Package: ALLMLL
Version: 1.2.13
Depends: R (>= 2.10), affy (>= 1.23.4)
License: GPL-2
Title: A subset of arrays from a large acute lymphoblastic leukemia
(ALL) study
Description: This package provides probe-level data for 20 HGU133A and
20 HGU133B arrays which are a subset of arrays from a large ALL
study. The data is for the MLL arrays. This data was published
in Mary E. Ross, Xiaodong Zhou, Guangchun Song, Sheila A.
Shurtleff, Kevin Girtman, W. Kent Williams, Hsi-Che Liu, Rami
Mahfouz, Susana C. Raimondi, Noel Lenny, Anami Patel, and James
R. Downing (2003) Classification of pediatric acute
lymphoblastic leukemia by gene expression profiling Blood 102:
2951-2959
biocViews: ExperimentData, Cancer, Leukemia
Author: B. M. Bolstad <bolstad@stat.berkeley.edu
Maintainer: B. M. Bolstad <bmb@bmbolstad.com>
MD5sum: 3d11a244a9e2c1aad246fbb5a3f0a6d4
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: ALL
Version: 1.4.13
Depends: R (>= 2.10), Biobase (>= 2.5.5)
Suggests: rpart
License: Artistic-2.0
Title: A data package
Description: Data of T- and B-cell Acute Lymphocytic Leukemia from the
Ritz Laboratory at the DFCI (includes Apr 2004 versions)
biocViews: ExperimentData, Cancer, Leukemia
Author: Xiaochun Li
Maintainer: Robert Gentleman <rgentlem@gmail.com>
MD5sum: 82a9bef4b94bf5de355f9aa0921e19b3
source.ver: src/contrib/ALL_1.4.13.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ALL_1.4.13.zip
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vignettes: vignettes/ALL/inst/doc/ALLintro.pdf
vignetteTitles: ALL data intro
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ALL/inst/doc/ALLintro.R
Package: AffymetrixDataTestFiles
Version: 0.1.5
Depends: R (>= 2.5.0)
License: LGPL-2.1
Title: Affymetrix data files (CEL, CDF, CHP, EXP, PSI) for testing
Description: This package contains annotation data files and sample
data files of Affymetrix file formats. The files originate
from the Affymetrix' Fusion SDK distribution.
biocViews: Microarray, OneChannel, AnnotationData, ExperimentData
Author: Henrik Bengtsson, James Bullard, Kasper Daniel Hansen
Maintainer: Henrik Bengtsson <hb@stat.berkeley.edu>
MD5sum: cf4a305543775a651cf1fd459af8fc09
source.ver: src/contrib/AffymetrixDataTestFiles_0.1.5.tar.gz
win.binary.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: AmpAffyExample
Version: 1.2.11
Depends: R (>= 2.4.0), affy (>= 1.23.4)
Suggests: hgu133acdf
License: LGPL (>= 2)
Title: Example of Amplified Data
Description: Six arrays. Three from amplified RNA, three from the
typical procedure.
biocViews: ExperimentData
Author: Rafael A. Irizarry
Maintainer: Rafael A. Irizarry <rafa@jhu.edu>
MD5sum: 284c0a5e5952f0a30b4ba9e5437b93b9
source.ver: src/contrib/AmpAffyExample_1.2.11.tar.gz
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: BeadArrayUseCases
Version: 1.0.9
Imports: beadarray (>= 2.3.18), limma, GEOquery
Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db,
illuminaHumanv2.db, illuminaHumanv3.db
License: GPL-2
Title: Analysing Illumina BeadArray expression data using Bioconductor
Description: Example data files and use cases for processing Illumina
BeadArray expression data using Bioconductor
biocViews: DifferentialExpression, Microarray
Author: Mark Dunning, Wei Shi, Andy Lynch, Mike Smith, Matt Ritchie
Maintainer: Mike Smith <Mike.L.Smith@cancer.org.uk>
MD5sum: 28217cc3bcaaba4e5ccec3aa052a28cf
source.ver: src/contrib/BeadArrayUseCases_1.0.9.tar.gz
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mac.binary.leopard.ver:
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vignettes: vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.pdf,
vignettes/BeadArrayUseCases/inst/doc/BeadChipSimple_old.pdf
vignetteTitles: BeadArrayUseCases.pdf, BeadChipSimple_old.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.R
Package: CCl4
Version: 1.0.13
Depends: R (>= 2.6.0), Biobase (>= 2.5.5), limma
License: Artistic-2.0
Title: Carbon Tetrachloride (CCl4) treated hepatocytes
Description: NChannelSet for rat hepatocytes treated with Carbon
Tetrachloride (CCl4) data from LGC company.
biocViews: ExperimentData
Author: Audrey Kauffmann, Wolfgang Huber
Maintainer: Audrey Kauffmann <audrey@ebi.ac.uk>
MD5sum: 726f3fe48c36c1e6c467c4a2bf490190
source.ver: src/contrib/CCl4_1.0.13.tar.gz
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vignettes: vignettes/CCl4/inst/doc/CCl4.pdf
vignetteTitles: CCl4
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CCl4/inst/doc/CCl4.R
Package: CLL
Version: 1.2.13
Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5)
License: LGPL
Title: A Package for CLL Gene Expression Data
Description: The CLL package contains the chronic lymphocytic leukemia
(CLL) gene expression data. The CLL data had 24 samples that
were either classified as progressive or stable in regards to
disease progression. The data came from Dr. Sabina Chiaretti
at Division of Hematology, Department of Cellular
Biotechnologies and Hematology, University La Sapienza, Rome,
Italy and Dr. Jerome Ritz at Department of Medicine, Brigham
and Women's Hospital, Harvard Medical School, Boston,
Massachusetts.
biocViews: ExperimentData, Cancer, Leukemia
Author: Elizabeth Whalen
Maintainer: Robert Gentleman <rgentlem@fhcrc.org>
MD5sum: 4bdb32614e7646d2abbfa44698a6d6dc
source.ver: src/contrib/CLL_1.2.13.tar.gz
win.binary.ver: bin/windows/contrib/2.15/CLL_1.2.13.zip
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: ChIPXpressData
Version: 0.99.1
Depends: bigmemory
License: GPL (>=2)
Title: ChIPXpress Pre-built Databases
Description: Contains pre-built mouse (GPL1261) and human (GPL570)
database of gene expression profiles to be used for ChIPXpress
ranking.
biocViews: AffymetrixChIP, Homo_sapiens, Mus_musculus
Author: George Wu
Maintainer: George Wu <gewu@jhsph.edu>
MD5sum: 5be3e4e821b655e2a50e0fb660cdd87c
source.ver: src/contrib/ChIPXpressData_0.99.1.tar.gz
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: DLBCL
Version: 1.3.5
Depends: R(>= 2.11.0), Biobase
License: GPL (>=2)
Title: Diffuse large B-cell lymphoma expression data
Description: This package provides additional expression data on
diffuse large B-cell lymphomas for the BioNet package.
biocViews: ExperimentData, Cancer
Author: Marcus Dittrich and Daniela Beisser
Maintainer: Marcus Dittrich
<marcus.dittrich@biocentrum.uni-wuerzburg.de>
URL: http://bionet.bioapps.biozentrum.uni-wuerzburg.de/
MD5sum: 8889ec3c1c743b821dd1275746feacf5
source.ver: src/contrib/DLBCL_1.3.5.tar.gz
win.binary.ver: bin/windows/contrib/2.15/DLBCL_1.3.5.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DLBCL_1.3.5.tgz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: EatonEtAlChIPseq
Version: 0.0.8
Depends: GenomicRanges (>= 1.5.42), ShortRead, rtracklayer
License: Artistic 2.0
Title: ChIP-seq data of ORC-binding sites in Yeast excerpted from Eaton
et al. 2010
Description: ChIP-seq analysis subset from "Conserved nucleosome
positioning defines replication origins" (PMID 20351051)
biocViews: ExperimentData, Yeast, ChIPseqData
Author: Patrick Aboyoun <paboyoun@fhcrc.org>
Maintainer: Patrick Aboyoun <paboyoun@fhcrc.org>
MD5sum: c9d30af21ebc8811367df4630bfdf885
source.ver: src/contrib/EatonEtAlChIPseq_0.0.8.tar.gz
win.binary.ver: bin/windows/contrib/2.15/EatonEtAlChIPseq_0.0.8.zip
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: FunciSNP.data
Version: 0.99.1
Depends: R (>= 2.14.0)
Imports: rtracklayer
License: GPL-3
Title: Various data sets for use with the FunciSNP package
Description: Data sets needed for FunciSNP to integrate information
from GWAS, 1000genomes and chromatin feature, in order to
identify functional SNP in coding or non-coding regions.
biocViews: Infrastructure, DataRepresentation, DataImport,
SequenceMatching, Annotation
Author: Simon G. Coetzee <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/
MD5sum: ae89ef71865a5958396cc4efad5bb467
source.ver: src/contrib/FunciSNP.data_0.99.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/FunciSNP.data_0.99.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/FunciSNP.data/inst/doc/FunciSNP.data.pdf
vignetteTitles: FunciSNP Vignette
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/FunciSNP.data/inst/doc/FunciSNP.data.R
Package: GGdata
Version: 1.0.20
Depends: R (>= 2.12.0), methods, Biobase (>= 2.5.5), GGBase, snpStats,
illuminaHumanv1.db, AnnotationDbi
Enhances: GGtools
License: LGPL
Title: all 90 hapmap CEU samples, 47K expression, 4mm SNP
Description: data exemplars dealing with hapmap SNP reports, GWAS, etc.
biocViews: ExperimentData, HapMap
Author: VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
MD5sum: c7f5e1246e73991e8001cceb92c0642a
source.ver: src/contrib/GGdata_1.0.20.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GGdata_1.0.20.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: ggtut
suggestsMe: encoDnaseI
Package: GSVAdata
Version: 0.99.9
Depends: R (>= 2.10), Biobase, GSEABase, hgu95a.db
License: GPL (>= 2)
Title: Data employed in the vignette of the GSVA package
Description: This package stores the data employed in the vignette of
the GSVA package. These data belong to the following
publications: Armstrong et al. Nat Genet 30:41-47, 2002; Cahoy
et al. J Neurosci 28:264-278, 2008; Carrel and Willard, Nature,
434:400-404, 2005; Huang et al. PNAS, 104:9758-9763, 2007;
Pickrell et al. Nature, 464:768-722, 2010; Skaletsky et al.
