetaGxData package compendium.
biocViews: ExpressionData, ExperimentHub, CancerData,
Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData,
ExperimentData
Author: Michael Zon <michaelzon7@gmail.com>, Deena M.A. Gendoo
<deena.gendoo@utoronto.ca>, Benjamin Haibe-Kains
<benjamin.haibe.kains@utoronto.ca>
Maintainer: Michael Zon <michaelzon7@gmail.com>
git_url: https://git.bioconductor.org/packages/MetaGxOvarian
git_branch: RELEASE_3_12
git_last_commit: f7fa049
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/MetaGxOvarian_1.10.0.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
dependencyCount: 92
Package: MetaGxPancreas
Version: 1.10.0
Depends: SummarizedExperiment, ExperimentHub, R (>= 3.6.0)
Imports: stats, impute, S4Vectors, AnnotationHub
Suggests: testthat, knitr, BiocStyle, rmarkdown
License: Artistic-2.0
MD5sum: f46a2c0a046236934312283551267921
NeedsCompilation: no
Title: Transcriptomic Pancreatic Cancer Datasets
Description: A collection of pancreatic Cancer transcriptomic datasets
that are part of the MetaGxData package compendium. This
package contains multiple pancreas cancer datasets that have
been downloaded from various resources and turned into
SummarizedExperiment objects. The details of how the authors
normalized the data can be found in the experiment data section
of the objects. Additionally, the location the data was
obtained from can be found in the url variables of the
experiment data portion of each SE.
biocViews: ExpressionData, ExperimentHub, CancerData,
Homo_sapiens_Data, ArrayExpress, GEO, NCI, MicroarrayData,
ExperimentData, SequencingData
Author: Michael Zon [aut, cre], Vandana Sandhu [aut], Benjamin
Haibe-Kains [aut]
Maintainer: Michael Zon <michaelzon7@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/MetaGxPancreas
git_branch: RELEASE_3_12
git_last_commit: 6525a6c
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/MetaGxPancreas_1.10.0.tar.gz
vignettes: vignettes/MetaGxPancreas/inst/doc/MetaGxPancreas.html
vignetteTitles: MetaGxPancreas: A Package for Pancreatic Cancer Gene
Expression Analysis
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MetaGxPancreas/inst/doc/MetaGxPancreas.R
dependencyCount: 92
Package: metaMSdata
Version: 1.26.0
License: GPL (>= 2)
MD5sum: 9f8ac3fb6158ed9235f678f8cb77cb05
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: Yann Guitton <yann.guitton@gmail.com>
git_url: https://git.bioconductor.org/packages/metaMSdata
git_branch: RELEASE_3_12
git_last_commit: 69e6aa1
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/metaMSdata_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: CluMSID, metaMS
dependencyCount: 0
Package: MethylAidData
Version: 1.22.0
Depends: MethylAid, R (>= 3.2)
Suggests: BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC
License: GPL (>= 2)
MD5sum: 5c52c3d758757ac600cc230cb3390c9d
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 <mviterson@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/MethylAidData
git_branch: RELEASE_3_12
git_last_commit: d71d35f
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/MethylAidData_1.22.0.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
suggestsMe: MethylAid
dependencyCount: 155
Package: MethylSeqData
Version: 1.0.0
Depends: SummarizedExperiment
Imports: ExperimentHub, HDF5Array, rhdf5, GenomeInfoDb, S4Vectors,
GenomicRanges, stats, IRanges, utils
Suggests: BiocFileCache, BiocStyle, data.table, knitr, rmarkdown
License: CC0
MD5sum: 2af02a8bed3a2b754209964afdef1239
NeedsCompilation: no
Title: Collection of Public DNA Methylation Sequencing Datasets
Description: Base-level (i.e. cytosine-level) counts for a collection
of public bisulfite-seq datasets (e.g., WGBS and RRBS),
provided as SummarizedExperiment objects with sample- and
base-level metadata.
biocViews: ExperimentHub, ExperimentData, SequencingData,
Homo_sapiens_Data, Mus_musculus_Data, MethylSeqData
Author: Peter Hickey [aut, cre]
Maintainer: Peter Hickey <peter.hickey@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/MethylSeqData
git_branch: RELEASE_3_12
git_last_commit: f8abcd3
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/MethylSeqData_1.0.0.tar.gz
vignettes: vignettes/MethylSeqData/inst/doc/MethylSeqData.html
vignetteTitles: User's Guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MethylSeqData/inst/doc/MethylSeqData.R
dependencyCount: 95
Package: methyvimData
Version: 1.12.0
Depends: R (>= 3.4.0), minfi
Suggests: Biobase, BiocStyle, SummarizedExperiment, knitr, rmarkdown
License: file LICENSE
MD5sum: 6d6ed82ae238729bf17d77c80bff1b50
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 <nhejazi@berkeley.edu>
VignetteBuilder: knitr
PackageStatus: Deprecated
git_url: https://git.bioconductor.org/packages/methyvimData
git_branch: RELEASE_3_12
git_last_commit: 58262df
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/methyvimData_1.12.0.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
suggestsMe: methyvim
dependencyCount: 130
Package: microRNAome
Version: 1.12.0
Depends: R (>= 3.4), SummarizedExperiment
Suggests: BiocGenerics, RUnit
License: GPL (>= 2)
MD5sum: 7fa776a9f0adeb0bc6a3d47baa7a7ad8
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 <mccallm@gmail.com>, Marc K. Halushka
<mhalush1@jhmi.edu>
Maintainer: Matthew N. McCall <mccallm@gmail.com>
git_url: https://git.bioconductor.org/packages/microRNAome
git_branch: RELEASE_3_12
git_last_commit: d63146a
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/microRNAome_1.12.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 26
Package: MIGSAdata
Version: 1.14.0
Depends: R (>= 3.4)
Suggests: BiocGenerics
License: GPL (>= 2)
MD5sum: b07b7a6f0ac2a4d561441a7efb88eef1
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 <jcrodriguez@bdmg.com.ar>
URL: http://www.bdmg.com.ar/
git_url: https://git.bioconductor.org/packages/MIGSAdata
git_branch: RELEASE_3_12
git_last_commit: 77a1c75
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/MIGSAdata_1.14.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: MIGSA
dependencyCount: 0
Package: minfiData
Version: 0.36.0
Depends: R (>= 3.3.0), minfi (>= 1.21.2),
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19
License: Artistic-2.0
MD5sum: 7be8e0f0c797c9e01af0d16b6109aef3
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 <kasperdanielhansen@gmail.com>
git_url: https://git.bioconductor.org/packages/minfiData
git_branch: RELEASE_3_12
git_last_commit: fa2879d
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/minfiData_0.36.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: methylationArrayAnalysis
suggestsMe: bigmelon, conumee, ENmix, funtooNorm, Harman, mCSEA, MEAL,
MethylAid, methyvim, minfi, missMethyl, MultiDataSet,
shinyMethyl, skewr, MethylAidData
dependencyCount: 132
Package: minfiDataEPIC
Version: 1.16.0
Depends: R (>= 3.3), minfi (>= 1.21.2),
IlluminaHumanMethylationEPICmanifest,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
License: Artistic-2.0
MD5sum: 1b73837c3ba0c2cbc4501da54dda4855
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 <kasperdanielhansen@gmail.com>
git_url: https://git.bioconductor.org/packages/minfiDataEPIC
git_branch: RELEASE_3_12
git_last_commit: 30645f1
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/minfiDataEPIC_1.16.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: MethylAid, minfi, REMP, MethylAidData
dependencyCount: 132
Package: minionSummaryData
Version: 1.20.0
Depends: R (>= 3.2.0)
Suggests: BiocStyle, knitr, rmarkdown
License: MIT + file LICENSE
MD5sum: 1f92bd6f0175e8073465fad0e37ddbba
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 <grimbough@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/minionSummaryData
git_branch: RELEASE_3_12
git_last_commit: 6053d53
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/minionSummaryData_1.20.0.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
suggestsMe: IONiseR
dependencyCount: 0
Package: miRcompData
Version: 1.20.0
Depends: R (>= 3.2),
Imports: utils
License: GPL-3 | file LICENSE
MD5sum: 53d2b44cd41d26e3c4fb2fdbc4c38b6b
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 <mccallm@gmail.com>
Maintainer: Matthew N. McCall <mccallm@gmail.com>
git_url: https://git.bioconductor.org/packages/miRcompData
git_branch: RELEASE_3_12
git_last_commit: 949ec31
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/miRcompData_1.20.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
dependsOnMe: miRcomp
dependencyCount: 1
Package: miRNATarget
Version: 1.28.0
Depends: R (>= 2.10), Biobase
License: GPL
MD5sum: dbb8088782dff5d7c43c48a62bac3ee8
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 <tag@granular.com>
Maintainer: Y-h. Taguchi <tag@granular.com>
git_url: https://git.bioconductor.org/packages/miRNATarget
git_branch: RELEASE_3_12
git_last_commit: b7ba873
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/miRNATarget_1.28.0.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
suggestsMe: MiRaGE
dependencyCount: 7
Package: mitoODEdata
Version: 1.26.0
Depends: R (>= 2.14.0)
Imports: methods, graphics
License: LGPL
MD5sum: e5b78fa55840c36c08a6ae09a887d71e
NeedsCompilation: no
Title: Experimental data associated to the paper "Dynamical modelling
of phenotypes in a genome-wide RNAi live-cell imaging assay"
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". 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 <pau.gregoire@gene.com>
SystemRequirements: <not required>
PackageStatus: Deprecated
git_url: https://git.bioconductor.org/packages/mitoODEdata
git_branch: RELEASE_3_12
git_last_commit: cb91b09
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/mitoODEdata_1.26.0.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
dependencyCount: 2
Package: MMAPPR2data
Version: 1.4.0
Depends: R (>= 3.6.0)
Imports: Rsamtools
Suggests: knitr, rmarkdown, BiocStyle, roxygen2, seqinr, readr
Enhances: MMAPPR2
License: GPL-3
MD5sum: 799f3d5d7ef8f9393ee54fdccfaf69f8
NeedsCompilation: no
Title: Sample Data for MMAPPR2
Description: Contains data for illustration purposes in the MMAPPR2
package, namely simulated BAM files containing RNA-Seq data for
a mutation in the slc24a5 gene, taken from the GRCz11 genome.
Also contains reference sequence and annotation files for the
region.
biocViews: RNASeqData, Danio_rerio_Data, SequencingData, Genome
Author: Kyle Johnsen [aut], Jonathon Hill [cre]
Maintainer: Jonathon Hill <jhill@byu.edu>
URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3613585/,
https://github.com/kjohnsen/MMAPPR2
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/MMAPPR2data
git_branch: RELEASE_3_12
git_last_commit: f0ff55d
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/MMAPPR2data_1.4.0.tar.gz
vignettes: vignettes/MMAPPR2data/inst/doc/MMAPPR2data.html
vignetteTitles: Using MMAPPR2data Resources
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MMAPPR2data/inst/doc/MMAPPR2data.R
suggestsMe: MMAPPR2
dependencyCount: 29
Package: MMDiffBamSubset
Version: 1.26.0
Suggests: MMDiff2
License: LGPL
MD5sum: 7331050e61076bdba1a2914d7062743a
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 <G.Schweikert@ed.ac.uk>
git_url: https://git.bioconductor.org/packages/MMDiffBamSubset
git_branch: RELEASE_3_12
git_last_commit: 20f772f
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/MMDiffBamSubset_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: MMDiff2
dependencyCount: 0
Package: MOFAdata
Version: 1.6.0
Depends: R (>= 3.5)
Suggests: knitr, MultiAssayExperiment
License: LGPL-3
MD5sum: c18255b015dd3ab41e1d935c9c859b17
NeedsCompilation: yes
Title: Data package for Multi-Omics Factor Analysis (MOFA)
Description: A collection of datasets to accompany the R package MOFA
and illustrate running and analysing MOFA models.
biocViews: ReproducibleResearch
Author: Ricard Argelaguet, Britta Velten, Damien Arnol, Florian
Buettner, Wolfgang Huber, Oliver Stegle
Maintainer: Britta Velten <britta.velten@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/MOFAdata
git_branch: RELEASE_3_12
git_last_commit: 1bcd0ae
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/MOFAdata_1.6.0.tar.gz
vignettes: vignettes/MOFAdata/inst/doc/MOFAdata.html
vignetteTitles: MOFAdata
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MOFAdata/inst/doc/MOFAdata.R
suggestsMe: MOFA
dependencyCount: 0
Package: mosaicsExample
Version: 1.28.0
Depends: R (>= 2.11.1)
License: GPL (>= 2)
MD5sum: e34adaddcf317e2d2bb62387adee5665
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 <dongjun.chung@gmail.com>
URL: http://groups.google.com/group/mosaics_user_group
git_url: https://git.bioconductor.org/packages/mosaicsExample
git_branch: RELEASE_3_12
git_last_commit: 0c24f1d
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/mosaicsExample_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: mosaics
dependencyCount: 0
Package: mouse4302barcodevecs
Version: 1.28.0
Depends: R (>= 2.10.0)
License: GPL (>= 2)
MD5sum: c2af8d2969541e5f77da51e42f992f0b
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 <mmccall@jhsph.edu>, Rafael A. Irizarry
<rafa@jhu.edu>
Maintainer: Matthew N. McCall <mmccall@jhsph.edu>
git_url: https://git.bioconductor.org/packages/mouse4302barcodevecs
git_branch: RELEASE_3_12
git_last_commit: e939425
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/mouse4302barcodevecs_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: MouseGastrulationData
Version: 1.4.0
Depends: R (>= 4.0), SingleCellExperiment, SummarizedExperiment
Imports: methods, ExperimentHub, BiocGenerics, S4Vectors
Suggests: BiocStyle, knitr, rmarkdown
License: GPL-3
MD5sum: 55b3d08082a5acfc85e1c4d02cacc25e
NeedsCompilation: no
Title: Single-Cell Transcriptomics Data across Mouse Gastrulation and
Early Organogenesis
Description: Provides processed and raw count matrices for single-cell
RNA sequencing data from a timecourse of mouse gastrulation and
early organogenesis.
biocViews: ExperimentData, ExpressionData, SequencingData, RNASeqData,
SingleCellData, ExperimentHub
Author: Jonathan Griffiths [aut, cre], Aaron Lun [aut]
Maintainer: Jonathan Griffiths <jonathan.griffiths.94@gmail.com>
URL: https://github.com/MarioniLab/MouseGastrulationData
VignetteBuilder: knitr
BugReports: https://github.com/MarioniLab/MouseGastrulationData/issues
git_url: https://git.bioconductor.org/packages/MouseGastrulationData
git_branch: RELEASE_3_12
git_last_commit: 0440a1c
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/MouseGastrulationData_1.4.0.tar.gz
vignettes:
vignettes/MouseGastrulationData/inst/doc/MouseGastrulationData.html
vignetteTitles: Available datasets
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/MouseGastrulationData/inst/doc/MouseGastrulationData.R
dependencyCount: 92
Package: msd16s
Version: 1.10.0
Depends: R (>= 2.10), Biobase, metagenomeSeq,
License: Artistic-2.0
MD5sum: 4ecc50918504769e729a9e8857446712
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 <jpaulson@umiacs.umd.edu>
URL: http://www.cbcb.umd.edu/research/projects/GEMS-pathogen-discovery
git_url: https://git.bioconductor.org/packages/msd16s
git_branch: RELEASE_3_12
git_last_commit: 270ed4c
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/msd16s_1.10.0.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
suggestsMe: metavizr
dependencyCount: 29
Package: msdata
Version: 0.30.0
Depends: R (>= 2.10)
Suggests: xcms, mzR, MSnbase
License: GPL (>= 2)
MD5sum: 03723043fc93835c6615b11e823a9f0b
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 <sneumann@ipb-halle.de>, Laurent Gatto
<laurent.gatto@uclouvain.be> with contriutions from Johannes
Rainer
Maintainer: Steffen Neumann <sneumann@ipb-halle.de>, Laurent Gatto
<laurent.gatto@uclouvain.be>
git_url: https://git.bioconductor.org/packages/msdata
git_branch: RELEASE_3_12
git_last_commit: 821821a
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/msdata_0.30.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: IPO, MSnbase, mzR, peakPantheR, QFeatures, Spectra, xcms,
RforProteomics
dependencyCount: 0
Package: MSMB
Version: 1.8.0
Depends: R (>= 2.10)
Suggests: knitr, BiocStyle
License: LGPL
MD5sum: 261e60bf66142bf66bcb7011c0d3a47c
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 <whuber@embl.de>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/MSMB
git_branch: RELEASE_3_12
git_last_commit: 5ce6b52
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/MSMB_1.8.0.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
dependencyCount: 0
Package: msPurityData
Version: 1.18.0
Suggests: knitr
License: GPL (>= 2)
MD5sum: 4fd99010fb927b81c3d37bdcf088a3ba
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 <thomas.nigel.lawson@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/msPurityData
git_branch: RELEASE_3_12
git_last_commit: d886117
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/msPurityData_1.18.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: msPurity
dependencyCount: 0
Package: msqc1
Version: 1.18.0
Depends: R (>= 3.6), lattice, stats, utils
Suggests: BiocStyle, knitr, testthat, specL (>= 1.2)
License: GPL
MD5sum: 9834d58363b4027a188fb06d9f0d5e7d
NeedsCompilation: no
Title: Sigma mix MSQC1 data
Description: contains eight technical replicate data set and a three
replicate dilution series of the MS Qual/Quant Quality Control
Mix standard sample (Sigma-Aldrich, Buchs, Switzerland)
measured on five different mass spectrometer platforms at the
Functional Genomics Center Zurich.