Nature, 423:825-837; Verhaak et al. Cancer Cell 17:98-110, 2010
biocViews: ExperimentData, RNAseqData, RNAExpressionData, Cancer,
Leukemia
Author: Robert Castelo <robert.castelo@upf.edu>
Maintainer: Robert Castelo <robert.castelo@upf.edu>
MD5sum: 3b73c1c0148607554dc252c742f56cf5
source.ver: src/contrib/GSVAdata_0.99.9.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GSVAdata_0.99.9.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: GWASdata
Version: 1.0.7
Depends: GWASTools
License: Artistic-2.0
Title: Data used in the examples and vignettes of the GWASTools package
Description: Selected Affymetrix and Illlumina SNP data for HapMap
subjects. Data provided by the Center for Inherited Disease
Research at Johns Hopkins University and the Broad Institute of
MIT and Harvard University.
biocViews: ExperimentData, SNP, Microarray
Author: Stephanie Gogarten
Maintainer: Stephanie Gogarten <sdmorris@u.washington.edu>
MD5sum: bf4ade53ed74bf97e417d535f1d7e6fa
source.ver: src/contrib/GWASdata_1.0.7.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GWASdata_1.0.7.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: HEEBOdata
Version: 1.0.4
License: LGPL
Title: HEEBO set and HEEBO controls.
Description: R objects describing the HEEBO oligo set.
biocViews: ExperimentData
Author: Agnes Paquet
Maintainer: Agnes Paquet <apaquet@medsfgh.ucsf.edu>
URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/
MD5sum: 6273c2678466fbcc5927e41866adbec7
source.ver: src/contrib/HEEBOdata_1.0.4.tar.gz
win.binary.ver: bin/windows/contrib/2.15/HEEBOdata_1.0.4.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: HIVcDNAvantWout03
Version: 1.2.7
License: GPL (>= 2)
Title: T cell line infections with HIV-1 LAI (BRU)
Description: The expression levels of approximately 4600 cellular RNA
transcripts were assessed in CD4+ T cell lines at different
times after infection with HIV-1BRU using DNA microarrays. This
data corresponds to the first block of a 12 block array image
(001030_08_1.GEL) in the first data set (2000095918 A) in the
first experiment (CEM LAI vs HI-LAI 24hr). There are two data
sets, which are part of a dye-swap experiment with replicates,
representing the Cy3 (green) absorption intensities for channel
1 (hiv1raw) and the Cy5 (red) absorption intensities for
channel 2 (hiv2raw).
biocViews: ExperimentData, HIV
Author: Dr. Angelique van't Wout, Department of Microbiology,
University of Washington
Maintainer: Chris Fraley <fraley@stat.washington.edu>
URL:
http://expression.microslu.washington.edu/expression/vantwoutjvi2002.html
MD5sum: e36c9b91936f04e8913edeea85a9f9c8
source.ver: src/contrib/HIVcDNAvantWout03_1.2.7.tar.gz
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mac.binary.leopard.ver:
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vignettes: vignettes/HIVcDNAvantWout03/inst/doc/hivData.pdf
vignetteTitles: hivData.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: ITALICSData
Version: 2.0.6
Depends: R (>= 2.0.0)
License: GPL
Title: ITALICSData
Description: Data needed to use the ITALICS package
biocViews: ExperimentData
Author: Guillem Rigaill
Maintainer: Guillem Rigaill <italics@curie.fr>
URL: http://bioinfo.curie.fr
MD5sum: 0ca0b93711a1e6be61185535041181ee
source.ver: src/contrib/ITALICSData_2.0.6.tar.gz
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: IlluminaHumanMethylation450kmanifest
Version: 0.2.1
Depends: R (>= 2.13.0), minfi
License: Artistic-2.0
Title: Annotation for Illumina's 450k methylation arrays
Description: Manifest for Illumina's 450k array data
biocViews: IlluminaChip, Homo_sapiens, DNAMethylation
Author: Kasper Daniel Hansen, Martin Aryee
Maintainer: Kasper Daniel Hansen <khansen@jhsph.edu>
MD5sum: c315afc7a66c0b3d9793b76d18867444
source.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: minfiData
Package: Iyer517
Version: 1.4.11
Depends: Biobase (>= 2.5.5)
License: Artistic-2.0
Title: exprSets for Iyer, Eisen et all 1999 Science paper
Description: representation of public Iyer data from
http://genome-www.stanford.edu/serum/clusters.html
biocViews: ExperimentData
Author: Vishy Iyer <vishy@cmgm.stanford.edu>
Maintainer: Vince Carey <stvjc@channing.harvard.edu>
MD5sum: cdadd8489bca5c30809f40b7dfcd93fa
source.ver: src/contrib/Iyer517_1.4.11.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Iyer517_1.4.11.zip
mac.binary.leopard.ver:
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vignettes: vignettes/Iyer517/inst/doc/Iyer517.pdf
vignetteTitles: Iyer517
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Iyer517/inst/doc/Iyer517.R
Package: KEGGdzPathwaysGEO
Version: 1.1.1
Depends: R (>= 2.13.0)
Imports: Biobase, BiocGenerics
License: GPL-2
Title: KEGG Disease Datasets from GEO
Description: This is a collection of 24 data sets for which the
phenotype is a disease with a corresponding pathway in the KEGG
database.This collection of datasets were used as gold standard
in comparing gene set analysis methods by the PADOG package.
Author: Gaurav Bhatti, Adi L. Tarca
Maintainer: Gaurav Bhatti <gbhatti@med.wayne.edu>
MD5sum: 38be40fadb76e1c9fea2178448e2cbe2
source.ver: src/contrib/KEGGdzPathwaysGEO_1.1.1.tar.gz
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hasREADME: FALSE
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Package: LiebermanAidenHiC2009
Version: 0.1.13
Depends: KernSmooth, IRanges
License: LGPL
Title: Selected data from the HiC paper of E. Lieberman-Aiden et al. in
Science (2009)
Description: This package provides data that were presented in the
article "Comprehensive mapping of long-range interactions
reveals folding principles of the human genome", Science 2009
Oct 9;326(5950):289-93. PMID: 19815776
biocViews: ExperimentData
Author: Wolfgang Huber, Felix Klein
Maintainer: Felix Klein <fklein@embl.de>
MD5sum: 06783b16e02cfdd0cde3c407cf53fd07
source.ver: src/contrib/LiebermanAidenHiC2009_0.1.13.tar.gz
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vignettes:
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vignetteTitles: Exploration of HiC data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: LungCancerLines
Version: 0.0.7
Imports: Rsamtools
License: Artistic-2.0
Title: Reads from Two Lung Cancer Cell Lines
Description: Reads from an RNA-seq experiment between two lung cancer
cell lines: H1993 (met) and H2073 (primary). The reads are
stored as Fastq files and are meant for use with the TP53Genome
object in the gmapR package.
Author: Cory Barr, Michael Lawrence
Maintainer: Cory Barr <barr.cory@gene.com>
MD5sum: ebe2c91e3efa42d8da594878e3413834
source.ver: src/contrib/LungCancerLines_0.0.7.tar.gz
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hasREADME: FALSE
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Package: MAQCsubsetAFX
Version: 1.0.9
Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5)
License: Artistic-2.0
Title: MAQC data subset for the Affymetrix platform
Description: MAQC data subset for the Affymetrix platform
biocViews: Microarray, ExperimentData
Author: Laurent Gatto
Maintainer: Laurent Gatto <lg390@cam.ac.uk>
MD5sum: ffb7d237a1d98c4cbbc757108910f77d
source.ver: src/contrib/MAQCsubsetAFX_1.0.9.tar.gz
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vignettes: vignettes/MAQCsubsetAFX/inst/doc/MAQCsubsetAFX.pdf
vignetteTitles: MAQCsubsetAFX: MAQC data subset for the Affymetrix
platform
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MAQCsubsetAFX/inst/doc/MAQCsubsetAFX.R
Package: MAQCsubsetILM
Version: 1.0.7
Depends: Biobase (>= 2.5.5), lumi
License: Artistic-2.0
Title: MAQC data subset for the Illumina platform
Description: MAQC data subset for the Illumina platform
biocViews: Microarray, ExperimentData
Author: Laurent Gatto
Maintainer: Laurent Gatto <lg390@cam.ac.uk>
MD5sum: c183ed0e8008c91726879c01ec90692f
source.ver: src/contrib/MAQCsubsetILM_1.0.7.tar.gz
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mac.binary.leopard.ver:
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Suggests: genefilter, codelink
License: Artistic-2.0
Title: Experimental Data Package: MAQCsubset
Description: Data Package automatically created on Sun Nov 19 15:59:29
2006.
biocViews: ExperimentData
Author: VJ Carey
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Package: MEDIPSData
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Title: Example data for the MEDIPS package.
Description: Data for the MEDIPS package, consisting of chromosome 22
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biocViews: ExperimentData, ChIPseq, DNAMethylation,
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License: LGPL
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Suggests: snow
License: Artistic-2.0
Title: Predicting functional networks and modules of chromatin factors
controlling adult stem cell fate from RNA interference screens
Description: This package provides functions to reproduce results and
figures in Mulder K. et. al. published in Nature Cell Biology
2012 and Wang X. et. al. published in PLoS Computational
Biology 2012.
biocViews: Bioinformatics
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vignetteTitles: Arora2010_PAN.pdf, Arora2010_sigMod.pdf, Main
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Title: Data for the NCIgraph software package
Description: Provides pathways from the NCI Pathways Database as R
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biocViews: Bioinformatics, GraphsAndNetworks
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Package: Neve2006
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Title: expression and CGH data on breast cancer cell lines
Description: Experimental organization of combined expression and CGH
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biocViews: ExperimentData, Cancer, Breast
Author: M. Neve et al. in Gray Lab at LBL
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Suggests: hgu133plus2.db, hgu133plus2cdf
License: Artistic-2.0
Title: expression and copy number data on clear cell renal carcinoma
samples
Description: Sample data for PREDA package. (annotations objects
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biocViews: ExperimentData, Cancer
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Package: PWMEnrich.Dmelanogaster.background
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Title: D. melanogaster background for PWMEnrich
Description: PWMEnrich pre-compiled background objects for Drosophila
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biocViews: AnnotationData, Drosophila_melanogaster
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Package: ProData
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Title: SELDI-TOF data of Breast cancer samples
Description: A data package of SELDI-TOF protein mass spectrometry data
of 167 breast cancer and normal samples.
biocViews: ExperimentData, Cancer, Breast
Author: Xiaochun Li
Maintainer: Xiaochun Li <xiaochun@jimmy.harvard.edu>
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Package: RMassBankData
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Suggests: RMassBank
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Title: Test dataset for RMassBank
Description: Example spectra, a example compound list and an example
annotation list for a narcotics dataset; required to test
RMassBank. The package is described in the man page for
RMassBankData.
biocViews: ExperimentData, MassSpectrometryData
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Package: RNASeqDataSubset
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Depends: Rsamtools (>= 1.9.8)
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Title: Subset of BAM files from the "TBX20" experiment
Description: Dual transcriptional activator and repressor roles of
TBX20 regulate adult cardiac structure and function. A subset
of the RNA-Seq data.
biocViews: ExperimentData, RNAseqData
Author: D. Bindreither
Maintainer: D. Bindreither <daniel.bindreither@gmail.com>
MD5sum: e41e8da740115c5e1c2d24487be93e60
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Suggests: qvalue, lattice
License: Artistic-2.0
Title: Mapping of Signalling Networks through Synthetic Genetic
Interaction Analysis by RNAi
Description: This package includes all data used in the paper -Mapping
of Signalling Networks through Synthetic Genetic Interaction
Analysis by RNAi- by Horn, Sandmann, Fischer et al.., Nat.
Methods, 2011. The package vignette shows the R code to
reproduce all figures in the paper.
biocViews: ExperimentData
Author: Bernd Fischer <bernd.fischer@embl.de>
Maintainer: Bernd Fischer <bernd.fischer@embl.de>
MD5sum: 16c2b4f2a367dbde56ef1f027661f243
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hasREADME: FALSE
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Rfiles: vignettes/RNAinteractMAPK/inst/doc/RNAinteractMAPK.R
Package: RnaSeqTutorial
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Depends: R (>= 2.15.0), methods, easyRNASeq
Suggests: Rsamtools, ShortRead, BSgenome.Dmelanogaster.UCSC.dm3,
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License: Artistic-2.0
Title: RNA-Seq Tutorial (EBI Cambridge UK, October 2011)
Description: A selection of RNA-Seq data to get familiar with the
related Bioconductor core packages and the easyRNASeq package.
biocViews: ExperimentData, RNAseqData
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MD5sum: d88099235d9c94370826963027559d18
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Rfiles: vignettes/RnaSeqTutorial/inst/doc/RnaSeqTutorial.R
Package: SNAData
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Depends: R (>= 2.4.0), graph
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License: LGPL
Title: Social Networks Analysis Data Examples
Description: Data from Wasserman & Faust (1999) "Social Network
Analysis"
biocViews: ExperimentData
Author: Denise Scholtens
Maintainer: Denise Scholtens <dscholtens@northwestern.edu>
MD5sum: 1188a8db8b01948821844e9cddd4a21b
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Rfiles: vignettes/SNAData/inst/doc/SNAData.R
Package: SpikeInSubset
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Title: Part of Affymetrix's Spike-In Experiment Data
Description: Includes probe-level and expression data for the HGU133
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biocViews: ExperimentData
Author: Rafael Irizarry <rafa@jhu.edu> and Zhijin Wu
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MD5sum: 6d39bb5107ac0f9046e0f463fb5a647b
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Package: SpikeIn
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Title: Affymetrix Spike-In Experiment Data
Description: Contains the HGU133 and HGU95 spikein experiment data.
biocViews: ExperimentData
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Package: TCGAMethylation450k
Version: 0.99.3
License: GPL-2
Title: The Cancer Genome Atlas Illumina 450k methylation example data
Description: The Cancer Genome Atlas (TCGA) is applying genomics
technologies to over 20 different types of cancer. This
package contains a small set of 450k array data in idat format.
Author: Sean Davis
Maintainer: Sean Davis <sdavis2@mail.nih.gov>
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Package: TargetSearchData
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Title: Example GC-MS data for TargetSearch Package
Description: This package provides example GC-MS data for TargetSearch
Package.
biocViews: ExperimentData
Author: Alvaro Cuadros-Inostroza, Henning Redestig, Matt Hannah
Maintainer: Alvaro Cuadros-Inostroza <inostroza@mpimp-golm.mpg.de>
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Package: XhybCasneuf
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License: Artistic-2.0
Title: EBI/PSB cross-hybridisation study package
Description: Cross-hybridisation study on the ATH1 Affymetrix GeneChip
biocViews: ExperimentData
Author: Tineke Casneuf <tine@ebi.ac.uk>
Maintainer: Tineke Casneuf <tine@ebi.ac.uk>
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Rfiles: vignettes/XhybCasneuf/inst/doc/Xhyb.R
Package: affycompData
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Title: affycomp data
Description: Data needed by the affycomp package.
biocViews: OneChannel, Microarray, Preprocessing
Author: Rafael A. Irizarry <rafa@jhu.edu> and Zhijin Wu
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Maintainer: Harris Jaffee <hj@jhu.edu>
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Package: affydata
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Depends: R (>= 2.4.0), affy (>= 1.23.4)
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Suggests: hgu95av2cdf, hgu133acdf
License: GPL (>= 2)
Title: Affymetrix Data for Demonstration Purpose
Description: Example datasets of a slightly large size. They represent
'real world examples', unlike the artificial examples included
in the package affy.
biocViews: ExperimentData, OneChannel, Microarray
Author: Laurent Gautier <laurent@cbs.dtu.dk>
Maintainer: Harris Jaffee <hj@jhu.edu>
MD5sum: 05607d16af3f189340ef6c38c4ec3803
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vignetteTitles: affydata primer
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Rfiles: vignettes/affydata/inst/doc/affydata.R
Package: beadarrayExampleData
Version: 1.0.5
Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>=
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License: GPL-2
Title: Example data for the beadarray package
Description: An small dataset that can be used to run examples from the
beadarray vignette and examples
biocViews: Microarray, OneChannel, QualityControl, Preprocessing,
ExperimentData
Author: Mark Dunning
Maintainer: Mark Dunning <Mark.Dunning@cancer.org.uk>
MD5sum: 5b81e5f2dd150a65a05d3609b145bfb0
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vignetteTitles: beadarrayExampleData: example data for the beadarray
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Package: beta7
Version: 1.0.4
Depends: R (>= 2.4.0), marray
License: LGPL
Title: Rodriguez et al. (2004) Differential Gene Expression by
Memory/Effector T Helper Cells Bearing the Gut-Homing Receptor
Integrin alpha4 beta7.
Description: Data from 6 gpr files aims to identify differential
expressed genes between the beta 7+ and beta 7- memory T helper
cells.
biocViews: ExperimentData
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Package: bladderbatch
Version: 1.0.4
Depends: Biobase
License: Artistic-2.0
Title: Bladder gene expression data illustrating batch effects
Description: This package contains microarray gene expression data on
57 bladder samples from 5 batches. The data are used as an
illustrative example for the sva package.
biocViews: ExperimentData,Cancer,RNAExpressionData
Author: Jeffrey T. Leek <jleek@jhsph.edu>
Maintainer: Jeffrey T. Leek <jleek@jhsph.edu>
MD5sum: ac11a60b1bbb2c0b5f13e78045cc855a
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vignettes: vignettes/bladderbatch/inst/doc/bladderbatch.pdf
vignetteTitles: bladderbatchTutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/bladderbatch/inst/doc/bladderbatch.R
Package: breastCancerMAINZ
Version: 1.0.4
Depends: R (>= 2.5.0)
Suggests: survcomp, genefu, Biobase
License: Artistic-2.0
Title: Gene expression dataset published by Schmidt et al. [2008]
(MAINZ).
Description: Gene expression data from the breast cancer study
published by Schmidt et al. in 2008, provided as an eSet.
biocViews: ExperimentData, Cancer, GeneExpression, Microarray
Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos
Sotiriou, Gianluca Bontempi, John Quackenbush
Maintainer: Markus Schroeder <mschroed@jimmy.harvard.edu>, Benjamin
Haibe-Kains <bhaibeka@jimmy.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: breastCancerNKI
Version: 1.0.4
Depends: R (>= 2.5.0)
Suggests: survcomp, genefu, Biobase
License: Artistic-2.0
Title: Genexpression dataset published by van't Veer et al. [2002] and
van de Vijver et al. [2002] (NKI).