biocViews: ExperimentData, MassSpectrometryData, ReproducibleResearch
Author: Tobias Kockmann [aut]
(<https://orcid.org/0000-0002-1847-885X>), Christian Trachsel
[aut], Christian Panse [aut, cre]
(<https://orcid.org/0000-0003-1975-3064>)
Maintainer: Christian Panse <cp@fgcz.ethz.ch>
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_12
git_last_commit: be38dc3
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/msqc1_1.18.0.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
dependencyCount: 6
Package: MSstatsBioData
Version: 1.12.0
Depends: R (>= 3.4)
Suggests: BiocStyle, knitr, MSstats
License: Artistic-2.0
MD5sum: 936e940e8a9511585b4708862b3d718d
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 <mnchoi67@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/MSstatsBioData
git_branch: RELEASE_3_12
git_last_commit: e2631a8
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/MSstatsBioData_1.12.0.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
suggestsMe: MSstats
dependencyCount: 0
Package: mtbls2
Version: 1.20.1
Depends: R (>= 2.10)
Suggests: xcms (>= 3.11.8), CAMERA, Risa (>= 1.0.0), knitr, Heatplus,
pcaMethods, sp
License: CC0
MD5sum: c212b7abdca4cf3309219a7479b251ca
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 <sneumann@ipb-halle.de>
Maintainer: Steffen Neumann <sneumann@ipb-halle.de>
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_12
git_last_commit: 01210c4
git_last_commit_date: 2020-11-28
Date/Publication: 2020-11-30
source.ver: src/contrib/mtbls2_1.20.1.tar.gz
vignettes: vignettes/mtbls2/inst/doc/MTBLS2-xcms3.html,
vignettes/mtbls2/inst/doc/MTBLS2.html
vignetteTitles: MTBLS2 Processing and Analysis with xcms3,, 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
suggestsMe: Autotuner, IPO, yamss
dependencyCount: 0
Package: MUGAExampleData
Version: 1.10.0
Depends: R (>= 2.10.0)
License: GPL-3
MD5sum: b76917129371e6dfeac211201cd9f90e
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 <Dan.Gatti@jax.org>
Maintainer: Daniel Gatti <Dan.Gatti@jax.org>
git_url: https://git.bioconductor.org/packages/MUGAExampleData
git_branch: RELEASE_3_12
git_last_commit: 418b1ed
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/MUGAExampleData_1.10.0.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
dependencyCount: 0
Package: muscData
Version: 1.4.0
Depends: R (>= 3.6), ExperimentHub, SingleCellExperiment
Imports: utils
Suggests: BiocStyle, dplyr, DropletUtils, knitr, GEOquery, Matrix,
matrixStats, methods, muscat, rmarkdown, R.utils, readxl,
scater, scds, Seurat
License: MIT + file LICENSE
MD5sum: ce6d68f9bd537bf18be48652b017f48a
NeedsCompilation: no
Title: Multi-sample multi-group scRNA-seq data
Description: Data package containing a collection of multi-sample
multi-group scRNA-seq datasets in SingleCellExperiment
Bioconductor object format.
biocViews: ExperimentHub, ExperimentData, ExpressionData, GEO,
Homo_sapiens_Data, ImmunoOncologyData, SingleCellData
Author: Helena L. Crowell [aut, cre]
Maintainer: Helena L. Crowell <helena.crowell@uzh.ch>
URL: https://github.com/HelenaLC/muscData
VignetteBuilder: knitr
BugReports: https://github.com/HelenaLC/muscData/issues
git_url: https://git.bioconductor.org/packages/muscData
git_branch: RELEASE_3_12
git_last_commit: 3a3a116
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/muscData_1.4.0.tar.gz
vignettes: vignettes/muscData/inst/doc/muscData.html
vignetteTitles: Multi-sample multi-group scRNA-seq data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/muscData/inst/doc/muscData.R
dependencyCount: 92
Package: mvoutData
Version: 1.26.0
Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4),
lumi
License: Artistic-2.0
MD5sum: 199cfe2ca4029544b91b148909877bf5
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 <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/mvoutData
git_branch: RELEASE_3_12
git_last_commit: e29ed31
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/mvoutData_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: arrayMvout
dependencyCount: 151
Package: NanoporeRNASeq
Version: 1.0.0
Depends: R(>= 4.0.0), ExperimentHub (>= 1.15.3)
Suggests: knitr, bambu, ggbio, BSgenome.Hsapiens.NCBI.GRCh38, circlize,
ComplexHeatmap, apeglm, rlang, GenomicAlignments, Rsamtools
Enhances: parallel
License: GPL-3 + file LICENSE
MD5sum: aea2d0400b2f9b2ff2c315642d520d59
NeedsCompilation: no
Title: Nanopore RNA-Seq Example data
Description: The NanoporeRNASeq package contains long read RNA-Seq data
generated using Oxford Nanopore Sequencing. The data consists
of 6 samples from two human cell lines (K562 and MCF7) that
were generated by the SG-NEx project. Each of these cell lines
has three replicates, with 1 direct RNA sequencing data and 2
cDNA sequencing data. Reads are aligned to chromosome 22
(Grch38) and stored as bam files. The original data is from the
SG-NEx project.
biocViews: ExperimentHub, ExperimentData, RNASeqData, Genome,
SequencingData
Author: Jonathan Goeke Developer [aut], Ying Chen Developer [cre], Yuk
Kei Wan Developer [aut]
Maintainer: Ying Chen Developer <chen_ying@gis.a-star.edu.sg>
URL: https://github.com/GoekeLab/NanoporeRNASeq
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/NanoporeRNASeq
git_branch: RELEASE_3_12
git_last_commit: f06482d
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/NanoporeRNASeq_1.0.0.tar.gz
vignettes: vignettes/NanoporeRNASeq/inst/doc/NanoporeRNASeq.html
vignetteTitles: NanoporeRNASeq
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/NanoporeRNASeq/inst/doc/NanoporeRNASeq.R
suggestsMe: bambu
dependencyCount: 77
Package: nanotubes
Version: 1.6.0
Depends: R (>= 3.6)
Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, rtracklayer,
CAGEfightR
License: GPL-3
MD5sum: c6eaa509f7d4968675a872cfd72549cd
NeedsCompilation: no
Title: Mouse nanotube CAGE data
Description: Cap Analysis of Gene Expression (CAGE) data from
"Identification of Gene Transcription Start Sites and Enhancers
Responding to Pulmonary Carbon Nanotube Exposure in Vivo" by
Bornholdt et al. supplied as CAGE Transcription Start Sites
(CTSSs).
biocViews: ExperimentData, SequencingData, ExpressionData
Author: Malte Thodberg
Maintainer: Malte Thodberg <maltethodberg@gmail.com>
URL: https://github.com/MalteThodberg/nanotubes
VignetteBuilder: knitr
BugReports: https://github.com/MalteThodberg/nanotubes/issues
git_url: https://git.bioconductor.org/packages/nanotubes
git_branch: RELEASE_3_12
git_last_commit: 70746bd
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/nanotubes_1.6.0.tar.gz
vignettes: vignettes/nanotubes/inst/doc/nanotubes.html
vignetteTitles: nanotubes
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/nanotubes/inst/doc/nanotubes.R
dependsOnMe: CAGEWorkflow
dependencyCount: 0
Package: NCIgraphData
Version: 1.26.0
Depends: R (>= 2.10.0)
Suggests: Rgraphviz
License: GPL-3
MD5sum: 39845152e5fedba7a016dafec26e8fb9
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 <laurent.jacob@gmail.com>
git_url: https://git.bioconductor.org/packages/NCIgraphData
git_branch: RELEASE_3_12
git_last_commit: 2dc6fca
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/NCIgraphData_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: NestLink
Version: 1.6.0
Depends: R (>= 3.6), AnnotationHub (>= 2.15), ExperimentHub (>= 1.0),
Biostrings (>= 2.51), gplots (>= 3.0), protViz (>= 0.4),
ShortRead (>= 1.41)
Imports: grDevices, graphics, stats, utils
Suggests: BiocStyle (>= 2.2), DT, ggplot2, knitr, rmarkdown, testthat,
specL, lattice, scales
License: GPL
MD5sum: 7c828fec20fe1af6e303d688801d787f
NeedsCompilation: no
Title: NestLink an R data package to guide through Engineered Peptide
Barcodes for In-Depth Analyzes of Binding Protein Ensembles
Description: Provides next-generation sequencing (NGS) and mass
spectrometry (MS) sample data, code snippets and replication
material used for developing NestLink. The NestLink approach is
a protein binder selection and identification technology able
to biophysically characterize thousands of library members at
once without handling individual clones at any stage of the
process. Data were acquired on NGS and MS platforms at the
Functional Genomics Center Zurich.
biocViews: ExperimentHub, ExperimentData, SequencingData,
MassSpectrometryData, ReproducibleResearch
Author: Pascal Egloff [aut] (<https://orcid.org/0000-0001-8948-3704>),
Iwan Zimmermann [ctb]
(<https://orcid.org/0000-0003-3476-4749>), Fabian M. Arnold
[ctb], Cedric A.J. Hutter [ctb]
(<https://orcid.org/0000-0002-8920-3343>), Lennart Opitz [aut,
cre] (<https://orcid.org/0000-0001-7945-6737>), Lucy Poveda
[ctb] (<https://orcid.org/0000-0002-5291-5582>), Hans-Anton
Keserue [ctb], Christian Panse [aut, ctb]
(<https://orcid.org/0000-0003-1975-3064>), Bernd Roschitzki
[aut] (<https://orcid.org/0000-0001-5756-9773>), Markus Seeger
[aut] (<https://orcid.org/0000-0003-1761-8571>)
Maintainer: Lennart Opitz <lopitz@fgcz.ethz.ch>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/NestLink
git_branch: RELEASE_3_12
git_last_commit: 02d40a4
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/NestLink_1.6.0.tar.gz
vignettes:
vignettes/NestLink/inst/doc/analyze-flycode-detectibilty.html,
vignettes/NestLink/inst/doc/compare-predicted-observed-flycodes.html,
vignettes/NestLink/inst/doc/link-nanobodies-flycodes.html,
vignettes/NestLink/inst/doc/make-data.html,
vignettes/NestLink/inst/doc/simulate-flycodes.html,
vignettes/NestLink/inst/doc/supplement-note1.html
vignetteTitles: 2. Analyze flycode detectability using ESP and SSRC
prediction, 3. Compare Predicted and Observed flycodes
hydrophobicity values using F255744., 1. Link high quality
flycode and nanobody sequences by NGS filtering., 5. make-data,
0. Simulate flycode properties., 4. Control experiment to
assess the robustness of protein detection via flycodes
(NMETH-A35040 Suppl. notes 1).
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/NestLink/inst/doc/analyze-flycode-detectibilty.R,
vignettes/NestLink/inst/doc/compare-predicted-observed-flycodes.R,
vignettes/NestLink/inst/doc/link-nanobodies-flycodes.R,
vignettes/NestLink/inst/doc/make-data.R,
vignettes/NestLink/inst/doc/simulate-flycodes.R,
vignettes/NestLink/inst/doc/supplement-note1.R
dependencyCount: 113
Package: Neve2006
Version: 0.28.0
Depends: R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0),
hgu133a.db, annotate
License: Artistic-2.0
MD5sum: d382b1d36d68afe7c08a41fd23833786
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 <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/Neve2006
git_branch: RELEASE_3_12
git_last_commit: 1fa3869
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/Neve2006_0.28.0.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
dependencyCount: 40
Package: NGScopyData
Version: 1.10.0
License: GPL (>=2)
MD5sum: 1269189e1a0ce421247335d808f88368
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 <xiaobei@binf.ku.dk>
URL:
http://www.bioconductor.org/packages/release/data/experiment/html/NGScopyData.html
git_url: https://git.bioconductor.org/packages/NGScopyData
git_branch: RELEASE_3_12
git_last_commit: 1be2f08
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/NGScopyData_1.10.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: oct4
Version: 1.6.0
Suggests: knitr
License: GPL (>= 2)
MD5sum: 1649199754337c520da0409e3d9c5b29
NeedsCompilation: no
Title: Conditional knockdown of OCT4 in mouse ESCs
Description: This package provides the output of running Salmon on a
set of 12 RNA-seq samples from King & Klose, "The pioneer
factor OCT4 requires the chromatin remodeller BRG1 to support
gene regulatory element function in mouse embryonic stem
cells", published in eLIFE, March 2017. For details on version
numbers and how the samples were processed see the package
vignette.
biocViews: ExperimentData, SequencingData, RNASeqData
Author: Michael Love
Maintainer: Michael Love <michaelisaiahlove@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/oct4
git_branch: RELEASE_3_12
git_last_commit: 875d1fa
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/oct4_1.6.0.tar.gz
vignettes: vignettes/oct4/inst/doc/oct4.html
vignetteTitles: Salmon quantifications for condition OCT4 knockdown in
mouse ESCs
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/oct4/inst/doc/oct4.R
dependencyCount: 0
Package: OMICsPCAdata
Version: 1.8.0
Depends: R (>= 3.5.0), MultiAssayExperiment
Suggests: knitr, kableExtra, rmarkdown
License: GPL-3
MD5sum: bf2d969591668d8217c27e90b31fee3d
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 <subhadeep1024@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/OMICsPCAdata
git_branch: RELEASE_3_12
git_last_commit: f114162
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/OMICsPCAdata_1.8.0.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
dependsOnMe: OMICsPCA
dependencyCount: 47
Package: OnassisJavaLibs
Version: 1.12.0
Depends: R (>= 3.4)
Imports: rJava
Suggests: BiocStyle, rmarkdown, knitr
License: GPL-2
MD5sum: dcad3f01f013848ce70ca4a7852dc100
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 <eugenia.galeota@gmail.com>
SystemRequirements: Java (>= 1.8)
VignetteBuilder: rmarkdown, knitr
git_url: https://git.bioconductor.org/packages/OnassisJavaLibs
git_branch: RELEASE_3_12
git_last_commit: e053621
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/OnassisJavaLibs_1.12.0.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
dependsOnMe: Onassis
dependencyCount: 2
Package: optimalFlowData
Version: 1.2.0
Depends: R (>= 4.0)
Suggests: knitr, BiocStyle, rmarkdown, magick
License: Artistic-2.0
MD5sum: 1a38124fe2886e193b38e0f8e24e7fda
NeedsCompilation: no
Title: optimalFlowData
Description: Data files used as examples and for testing of the
software provided in the optimalFlow package.