Description: Genexpression data from a breast cancer study published by
van't Veer et al. in 2002 and van de Vijver et al. in 2002,
provided as an eSet.
biocViews: ExperimentData, Cancer, GeneExpression, Microarray
Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos
Sotiriou, Gianluca Bontempi, John Quackenbush
Maintainer: Markus Schroeder <mschroed@jimmy.harvard.edu>, Benjamin
Haibe-Kains <bhaibeka@jimmy.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
MD5sum: 06b7c476f70762247c52a3d784423161
source.ver: src/contrib/breastCancerNKI_1.0.4.tar.gz
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: breastCancerTRANSBIG
Version: 1.0.4
Depends: R (>= 2.5.0)
Suggests: survcomp, genefu, Biobase
License: Artistic-2.0
Title: Gene expression dataset published by Desmedt et al. [2007]
(TRANSBIG).
Description: Gene expression data from a breast cancer study published
by Desmedt et al. in 2007, provided as an eSet.
biocViews: ExperimentData, Cancer, GeneExpression, Microarray
Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos
Sotiriou, Gianluca Bontempi, John Quackenbush
Maintainer: Markus Schroeder <mschroed@jimmy.harvard.edu>, Benjamin
Haibe-Kains <bhaibeka@jimmy.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
MD5sum: dfcbb2d08313f001df93e397ebcc7ff7
source.ver: src/contrib/breastCancerTRANSBIG_1.0.4.tar.gz
win.binary.ver: bin/windows/contrib/2.15/breastCancerTRANSBIG_1.0.4.zip
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: breastCancerUNT
Version: 1.0.4
Depends: R (>= 2.5.0)
Suggests: survcomp, genefu, Biobase
License: Artistic-2.0
Title: Gene expression dataset published by Sotiriou et al. [2007]
(UNT).
Description: Gene expression data from a breast cancer study published
by Sotiriou et al. in 2007, provided as an eSet.
biocViews: ExperimentData, Cancer, GeneExpression, Microarray
Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos
Sotiriou, Gianluca Bontempi, John Quackenbush
Maintainer: Markus Schroeder <mschroed@jimmy.harvard.edu>, Benjamin
Haibe-Kains <bhaibeka@jimmy.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
MD5sum: 3a58f30e6f10a8556752672535939053
source.ver: src/contrib/breastCancerUNT_1.0.4.tar.gz
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: breastCancerUPP
Version: 1.0.4
Depends: R (>= 2.5.0)
Suggests: survcomp, genefu, Biobase
License: Artistic-2.0
Title: Gene expression dataset published by Miller et al. [2005] (UPP).
Description: Gene expression data from a breast cancer study published
by Miller et al. in 2005, provided as an eSet.
biocViews: ExperimentData, Cancer, GeneExpression, Microarray
Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos
Sotiriou, Gianluca Bontempi, John Quackenbush
Maintainer: Markus Schroeder <mschroed@jimmy.harvard.edu>, Benjamin
Haibe-Kains <bhaibeka@jimmy.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
MD5sum: 251093b9162e7eb439035147c8ac8012
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: breastCancerVDX
Version: 1.0.4
Depends: R (>= 2.5.0)
Suggests: survcomp, genefu, Biobase
License: Artistic-2.0
Title: Gene expression datasets published by Wang et al. [2005] and
Minn et al. [2007] (VDX).
Description: Gene expression data from a breast cancer study published
by Wang et al. in 2005 and Minn et al. in 2007, provided as an
eSet.
biocViews: ExperimentData, Cancer, GeneExpression, Microarray
Author: Markus Schroeder, Benjamin Haibe-Kains, Aedin Culhane, Christos
Sotiriou, Gianluca Bontempi, John Quackenbush
Maintainer: Markus Schroeder <mschroed@jimmy.harvard.edu>, Benjamin
Haibe-Kains <bhaibeka@jimmy.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
MD5sum: d516e7d4339c7c75feb7a12e5e89248b
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: bronchialIL13
Version: 1.0.10
Depends: R(>= 2.10.0), affy (>= 1.23.4)
License: GPL-2
Title: time course experiment involving il13
Description: derived from CNMC (pepr.cnmcresearch.org)
http://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=95
Human Bronchial Cell line A549
biocViews: ExperimentData, TimeCourse
Author: Vince Carey <stvjc@channing.harvard.edu>
Maintainer: Vince Carey <stvjc@channing.harvard.edu>
URL: http://www.biostat.harvard.edu/~carey
MD5sum: d2573a0809c0421e1db0ed42503ced87
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: bsseqData
Version: 0.1.2
Depends: R (>= 2.15), bsseq
License: Artistic-2.0
Title: Example whole genome bisulfite data for the bsseq package
Description: Example whole genome bisulfite data for the bsseq package
biocViews: DNAMethylation
Author: Kasper Daniel Hansen
Maintainer: Kasper Daniel Hansen <khansen@jhsph.edu>
MD5sum: 37a07d9a89719bbf275271bbe4b8ab8b
source.ver: src/contrib/bsseqData_0.1.2.tar.gz
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: cancerdata
Version: 1.1.1
Depends: R (>= 2.10.1), Biobase
License: GPL (>= 2)
Title: Development and validation of diagnostic tests from
high-dimensional molecular data: Datasets
Description: Dataset for the R package cancerclass
biocViews: Cancer, Microarray, Classification, Visualization
Author: Jan Budczies, Daniel Kosztyla
Maintainer: Daniel Kosztyla <danielkossi@hotmail.com>
MD5sum: 486b38adf47a10a1d62afef2b9e3c691
source.ver: src/contrib/cancerdata_1.1.1.tar.gz
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: ccTutorial
Version: 1.0.22
Depends: R (>= 2.10), Ringo(>= 1.9.8), affy(>= 1.23.4), topGO(>=
1.13.1)
Imports: Biobase
Suggests: biomaRt, Biobase(>= 2.5.5), xtable
License: Artistic-2.0
Title: Data package for ChIP-chip tutorial
Description: This is a data package that accompanies a ChIP-chip
tutorial, which has been published in PLoS Computational
Biology. The data and source code in this package allow the
reader to completely reproduce the steps in the tutorial.
biocViews: ExperimentData, ChIPchipData
Author: Joern Toedling, Wolfgang Huber
Maintainer: Joern Toedling <joern.toedling@curie.fr>
MD5sum: e28eba83729e6651159966f2cc7853a1
source.ver: src/contrib/ccTutorial_1.0.22.tar.gz
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mac.binary.leopard.ver:
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vignettes: vignettes/ccTutorial/inst/doc/ccTutorial.pdf,
vignettes/ccTutorial/inst/doc/ccTutorialSupplement.pdf
vignetteTitles: A tutorial on how to analyze ChIP-chip readouts using
Bioconductor, Supplement to A tutorial on how to analyze
ChIP-chip readouts using Bioconductor
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ccTutorial/inst/doc/ccTutorial.R,
vignettes/ccTutorial/inst/doc/ccTutorialSupplement.R
Package: ceu1kg
Version: 0.0.31
Depends: R (>= 2.12.0), GGBase (>= 3.9.0), GGtools, Biobase
Suggests: SNPlocs.Hsapiens.dbSNP.20101109
License: Artistic-2.0
Title: CEU (N=60) genotypes from 1000 genomes pilot phase I
Description: CEU genotypes from 1000 genomes "low coverage" pilot phase
I (approx 8 million SNP calls released July 2010); includes
Wellcome trust GENEVAR expression for 43 indiv
biocViews: Genetics, SNP
Author: VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
MD5sum: 3a4246d9fe04ce2a5a477bd544549f64
source.ver: src/contrib/ceu1kg_0.0.31.tar.gz
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vignettes: vignettes/ceu1kg/inst/doc/ceu1kg.pdf
vignetteTitles: ceu1kg overview
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ceu1kg/inst/doc/ceu1kg.R
Package: ceuhm3
Version: 0.0.14
Depends: R (>= 2.12.0), GGBase, Biobase
Imports: GGtools
License: Artistic-2.0
Title: ceuhm3: genotype (HapMap phase III) and expression data for CEPH
CEU cohort
Description: ceuhm3: genotype (HapMap phase III) and expression data
for CEPH CEU cohort
biocViews: Genetics, GeneExpression, GeneticVariability, SNP
Author: VJ Carey
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
MD5sum: acf64a41cdbe20369342dfacedb1e5c2
source.ver: src/contrib/ceuhm3_0.0.14.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ceuhm3_0.0.14.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: cgdv17
Version: 0.0.18
Depends: R (>= 2.15), VariantAnnotation, org.Hs.eg.db, methods,
GGtools, TxDb.Hsapiens.UCSC.hg19.knownGene, parallel
Imports: Biobase, IRanges
License: Artistic 2.0
Title: Complete Genomics Diversity Panel, chr17 on 46 individuals
Description: Complete Genomics Diversity Panel, chr17 on 46 individuals
biocViews: genetics
Author: VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
MD5sum: 0fe56f0c6403b7c9f82b45c80f55e8da
source.ver: src/contrib/cgdv17_0.0.18.tar.gz
win.binary.ver: bin/windows/contrib/2.15/cgdv17_0.0.18.zip
mac.binary.leopard.ver:
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vignettes: vignettes/cgdv17/inst/doc/cgdv.pdf
vignetteTitles: cgdv17: extract from Complete Genomics diversity panel
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/cgdv17/inst/doc/cgdv.R
Package: charmData
Version: 0.99.7
Depends: R(>= 2.11.0), charm, pd.charm.hg18.example
License: LGPL (>= 2)
Title: An example dataset for use with the charm package
Description: An example dataset for use with the charm package
biocViews: ExperimentData
Author: Martin Aryee
Maintainer: Martin Aryee <aryee@jhu.edu>
MD5sum: aabc6ca1cb940b416c806616568b783d
source.ver: src/contrib/charmData_0.99.7.tar.gz
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: cheung2010
Version: 0.0.26
Depends: R (>= 2.13.0), Biobase, GGtools, GenomicRanges, hgfocus.db
Imports: AnnotationDbi
Suggests: SNPlocs.Hsapiens.dbSNP.20100427,
SNPlocs.Hsapiens.dbSNP.20101109,
Enhances: parallel
License: Artistic 2.0
Title: resources for genetics of gene expression based on Cheung et al
2010
Description: Data resources related to the PLoS Biology paper
Polymorphic Cis- and Trans-Regulation of Human Gene Expression,
including small-footprint smlSet support for 147 hgfocus arrays
and corresponding HapMap genotypes at 1.3 million SNP; 0.0.22+
includes cheung_eset... from Leek et al RECOUNT myrna output
biocViews: GeneticVariability, RNAseqData
Author: Vince Carey <stvjc@channing.harvard.edu>
Maintainer: Vince Carey <stvjc@channing.harvard.edu>
MD5sum: 12f4e4efcc6ae71cb37c5215017d48b8
source.ver: src/contrib/cheung2010_0.0.26.tar.gz
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mac.binary.leopard.ver:
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vignettes: vignettes/cheung2010/inst/doc/arr2hap.pdf,
vignettes/cheung2010/inst/doc/cheungTrans.pdf
vignetteTitles: arr2hap.pdf, cheungTrans: checking trans eQTL with
hgfocus arrays
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/cheung2010/inst/doc/cheungTrans.R
dependsOnMe: ggtut
Package: cnvGSAdata
Version: 0.99.3
Depends: R (>= 2.10), cnvGSA
License: LGPL
Title: Data used in the vignette of the cnvGSA package
Description: This package contains the data used in the vignette of the
cnvGSA package.