biocViews: ExperimentData, PackageTypeData, ImmunoOncologyData,
FlowCytometryData
Author: Hristo Inouzhe <hristo.inouzhe@gmail.com>
Maintainer: Hristo Inouzhe <hristo.inouzhe@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/optimalFlowData
git_branch: RELEASE_3_12
git_last_commit: 930e8b9
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/optimalFlowData_1.2.0.tar.gz
vignettes:
vignettes/optimalFlowData/inst/doc/optimalFlowData_vignette.html
vignetteTitles: optimalFlow: optimal-transport approach to Flow
Cytometry analysis
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/optimalFlowData/inst/doc/optimalFlowData_vignette.R
dependsOnMe: optimalFlow
dependencyCount: 0
Package: parathyroidSE
Version: 1.28.0
Depends: SummarizedExperiment, R (>= 2.10)
Suggests: Rsamtools, GenomicAlignments, GEOquery, SRAdb,
GenomicFeatures, BiocStyle
License: LGPL
MD5sum: 120a4b8889f5c1783dbbcd436764c9a7
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 <michaelisaiahlove@gmail.com>
git_url: https://git.bioconductor.org/packages/parathyroidSE
git_branch: RELEASE_3_12
git_last_commit: 3608789
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/parathyroidSE_1.28.0.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
suggestsMe: ClassifyR, DEXSeq, simulatorZ
dependencyCount: 26
Package: pasilla
Version: 1.18.1
Depends: R (>= 3.3.0)
Suggests: DEXSeq, rmarkdown, BiocStyle, knitr
License: LGPL
MD5sum: 29c5ffe2e8a95525d33cda768bfbb8b4
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 <alejandro.reyes.ds@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/pasilla
git_branch: RELEASE_3_12
git_last_commit: 1889939
git_last_commit_date: 2020-12-23
Date/Publication: 2020-12-24
source.ver: src/contrib/pasilla_1.18.1.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
importsMe: blacksheepr
suggestsMe: BADER, DESeq2, DEXSeq, EnhancedVolcano, regionReport,
ReportingTools, tidybulk, IHWpaper, pasillaBamSubset
dependencyCount: 0
Package: pasillaBamSubset
Version: 0.28.0
Suggests: pasilla
License: LGPL
MD5sum: 050cd33be3e9af1da31a1576b530284b
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 <hpages.on.github@gmail.com>
git_url: https://git.bioconductor.org/packages/pasillaBamSubset
git_branch: RELEASE_3_12
git_last_commit: 6e5cec4
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/pasillaBamSubset_0.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: GenomicAlignments, GenomicFeatures, GenomicRanges, gmoviz,
IRanges, karyoploteR, plyranges, TransView
dependencyCount: 0
Package: PasillaTranscriptExpr
Version: 1.18.0
Depends: R (>= 3.3.0)
Suggests: rtracklayer, BiocStyle, knitr, testthat
License: GPL (>= 3)
MD5sum: 0b60db6e5deb47ef3ca351ba96cea648
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 <gosia.nowicka@uzh.ch>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/PasillaTranscriptExpr
git_branch: RELEASE_3_12
git_last_commit: 03d7bd7
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/PasillaTranscriptExpr_1.18.0.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
suggestsMe: DRIMSeq
dependencyCount: 0
Package: PathNetData
Version: 1.26.0
Depends: R (>= 1.14.0)
License: GPL-3
MD5sum: 7e3f6b58403749727af386484b41563c
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 <bhaskar.dutta@gmail.com>, Anders Wallqvist
<awallqvist@bhsai.org>, and Jaques Reifman <jreifman@bhsai.org>
Maintainer: Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>
git_url: https://git.bioconductor.org/packages/PathNetData
git_branch: RELEASE_3_12
git_last_commit: b8cddbb
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/PathNetData_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: PathNet
dependencyCount: 0
Package: pathprintGEOData
Version: 1.20.0
Depends: R (>= 3.4)
Suggests: pathprint, SummarizedExperiment
License: GPL
MD5sum: c36a4a01d3aeca864e22f3218578964c
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 <s.kariotis@sheffield.ac.uk>
PackageStatus: Deprecated
git_url: https://git.bioconductor.org/packages/pathprintGEOData
git_branch: RELEASE_3_12
git_last_commit: 545e7c7
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/pathprintGEOData_1.20.0.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
dependencyCount: 0
Package: pcaGoPromoter.Hs.hg19
Version: 1.26.0
License: GPL (>= 2)
MD5sum: 6276608a745d2e02550f625fa7e2d003
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 <mhansen@sund.ku.dk>
Maintainer: Morten Hansen <mhansen@sund.ku.dk>
PackageStatus: Deprecated
git_url: https://git.bioconductor.org/packages/pcaGoPromoter.Hs.hg19
git_branch: RELEASE_3_12
git_last_commit: c1f37ef
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/pcaGoPromoter.Hs.hg19_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: pcaGoPromoter.Mm.mm9
Version: 1.26.0
License: GPL (>= 2)
MD5sum: f8537b219b1a7c35d1a26b6ea2b0de3c
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, <mhansen@sund.ku.dk>
Maintainer: Morten Hansen <mhansen@sund.ku.dk>
PackageStatus: Deprecated
git_url: https://git.bioconductor.org/packages/pcaGoPromoter.Mm.mm9
git_branch: RELEASE_3_12
git_last_commit: fdfcb4f
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/pcaGoPromoter.Mm.mm9_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: pcaGoPromoter.Rn.rn4
Version: 1.26.0
License: GPL (>= 2)
MD5sum: 2086f764f93b01317fabb0615bc52071
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 <mhansen@sund.ku.dk>
Maintainer: Morten Hansen, <mhansen@sund.ku.dk>
PackageStatus: Deprecated
git_url: https://git.bioconductor.org/packages/pcaGoPromoter.Rn.rn4
git_branch: RELEASE_3_12
git_last_commit: 5262b47
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/pcaGoPromoter.Rn.rn4_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: PCHiCdata
Version: 1.18.0
Depends: R (>= 3.2), Chicago
Suggests: testthat, BiocStyle, knitr
License: Artistic-2.0
MD5sum: eb70f3ccb1adbc8919388c55902f84ec
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
<paula.freire-pritchett@babraham.ac.uk>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/PCHiCdata
git_branch: RELEASE_3_12
git_last_commit: 3d342b9
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/PCHiCdata_1.18.0.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
suggestsMe: Chicago
dependencyCount: 72
Package: pcxnData
Version: 2.12.0
Depends: R (>= 3.4)
Suggests: pcxn
License: MIT + file LICENSE
MD5sum: 1931ae0b35e02acd7c06f412c658c7d7
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 <s.kariotis@sheffield.ac.uk>
git_url: https://git.bioconductor.org/packages/pcxnData
git_branch: RELEASE_3_12
git_last_commit: bb367e2
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/pcxnData_2.12.0.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
dependsOnMe: pcxn
dependencyCount: 0
Package: pd.atdschip.tiling
Version: 0.28.0
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: 62557a240f954bd28636afe2a01734f6
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 <kristof.debeuf@ugent.be>
git_url: https://git.bioconductor.org/packages/pd.atdschip.tiling
git_branch: RELEASE_3_12
git_last_commit: 0eff76b
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/pd.atdschip.tiling_0.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 54
Package: pepDat
Version: 1.10.0
Depends: R(>= 3.0.0)
Imports: GenomicRanges
Suggests: knitr
License: Artistic-2.0
MD5sum: c761ec707c83cd3a216065db41625767
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 <rsautera@fhcrc.org>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/pepDat
git_branch: RELEASE_3_12
git_last_commit: 6dd4be5
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/pepDat_1.10.0.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
suggestsMe: pepStat, Pviz
dependencyCount: 17
Package: PepsNMRData
Version: 1.8.0
Depends: R (>= 3.5)
Suggests: knitr, markdown, rmarkdown, BiocStyle
License: GPL-2 | file LICENSE
MD5sum: 023e8a1b78b0f10590c67f2dc7308e30
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 <manon.martin@uclouvain.be>
BugReports: https://github.com/ManonMartin/PepsNMRData/issues
git_url: https://git.bioconductor.org/packages/PepsNMRData
git_branch: RELEASE_3_12
git_last_commit: 557d701
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/PepsNMRData_1.8.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
suggestsMe: PepsNMR
dependencyCount: 0
Package: PhyloProfileData
Version: 1.4.0
Depends: R (>= 3.6.0)
Imports: ExperimentHub, Biostrings
Suggests: knitr
License: MIT + file LICENSE
MD5sum: d5da0364c4e4205ff9b4d96c75eb6da9
NeedsCompilation: yes
Title: Data package for phylogenetic profile analysis using
PhyloProfile tool
Description: Two experimental datasets to illustrate running and
analysing phylogenetic profiles with PhyloProfile package.
biocViews: ExperimentData, ReproducibleResearch, ExperimentHub
Author: Ingo Ebersberger, Arpit Jain, Hannah Mülbaier, Vinh Tran
Maintainer: Vinh Tran <tran@bio.uni-frankfurt.de>
URL: https://github.com/BIONF/PhyloProfileData
VignetteBuilder: knitr
BugReports: https://github.com/trvinh/PhyloProfileData/issues
git_url: https://git.bioconductor.org/packages/PhyloProfileData
git_branch: RELEASE_3_12
git_last_commit: f963b1b
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/PhyloProfileData_1.4.0.tar.gz
vignettes: vignettes/PhyloProfileData/inst/doc/PhyloProfileData.html
vignetteTitles: PhyloProfileData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/PhyloProfileData/inst/doc/PhyloProfileData.R
dependencyCount: 80
Package: plasFIA
Version: 1.18.0
Depends: proFIA
License: LGPL
MD5sum: 68bda04abd8377f101776fdfed8378b2
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 <alexis.delabriere@outlook.fr>
git_url: https://git.bioconductor.org/packages/plasFIA
git_branch: RELEASE_3_12
git_last_commit: 9fc459b
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/plasFIA_1.18.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: proFIA
dependencyCount: 103
Package: ppiData
Version: 0.28.0
Depends: graph
Imports: AnnotationDbi
Suggests: org.Sc.sgd.db, ppiStats
License: Artistic-2.0
MD5sum: 4c12874544a3ce347b66a04169957c61
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
<maintainer@bioconductor.org>
git_url: https://git.bioconductor.org/packages/ppiData
git_branch: RELEASE_3_12
git_last_commit: 86de2bb
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ppiData_0.28.0.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
dependsOnMe: PCpheno, ppiStats
suggestsMe: ScISI
dependencyCount: 27
Package: prebsdata
Version: 1.26.0
Depends: R (>= 2.14.0)
License: Artistic-2.0
MD5sum: 68d86474c0b61b7adc5950b96b53c3e7
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 <karolis.uziela@scilifelab.se>
git_url: https://git.bioconductor.org/packages/prebsdata
git_branch: RELEASE_3_12
git_last_commit: 827eed6
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/prebsdata_1.26.0.tar.gz
vignettes: vignettes/prebsdata/inst/doc/prebsdata.pdf
vignetteTitles: prebsdata User Guide
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: prebs, SigFuge
dependencyCount: 0
Package: PREDAsampledata
Version: 0.30.0
Depends: R (>= 2.10.0), methods, PREDA, Biobase, affy, annotate
Suggests: hgu133plus2.db, hgu133plus2cdf
License: Artistic-2.0
MD5sum: 196ea85e4e11d75d7904fd42e52705d3
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 <francesco.ferrari@ifom.eu>
git_url: https://git.bioconductor.org/packages/PREDAsampledata
git_branch: RELEASE_3_12
git_last_commit: 7fe7bf2
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/PREDAsampledata_0.30.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: PREDA
dependencyCount: 54
Package: ProData
Version: 1.28.0
Depends: R (>= 2.4.0), Biobase (>= 2.5.5)
License: GPL
MD5sum: f6ad22c62345f4264ea027e603ab7ed5
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 <xiaochun@jimmy.harvard.edu>
git_url: https://git.bioconductor.org/packages/ProData
git_branch: RELEASE_3_12
git_last_commit: 39a00e5
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ProData_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: CorrectedFDR
dependencyCount: 7
Package: pRolocdata
Version: 1.28.0
Depends: R (>= 3.6.3), MSnbase
Imports: Biobase, utils
Suggests: pRoloc (>= 1.13.8), testthat
License: GPL-2
MD5sum: 5ee41d08e66faba9bfb7e174bdba5c05
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, Oliver M. Crook and Lisa M. Breckels
Maintainer: Laurent Gatto <laurent.gatto@uclouvain.be>
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_12
git_last_commit: 1764dcb
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/pRolocdata_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: proteomics
suggestsMe: MSnbase, pRoloc, pRolocGUI, RforProteomics
dependencyCount: 74
Package: prostateCancerCamcap
Version: 1.18.0
Depends: Biobase, R (>= 3.3)
Suggests: GEOquery
License: Artistic-2.0
MD5sum: 2b1fa1c883bf7dbded0cb728abd53f70
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 <mark.dunning@cruk.cam.ac.uk>
git_url: https://git.bioconductor.org/packages/prostateCancerCamcap
git_branch: RELEASE_3_12
git_last_commit: 65f5bfc
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/prostateCancerCamcap_1.18.0.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
dependencyCount: 7
Package: prostateCancerGrasso
Version: 1.18.0
Depends: Biobase, R (>= 3.3)
Suggests: GEOquery
License: Artistic-2.0
MD5sum: 37acc8f486549ba417079204c202e237
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 <mark.dunning@cruk.cam.ac.uk>
git_url: https://git.bioconductor.org/packages/prostateCancerGrasso
git_branch: RELEASE_3_12
git_last_commit: cd66d64
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/prostateCancerGrasso_1.18.0.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
dependencyCount: 7
Package: prostateCancerStockholm
Version: 1.18.0
Depends: Biobase , R (>= 3.3)
Suggests: GEOquery
License: Artistic-2.0
MD5sum: dd95c3fe63eed97ff7dcb7dee3de8ccb
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 <mark.dunning@cruk.cam.ac.uk>
git_url: https://git.bioconductor.org/packages/prostateCancerStockholm
git_branch: RELEASE_3_12
git_last_commit: 0b0c3e1
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/prostateCancerStockholm_1.18.0.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
dependencyCount: 7
Package: prostateCancerTaylor
Version: 1.18.0
Depends: Biobase, R (>= 3.3)
Suggests: GEOquery, org.Hs.eg.db
License: Artistic-2.0
MD5sum: 315f32f75f7b8f7e3577c0f80d6a60e1
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 <mark.dunning@cruk.cam.ac.uk>
git_url: https://git.bioconductor.org/packages/prostateCancerTaylor
git_branch: RELEASE_3_12
git_last_commit: 4f5143f
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/prostateCancerTaylor_1.18.0.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
dependencyCount: 7
Package: prostateCancerVarambally
Version: 1.18.0
Depends: Biobase, R (>= 3.3)
Suggests: GEOquery
License: Artistic-2.0
MD5sum: 12a3ae30f7460c5cc6ed4236e6c3a904
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 <mark.dunning@cruk.cam.ac.uk>
git_url: https://git.bioconductor.org/packages/prostateCancerVarambally
git_branch: RELEASE_3_12
git_last_commit: 8f71824
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/prostateCancerVarambally_1.18.0.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
dependencyCount: 7
Package: PtH2O2lipids
Version: 1.16.0
Depends: R (>= 3.3), xcms, CAMERA, LOBSTAHS, methods, utils
Suggests: gplots, RColorBrewer, cluster, vegan, clustsig
License: MIT + file LICENSE
MD5sum: 4974fcaef00b3f026cd9c25576a4e050
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 <james.r.collins@aya.yale.edu>
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_12
git_last_commit: 906a1b5
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/PtH2O2lipids_1.16.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
suggestsMe: LOBSTAHS
dependencyCount: 127
Package: pumadata
Version: 2.26.0
Depends: R (>= 3.2.0), Biobase (>= 2.5.5),puma, oligo(>= 1.32.0)
License: LGPL
MD5sum: 2077713140f2990ee39a20b6eb03edf1
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: Xuejun liu <xuejun.liu@nuaa.edu.cn>
URL: http://umber.sbs.man.ac.uk/resources/puma
git_url: https://git.bioconductor.org/packages/pumadata
git_branch: RELEASE_3_12
git_last_commit: 0a89e6f
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/pumadata_2.26.0.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
suggestsMe: puma
dependencyCount: 57
Package: PWMEnrich.Dmelanogaster.background
Version: 4.24.0
Depends: methods, PWMEnrich
License: GPL-3
MD5sum: e6b46ce8b619bd07902b43b1a0596d31
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: Diego Diez <diego10ruiz@gmail.com>
git_url:
https://git.bioconductor.org/packages/PWMEnrich.Dmelanogaster.background
git_branch: RELEASE_3_12
git_last_commit: 91f16e6
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver:
src/contrib/PWMEnrich.Dmelanogaster.background_4.24.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: PWMEnrich
dependencyCount: 21
Package: PWMEnrich.Hsapiens.background
Version: 4.24.0
Depends: R (>= 2.10), methods, PWMEnrich
License: GPL-3
MD5sum: f9110634c557cbef10df0b45788b5b7b
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: Diego Diez <diego10ruiz@gmail.com>
git_url:
https://git.bioconductor.org/packages/PWMEnrich.Hsapiens.background
git_branch: RELEASE_3_12
git_last_commit: 9cf6a9a
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/PWMEnrich.Hsapiens.background_4.24.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: PWMEnrich
dependencyCount: 21
Package: PWMEnrich.Mmusculus.background
Version: 4.24.0
Depends: R (>= 2.10), methods, PWMEnrich
License: GPL-3
MD5sum: 7064bd9b2897bc609ae70da70659e69d
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: Diego Diez <diego10ruiz@gmail.com>
git_url:
https://git.bioconductor.org/packages/PWMEnrich.Mmusculus.background
git_branch: RELEASE_3_12
git_last_commit: 4c7cff2
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/PWMEnrich.Mmusculus.background_4.24.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: PWMEnrich
dependencyCount: 21
Package: pwrEWAS.data
Version: 1.4.0
Imports: ExperimentHub
Suggests: knitr, RUnit, BiocGenerics
License: Artistic-2.0
MD5sum: cb3ce70b6132afcde57b4a294f01738c
NeedsCompilation: no
Title: pwrEWAS.data: Reference data accompanying pwrEWAS
Description: This package provides reference data required for pwrEWAS.
pwrEWAS is a user-friendly tool to estimate power in EWAS as a
function of sample and effect size for two-group comparisons of
DNAm (e.g., case vs control, exposed vs non-exposed, etc.).
biocViews: ExperimentHub, MethylationArrayData, MicroarrayData,
TissueMicroarrayData, Tissue
Author: Stefan Graw
Maintainer: Stefan Graw <shgraw@uams.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/pwrEWAS.data
git_branch: RELEASE_3_12
git_last_commit: be93ea2
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/pwrEWAS.data_1.4.0.tar.gz
vignettes: vignettes/pwrEWAS.data/inst/doc/pwrEWAS.data.pdf
vignetteTitles: pwrEWAS.data: Reference data accompanying pwrEWAS
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
importsMe: pwrEWAS
dependencyCount: 77
Package: QDNAseq.hg19
Version: 1.20.0
Depends: R (>= 3.2.1), QDNAseq
License: GPL
MD5sum: bda22c86fc59317e07ac4f9041a263f7
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 <d.sie@vumc.nl>
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_12
git_last_commit: dec68e5
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/QDNAseq.hg19_1.20.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: biscuiteer, QDNAseq
dependencyCount: 49
Package: QDNAseq.mm10
Version: 1.20.0
Depends: R (>= 3.2.1), QDNAseq
License: GPL
MD5sum: cd65e7df93f4a4765f7f338b62191de6
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 <d.sie@vumc.nl>
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_12
git_last_commit: a71709e
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/QDNAseq.mm10_1.20.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: biscuiteer, QDNAseq
dependencyCount: 49
Package: qPLEXdata
Version: 1.8.0
Depends: R (>= 3.5), qPLEXanalyzer
Imports: utils, knitr, MSnbase, dplyr
License: GPL-2
MD5sum: a9545e21a0e553f6faf5787984f8c4f7
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 <kamal.fartiyal84@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/qPLEXdata
git_branch: RELEASE_3_12
git_last_commit: 869fe2a
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/qPLEXdata_1.8.0.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
suggestsMe: qPLEXanalyzer
dependencyCount: 98
Package: QUBICdata
Version: 1.18.0
Depends: R (>= 3.1)
Suggests: knitr, rmarkdown
License: Unlimited | file LICENSE
MD5sum: da5cf90f8d08212eaef5a718a6da2be1
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 <zy26@jlu.edu.cn>
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_12
git_last_commit: cea4c13
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/QUBICdata_1.18.0.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
suggestsMe: QUBIC
dependencyCount: 0
Package: rcellminerData
Version: 2.12.0
Depends: R (>= 3.1.1), Biobase
Suggests: knitr, testthat, BiocStyle, rcellminer
License: LGPL-3 + file LICENSE
MD5sum: c981f721c32746a7d63c8d0ba2a78c66
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 <lunaa@cbio.mskcc.org>, Vinodh Rajapakse
<vinodh.rajapakse@nih.gov>, Fathi Elloumi
<fathi.elloumi@nih.gov>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/rcellminerData
git_branch: RELEASE_3_12
git_last_commit: a135de0
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/rcellminerData_2.12.0.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
dependsOnMe: rcellminer
dependencyCount: 7
Package: RcisTarget.hg19.motifDBs.cisbpOnly.500bp
Version: 1.10.0
Depends: R (>= 3.3)
Imports: data.table
License: GPL-3
MD5sum: 9618daa214589c03ea720088cfcb6c29
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 <sara.aibar@kuleuven.vib.be>
URL: http://scenic.aertslab.org
git_url:
https://git.bioconductor.org/packages/RcisTarget.hg19.motifDBs.cisbpOnly.500bp
git_branch: RELEASE_3_12
git_last_commit: 5491126
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver:
src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.10.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: RcisTarget
dependencyCount: 2
Package: ReactomeGSA.data
Version: 1.4.0
Depends: R (>= 3.6), limma, edgeR, ReactomeGSA, Seurat
License: Artistic-2.0
MD5sum: adbf24701a53d3e0b3c169c175226e38
NeedsCompilation: no
Title: Companion data package for the ReactomeGSA package
Description: Companion data sets to showcase the functionality of the
ReactomeGSA package. This package contains proteomics and
RNA-seq data of the melanoma B-cell induction study by Griss et
al. and scRNA-seq data from Jerby-Arnon et al.
biocViews: ExpressionData, RNASeqData, Proteome, Homo_sapiens_Data
Author: Johannes Griss [aut, cre]
(<https://orcid.org/0000-0003-2206-9511>)
Maintainer: Johannes Griss <johannes.griss@meduniwien.ac.at>
URL: https://github.com/reactome/ReactomeGSA.data/issues
BugReports: https://github.com/reactome/ReactomeGSA.data
git_url: https://git.bioconductor.org/packages/ReactomeGSA.data
git_branch: RELEASE_3_12
git_last_commit: 34d0432
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/ReactomeGSA.data_1.4.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: ReactomeGSA
dependencyCount: 145
Package: RegParallel
Version: 1.8.0
Depends: doParallel, foreach, parallel, iterators, data.table, stringr,
survival, arm, stats, utils, methods
Suggests: RUnit, BiocGenerics, knitr, DESeq2, airway, magrittr,
Biobase, GEOquery, biomaRt, survminer, survey
License: GPL-3
MD5sum: 132d98edb956ba2fa222f919aa96d64f
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, and Bayesian logistic
regression. Also caters for generalised linear models that
utilise survey weights created by the 'survey' CRAN package and
that utilise 'survey::svyglm'.
biocViews: DiseaseModel
Author: Kevin Blighe [aut, cre], Sarega Gurudas [ctb], Jessica Lasky-Su
[aut]
Maintainer: Kevin Blighe <kevin@clinicalbioinformatics.co.uk>
URL: https://github.com/kevinblighe/RegParallel
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/RegParallel
git_branch: RELEASE_3_12
git_last_commit: 1526474
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RegParallel_1.8.0.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
dependencyCount: 84
Package: restfulSEData
Version: 1.12.0
Depends: R (>= 3.4), SummarizedExperiment, ExperimentHub
Imports: utils, methods
Suggests: knitr
License: Artistic-2.0
MD5sum: 3b5a5f351916c2b5b16bff0709dfe2bb
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
<maintainer@bioconductor.org>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/restfulSEData
git_branch: RELEASE_3_12
git_last_commit: a0966bb
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/restfulSEData_1.12.0.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
suggestsMe: restfulSE
dependencyCount: 91
Package: RforProteomics
Version: 1.28.1
Depends: R (>= 3.5), MSnbase (>= 2.5.3)
Imports: R.utils, shiny, biocViews, BiocManager
Suggests: AnnotationDbi, rpx (>= 1.16.1), DT, knitr, rmarkdown,
BiocStyle, mzR, xcms, msdata, isobar, MALDIquant (>= 1.12),
MALDIquantForeign, readBrukerFlexData, synapter, synapterdata,
Rdisop, OrgMassSpecR, SummarizedExperiment, BRAIN, rols, hpar,
GO.db, org.Hs.eg.db, e1071, biomaRt, RColorBrewer, ggplot2,
reshape2, xtable, lattice, mzID, pRoloc, pRolocdata, MSnID,
msmsTests, msmsEDA, DEP, corrplot, beanplot, Heatplus, gplots,
VennDiagram, protViz, genefilter, plotly, gridExtra, dplyr,
lubridate, magick, cleaver
License: Artistic-2.0
MD5sum: 71957a7234ce2c5758dea84b1254771d
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], Sebastian Gibb [ctb], Vlad Petyuk
[ctb], Thomas Pedersen Lin [ctb]
Maintainer: Laurent Gatto <laurent.gatto@uclouvain.be>
URL: http://lgatto.github.com/RforProteomics/
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/RforProteomics
git_branch: RELEASE_3_12
git_last_commit: 96a57e3
git_last_commit_date: 2021-01-15
Date/Publication: 2021-01-18
source.ver: src/contrib/RforProteomics_1.28.1.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
suggestsMe: MSstatsQC, qcmetrics
dependencyCount: 102
Package: RGMQLlib
Version: 1.10.0
Depends: R(>= 3.4.2)
Suggests: BiocStyle, knitr, rmarkdown
License: Artistic-2.0
MD5sum: 29dad94fa077f0b9aa608ec34a5f441c
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 <simonepallotta@hotmail.com>
URL: http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/RGMQLlib
git_branch: RELEASE_3_12
git_last_commit: 8f25360
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RGMQLlib_1.10.0.tar.gz
vignettes: vignettes/RGMQLlib/inst/doc/RGMQLlib.pdf
vignetteTitles: RGMQLlib: scala Libraries to support GMQL
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: RGMQL
dependencyCount: 0
Package: rheumaticConditionWOLLBOLD
Version: 1.28.0
Depends: R (>= 2.10.0)
Suggests: genefilter, Biobase, hgu133plus2.db
License: Artistic-2.0
MD5sum: e6dd8c70198e59afc648fe567e55ca58
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 <aquiroz@hsph.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
git_url:
https://git.bioconductor.org/packages/rheumaticConditionWOLLBOLD
git_branch: RELEASE_3_12
git_last_commit: 48b344b
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/rheumaticConditionWOLLBOLD_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: RITANdata
Version: 1.14.0
Depends: R (>= 3.4)
License: file LICENSE
MD5sum: 61372f17e03d8dcfc9651d8822b73127
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 <zimmermann.michael@mayo.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/RITANdata
git_branch: RELEASE_3_12
git_last_commit: e9a2293
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RITANdata_1.14.0.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
importsMe: RITAN
dependencyCount: 0
Package: RMassBankData
Version: 1.28.0
Suggests: RMassBank
License: Artistic-2.0
MD5sum: 3cc5ee0065cf23bedc59addd8fb7baa3
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 <massbank@eawag.ch>
git_url: https://git.bioconductor.org/packages/RMassBankData
git_branch: RELEASE_3_12
git_last_commit: 0fe2270
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RMassBankData_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: RNAinteractMAPK
Version: 1.28.2
Depends: R (>= 2.12.0), sparseLDA, RNAinteract
Imports: grid, gdata, MASS, genefilter, methods, fields, utils,
lattice, Biobase
Suggests: qvalue
License: Artistic-2.0
MD5sum: 4f2bbb8a9aadd75159d44d8556bea3ff
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 [aut], Wolfgang Huber [ctb], Mike Smith [cre]
Maintainer: Mike Smith <mike.smith@embl.de>
git_url: https://git.bioconductor.org/packages/RNAinteractMAPK
git_branch: RELEASE_3_12
git_last_commit: 425e384
git_last_commit_date: 2020-12-22
Date/Publication: 2020-12-24
source.ver: src/contrib/RNAinteractMAPK_1.28.2.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
dependencyCount: 113
Package: RNAmodR.Data
Version: 1.4.0
Depends: R (>= 3.6), ExperimentHub, ExperimentHubData (>= 1.9.2)
Imports: utils
Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, sessioninfo,
testthat
License: Artistic-2.0
MD5sum: 76a39b40b6dc9e54d5f0513896e93153
NeedsCompilation: no
Title: Example data for the RNAmodR package
Description: RNAmodR.Data contains example data, which is used for
vignettes and example workflows in the RNAmodR and dependent
packages.
biocViews: ExperimentData, SequencingData, RNASeqData
Author: Felix G.M. Ernst [aut, cre], Denis L.J. Lafontaine [ctb, fnd]
Maintainer: Felix G.M. Ernst <felix.gm.ernst@outlook.com>
URL: https://github.com/FelixErnst/RNAmodR.Data
VignetteBuilder: knitr
BugReports: https://github.com/FelixErnst/RNAmodR.Data/issues
git_url: https://git.bioconductor.org/packages/RNAmodR.Data
git_branch: RELEASE_3_12
git_last_commit: 8fe16f1
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RNAmodR.Data_1.4.0.tar.gz
vignettes: vignettes/RNAmodR.Data/inst/doc/RNAmodR.Data.html
vignetteTitles: RNAmodR.Data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RNAmodR.Data/inst/doc/RNAmodR.Data.R
suggestsMe: RNAmodR, RNAmodR.AlkAnilineSeq, RNAmodR.ML,
RNAmodR.RiboMethSeq
dependencyCount: 130
Package: RNAseqData.HNRNPC.bam.chr14
Version: 0.28.0
Suggests: GenomicAlignments, BiocManager
License: LGPL
MD5sum: 1025906a7f6a12e4342a628d563011ca
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 <hpages.on.github@gmail.com>
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_12
git_last_commit: 8a9881d
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RNAseqData.HNRNPC.bam.chr14_0.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: sequencing
suggestsMe: BiocParallel, GenomicAlignments, GenomicFiles,
GenomicRanges, roar, Rsamtools, SplicingGraphs
dependencyCount: 0
Package: RNASeqRData
Version: 1.8.0
Depends: R (>= 3.5.0)
Suggests: png, grid
License: Artistic-2.0
MD5sum: 61afda2f15d7fc1239252c5c59329d8e
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 <ntueeb05howard@gmail.com>
git_url: https://git.bioconductor.org/packages/RNASeqRData
git_branch: RELEASE_3_12
git_last_commit: 095ea4b
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RNASeqRData_1.8.0.tar.gz
vignettes: vignettes/RNASeqRData/inst/doc/RNASeqRData.html
vignetteTitles: RNASeqRData.html
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: RNASeqR
dependencyCount: 0
Package: RnaSeqSampleSizeData
Version: 1.22.0
Depends: edgeR,R (>= 2.10)
Suggests: BiocStyle, knitr
License: GPL (>= 2)
MD5sum: ddef4d25b2214d2607342546e4349b77
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 <zhaoshilin@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/RnaSeqSampleSizeData
git_branch: RELEASE_3_12
git_last_commit: 0e389c8
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RnaSeqSampleSizeData_1.22.0.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
dependsOnMe: RnaSeqSampleSize
dependencyCount: 11
Package: RnBeads.hg19
Version: 1.22.0
Depends: R (>= 3.0.0), GenomicRanges
Suggests: RnBeads
License: GPL-3
MD5sum: 1358bfdb643b632aeaaca13ada2e68e8
NeedsCompilation: no
Title: RnBeads.hg19
Description: Automatically generated RnBeads annotation package for the
assembly hg19.