biocViews: ExperimentData
Author: Robert Ziman <rziman@gmail.com>
Maintainer: Robert Ziman <rziman@gmail.com>
MD5sum: d015d66de87dccddf508616c88785b09
source.ver: src/contrib/cnvGSAdata_0.99.3.tar.gz
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: colonCA
Version: 1.4.10
Depends: Biobase (>= 2.5.5)
License: LGPL
Title: exprSet for Alon et al. (1999) colon cancer data
Description: exprSet for Alon et al. (1999) colon cancer data
biocViews: ExperimentData, Cancer, Colon
Author: Sylvia Merk
Maintainer: W Sylvia Merk <sylvia.merk@ukmuenster.de>
MD5sum: 1d1227d669a025825e4f12bde49e7a6c
source.ver: src/contrib/colonCA_1.4.10.tar.gz
win.binary.ver: bin/windows/contrib/2.15/colonCA_1.4.10.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: davidTiling
Version: 1.2.16
Depends: R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db
License: LGPL
Title: Data and analysis scripts for David, Huber et al. yeast tiling
array paper
Description: This package contains the data for the paper by L. David
et al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix
genechips, an ExpressionSet object with the raw feature data, a
probe annotation data structure for the chip and the yeast
genome annotation (GFF file) that was used. In addition, some
custom-written analysis functions are provided, as well as R
scripts in the scripts directory.
biocViews: ExperimentData, Yeast
Author: Wolfgang Huber <huber@ebi.ac.uk>, Joern Toedling
<toedling@ebi.ac.uk>
Maintainer: Wolfgang Huber <huber@ebi.ac.uk>
URL: http://www.ebi.ac.uk/huber
MD5sum: cc768c586887bb06f6c7502559308ef4
source.ver: src/contrib/davidTiling_1.2.16.tar.gz
win.binary.ver: bin/windows/contrib/2.15/davidTiling_1.2.16.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: dressCheck
Version: 0.1.6
Depends: R (>= 2.10.1), methods, Biobase (>= 2.5.5)
Suggests: survival, chron
License: Artistic-2.0
Title: data and software for checking Dressman JCO 25(5) 2007
Description: data and software for checking Dressman JCO 25(5) 2007
biocViews: Statistics, ExperimentData
Author: Vincent Carey <stvjc@channing.harvard.edu>
Maintainer: Vincent Carey <stvjc@channing.harvard.edu>
MD5sum: ead3df6340deefee6ad38b5149300169
source.ver: src/contrib/dressCheck_0.1.6.tar.gz
win.binary.ver: bin/windows/contrib/2.15/dressCheck_0.1.6.zip
mac.binary.leopard.ver:
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vignettes: vignettes/dressCheck/inst/doc/short.pdf
vignetteTitles: short review of dressCheck contents
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/dressCheck/inst/doc/short.R
Package: dsQTL
Version: 0.0.22
Depends: R (>= 2.15.0), utils, GenomicRanges, Biobase, GGBase
License: Artistic-2.0
Title: dsQTL, data excerpt from Degner et al. 2012 Nature letter
Description: dsQTL, excerpt from Degner et al. 2012 Nature letter on
DNA variants associated with DnaseI hypersensitivity
biocViews: genetics, HighThroughputSequencingData, ExperimentData
Author: VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
MD5sum: 39a893353d96a9b4e0f1909bedd38489
source.ver: src/contrib/dsQTL_0.0.22.tar.gz
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mac.binary.leopard.ver:
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vignettes: vignettes/dsQTL/inst/doc/dsq.pdf
vignetteTitles: dsQTL,, data excerpt from Degner et al. 2012 Nature
letter
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/dsQTL/inst/doc/dsq.R
Package: dyebiasexamples
Version: 1.0.9
Depends: R (>= 1.4.1), marray, GEOquery
Suggests: dyebias, convert, Biobase
License: GPL-3
Title: Example data for the dyebias package, which implements the
GASSCO method.
Description: Data for the dyebias package, consisting of 4 self-self
hybrizations of self-spotted yeast slides, as well as data from
Array Express accession E-MTAB-32
biocViews: Microarray, TwoChannel, ExperimentData
Author: Philip Lijnzaad <p.lijnzaad@umcutrecht.nl> and Thanasis
Margaritis <a.margaritis@umcutrecht.nl>
Maintainer: Philip Lijnzaad <p.lijnzaad@umcutrecht.nl>
URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad
MD5sum: 04b4a386c8340b40e753cf0c0b3dae58
source.ver: src/contrib/dyebiasexamples_1.0.9.tar.gz
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mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Package: ecoliLeucine
Version: 1.2.9
Depends: R (>= 1.9.0), affy (>= 1.23.4), ecolicdf
License: GPL (>= 2)
Title: Experimental data with Affymetrix E. coli chips
Description: Experimental data with Affymetrix E. coli chips, as
reported in She-pin Hung, Pierre Baldi, and G. Wesley Hatfield,
J. Biol. Chem., Vol. 277, Issue 43, 40309-40323, October 25,
2002
biocViews: ExperimentData, EColiData
Author: Laurent Gautier
Maintainer: Laurent Gautier <lgautier@gmail.com>
MD5sum: 9151d4bf456fcb939108510d1ac83357
source.ver: src/contrib/ecoliLeucine_1.2.9.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ecoliLeucine_1.2.9.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: encoDnaseI
Version: 0.1.15
Depends: R (>= 2.15.0), methods, Biobase (>= 2.5.5), lattice, GGtools,
GGBase
Suggests: GGdata
License: Artistic-2.0
Title: data provided by UCSC for Cd4 raw measures of DnaseI
hypersensitivity
Description: data provided by UCSC for Cd4 raw measures of DnaseI
hypersensitivity
biocViews: ExperimentData
Author: VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
MD5sum: 74d9ca996ff945f8727492792c2d601a
source.ver: src/contrib/encoDnaseI_0.1.15.tar.gz
win.binary.ver: bin/windows/contrib/2.15/encoDnaseI_0.1.15.zip
mac.binary.leopard.ver:
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vignettes: vignettes/encoDnaseI/inst/doc/dnaseUse.pdf
vignetteTitles: ENCODE/hg18 track demo: DNaseI hypersensitivity
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/encoDnaseI/inst/doc/dnaseUse.R
Package: estrogen
Version: 1.8.9
Depends: R (>= 1.9.0), affy (>= 1.4)
Suggests: Biobase (>= 1.13.16), affy, vsn, hgu95av2.db, genefilter
License: LGPL
Title: 2x2 factorial design exercise for the Bioconductor short course
Description: Data from 8 Affymetrix genechips, looking at a 2x2
factorial design (with 2 repeats per level)
biocViews: ExperimentData
Author: Wolfgang Huber, Robert Gentleman
Maintainer: R. Gentleman <rgentlem@hsph.harvard.edu>
MD5sum: 798a4315c61381be9f5498fe50a5a097
source.ver: src/contrib/estrogen_1.8.9.tar.gz
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vignettes: vignettes/estrogen/inst/doc/estrogen.pdf
vignetteTitles: estrogen
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/estrogen/inst/doc/estrogen.R
Package: faahKO
Version: 1.2.12
Depends: xcms
License: LGPL
Title: Saghatelian et al. (2004) FAAH knockout LC/MS data
Description: Positive ionization mode data in NetCDF file format.