Author: RnBeadsAnnotationCreator
Maintainer: RnBeadsAnnotationCreator <rnbeads@mpi-inf.mpg.de>
git_url: https://git.bioconductor.org/packages/RnBeads.hg19
git_branch: RELEASE_3_12
git_last_commit: c27ee43
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RnBeads.hg19_1.22.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: RnBeads
dependencyCount: 17
Package: RnBeads.hg38
Version: 1.22.0
Depends: R (>= 3.0.0), GenomicRanges
Suggests: RnBeads
License: GPL-3
MD5sum: b0e5d03c6a3e1b76cd9503d7676bfa50
NeedsCompilation: no
Title: RnBeads.hg38
Description: Automatically generated RnBeads annotation package for the
assembly hg38.
Author: RnBeadsAnnotationCreator
Maintainer: RnBeadsAnnotationCreator <rnbeads@mpi-inf.mpg.de>
git_url: https://git.bioconductor.org/packages/RnBeads.hg38
git_branch: RELEASE_3_12
git_last_commit: 1e100ef
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RnBeads.hg38_1.22.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 17
Package: RnBeads.mm10
Version: 1.22.0
Depends: R (>= 3.0.0), GenomicRanges
Suggests: RnBeads
License: GPL-3
MD5sum: 3dcef33b4fb917282b932410facf6dfa
NeedsCompilation: no
Title: RnBeads.mm10
Description: Automatically generated RnBeads annotation package for the
assembly mm10.
Author: RnBeadsAnnotationCreator
Maintainer: RnBeadsAnnotationCreator <rnbeads@mpi-inf.mpg.de>
git_url: https://git.bioconductor.org/packages/RnBeads.mm10
git_branch: RELEASE_3_12
git_last_commit: a5c65a5
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RnBeads.mm10_1.22.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 17
Package: RnBeads.mm9
Version: 1.22.0
Depends: R (>= 3.0.0), GenomicRanges
Suggests: RnBeads
License: GPL-3
MD5sum: e7464eae153a04268efc60dc41e934c0
NeedsCompilation: no
Title: RnBeads.mm9
Description: Automatically generated RnBeads annotation package for the
assembly mm9.
Author: RnBeadsAnnotationCreator
Maintainer: RnBeadsAnnotationCreator <rnbeads@mpi-inf.mpg.de>
git_url: https://git.bioconductor.org/packages/RnBeads.mm9
git_branch: RELEASE_3_12
git_last_commit: 8f7475c
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RnBeads.mm9_1.22.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: RnBeads
dependencyCount: 17
Package: RnBeads.rn5
Version: 1.22.0
Depends: R (>= 3.0.0), GenomicRanges
Suggests: RnBeads
License: GPL-3
MD5sum: 1a5a8735c728edb6f3c64a72ef2d680d
NeedsCompilation: no
Title: RnBeads.rn5
Description: Automatically generated RnBeads annotation package for the
assembly rn5.
Author: RnBeadsAnnotationCreator
Maintainer: RnBeadsAnnotationCreator <rnbeads@mpi-inf.mpg.de>
git_url: https://git.bioconductor.org/packages/RnBeads.rn5
git_branch: RELEASE_3_12
git_last_commit: d1dc5ff
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RnBeads.rn5_1.22.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 17
Package: RRBSdata
Version: 1.10.0
Depends: R (>= 3.1.0), BiSeq (>= 1.9.2)
License: LGPL-3
MD5sum: 1fd71908f0416a54d9445d091918f2b3
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 <katja.hebestreit@gmail.com>
git_url: https://git.bioconductor.org/packages/RRBSdata
git_branch: RELEASE_3_12
git_last_commit: b573878
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RRBSdata_1.10.0.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
dependencyCount: 80
Package: rRDPData
Version: 1.10.0
Depends: rRDP
License: GPL-2
MD5sum: 51a4076759f1dcbd9656a845d7ac64c1
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 <mhahsler@lyle.smu.edu>
SystemRequirements: Java
git_url: https://git.bioconductor.org/packages/rRDPData
git_branch: RELEASE_3_12
git_last_commit: 5d9752b
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/rRDPData_1.10.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: rRDP
dependencyCount: 16
Package: RTCGA.clinical
Version: 20151101.20.0
Depends: R (>= 3.2.0), RTCGA
Suggests: knitr
License: GPL-2
MD5sum: 49276179a16b54de3cd2b7fac99ba008
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 <m.p.kosinski@gmail.com>
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
VignetteBuilder: knitr
BugReports: https://github.com/RTCGA/RTCGA/issues
git_url: https://git.bioconductor.org/packages/RTCGA.clinical
git_branch: RELEASE_3_12
git_last_commit: 098f383
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RTCGA.clinical_20151101.20.0.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
suggestsMe: RTCGA
dependencyCount: 133
Package: RTCGA.CNV
Version: 1.18.0
Depends: R (>= 3.3.0), RTCGA
Suggests: knitr
License: GPL-2
MD5sum: 56553c5cfc97460e6e1baa782b97a37b
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 <przemyslaw.biecek@gmail.com>
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
VignetteBuilder: knitr
BugReports: https://github.com/RTCGA/RTCGA/issues
git_url: https://git.bioconductor.org/packages/RTCGA.CNV
git_branch: RELEASE_3_12
git_last_commit: de50b10
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RTCGA.CNV_1.18.0.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: TRUE
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
suggestsMe: RTCGA
dependencyCount: 133
Package: RTCGA.methylation
Version: 1.18.0
Depends: R (>= 3.3.0), RTCGA
Suggests: knitr
License: GPL-2
MD5sum: e35fd39ede52974f7a370301d0cd100b
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 <m.p.kosinski@gmail.com>
VignetteBuilder: knitr
BugReports: https://github.com/RTCGA/RTCGA/issues
git_url: https://git.bioconductor.org/packages/RTCGA.methylation
git_branch: RELEASE_3_12
git_last_commit: 6f0d63b
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RTCGA.methylation_1.18.0.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
suggestsMe: RTCGA
dependencyCount: 133
Package: RTCGA.miRNASeq
Version: 1.18.0
Depends: R (>= 3.3.0), RTCGA
Suggests: knitr
License: GPL-2
MD5sum: 1689a88880bd360d1c70106f11f64262
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 <witoldchodor@gmail.com>
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
VignetteBuilder: knitr
BugReports: https://github.com/RTCGA/RTCGA/issues
git_url: https://git.bioconductor.org/packages/RTCGA.miRNASeq
git_branch: RELEASE_3_12
git_last_commit: a3170df
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RTCGA.miRNASeq_1.18.0.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: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles:
vignettes/RTCGA.miRNASeq/inst/doc/downloading_miRNASeq_datasets.R
suggestsMe: RTCGA
dependencyCount: 133
Package: RTCGA.mRNA
Version: 1.18.0
Depends: R (>= 3.3.0), RTCGA
Suggests: knitr
License: GPL-2
MD5sum: 4efaa7ff5133a37f3018daf851edbf17
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 <witoldchodor@gmail.com>
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
VignetteBuilder: knitr
BugReports: https://github.com/RTCGA/RTCGA/issues
git_url: https://git.bioconductor.org/packages/RTCGA.mRNA
git_branch: RELEASE_3_12
git_last_commit: 4e20464
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RTCGA.mRNA_1.18.0.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: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RTCGA.mRNA/inst/doc/downloading_mRNA_datasets.R
suggestsMe: CancerSubtypes, RTCGA
dependencyCount: 133
Package: RTCGA.mutations
Version: 20151101.20.0
Depends: R (>= 3.2.0), RTCGA
Suggests: knitr
License: GPL-2
MD5sum: d2ed408e34a0429e0638afef954ce189
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 <m.p.kosinski@gmail.com>
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
VignetteBuilder: knitr
BugReports: https://github.com/RTCGA/RTCGA/issues
git_url: https://git.bioconductor.org/packages/RTCGA.mutations
git_branch: RELEASE_3_12
git_last_commit: 25d0255
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RTCGA.mutations_20151101.20.0.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
suggestsMe: RTCGA
dependencyCount: 133
Package: RTCGA.PANCAN12
Version: 1.18.0
Depends: R (>= 3.3.0), RTCGA
Suggests: knitr
License: GPL-2
MD5sum: 46773c210d21b9adaa0b6fee183b1b7c
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 <przemyslaw.biecek@gmail.com>
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
VignetteBuilder: knitr
BugReports: https://github.com/RTCGA/RTCGA/issues
git_url: https://git.bioconductor.org/packages/RTCGA.PANCAN12
git_branch: RELEASE_3_12
git_last_commit: 6486bf5
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RTCGA.PANCAN12_1.18.0.tar.gz
vignettes: vignettes/RTCGA.PANCAN12/inst/doc/pancan12.html
vignetteTitles: Using RTCGA.PANCAN12 to compare time to death
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RTCGA.PANCAN12/inst/doc/pancan12.R
suggestsMe: GOpro, RTCGA
dependencyCount: 133
Package: RTCGA.rnaseq
Version: 20151101.20.0
Depends: R (>= 3.2.0), RTCGA
Suggests: knitr
License: GPL-2
MD5sum: 9b949ae0aef4bb42381eedc853d6cd25
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 <m.p.kosinski@gmail.com>
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
VignetteBuilder: knitr
BugReports: https://github.com/RTCGA/RTCGA/issues
git_url: https://git.bioconductor.org/packages/RTCGA.rnaseq
git_branch: RELEASE_3_12
git_last_commit: 09009ff
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RTCGA.rnaseq_20151101.20.0.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: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RTCGA.rnaseq/inst/doc/downloading_rnaseq_datasets.R
suggestsMe: RTCGA, FSelectorRcpp
dependencyCount: 133
Package: RTCGA.RPPA
Version: 1.18.0
Depends: R (>= 3.3.0), RTCGA
Suggests: knitr
License: GPL-2
MD5sum: 633094117181e59aae4b4dde340b4c05
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 <witoldchodor@gmail.com>
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
VignetteBuilder: knitr
BugReports: https://github.com/RTCGA/RTCGA/issues
git_url: https://git.bioconductor.org/packages/RTCGA.RPPA
git_branch: RELEASE_3_12
git_last_commit: 982cbf4
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RTCGA.RPPA_1.18.0.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: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RTCGA.RPPA/inst/doc/downloading_RPPA_datasets.R
suggestsMe: RTCGA
dependencyCount: 133
Package: RUVnormalizeData
Version: 1.10.0
Depends: R (>= 2.10.0), Biobase
License: GPL-3
MD5sum: 248e26e3fa9bff5a7aac430397cd1822
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 <laurent.jacob@univ-lyon1.fr>
git_url: https://git.bioconductor.org/packages/RUVnormalizeData
git_branch: RELEASE_3_12
git_last_commit: 781ff5e
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/RUVnormalizeData_1.10.0.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
importsMe: RUVnormalize
dependencyCount: 7
Package: sampleClassifierData
Version: 1.14.1
Depends: R (>= 3.4), SummarizedExperiment
Suggests: BiocStyle
License: Artistic-2.0
MD5sum: 3981f88bbe0a20afbe85843c0bd4581f
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 <khadija.el-amrani@charite.de>
git_url: https://git.bioconductor.org/packages/sampleClassifierData
git_branch: RELEASE_3_12
git_last_commit: 558c056
git_last_commit_date: 2021-01-19
Date/Publication: 2021-01-21
source.ver: src/contrib/sampleClassifierData_1.14.1.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
suggestsMe: sampleClassifier
dependencyCount: 26
Package: SBGNview.data
Version: 1.4.1
Depends: R (>= 3.6)
Imports: knitr, rmarkdown, bookdown
Suggests: SummarizedExperiment
License: AGPL-3
MD5sum: 853cf8c818d5f406bb2c6be72c93182c
NeedsCompilation: no
Title: Demo gene expression datasets for SBGNview package
Description: This package contains: 1. A microarray gene expression
dataset from a human breast cancer study. 2. A RNA-Seq gene
expression dataset from a mouse study on IFNG knockout. 3. ID
mapping tables between gene IDs and SBGN-ML file glyph IDs. 4.
Percent of orthologs detected in other species of the genes in
a pathway. Cutoffs of this percentage for defining if a pathway
exists in another species. 5. XML text of SBGN-ML files for all
pre-collected pathways.
biocViews: ExperimentData, CancerData, BreastCancerData,
MicroarrayData, GEO, RNASeqData
Author: Xiaoxi Dong*, Kovidh Vegesna*, Weijun Luo
Maintainer: Weijun Luo <luo_weijun@yahoo.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/SBGNview.data
git_branch: RELEASE_3_12
git_last_commit: 24dae23
git_last_commit_date: 2021-02-25
Date/Publication: 2021-03-01
source.ver: src/contrib/SBGNview.data_1.4.1.tar.gz
vignettes: vignettes/SBGNview.data/inst/doc/SBGNview.data.vignette.html
vignetteTitles: SBGNview functions
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SBGNview.data/inst/doc/SBGNview.data.vignette.R
dependsOnMe: SBGNview
dependencyCount: 24
Package: SCATEData
Version: 1.0.0
Depends: ExperimentHub, GenomicAlignments, GenomicRanges, base
Imports: utils
Suggests: knitr, rmarkdown
License: MIT + file LICENSE
MD5sum: 6670e17bf9845cf95c848d8df0ce3bbd
NeedsCompilation: no
Title: Data for SCATE (Single-cell ATAC-seq Signal Extraction and
Enhancement)
Description: SCATEData is an ExperimentHub package for SCATE which is a
software tool for extracting and enhancing the sparse and
discrete Single-cell ATAC-seq Signal.
biocViews: ExperimentHub, ExperimentData
Author: Zhicheng Ji [aut], Weiqiang Zhou [aut], Wenpin Hou [cre, aut]
(<https://orcid.org/0000-0003-0972-2192>), Hongkai Ji [aut]
Maintainer: Wenpin Hou <wp.hou3@gmail.com>
VignetteBuilder: knitr
BugReports: https://github.com/Winnie09/SCATEData/issues
git_url: https://git.bioconductor.org/packages/SCATEData
git_branch: RELEASE_3_12
git_last_commit: 4c42627
git_last_commit_date: 2020-10-27
Date/Publication: 2020-11-09
source.ver: src/contrib/SCATEData_1.0.0.tar.gz
vignettes: vignettes/SCATEData/inst/doc/SCATEData_package.html
vignetteTitles: 1. SCATEData package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/SCATEData/inst/doc/SCATEData_package.R
dependsOnMe: SCATE
dependencyCount: 103
Package: SCLCBam
Version: 1.22.0
Depends: R(>= 2.10)
Suggests: BiocStyle
License: GPL-2
MD5sum: 97a1d00b7bc1ce93f5bb8199c8f5a507
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 <o.krijgsman@nki.nl>
git_url: https://git.bioconductor.org/packages/SCLCBam
git_branch: RELEASE_3_12
git_last_commit: 207d811
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/SCLCBam_1.22.0.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
suggestsMe: CopywriteR
dependencyCount: 0
Package: scRNAseq
Version: 2.4.0
Depends: SingleCellExperiment
Imports: utils, methods, BiocGenerics, S4Vectors, GenomicRanges,
SummarizedExperiment, ExperimentHub, AnnotationHub,
AnnotationDbi, ensembldb, GenomicFeatures
Suggests: BiocStyle, knitr, rmarkdown, BiocFileCache, testthat
License: CC0
MD5sum: 2a68fa4f52d25c91dda4354ae49b4838
NeedsCompilation: no
Title: Collection of Public Single-Cell RNA-Seq Datasets
Description: Gene-level counts for a collection of public scRNA-seq
datasets, provided as SingleCellExperiment objects with cell-
and gene-level metadata.