Centroided subset from 200-600 m/z and 2500-4500 seconds. Data
originally reported in "Assignment of Endogenous Substrates to
Enzymes by Global Metabolite Profiling" Biochemistry; 2004;
43(45). Also includes detected peaks in an xcmsSet.
biocViews: ExperimentData, MassSpectrometryData
Author: Colin A. Smith <csmith@scripps.edu>
Maintainer: Colin A. Smith <csmith@scripps.edu>
URL: http://dx.doi.org/10.1021/bi0480335
MD5sum: 0949ce9f156ddc03dde092aced5ab7b8
source.ver: src/contrib/faahKO_1.2.12.tar.gz
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: fabiaData
Version: 1.0.1
Depends: R (>= 2.10.0), Biobase
Imports: utils
Suggests: fabia
License: LGPL (>= 2.1)
Title: Data sets for FABIA (Factor Analysis for Bicluster Acquisition)
Description: Supplying gene expression data sets for the demos of the
biclustering method "Factor Analysis for Bicluster Acquisition"
(FABIA). The following three data sets are provided: A) breast
cancer (van't Veer, Nature, 2002), B) multiple tissues (Su,
PNAS, 2002), and C) diffuse large-B-cell lymphoma (Rosenwald, N
Engl J Med, 2002).
biocViews: Bioinformatics, Statistics, Microarray,
DifferentialExpression, MultipleComparisons, Clustering,
Visualization
Author: Sepp Hochreiter <hochreit@bioinf.jku.at>
Maintainer: Sepp Hochreiter <hochreit@bioinf.jku.at>
URL: http://www.bioinf.jku.at/software/fabia/fabia.html
MD5sum: 020ead8db413d8776d4249be98468089
source.ver: src/contrib/fabiaData_1.0.1.tar.gz
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mac.binary.leopard.ver:
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vignettes: vignettes/fabiaData/inst/doc/fabiaData.pdf
vignetteTitles: fabiaData: Manual for the R Package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/fabiaData/inst/doc/fabiaData.R
Package: facsDorit
Version: 1.4.6
Depends: R (>= 1.9.1), prada (>= 1.0.5)
License: GPL-2
Title: DKFZ FACS example data
Description: FACS example data for cell-based assays. This data is used
in the examples and vignettes of the package prada.
biocViews: ExperimentData
Author: Florian Hahne <f.hahne@dfkz-heidelberg.de>
Maintainer: Florian Hahne <f.hahne@dfkz-heidelberg.de>
URL: http://www.dkfz.de/mga
MD5sum: 143415b3da3f9b24b442f7058470d4f5
source.ver: src/contrib/facsDorit_1.4.6.tar.gz
win.binary.ver: bin/windows/contrib/2.15/facsDorit_1.4.6.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: ffpeExampleData
Version: 1.0.2
Depends: R (>= 2.10.0), lumi
Suggests: genefilter, affy
License: GPL (>2)
Title: Illumina DASL example microarray data
Description: A subset of GSE17565 (April et al. 2009) containing 32
FFPE samples of Burkitts Lymphoma and Breast Adenocarcinoma,
with a dilution series in technical duplicate.
biocViews: Microarray, GeneExpression
Author: Levi Waldron
Maintainer: Levi Waldron <lwaldron@hsph.harvard.edu>
MD5sum: 11f4327c77abdb4cc036f3ee5d9d06ed
source.ver: src/contrib/ffpeExampleData_1.0.2.tar.gz
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: fibroEset
Version: 1.4.8
Depends: Biobase (>= 2.5.5)
License: LGPL
Title: exprSet for Karaman et al. (2003) fibroblasts data
Description: exprSet for Karaman et al. (2003) human, bonobo and
gorilla fibroblasts data
biocViews: ExperimentData
Author: Sylvia Merk
Maintainer: Sylvia Merk <merk@ibe.med.uni-muenchen.de>
MD5sum: 6dc1efaed7441246d44b14a3b44c39ed
source.ver: src/contrib/fibroEset_1.4.8.tar.gz
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: flowWorkspaceData
Version: 0.99.8
License: GPL-2
Title: A data package containing a flowJo xml workspace and associated
fcs files for testing the flowWorkspace package.
Description: The necessary external data to run the flowWorkspace
vignette is found in this package.
biocViews: ExperimentData
Author: Greg Finak
Maintainer: Greg Finak <gfinak@fhcrc.org>
MD5sum: cf8050ad9bfbecceb9869e4c9ba5cf45
source.ver: src/contrib/flowWorkspaceData_0.99.8.tar.gz
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: frmaExampleData
Version: 0.99.4
Depends: R (>= 2.10.0)
License: GPL (>= 2)
Title: Frma Example Data
Description: Data files used by the examples in frma and frmaTools
packages
biocViews: Microarray, AffymetrixChip, Homo_sapiens
Author: Matthew N. McCall <mmccall@jhsph.edu>
Maintainer: Matthew N. McCall <mmccall@jhsph.edu>
MD5sum: 2610fc6cbac9cc57d35befaa01c57218
source.ver: src/contrib/frmaExampleData_0.99.4.tar.gz
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: gageData
Version: 1.1.5
Suggests: gage, genefilter
License: GPL (>=2.0)
Title: Auxillary data for gage package
Description: This is a supportive data package for the software
package, gage. However, the data supplied here are also useful
for gene set or pathway analysis or microarray data analysis in
general. In this package, we provide two demo microarray
dataset: GSE16873 (a breast cancer dataset from GEO) and BMP6
(originally published as an demo dataset for GAGE, also
registered as GSE13604 in GEO). This package also includes
commonly used gene set data based on KEGG pathways and GO terms
for major research species, including human, mouse, rat and
budding yeast. Mapping data between common gene IDs for budding
yeast are also included.
biocViews: ExperimentData, Cancer
Author: Weijun Luo
Maintainer: Weijun Luo <luo@cshl.edu>
MD5sum: 6f5b68abe7c67dc000f6ef63ab9db8ef
source.ver: src/contrib/gageData_1.1.5.tar.gz
win.binary.ver: bin/windows/contrib/2.15/gageData_1.1.5.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: gaschYHS
Version: 1.0.10
Depends: R (>= 2.14.0), Biobase (>= 2.5.5)
License: Artistic-2.0
Title: ExpressionSet for response of yeast to heat shock and other
environmental stresses
Description: Data from PMID 11102521
biocViews: ExperimentData, Yeast
Author: Audrey Gasch and colleagues
Maintainer: Vince Carey <stvjc@channing.harvard.edu>
URL:
http://genome-www.stanford.edu/yeast_stress/data/rawdata/complete_dataset.txt
MD5sum: 77e8c1fed946b6e5348e74fcd8beac5c
source.ver: src/contrib/gaschYHS_1.0.10.tar.gz
win.binary.ver: bin/windows/contrib/2.15/gaschYHS_1.0.10.zip
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: gatingMLData
Version: 1.0.6
Depends: R (>= 1.9.0)
Suggests: flowUtils
License: GPL
Title: Data and XML files for GatingML Test suite
Description: Test data & XML files for Testing compliance with the
GatingML 1.5 standards in package flowUtils.