biocViews: ExperimentHub, ExperimentData, ExpressionData,
SequencingData, RNASeqData, SingleCellData
Author: Davide Risso [aut, cph], Michael Cole [aut], Aaron Lun [ctb,
cre], Alan O'Callaghan [ctb], Jens Preussner [ctb], Charlotte
Soneson [ctb], Stephany Orjuela [ctb]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/scRNAseq
git_branch: RELEASE_3_12
git_last_commit: 61f2c38
git_last_commit_date: 2020-10-27
Date/Publication: 2020-11-09
source.ver: src/contrib/scRNAseq_2.4.0.tar.gz
vignettes: vignettes/scRNAseq/inst/doc/scRNAseq.html
vignetteTitles: User's Guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/scRNAseq/inst/doc/scRNAseq.R
importsMe: singleCellTK
suggestsMe: batchelor, bluster, dittoSeq, iSEE, iSEEu, scater,
scDblFinder, scFeatureFilter, scone, scran, scuttle,
SingleCellExperiment, SingleR, snifter, SummarizedBenchmark,
velociraptor, zellkonverter, zinbwave
dependencyCount: 116
Package: scTHI.data
Version: 1.2.0
Depends: R (>= 4.0)
License: GPL-2
MD5sum: a5b6b2a786120dff265800f5beeaa108
NeedsCompilation: no
Title: The package contains examples of single cell data used in
vignettes and examples of the scTHI package; data contain both
tumor cells and immune cells from public dataset of glioma
Description: Data for the vignette and tutorial of the package scTHI.
biocViews: ExperimentData, SingleCellData
Author: Francesca Pia Caruso [aut], Michele Ceccarelli [aut, cre]
Maintainer: Michele Ceccarelli <m.ceccarelli@gmail.com>
git_url: https://git.bioconductor.org/packages/scTHI.data
git_branch: RELEASE_3_12
git_last_commit: b6a8c5a
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/scTHI.data_1.2.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: scTHI
dependencyCount: 0
Package: seq2pathway.data
Version: 1.22.0
Depends: R (>= 2.10.0)
License: GPL (>= 2)
MD5sum: 8fb6db12ac9673267562e1404d959c06
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 <binw@uchicago.edu>
Maintainer: Xinan Holly Yang <xyang2@uchicago.edu>
git_url: https://git.bioconductor.org/packages/seq2pathway.data
git_branch: RELEASE_3_12
git_last_commit: 5ba32cf
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/seq2pathway.data_1.22.0.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
importsMe: seq2pathway
dependencyCount: 0
Package: seqc
Version: 1.24.0
Depends: R (>= 2.10)
Imports: utils, Biobase
License: GPL-3
MD5sum: 0fc3dca59ff6ec7f05397f0c71e86ce3
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 <Yang.Liao@onjcri.org.au> and Wei Shi
<Wei.Shi@onjcri.org.au>
URL:
http://bioconductor.org/packages/release/data/experiment/html/seqc.html
git_url: https://git.bioconductor.org/packages/seqc
git_branch: RELEASE_3_12
git_last_commit: 64b0931
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/seqc_1.24.0.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
dependencyCount: 7
Package: seqCNA.annot
Version: 1.26.0
Depends: R (>= 2.10)
License: GPL-3
MD5sum: 4113813d5c84463543ae336d3b5011d5
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 <dmosen.gn@cicbiogune.es>
git_url: https://git.bioconductor.org/packages/seqCNA.annot
git_branch: RELEASE_3_12
git_last_commit: 1e2cfa6
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/seqCNA.annot_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: seqCNA
dependencyCount: 0
Package: serumStimulation
Version: 1.26.0
Depends: R (>= 2.10)
License: GPL (>= 2)
MD5sum: f7f0e6996e6e155adbf439a1e7508320
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 <mhansen@sund.ku.dk>
Maintainer: Morten Hansen, <mhansen@sund.ku.dk>
git_url: https://git.bioconductor.org/packages/serumStimulation
git_branch: RELEASE_3_12
git_last_commit: 9162b24
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/serumStimulation_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: sesameData
Version: 1.8.10
Depends: R (>= 4.0), ExperimentHub, AnnotationHub, rmarkdown
Imports: utils, curl
Suggests: GenomicRanges, BiocGenerics, sesame, testthat, knitr
License: Artistic-2.0
MD5sum: e426c8dd46c862c9a0bd42790fcb836c
NeedsCompilation: no
Title: Supporting Data for SeSAMe Package
Description: Provides supporting annotation and test data for SeSAMe
package. This includes chip tango addresses, mapping
information, performance annotation, and trained predictor for
Infinium array data. This package provides user access to
essential annotation data for working with many generations of
the Infinium DNA methylation array. Current we support human
array (HM27, HM450, EPIC), mouse array (MM285) and the
HorvathMethylChip40 (Mammal40) array.
biocViews: ExperimentData, MicroarrayData, Genome, ExperimentHub,
MethylationArrayData
Author: Wanding Zhou [aut, cre], Hui Shen [aut], Timothy Triche [ctb]
Maintainer: Wanding Zhou <zhouwanding@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/sesameData
git_branch: RELEASE_3_12
git_last_commit: e98950a
git_last_commit_date: 2021-04-25
Date/Publication: 2021-04-26
source.ver: src/contrib/sesameData_1.8.10.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
dependsOnMe: sesame
importsMe: MethReg
suggestsMe: ELMER
dependencyCount: 86
Package: seventyGeneData
Version: 1.26.0
Depends: R (>= 2.13.0)
Suggests: Biobase, gdata, limma, breastCancerNKI
License: Artistic-2.0
MD5sum: f79a5b674497a5b11a044ec86673a1a6
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 <marchion@jhu.edu>
Maintainer: Luigi Marchionni <marchion@jhu.edu>
URL: http://luigimarchionni.org/breastTSP.html
git_url: https://git.bioconductor.org/packages/seventyGeneData
git_branch: RELEASE_3_12
git_last_commit: 6f93804
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/seventyGeneData_1.26.0.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
dependencyCount: 0
Package: shinyMethylData
Version: 1.10.0
Depends: R (>= 3.0.0)
License: Artistic-2.0
MD5sum: e201fa0f3ea58fcfb78a5b3183748ca8
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 <jfortin@jhsph.edu>
git_url: https://git.bioconductor.org/packages/shinyMethylData
git_branch: RELEASE_3_12
git_last_commit: 47df22d
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/shinyMethylData_1.10.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: shinyMethyl
dependencyCount: 0
Package: signatureSearchData
Version: 1.4.0
Depends: R (>= 3.6)
Imports: ExperimentHub, utils, affy, limma, Biobase, magrittr, dplyr,
R.utils, stats, signatureSearch, rhdf5
Suggests: knitr, rmarkdown
License: Artistic-2.0
MD5sum: 638bec4cef7d3195b0effb863d68f52e
NeedsCompilation: no
Title: Datasets for signatureSearch package
Description: CMAP/LINCS hdf5 databases and other annotations used for
signatureSearch software package.
biocViews: ExperimentHub, ExperimentData, ExpressionData
Author: Yuzhu Duan <yduan004@ucr.edu>, Thomas Girke
<thomas.girke@ucr.edu>
Maintainer: Yuzhu Duan <yduan004@ucr.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/signatureSearchData
git_branch: RELEASE_3_12
git_last_commit: 6e452bf
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/signatureSearchData_1.4.0.tar.gz
vignettes:
vignettes/signatureSearchData/inst/doc/signatureSearchData.html
vignetteTitles: signatureSearchData
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/signatureSearchData/inst/doc/signatureSearchData.R
dependencyCount: 166
Package: simpIntLists
Version: 1.26.0
License: GPL (>= 2)
MD5sum: d655210439afa09dab079e3efe24a04d
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 <e102771@ceng.metu.edu.tr>
git_url: https://git.bioconductor.org/packages/simpIntLists
git_branch: RELEASE_3_12
git_last_commit: 11e24c3
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/simpIntLists_1.26.0.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
dependsOnMe: ibh
suggestsMe: GeneNetworkBuilder
dependencyCount: 0
Package: Single.mTEC.Transcriptomes
Version: 1.18.0
Depends: R (>= 3.5.0)
Suggests: DESeq2, GenomicRanges, GenomicFeatures, genefilter, statmod,
gdata, RColorBrewer, ggplot2, gplots, cluster, clue, grid,
gridExtra, ggbio, Gviz, geneplotter, matrixStats, pheatmap,
BiocStyle, knitr
License: LGPL
MD5sum: dc96320ac09f9b5816d9cb0a70419d9b
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 <alejandro.reyes@embl.de>
VignetteBuilder: knitr
git_url:
https://git.bioconductor.org/packages/Single.mTEC.Transcriptomes
git_branch: RELEASE_3_12
git_last_commit: f6ad28b
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/Single.mTEC.Transcriptomes_1.18.0.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
dependencyCount: 0
Package: SingleCellMultiModal
Version: 1.2.4
Depends: R (>= 4.0.0), MultiAssayExperiment
Imports: AnnotationHub, BiocFileCache, BiocGenerics, ExperimentHub,
HCAMatrixBrowser, HDF5Array, S4Vectors, SingleCellExperiment,
SpatialExperiment, SummarizedExperiment, Matrix, methods, utils
Suggests: knitr, scran
License: Artistic-2.0
MD5sum: 2f13c8eebf694b3a36d1d2b5f8f56e08
NeedsCompilation: no
Title: Integrating Multi-modal Single Cell Experiment datasets
Description: SingleCellMultiModal is an ExperimentHub package that
serves multiple datasets obtained from GEO and other sources
and represents them as MultiAssayExperiment objects. The
current focus is on datasets that use new technologies such as
scNMT and scM&T.
biocViews: ExperimentData, SingleCellData, ReproducibleResearch,
ExperimentHub, GEO
Author: Marcel Ramos [aut, cre]
(<https://orcid.org/0000-0002-3242-0582>), Ricard Argelaguet
[aut], Dario Righelli [aut], Kelly Eckenrode [aut], Levi
Waldron [aut]
Maintainer: Marcel Ramos <marcel.ramos@roswellpark.org>
VignetteBuilder: knitr
BugReports: https://github.com/waldronlab/SingleCellMultiModal/issues
git_url: https://git.bioconductor.org/packages/SingleCellMultiModal
git_branch: RELEASE_3_12
git_last_commit: de087cd
git_last_commit_date: 2021-01-22
Date/Publication: 2021-01-28
source.ver: src/contrib/SingleCellMultiModal_1.2.4.tar.gz
vignettes: vignettes/SingleCellMultiModal/inst/doc/CITEseq.html,
vignettes/SingleCellMultiModal/inst/doc/ECCITEseq.html,
vignettes/SingleCellMultiModal/inst/doc/PBMC.html,
vignettes/SingleCellMultiModal/inst/doc/scNMT.html,
vignettes/SingleCellMultiModal/inst/doc/SCoPE2.html,
vignettes/SingleCellMultiModal/inst/doc/seqFISH.html
vignetteTitles: CITEseq Cord Blood, ECCITEseq Peripheral Blood, PBMC
10x multiome, scNMT Mouse Gastrulation, SCoPE2: macrophage vs
monocytes, seqFISH Mouse Visual Cortex
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SingleCellMultiModal/inst/doc/CITEseq.R,
vignettes/SingleCellMultiModal/inst/doc/ECCITEseq.R,
vignettes/SingleCellMultiModal/inst/doc/PBMC.R,
vignettes/SingleCellMultiModal/inst/doc/scNMT.R,
vignettes/SingleCellMultiModal/inst/doc/SCoPE2.R,
vignettes/SingleCellMultiModal/inst/doc/seqFISH.R
dependencyCount: 110
Package: SNAData
Version: 1.36.0
Depends: R (>= 2.4.0), graph
Suggests: Rgraphviz
License: LGPL
MD5sum: b37133b8d98bd2e5b3e9f5dde1d9b746
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 <dscholtens@northwestern.edu>
git_url: https://git.bioconductor.org/packages/SNAData
git_branch: RELEASE_3_12
git_last_commit: fc0ef6a
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/SNAData_1.36.0.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
dependencyCount: 8
Package: SNAGEEdata
Version: 1.26.0
Depends: R (>= 2.6.0)
Suggests: ALL, hgu95av2.db, SNAGEE
License: Artistic-2.0
MD5sum: 9951bf260fe26f22b0c69b704e13cccf
NeedsCompilation: no
Title: SNAGEE data
Description: SNAGEE data - gene list and correlation matrix
biocViews: MicroarrayData
Author: David Venet <davenet@ulb.ac.be>
Maintainer: David Venet <davenet@ulb.ac.be>
URL: http://fleming.ulb.ac.be/SNAGEE
git_url: https://git.bioconductor.org/packages/SNAGEEdata
git_branch: RELEASE_3_12
git_last_commit: e4e0b31
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/SNAGEEdata_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: SNAGEE
dependencyCount: 0
Package: SNPhoodData
Version: 1.20.0
Depends: R (>= 3.2)
Suggests: BiocStyle,knitr,rmarkdown
License: LGPL (>= 3)
MD5sum: 3fa7b5d70c31be14b6864b7993dd6ce4
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 <christian.arnold@embl.de>
VignetteBuilder: knitr
BugReports: christian.arnold@embl.de
git_url: https://git.bioconductor.org/packages/SNPhoodData
git_branch: RELEASE_3_12
git_last_commit: 233b829
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/SNPhoodData_1.20.0.tar.gz
vignettes: vignettes/SNPhoodData/inst/doc/SNPhoodData.html
vignetteTitles: The *SNPhoodData* package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: SNPhood
dependencyCount: 0
Package: SomatiCAData
Version: 1.28.0
Depends: R (>= 2.14)
License: Artistic-2.0
MD5sum: 0e95d82bf6efb7d3208ea5bf74ef888a
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 <mengjie.chen@yale.edu>
git_url: https://git.bioconductor.org/packages/SomatiCAData
git_branch: RELEASE_3_12
git_last_commit: 1aba49c
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/SomatiCAData_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: SomaticCancerAlterations
Version: 1.26.0
Depends: R (>= 3.0.0)
Imports: GenomicRanges, exomeCopy, stringr, IRanges, S4Vectors
Suggests: testthat, ggbio, ggplot2, knitr
License: GPL-3
MD5sum: 01eab508abaff3a3500479b8bfa82c05
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 <jg-bioc@gmx.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/SomaticCancerAlterations
git_branch: RELEASE_3_12
git_last_commit: e6b9385
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/SomaticCancerAlterations_1.26.0.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
suggestsMe: SomaticSignatures
dependencyCount: 34
Package: spatialLIBD
Version: 1.2.1
Depends: SingleCellExperiment, R (>= 3.6)
Imports: shiny, golem, ggplot2, cowplot, plotly, viridisLite,
shinyWidgets, Polychrome, sessioninfo, grid, grDevices,
methods, AnnotationHub, utils, png, scater, DT, ExperimentHub,
RColorBrewer, SummarizedExperiment, stats, graphics, S4Vectors,
IRanges, fields, benchmarkme, SpatialExperiment, BiocFileCache,
jsonlite, tibble, readbitmap
Suggests: knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0),
covr, here, BiocManager
License: Artistic-2.0
MD5sum: 5d1f8b2ef147899634e29e036ec077f7
NeedsCompilation: no
Title: LIBD Visium spatial transcriptomics human pilot data inspector
Description: Inspect interactively the spatial transcriptomics 10x
Genomics Visium data from Maynard, Collado-Torres et al, 2020
analyzed by Lieber Institute for Brain Development researchers
and collaborators.
biocViews: Homo_sapiens_Data, ExperimentHub, SequencingData,
SingleCellData, ExpressionData, Tissue, PackageTypeData
Author: Leonardo Collado-Torres [aut, cre]
(<https://orcid.org/0000-0003-2140-308X>), Kristen R. Maynard
[ctb] (<https://orcid.org/0000-0003-0031-8468>), Andrew E.