biocViews: ExperimentData
Author: Nishant Gopalakrishnan
Maintainer: Nishant Gopalakrishnan <ngopalak@fhcrc.org>
MD5sum: b4d3030bdff64ac4e2f10c20d7098c53
source.ver: src/contrib/gatingMLData_1.0.6.tar.gz
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: gcspikelite
Version: 1.0.8
Depends: R (>= 2.5.0)
License: LGPL
Title: Spike-in data for GC/MS data and methods within flagme
Description: Spike-in data for GC/MS data and methods within flagme
biocViews: MassSpectrometryData
Author: Mark Robinson <mrobinson@wehi.edu.au>
Maintainer: Mark Robinson <mrobinson@wehi.edu.au>
MD5sum: f05aed2968966680bd61f659a1cb1983
source.ver: src/contrib/gcspikelite_1.0.8.tar.gz
win.binary.ver: bin/windows/contrib/2.15/gcspikelite_1.0.8.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: geneLenDataBase
Version: 0.99.10
Depends: R (>= 2.11.0)
Imports: utils, rtracklayer, GenomicFeatures (>= 1.3.15)
License: LGPL (>= 2)
Title: Lengths of mRNA transcripts for a number of genomes
Description: Length of mRNA transcripts for a number of genomes and
gene ID formats, largely based on UCSC table browser
biocViews: HighThroughputSequencingData, ExperimentData, Transcription,
RNAseq
Author: Matthew Young
Maintainer: Matthew Young <myoung@wehi.edu.au>, Nadia Davidson
<nadia.davidson@mcri.edu.au>
MD5sum: 27426f2b64ee116d57acdeb51bf584f9
source.ver: src/contrib/geneLenDataBase_0.99.10.tar.gz
win.binary.ver: bin/windows/contrib/2.15/geneLenDataBase_0.99.10.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: ggtut
Version: 0.0.43
Depends: R (>= 2.14.0), GGtools (>= 3.11.32), ff, GenomicRanges,
snpStats, GGdata, GenomicFeatures, ChIPpeakAnno, Rsamtools(>=
1.5.35), cheung2010, SNPlocs.Hsapiens.dbSNP.20090506, hmyriB36
Suggests: rtracklayer, GenomicFeatures, ChIPpeakAnno,
TxDb.Hsapiens.UCSC.hg18.knownGene
License: Artistic-2.0
Title: support for tutorial on genetics of gene expression ISMB 2011
Description: various resources for genetics of expression with R/bioc
Author: VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
MD5sum: 517b906a283f23f2e7093f48ca06aa92
source.ver: src/contrib/ggtut_0.0.43.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ggtut_0.0.43.zip
mac.binary.leopard.ver:
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vignettes: vignettes/ggtut/inst/doc/careyGGtutslides.pdf,
vignettes/ggtut/inst/doc/extras.pdf,
vignettes/ggtut/inst/doc/tut11.pdf,
vignettes/ggtut/inst/doc/tut12.pdf
vignetteTitles: careyGGtutslides.pdf, extras.pdf, tut11.pdf, tut12.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: golubEsets
Version: 1.4.12
Depends: R (>= 2.14.0), Biobase (>= 2.5.5)
License: LGPL
Title: exprSets for golub leukemia data
Description: representation of public golub data with some covariate
data of provenance unknown to the maintainer at present; now
employs ExpressionSet format
biocViews: ExperimentData, Cancer, Leukemia
Author: Todd Golub <golub@wi.mit.edu>
Maintainer: Vince Carey <stvjc@channing.harvard.edu>
MD5sum: 710f544de4147ff46561f9062e78a5d4
source.ver: src/contrib/golubEsets_1.4.12.tar.gz
win.binary.ver: bin/windows/contrib/2.15/golubEsets_1.4.12.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
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Package: hapmap100khind
Version: 1.4.1
Suggests: oligo
License: GPL
Title: Sample data - Hapmap 100K HIND Affymetrix
Description: Sample dataset obtained from http://www.hapmap.org
biocViews: ExperimentData, HapMap
Author: Hapmap Consortium
Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
MD5sum: 90bb0d3ee1f2608528b48ec2c9a03930
source.ver: src/contrib/hapmap100khind_1.4.1.tar.gz
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: hapmap100kxba
Version: 1.4.1
Suggests: oligo
License: GPL
Title: Sample data - Hapmap 100K XBA Affymetrix
Description: Sample dataset obtained from http://www.hapmap.org
biocViews: ExperimentData, HapMap
Author: Hapmap Consortium
Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
MD5sum: 0bbe24e0a59d8c4863f45a8b6018f760
source.ver: src/contrib/hapmap100kxba_1.4.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/hapmap100kxba_1.4.1.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: hapmap500knsp
Version: 1.4.1
Suggests: oligo
License: GPL
Title: Sample data - Hapmap 500K NSP Affymetrix
Description: Sample dataset obtained from http://www.hapmap.org
biocViews: ExperimentData, HapMap
Author: Hapmap Consortium
Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
MD5sum: 940b1a5de5a889127c217f487b3ef8cd
source.ver: src/contrib/hapmap500knsp_1.4.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/hapmap500knsp_1.4.1.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: hapmap500ksty
Version: 1.4.1
Suggests: oligo
License: GPL
Title: Sample data - Hapmap 500K STY Affymetrix
Description: Sample dataset obtained from http://www.hapmap.org
biocViews: ExperimentData, HapMap
Author: Hapmap Consortium
Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
MD5sum: 15d8aeadc63a50c7ff74451732387908
source.ver: src/contrib/hapmap500ksty_1.4.1.tar.gz
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
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Package: hapmapsnp5
Version: 1.4.1
Suggests: oligo
License: GPL
Title: Sample data - Hapmap SNP 5.0 Affymetrix
Description: Sample dataset obtained from http://www.hapmap.org
biocViews: ExperimentData, HapMap
Author: Hapmap Consortium
Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
MD5sum: 00632863cad40f16c800d76b6ea48323
source.ver: src/contrib/hapmapsnp5_1.4.1.tar.gz
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: hapmapsnp6
Version: 1.4.1
Depends: R (>= 2.15)
Suggests: oligo, oligoClasses
License: GPL
Title: Sample data - Hapmap SNP 6.0 Affymetrix
Description: Sample dataset obtained from http://www.hapmap.org
biocViews: ExperimentData, HapMap
Author: Hapmap Consortium
Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
MD5sum: ed23f0e2c0638bda4f7cbc507b6c0849
source.ver: src/contrib/hapmapsnp6_1.4.1.tar.gz
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
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Package: harbChIP
Version: 1.0.9
Depends: R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5),
Biostrings
Imports: methods, stats
License: Artistic-2.0
Title: Experimental Data Package: harbChIP
Description: data from a yeast ChIP-chip experiment
biocViews: ExperimentData, Yeast, ChIPchip
Author: VJ Carey
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
MD5sum: 3dd761e532920f7c734a3bb92d55626b
source.ver: src/contrib/harbChIP_1.0.9.tar.gz
win.binary.ver: bin/windows/contrib/2.15/harbChIP_1.0.9.zip
mac.binary.leopard.ver:
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vignettes: vignettes/harbChIP/inst/doc/yeastUpstream.pdf
vignetteTitles: upstream sequence management for yeast
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/harbChIP/inst/doc/yeastUpstream.R
Package: hgu133abarcodevecs
Version: 1.0.5
Depends: R (>= 2.10.0)
License: GPL (>= 2)
Title: hgu133a data for barcode
Description: Data used by the barcode package for microarrays of type
hgu133a.
biocViews: AnnotationData, AffymetrixChip, hgu133a, Homo_sapiens
Author: Matthew N. McCall <mmccall@jhsph.edu>, Rafael A. Irizarry
<rafa@jhu.edu>
Maintainer: Matthew N. McCall <mmccall@jhsph.edu>
MD5sum: d6317e163a823f743e92baeed3d383c0
source.ver: src/contrib/hgu133abarcodevecs_1.0.5.tar.gz
win.binary.ver: bin/windows/contrib/2.15/hgu133abarcodevecs_1.0.5.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: hgu133afrmavecs
Version: 1.1.10
Depends: R (>= 2.10.0)
License: GPL (>= 2)
Title: Vectors used by frma for microarrays of type hgu133a
Description: This package was created by frmaTools version 1.9.1.
biocViews: AnnotationData, AffymetrixChip, hgu133a, Homo_sapiens
Author: Matthew N. McCall <mmccall@jhsph.edu>, Rafael A. Irizarry
<rafa@jhu.edu>
Maintainer: Matthew N. McCall <mmccall@jhsph.edu>
MD5sum: 9408a62f173a117a2c88246a79d76c9e
source.ver: src/contrib/hgu133afrmavecs_1.1.10.tar.gz
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
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Package: hgu133plus2barcodevecs
Version: 1.0.5
Depends: R (>= 2.10.0)
License: GPL (>= 2)
Title: hgu133plus2 data for barcode
Description: Data used by the barcode package for microarrays of type
hgu133plus2.
biocViews: AnnotationData, AffymetrixChip, hgu133plus2, Homo_sapiens
Author: Matthew N. McCall <mmccall@jhsph.edu>, Rafael A. Irizarry
<rafa@jhu.edu>
Maintainer: Matthew N. McCall <mmccall@jhsph.edu>
MD5sum: a53aa05904a0550fb67d2789722c4c67
source.ver: src/contrib/hgu133plus2barcodevecs_1.0.5.tar.gz
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hasINSTALL: FALSE
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Package: hgu133plus2frmavecs
Version: 1.1.10
Depends: R (>= 2.10.0)
License: GPL (>= 2)
Title: Vectors used by frma for microarrays of type hgu133plus2
Description: This package was created by frmaTools version 1.9.1.
biocViews: AnnotationData, AffymetrixChip, hgu133plus2, Homo_sapiens
Author: Matthew N. McCall <mmccall@jhsph.edu>, Rafael A. Irizarry
<rafa@jhu.edu>
Maintainer: Matthew N. McCall <mmccall@jhsph.edu>
MD5sum: 36d778aa26421b55eca6dc44e2a06cd3
source.ver: src/contrib/hgu133plus2frmavecs_1.1.10.tar.gz
win.binary.ver: bin/windows/contrib/2.15/hgu133plus2frmavecs_1.1.10.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: hgu2beta7
Version: 1.2.7
Depends: R (>= 2.0.0)
License: Artistic-2.0
Title: A data package containing annotation data for hgu2beta7
Description: Annotation data file for hgu2beta7 assembled using data
from public data repositories
biocViews: AnnotationData
Author: Chenwei Lin
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: e9d5700fbb5df7e74308a75a8296f321
source.ver: src/contrib/hgu2beta7_1.2.7.tar.gz
win.binary.ver: bin/windows/contrib/2.15/hgu2beta7_1.2.7.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: hmyriB36
Version: 0.99.16
Depends: R (>= 2.13.0), methods, Biobase (>= 2.5.5), GGBase
Suggests: GGtools, illuminaHumanv1.db
License: Artistic-2.0
Title: YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes
Description: YRI hapmap + expression (GENEVAR), Build 36, r23a
genotypes
biocViews: Statistics, ExperimentData
Author: Vincent Carey <stvjc@channing.harvard.edu>
Maintainer: Vincent Carey <stvjc@channing.harvard.edu>
MD5sum: 7ff01207211dcb929ee55181d9e8e381
source.ver: src/contrib/hmyriB36_0.99.16.tar.gz
win.binary.ver: bin/windows/contrib/2.15/hmyriB36_0.99.16.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: ggtut
suggestsMe: ind1KG
Package: humanStemCell
Version: 0.2.7
Depends: Biobase (>= 2.5.5), hgu133plus2.db
License: Artistic-2.0
Title: Human Stem Cells time course experiment
Description: Affymetrix time course experiment on human stem cells (two
time points: undifferentiated and differentiated).