Jaffe [ctb] (<https://orcid.org/0000-0001-6886-1454>), Brenda
Pardo [ctb] (<https://orcid.org/0000-0001-8103-7136>)
Maintainer: Leonardo Collado-Torres <lcolladotor@gmail.com>
URL: https://github.com/LieberInstitute/spatialLIBD
VignetteBuilder: knitr
BugReports: https://support.bioconductor.org/t/spatialLIBD
git_url: https://git.bioconductor.org/packages/spatialLIBD
git_branch: RELEASE_3_12
git_last_commit: a78c6d3
git_last_commit_date: 2020-12-17
Date/Publication: 2020-12-21
source.ver: src/contrib/spatialLIBD_1.2.1.tar.gz
vignettes: vignettes/spatialLIBD/inst/doc/spatialLIBD.html
vignetteTitles: Introduction to spatialLIBD
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/spatialLIBD/inst/doc/spatialLIBD.R
suggestsMe: BayesSpace
dependencyCount: 196
Package: SpikeIn
Version: 1.32.0
Depends: R (>= 1.6), affy (>= 1.23.4)
License: Artistic-2.0
MD5sum: 0a55a618bef51e548e2201d3fa8d7fe8
NeedsCompilation: no
Title: Affymetrix Spike-In Experiment Data
Description: Contains the HGU133 and HGU95 spikein experiment data.
biocViews: ExperimentData, MicroarrayData
Author: Rafael Irizarry <rafa@jhu.edu>
Maintainer: Rafael A. Irizarry <rafa@jhu.edu>
git_url: https://git.bioconductor.org/packages/SpikeIn
git_branch: RELEASE_3_12
git_last_commit: 07cde8e
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/SpikeIn_1.32.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: PECA
dependencyCount: 13
Package: SpikeInSubset
Version: 1.30.0
Depends: R (>= 2.4.0), Biobase (>= 2.5.5), affy (>= 1.23.4)
License: LGPL
MD5sum: 8d161157f44ae59e5e95e8be8fef2b68
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 <rafa@jhu.edu> and Zhijin Wu
Maintainer: Rafael A. Irizarry <rafa@jhu.edu>
git_url: https://git.bioconductor.org/packages/SpikeInSubset
git_branch: RELEASE_3_12
git_last_commit: 7628919
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/SpikeInSubset_1.30.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: logitT
dependencyCount: 13
Package: spqnData
Version: 1.2.0
Depends: R (>= 4.0), SummarizedExperiment
License: Artistic-2.0
MD5sum: 60ab50fa06b3eb5014ce6e19cc7e6422
NeedsCompilation: no
Title: Data for the spqn package
Description: Bulk RNA-seq from GTEx on 4,000 randomly selected,
expressed genes. Data has been processed for co-expression
analysis.
biocViews: Homo_sapiens_Data, ExpressionData, Tissue, RNASeqData
Author: Yi Wang [cre, aut], Kasper Daniel Hansen [aut]
Maintainer: Yi Wang <yiwangthu5@gmail.com>
git_url: https://git.bioconductor.org/packages/spqnData
git_branch: RELEASE_3_12
git_last_commit: 09e8a13
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/spqnData_1.2.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: spqn
dependencyCount: 26
Package: stemHypoxia
Version: 1.26.0
Depends: R (>= 2.14.1)
License: GPL (>=2)
MD5sum: 3fb87ef5cdeaddd8553e2ed31066f7d9
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 <cristobalfresno@gmail.com>
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_12
git_last_commit: 66be421
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/stemHypoxia_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: lmdme
dependencyCount: 0
Package: stjudem
Version: 1.30.0
Depends: R (>= 2.10), utils
License: LGPL (>= 2)
MD5sum: 020817d16c315fc572f13d1145861702
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 <toedling@ebi.ac.uk>
git_url: https://git.bioconductor.org/packages/stjudem
git_branch: RELEASE_3_12
git_last_commit: fefa5d7
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/stjudem_1.30.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: macat
dependencyCount: 1
Package: SVM2CRMdata
Version: 1.22.0
Depends: R(>= 3.2.0)
License: LGPL (>= 2)
MD5sum: b6da6180ff95e623d6f9637f874d8ad4
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
<guidantonio.malagolitagliazucchi@unimore.it>
git_url: https://git.bioconductor.org/packages/SVM2CRMdata
git_branch: RELEASE_3_12
git_last_commit: 0309604
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/SVM2CRMdata_1.22.0.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
dependencyCount: 0
Package: synapterdata
Version: 1.28.0
Depends: R (>= 2.10), synapter (>= 1.99.2)
Imports: utils
License: GPL-2
MD5sum: a2be9b10dcda1e3f3c41ec9c797b8438
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 <lg390@cam.ac.uk>
git_url: https://git.bioconductor.org/packages/synapterdata
git_branch: RELEASE_3_12
git_last_commit: 08f1c73
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/synapterdata_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: synapter, RforProteomics
dependencyCount: 101
Package: systemPipeRdata
Version: 1.18.2
Depends: methods
Imports: BiocGenerics, jsonlite, remotes
Suggests: RUnit, BiocStyle, knitr, rmarkdown, systemPipeR
License: Artistic-2.0
MD5sum: 89ff9c9ff7ef9d4a1101b1019b181e71
NeedsCompilation: no
Title: systemPipeRdata: 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, ImmunoOncology,
RiboSeq, WorkflowStep
Author: Thomas Girke
Maintainer: Thomas Girke <thomas.girke@ucr.edu>
URL: https://github.com/tgirke/systemPipeRdata
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/systemPipeRdata
git_branch: RELEASE_3_12
git_last_commit: 38a38e3
git_last_commit_date: 2021-05-01
Date/Publication: 2021-05-03
source.ver: src/contrib/systemPipeRdata_1.18.2.tar.gz
vignettes: vignettes/systemPipeRdata/inst/doc/systemPipeChIPseq.html,
vignettes/systemPipeRdata/inst/doc/systemPipeRdata.html,
vignettes/systemPipeRdata/inst/doc/systemPipeRIBOseq.html,
vignettes/systemPipeRdata/inst/doc/systemPipeRNAseq.html,
vignettes/systemPipeRdata/inst/doc/systemPipeVARseq.html
vignetteTitles: WF: ChIP-Seq Workflow Template, systemPipeRdata:
Workflow templates and sample data, WF: RIBO-Seq Workflow
Template, WF: RNA-Seq Workflow Template, WF: VAR-Seq Template
hasREADME: TRUE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/systemPipeRdata/inst/doc/systemPipeChIPseq.R,
vignettes/systemPipeRdata/inst/doc/systemPipeRdata.R,
vignettes/systemPipeRdata/inst/doc/systemPipeRIBOseq.R,
vignettes/systemPipeRdata/inst/doc/systemPipeRNAseq.R,
vignettes/systemPipeRdata/inst/doc/systemPipeVARseq.R
importsMe: RNASeqR
suggestsMe: systemPipeR, systemPipeShiny
dependencyCount: 9
Package: TabulaMurisData
Version: 1.8.0
Depends: R (>= 3.5)
Imports: ExperimentHub, utils
Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran,
scater, iSEE, testthat
License: MIT + file LICENSE
MD5sum: 594d805f9c6d0f27d27c387bfd9009d4
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 [aut, cre]
(<https://orcid.org/0000-0003-3833-2169>)
Maintainer: Charlotte Soneson <charlottesoneson@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/TabulaMurisData
git_branch: RELEASE_3_12
git_last_commit: 03b050d
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/TabulaMurisData_1.8.0.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
dependencyCount: 77
Package: TargetScoreData
Version: 1.26.0
Suggests: TargetScore, gplots
License: GPL-2
MD5sum: 31e4471f23f72d785dd56ef323748780
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 <yueli@cs.toronto.edu>
git_url: https://git.bioconductor.org/packages/TargetScoreData
git_branch: RELEASE_3_12
git_last_commit: db41481
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/TargetScoreData_1.26.0.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
suggestsMe: TargetScore
dependencyCount: 0
Package: TargetSearchData
Version: 1.28.0
License: GPL (>= 2)
MD5sum: a747a8e44a7cddeacc2074a375776b65
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 <acuadros+bioc@gmail.com>
git_url: https://git.bioconductor.org/packages/TargetSearchData
git_branch: RELEASE_3_12
git_last_commit: 98d93e0
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/TargetSearchData_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: TargetSearch
dependencyCount: 0
Package: tartare
Version: 1.4.0
Depends: R (>= 3.6), AnnotationHub (>= 2.16), ExperimentHub (>= 1.0)
Imports: utils
Suggests: BiocStyle, knitr, testthat, tools
License: GPL-3
MD5sum: 5a72965c07427ac22bf8eb4d200a1b6e
NeedsCompilation: no
Title: Raw ground spectra recorded on Thermo Fisher Scientific mass
spectrometers
Description: provides raw files (size=278MBytes) recorded on different
Liquid Chromatography Mass Spectrometry (LC-MS) instruments.
All included MS instruments are manufactured by Thermo Fisher
Scientific and belong to the Orbitrap Tribrid or Q Exactive
Orbitrap family of instruments. Despite their common origin and
shared hardware components (e.g. Orbitrap mass analyser), the
above instruments tend to write data in different "dialects" in
a shared binary file format (.raw). The intention behind
tartare is to provide complex but slim real-world files that
can be used to make code robust with respect to this diversity.
In other words, it is intended for enhanced unit testing. The
package is considered to be used with the rawDiag package
(Trachsel, 2018 <doi:10.1021/acs.jproteome.8b00173>) and the
Spectra MsBackends.
biocViews: ExperimentData, MassSpectrometryData, ExperimentHub
Author: Christian Panse [aut, cre]
(<https://orcid.org/0000-0003-1975-3064>), Tobias Kockmann
[aut] (<https://orcid.org/0000-0002-1847-885X>)
Maintainer: Christian Panse <cp@fgcz.ethz.ch>
URL: https://github.com/cpanse/tartare
VignetteBuilder: knitr
BugReports: https://github.com/cpanse/tartare/issues
git_url: https://git.bioconductor.org/packages/tartare
git_branch: RELEASE_3_12
git_last_commit: fafd789
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/tartare_1.4.0.tar.gz
vignettes: vignettes/tartare/inst/doc/tartare.html
vignetteTitles: make and use tartare data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/tartare/inst/doc/tartare.R
dependencyCount: 77
Package: TBX20BamSubset
Version: 1.26.0
Depends: Rsamtools (>= 1.9.8)
Imports: xtable
License: LGPL
MD5sum: 1998a04cdc3472b7a00471bf2efbb539
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 <daniel.bindreither@gmail.com>
git_url: https://git.bioconductor.org/packages/TBX20BamSubset
git_branch: RELEASE_3_12
git_last_commit: 4d093dd
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/TBX20BamSubset_1.26.0.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
importsMe: Rmmquant
suggestsMe: APAlyzer
dependencyCount: 30
Package: TCGAbiolinksGUI.data
Version: 1.10.0
Depends: R (>= 3.5.0)
Suggests: BiocStyle, knitr, readr, DT
License: GPL-3
MD5sum: bb7f8eb16b13e00ec659e4719c42cceb
NeedsCompilation: no
Title: Data for the TCGAbiolinksGUI package
Description: Supporting data for the TCGAbiolinksGUI package.
biocViews: AssayDomainData, TechnologyData, OrganismData
Author: Tiago Chedraoui Silva
Maintainer: Tiago Chedraoui Silva <tiagochst@usp.br>
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_12
git_last_commit: c5c0e4c
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/TCGAbiolinksGUI.data_1.10.0.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
dependsOnMe: TCGAbiolinksGUI
importsMe: TCGAbiolinks
dependencyCount: 0
Package: TCGAcrcmiRNA
Version: 1.10.0
Depends: R (>= 3.0), Biobase
License: GPL-2
MD5sum: bcf3267c998bce384b1294b76803600d
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 <claudio.isella@ircc.it>
git_url: https://git.bioconductor.org/packages/TCGAcrcmiRNA
git_branch: RELEASE_3_12
git_last_commit: ec8776b
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/TCGAcrcmiRNA_1.10.0.tar.gz
vignettes: vignettes/TCGAcrcmiRNA/inst/doc/TcgaCrcVignette.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TCGAcrcmiRNA/inst/doc/TcgaCrcVignette.R
dependencyCount: 7
Package: TCGAcrcmRNA
Version: 1.10.0
Depends: R (>= 3.0), Biobase
License: GPL-2
MD5sum: 60f50f5dfe358d4bfd393daeca07aaf4
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 <claudio.isella@ircc.it>
git_url: https://git.bioconductor.org/packages/TCGAcrcmRNA
git_branch: RELEASE_3_12
git_last_commit: 9ad8507
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/TCGAcrcmRNA_1.10.0.tar.gz
vignettes: vignettes/TCGAcrcmRNA/inst/doc/TcgaCrcVignette.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TCGAcrcmRNA/inst/doc/TcgaCrcVignette.R
dependencyCount: 7
Package: TCGAMethylation450k
Version: 1.26.0
License: GPL-2
MD5sum: 7212b9155400bcb2ac808e36cb57f238
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 <sdavis2@mail.nih.gov>
git_url: https://git.bioconductor.org/packages/TCGAMethylation450k
git_branch: RELEASE_3_12
git_last_commit: c182148
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/TCGAMethylation450k_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: methylumi
dependencyCount: 0
Package: tcgaWGBSData.hg19
Version: 1.8.0
Depends: R (>= 3.5.0), ExperimentHub
Imports: bsseq, knitr
License: GPL-2
MD5sum: 0491742975afb83b01f8cd5a4c60c241
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 <divyswar01@g.harvard.edu>
Maintainer: Divy Kangeyan <divyswar01@g.harvard.edu>
VignetteBuilder: knitr
BugReports: https://github.com/aryeelab/tcgaWGBSData.hg19/issues
git_url: https://git.bioconductor.org/packages/tcgaWGBSData.hg19
git_branch: RELEASE_3_12
git_last_commit: 8a8967a
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/tcgaWGBSData.hg19_1.8.0.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
dependencyCount: 135
Package: TCGAWorkflowData
Version: 1.14.0
Depends: R (>= 3.5.0)
Imports: SummarizedExperiment
Suggests: knitr, rmarkdown, pander, testthat
License: GPL-3
MD5sum: 7322a7c134fe9c97e2e860ec8885ecf0
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 <tiagochst@usp.br>
Maintainer: Tiago Chedraoui Silva <tiagochst@usp.br>
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_12
git_last_commit: c2b1aa3
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/TCGAWorkflowData_1.14.0.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: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TCGAWorkflowData/inst/doc/TCGAWorkflowData.R
importsMe: TCGAWorkflow
dependencyCount: 26
Package: TENxBrainData
Version: 1.10.0
Depends: SingleCellExperiment, HDF5Array
Imports: AnnotationHub (>= 2.9.22), ExperimentHub
Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel,
data.table
License: CC BY 4.0
MD5sum: e085743f73d5fada27265ce1956f4286
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
<maintainer@bioconductor.org>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/TENxBrainData
git_branch: RELEASE_3_12
git_last_commit: b17ec93
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/TENxBrainData_1.10.0.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
suggestsMe: HDF5Array
dependencyCount: 96
Package: TENxBUSData
Version: 1.4.0
Imports: ExperimentHub, AnnotationHub, utils, BiocGenerics
Suggests: knitr, rmarkdown, BiocStyle
License: BSD_2_clause + file LICENSE
MD5sum: 845b21dc544617f8e05677225fc41762
NeedsCompilation: no
Title: Single cell dataset from 10x in BUS format
Description: Download Barcode, UMI, and Set (BUS) format of 10x
datasets from within R. This package accompanies the package
BUSpaRse, which can load BUS format into R as a sparse matrix,
and which has utility functions related to using the C++
command line package bustools.
biocViews: SingleCellData, SequencingData, ExperimentHub,
ExperimentData, ExpressionData
Author: Lambda Moses [aut, cre]
(<https://orcid.org/0000-0002-7092-9427>)
Maintainer: Lambda Moses <dlu2@caltech.edu>
URL: https://github.com/BUStools/TENxBUSData
VignetteBuilder: knitr
BugReports: https://github.com/BUStools/TENxBUSData/issues
git_url: https://git.bioconductor.org/packages/TENxBUSData
git_branch: RELEASE_3_12
git_last_commit: 6c30472
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/TENxBUSData_1.4.0.tar.gz
vignettes:
vignettes/TENxBUSData/inst/doc/downloading-10x-hgmm-data.html
vignetteTitles: Downloading BUS data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/TENxBUSData/inst/doc/downloading-10x-hgmm-data.R
suggestsMe: BUSpaRse
dependencyCount: 77
Package: TENxPBMCData
Version: 1.8.0
Depends: SingleCellExperiment, HDF5Array
Imports: AnnotationHub, ExperimentHub
Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel
License: CC BY 4.0
MD5sum: b4fadbce37bf648c02a3626fc755349c
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 <shicks19@jhu.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/TENxPBMCData
git_branch: RELEASE_3_12
git_last_commit: 5f34edd
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/TENxPBMCData_1.8.0.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
importsMe: singleCellTK
suggestsMe: celda, ExperimentSubset, fcoex, glmGamPoi, iSEE, mbkmeans,
schex, scry
dependencyCount: 96
Package: timecoursedata
Version: 1.0.0
Depends: R (>= 4.0), SummarizedExperiment
Suggests: testthat (>= 1.0.0), knitr, rmarkdown, covr, BiocStyle
License: BSD 3-clause License + file LICENSE
MD5sum: ed81142a31e819fb0fab8140ae5cd8a1
NeedsCompilation: no
Title: A data package for timecourse RNA-seq and microarray gene
expression data sets
Description: This data package contains timecourse gene expression data
sets. The first dataset, from Shoemaker et al, consists of
microarray samples from lung tissue of mice exposed to
different influenzy strains from 14 timepoints. The two other
datasets are leaf and root samples from sorghum crops exposed
to pre- and post-flowering drought stress and a control
condition, sampled across the plants lifetime.
biocViews: ExpressionData, MicroarrayData, RNASeqData
Author: Elizabeth Purdom [aut]
(<https://orcid.org/0000-0001-9455-7990>), Nelle Varoquaux
[aut, cre] (<https://orcid.org/0000-0002-8748-6546>)
Maintainer: Nelle Varoquaux <nelle.varoquaux@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/timecoursedata
git_branch: RELEASE_3_12
git_last_commit: 337b3bd
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/timecoursedata_1.0.0.tar.gz
vignettes: vignettes/timecoursedata/inst/doc/documentation.html
vignetteTitles: timecoursedata: Time course gene expression datasets
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/timecoursedata/inst/doc/documentation.R
dependencyCount: 26
Package: TimerQuant
Version: 1.20.0
Depends: shiny
Imports: ggplot2, grid, gridExtra, deSolve, dplyr, locfit
Suggests: BiocStyle, reshape2, knitr, shinyBS
License: Artistic-2.0
MD5sum: 2e01e61900332c9c245f0b8d704194b7
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 <joseph.barry@embl.de>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/TimerQuant
git_branch: RELEASE_3_12
git_last_commit: 7757f9d
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/TimerQuant_1.20.0.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
dependencyCount: 65
Package: tinesath1cdf
Version: 1.28.0
License: Artistic-2.0
MD5sum: 5fe7aec027da2e8e73f3a15828f59759
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 <tine@ebi.ac.uk>
git_url: https://git.bioconductor.org/packages/tinesath1cdf
git_branch: RELEASE_3_12
git_last_commit: 790d139
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/tinesath1cdf_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: XhybCasneuf
dependencyCount: 0
Package: tinesath1probe
Version: 1.28.0
Depends: R (>= 1.6), AnnotationDbi (>= 1.11.9)
License: LGPL
MD5sum: f3ac30fde273358f9a68faa36aad58dd
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 <tine@ebi.ac.uk>
git_url: https://git.bioconductor.org/packages/tinesath1probe
git_branch: RELEASE_3_12
git_last_commit: 71e5153
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/tinesath1probe_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 26
Package: tissueTreg
Version: 1.10.0
Depends: R (>= 3.5)
Suggests: BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq,
SummarizedExperiment
License: GPL (>= 2)
MD5sum: 3b1721e4047f6446069ce776038636cd
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 <c.imbusch@dkfz.de>
URL: https://github.com/cimbusch/tissueTreg
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/tissueTreg
git_branch: RELEASE_3_12
git_last_commit: d504da1
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/tissueTreg_1.10.0.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
dependencyCount: 0
Package: TMExplorer
Version: 1.0.1
Depends: R (>= 4.0), SingleCellExperiment
Imports: methods, Matrix
Suggests: BiocStyle, knitr, rmarkdown
License: Artistic-2.0
MD5sum: 950a8242d2704ac4eadf0c190c3111fd
NeedsCompilation: no
Title: A Collection of Tumour Microenvironment Single-cell RNA
Sequencing Datasets and Correspodnding Metadata
Description: This package provides a tool to search and download a
collection of tumour microenvironment single-cell RNA
sequencing datasets and their metadata. TMExplorer aims to act
as a single point of entry for users looking to study the
tumour microenvironment at the single cell level. Users can
quickly search available datasets using the metadata table and
then download the ones they are interested in for analysis.
biocViews: CancerData, SingleCellData, RNASeqData, SequencingData,
ExpressionData, GEO, PackageTypeData
Author: Erik Christensen [aut, cre], Alaine Naidas [aut], Parisa
Shooshtari [aut]
Maintainer: Erik Christensen <echris3@uwo.ca>
VignetteBuilder: knitr
BugReports: https://github.com/shooshtarilab/TMExplorer/issues
git_url: https://git.bioconductor.org/packages/TMExplorer
git_branch: RELEASE_3_12
git_last_commit: e19400c
git_last_commit_date: 2021-01-13
Date/Publication: 2021-01-14
source.ver: src/contrib/TMExplorer_1.0.1.tar.gz
vignettes: vignettes/TMExplorer/inst/doc/TMExplorer.html
vignetteTitles: TMExplorer
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TMExplorer/inst/doc/TMExplorer.R
dependencyCount: 27
Package: tofsimsData
Version: 1.18.0
Depends: R (>= 3.2.0)
Suggests: knitr, rmarkdown, tools
License: GPL-3
MD5sum: 0d50184b61ff71003b1244abaa08d5a9
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 <genfys@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/tofsimsData
git_branch: RELEASE_3_12
git_last_commit: 73360be
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/tofsimsData_1.18.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: tofsims
dependencyCount: 0
Package: topdownrdata
Version: 1.12.0
Depends: topdownr
License: GPL (>= 3)
MD5sum: c47120469cb5ca3c8a436edbc3f853da
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 <mail@sebastiangibb.de>
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_12
git_last_commit: e045a19
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/topdownrdata_1.12.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: topdownr
dependencyCount: 78
Package: tweeDEseqCountData
Version: 1.28.0
Depends: Biobase, R (>= 2.10)
License: GPL (>=2)
MD5sum: 7b1928bf23ebda984f9a537c9ba43535
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 <jrgonzalez@creal.cat> and Mikel Esnaola
<mesnaola@creal.cat> (with contributions from Robert Castelo
<robert.castelo@upf.edu>)
Maintainer: Juan R Gonzalez <jrgonzalez@creal.cat>
URL: http://www.creal.cat/jrgonzalez/software.htm
git_url: https://git.bioconductor.org/packages/tweeDEseqCountData
git_branch: RELEASE_3_12
git_last_commit: 197ce26
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/tweeDEseqCountData_1.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: GSAR, missMethyl, tweeDEseq
dependencyCount: 7
Package: tximportData
Version: 1.18.0
Suggests: knitr
License: GPL (>= 2)
MD5sum: 8cd06bd336aedef19f19fd75615c92e8
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 <michaelisaiahlove@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/tximportData
git_branch: RELEASE_3_12
git_last_commit: 24945f8
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/tximportData_1.18.0.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
suggestsMe: DESeq2, fishpond, HumanTranscriptomeCompendium, tximeta,
tximport, variancePartition
dependencyCount: 0
Package: VariantToolsData
Version: 1.14.0
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: 943b64e4ff261fe355a02a4a1b6eaa60
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 <michafla@gene.com>
git_url: https://git.bioconductor.org/packages/VariantToolsData
git_branch: RELEASE_3_12
git_last_commit: 882b063
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/VariantToolsData_1.14.0.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
dependencyCount: 90
Package: vulcandata
Version: 1.12.0
Imports: utils
License: LGPL-3
MD5sum: ad53e1b94cd41c14df136d8ba7eb250a
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 <federico.giorgi@gmail.com>
git_url: https://git.bioconductor.org/packages/vulcandata
git_branch: RELEASE_3_12
git_last_commit: 4e5dc2c
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/vulcandata_1.12.0.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
suggestsMe: vulcan
dependencyCount: 1
Package: waveTilingData
Version: 1.26.0
Depends: R (>= 2.14.0)
License: GPL (>= 2)
MD5sum: b52fb120bef93cb2dfca4493f2728957
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 <kristof.debeuf@ugent.be>
Maintainer: Kristof De Beuf <kristof.debeuf@ugent.be>
PackageStatus: Deprecated
git_url: https://git.bioconductor.org/packages/waveTilingData
git_branch: RELEASE_3_12
git_last_commit: 4b0dba0
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/waveTilingData_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: WES.1KG.WUGSC
Version: 1.22.0
License: GPL-2
MD5sum: 33e3d778c0da4283cb15eccca2fe72b5
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 <yuchaoj@wharton.upenn.edu>
git_url: https://git.bioconductor.org/packages/WES.1KG.WUGSC
git_branch: RELEASE_3_12
git_last_commit: f341ebe
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/WES.1KG.WUGSC_1.22.0.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
suggestsMe: CODEX, iCNV
dependencyCount: 0
Package: WGSmapp
Version: 1.2.0
Depends: R (>= 3.6.0), GenomicRanges
License: GPL-2
MD5sum: 150eaf7f0cf8a38f9f4eeea6c1d77894
NeedsCompilation: no
Title: Mappability tracks of Whole-genome Sequencing from the ENCODE
Project
Description: This package provides whole-genome mappability tracks on
human hg19/hg38 assembly. We employed the 100-mers mappability
track from the ENCODE Project and computed weighted average of
the mappability scores if multiple ENCODE regions overlap with
the same bin. “Blacklist†bins, including segmental duplication
regions and gaps in reference assembly from telomere,
centromere, and/or heterochromatin regions are included. The
dataset consists of three assembled .bam files of single-cell
whole genome sequencing from 10X for illustration purposes.
biocViews: ExperimentData, SequencingData, DNASeqData, SingleCellData,
Homo_sapiens_Data, Genome, ENCODE
Author: Rujin Wang
Maintainer: Rujin Wang <rujin@email.unc.edu>
git_url: https://git.bioconductor.org/packages/WGSmapp
git_branch: RELEASE_3_12
git_last_commit: 51622c7
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/WGSmapp_1.2.0.tar.gz
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: SCOPE
dependencyCount: 17
Package: XhybCasneuf
Version: 1.28.0
Depends: R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf ,
RColorBrewer , methods, grid
License: Artistic-2.0
MD5sum: 06021f1c339927f0417d2eb228368700
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 <tine@ebi.ac.uk>
Maintainer: Tineke Casneuf <tine@ebi.ac.uk>
git_url: https://git.bioconductor.org/packages/XhybCasneuf
git_branch: RELEASE_3_12
git_last_commit: db88792
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/XhybCasneuf_1.28.0.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
dependencyCount: 36
Package: yeastCC
Version: 1.30.0
Depends: Biobase (>= 2.5.5)
License: Artistic-2.0
MD5sum: 4ffe10f0fecf43d1e888704d295b294e
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 <sandrine@stat.berkeley.edu>
Maintainer: Sandrine Dudoit <sandrine@stat.berkeley.edu>
git_url: https://git.bioconductor.org/packages/yeastCC
git_branch: RELEASE_3_12
git_last_commit: a34138a
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/yeastCC_1.30.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: LiquidAssociation
suggestsMe: fastLiquidAssociation, ibh
dependencyCount: 7
Package: yeastExpData
Version: 0.36.0
Depends: R (>= 2.4), graph (>= 1.9.26)
Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db
License: GPL
MD5sum: b761c451ec244671fc5ad1ff20464bbd
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 <rgentlem@fhcrc.org>
git_url: https://git.bioconductor.org/packages/yeastExpData
git_branch: RELEASE_3_12
git_last_commit: 76d3d55
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/yeastExpData_0.36.0.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
dependsOnMe: PPInfer
suggestsMe: BiocCaseStudies, ClusterJudge, ppiStats
dependencyCount: 8
Package: yeastGSData
Version: 0.28.0
License: Artistic-2.0
MD5sum: b23b5a8c2896b2c614069d45bc4c533a
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 <rgentlem@fhcrc.org>
git_url: https://git.bioconductor.org/packages/yeastGSData
git_branch: RELEASE_3_12
git_last_commit: aa208a7
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/yeastGSData_0.28.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependencyCount: 0
Package: yeastNagalakshmi
Version: 1.26.0
License: Artistic-2.0
MD5sum: 8bbfff7430c654e9546aecaa4b3b0e9f
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 <mtmorgan@fhcrc.org>
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
git_url: https://git.bioconductor.org/packages/yeastNagalakshmi
git_branch: RELEASE_3_12
git_last_commit: 5f4bcd1
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/yeastNagalakshmi_1.26.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: ShortRead
dependencyCount: 0
Package: yeastRNASeq
Version: 0.28.0
Depends: R (>= 2.4)
Suggests: Biobase, ShortRead, IRanges
License: GPL
MD5sum: 4e3ca6ed952a67f0c652fac815525db7
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 <bullard@stat.berkeley.edu>
git_url: https://git.bioconductor.org/packages/yeastRNASeq
git_branch: RELEASE_3_12
git_last_commit: 2a96d83
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/yeastRNASeq_0.28.0.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
suggestsMe: EDASeq
dependencyCount: 0
Package: yri1kgv
Version: 0.32.0
Depends: GGBase
Imports: Biobase
License: Artistic-2.0
MD5sum: 6ef0871237bcd859a0b87adbae5aaf4e
NeedsCompilation: no
Title: expression + genotype on 79 unrelated YRI individuals
Description: expression + genotype on 79 unrelated YRI individuals
biocViews: ArrayExpress
Author: VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
git_url: https://git.bioconductor.org/packages/yri1kgv
git_branch: RELEASE_3_12
git_last_commit: 622195e
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/yri1kgv_0.32.0.tar.gz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: eQTL
dependencyCount: 60
Package: yriMulti
Version: 0.19.0
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: 1be47b590d01aa030ffae8e32754c23b
NeedsCompilation: no
Title: support for expression, methylation, DHS, VCF for YRI
Description: expression, methylation, DHS for YRI
Author: VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/yriMulti
git_branch: master
git_last_commit: 5558af5
git_last_commit_date: 2020-04-27
Date/Publication: 2020-04-30
source.ver: src/contrib/yriMulti_0.19.0.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
dependencyCount: 129
Package: zebrafishRNASeq
Version: 1.10.0
Depends: R (>= 2.10)
Suggests: BiocStyle, knitr
License: GPL
MD5sum: 9c4a233f00916d399030cc394ec174f4
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 <risso.davide@gmail.com>
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/zebrafishRNASeq
git_branch: RELEASE_3_12
git_last_commit: 5f95ce3
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-29
source.ver: src/contrib/zebrafishRNASeq_1.10.0.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
suggestsMe: RUVSeq, sva
dependencyCount: 0
Package: FunciSNP.data
Version: 1.26.0
Depends: R (>= 2.14.0), IRanges
Imports: rtracklayer
License: GPL-3
Title: Various data sets for use with the FunciSNP package
Description: Data sets needed for FunciSNP to integrate information
from GWAS, 1000genomes and chromatin feature, in order to
identify functional SNP in coding or non-coding regions.
biocViews: SNPData, Project1000genomes, ENCODE
Author: Simon G. Coetzee <simon@simoncoetzee.com> and Houtan Noushmehr,
PhD <houtan@usp.br>
Maintainer: Simon G. Coetzee <scoetzee@gmail.com>
URL: http://coetzeeseq.usc.edu/publication/Coetzee_SG_et_al_2012/
PackageStatus: Deprecated
Package: Mulder2012
Version: 0.30.0
Depends: R (>= 2.14), org.Hs.eg.db, KEGG.db
Imports: igraph, HTSanalyzeR, PANR, RedeR, pvclust, MASS
Suggests: snow
License: Artistic-2.0
Title: Predicting functional networks and modules of chromatin factors
controlling adult stem cell fate from RNA interference screens
Description: This package provides functions to reproduce results and
figures in Mulder K. et. al. published in Nature Cell Biology
2012 and Wang X. et. al. published in PLoS Computational
Biology 2012.
biocViews: StemCell, CancerData
Author: Xin Wang <Xin.Wang@cancer.org.uk>, Florian Markowetz
<Florian.Markowetz@cancer.org.uk>
Maintainer: Xin Wang <Xin.Wang@cancer.org.uk>
PackageStatus: Deprecated