biocViews: ExperimentData, StemCells
Author: R. Gentleman, N. Le Meur, M. Tewari
Maintainer: R. Gentleman <rgentlem@fhcrc.org>
MD5sum: 4feccf2c8ea4e8ccc9466c4f5e0ed19a
source.ver: src/contrib/humanStemCell_0.2.7.tar.gz
win.binary.ver: bin/windows/contrib/2.15/humanStemCell_0.2.7.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: ind1KG
Version: 0.1.14
Depends: R (>= 2.10.1), chopsticks
Suggests: Rsamtools, rtracklayer, GenomicFeatures, org.Hs.eg.db,
SNPlocs.Hsapiens.dbSNP.20090506,
TxDb.Hsapiens.UCSC.hg18.knownGene, lumiHumanIDMapping, GGBase,
GGtools, hmyriB36
License: Artistic-2.0
Title: Data from 1000 Genomes, NA19240 (female) chr6 excerpt
Description: Elements of samtools/bioc workflow for dealing with
personal sequence focusing on identification and interpretation
of rare variants
biocViews: Genetics, HighThroughputSequencing
Author: VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
MD5sum: 4163c74fba5f9cff677827416d3f27e3
source.ver: src/contrib/ind1KG_0.1.14.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ind1KG_0.1.14.zip
mac.binary.leopard.ver:
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vignettes: vignettes/ind1KG/inst/doc/ind1KG.pdf,
vignettes/ind1KG/inst/doc/nov09rv.pdf
vignetteTitles: ind1KG -- 1000 genomes data demo, Notes for eSet
developers
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ind1KG/inst/doc/ind1KG.R,
vignettes/ind1KG/inst/doc/nov09rv.R
Package: iontreeData
Version: 0.99.7
License: GPL-2
Title: Data provided to show the usage of functions in iontree package
Description: Raw MS2, MS3 scans from direct infusion mass spectrometry
(DIMS) and a demo ion tree database 'mzDB' derived from the
DIMS data are included. The demo database is used to show the
functionalities provided by the 'iontree' package, not for the
purpose of compound identification by any means.
biocViews: ExperimentData, Metabolomics
Author: Mingshu Cao
Maintainer: Mingshu Cao <mingshu.cao@agresearch.co.nz>
MD5sum: aa0dffc3ed90fa0d7c6724664a8e0cc3
source.ver: src/contrib/iontreeData_0.99.7.tar.gz
win.binary.ver: bin/windows/contrib/2.15/iontreeData_0.99.7.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: kidpack
Version: 1.5.11
Depends: R (>= 2.6.0), Biobase (>= 2.5.5)
License: GPL-2
Title: DKFZ kidney package
Description: kidney microarray data
biocViews: ExperimentData, Cancer, Kidney
Author: Wolfgang Huber <huber@ebi.ac.uk>
Maintainer: Wolfgang Huber <huber@ebi.ac.uk>
URL: http://www.dkfz.de/mga
MD5sum: d22c4a447cd6cc7593b82cc7ee968353
source.ver: src/contrib/kidpack_1.5.11.tar.gz
win.binary.ver: bin/windows/contrib/2.15/kidpack_1.5.11.zip
mac.binary.leopard.ver:
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vignettes: vignettes/kidpack/inst/doc/kidpack.pdf
vignetteTitles: kidpack - overview over the DKFZ kidney data package
hasREADME: TRUE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/kidpack/inst/doc/kidpack.R
Package: leeBamViews
Version: 0.99.20
Depends: R (>= 2.15.0), Biobase, Rsamtools (>= 0.1.50), BSgenome
Imports: GenomicRanges, methods
Suggests: GenomeGraphs, biomaRt, org.Sc.sgd.db, edgeR
Enhances: multicore
License: Artistic 2.0
Title: leeBamViews -- multiple yeast RNAseq samples excerpted from Lee
2009
Description: data from PMID 19096707; prototype for managing multiple
NGS samples
biocViews: HighThroughputSequencing, RNAseq, CellBiology, Genetics,
DifferentialExpression, RNAseqData
Author: VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
MD5sum: 95f6ec79289dbce2c9c8158d6bbe4022
source.ver: src/contrib/leeBamViews_0.99.20.tar.gz
win.binary.ver: bin/windows/contrib/2.15/leeBamViews_0.99.20.zip
mac.binary.leopard.ver:
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vignettes: vignettes/leeBamViews/inst/doc/leeViews.pdf
vignetteTitles: managing multiple NGS samples with bamViews
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/leeBamViews/inst/doc/leeViews.R
Package: lumiBarnes
Version: 1.3.9
Depends: R (>= 2.0), Biobase (>= 2.5.5), lumi (>= 1.1.0)
License: LGPL
Title: Barnes Benchmark Illumina Tissues Titration Data
Description: The Barnes benchmark dataset can be used to evaluate the
algorithms for Illumina microarrays. It measured a titration
series of two human tissues, blood and placenta, and includes
six samples with the titration ratio of blood and placenta as
100:0, 95:5, 75:25, 50:50, 25:75 and 0:100. The samples were
hybridized on HumanRef-8 BeadChip (Illumina, Inc) in duplicate.
The data is loaded as an LumiBatch Object (see documents in the
lumi package).
biocViews: ExperimentData, OneChannel, RNAExpressionData, NormalTissue
Author: Pan Du
Maintainer: Pan Du <dupan@northwestern.edu>
MD5sum: 2833c447dded2ec91d6ac959ed37cc6e
source.ver: src/contrib/lumiBarnes_1.3.9.tar.gz
win.binary.ver: bin/windows/contrib/2.15/lumiBarnes_1.3.9.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: lungExpression
Version: 0.0.14
Depends: R (>= 2.4.0), Biobase (>= 2.5.5)
License: GPL (>= 2)
Title: ExpressionSets for Parmigiani et al., 2004 Clinical Cancer
Research paper
Description: Data from three large lung cancer studies provided as
ExpressionSets
biocViews: ExperimentData, Cancer, Lung
Author: Robert Scharpf <rscharpf@jhsph.edu>, Simens Zhong
<zhong@mts.jhu.edu>, Giovanni Parmigiani <gp@jhu.edu>
Maintainer: Robert Scharpf <rscharpf@jhsph.edu>
MD5sum: 3509fe2c15027a69ad84f5e4428f54fb
source.ver: src/contrib/lungExpression_0.0.14.tar.gz
win.binary.ver: bin/windows/contrib/2.15/lungExpression_0.0.14.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: maqcExpression4plex
Version: 1.6.1
Suggests: oligo, pdInfoBuilder
License: GPL
Title: Sample Expression Data - MAQC / HG18 - NimbleGen
Description: Data from human (HG18) 4plex NimbleGen array. It has 24k
genes with 3 60mer probes per gene.
biocViews: ExperimentData
Author: NimbleGen Systems
Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
MD5sum: 031eaf937ae6c1dfff490e8460f7f985
source.ver: src/contrib/maqcExpression4plex_1.6.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/maqcExpression4plex_1.6.1.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: miRNATarget
Version: 0.99.2
Depends: R (>= 2.10), Biobase
License: GPL
Title: gene target tabale of miRNA for human/mouse used for MiRaGE
package
Description: gene target tabale of miRNA for human/mouse used for
MiRaGE package
biocViews: ExperimentData,
Author: Y-h. Taguchi <tag@granular.com>
Maintainer: Y-h. Taguchi <tag@granular.com>
MD5sum: a361580afde690924326033289f6ae7a
source.ver: src/contrib/miRNATarget_0.99.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/miRNATarget_0.99.2.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/miRNATarget_0.99.2.tgz
vignettes: vignettes/miRNATarget/inst/doc/miRNATarget.pdf
vignetteTitles: miRNATargetTutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/miRNATarget/inst/doc/miRNATarget.R
Package: minfiData
Version: 0.3.1
Depends: R (>= 2.13.0), minfi, IlluminaHumanMethylation450kmanifest
License: Artistic-2.0
Title: Example data for the Illumina Methylation 450k array
Description: Data from 6 samples across 2 groups from 450k methylation
arrays
biocViews: DNAMethylation
Author: Kasper Daniel Hansen, Martin Aryee, Winston Timp
Maintainer: Kasper Daniel Hansen <khansen@jhsph.edu>
MD5sum: e89877821218a03f1e0bfc191681d44d
source.ver: src/contrib/minfiData_0.3.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/minfiData_0.3.1.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: mosaicsExample
Version: 0.99.7
Depends: R (>= 2.11.1)
License: GPL (>= 2)
Title: Example data for the mosaics package, which implements MOSAiCS,
a statistical framework to analyze one-sample or two-sample
ChIP-seq data
Description: Data for the mosaics package, consisting of chromosome 21
ChIP and control sample data from a ChIP-seq experiment of
STAT1 binding, with mappability, GC content, and sequence
ambiguity scores of human genome HG18.
biocViews: ExperimentData, ChIPseqData, Homo_sapiens
Author: Dongjun Chung, Pei Fen Kuan, Sunduz Keles
Maintainer: Dongjun Chung <chungdon@stat.wisc.edu>
URL: http://groups.google.com/group/mosaics_user_group
MD5sum: 226c39c6fa72b70120445f14098dc271
source.ver: src/contrib/mosaicsExample_0.99.7.tar.gz
win.binary.ver: bin/windows/contrib/2.15/mosaicsExample_0.99.7.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: mouse4302barcodevecs
Version: 1.0.5
Depends: R (>= 2.10.0)
License: GPL (>= 2)
Title: mouse4302 data for barcode
Description: Data used by the barcode package for microarrays of type
mouse4302.
biocViews: AnnotationData, AffymetrixChip, mouse4302, Mus_musculus
Author: Matthew N. McCall <mmccall@jhsph.edu>, Rafael A. Irizarry
<rafa@jhu.edu>
Maintainer: Matthew N. McCall <mmccall@jhsph.edu>
MD5sum: 7efcd3d6812334fa2c351cb06ee8abb5
source.ver: src/contrib/mouse4302barcodevecs_1.0.5.tar.gz
win.binary.ver: bin/windows/contrib/2.15/mouse4302barcodevecs_1.0.5.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: mouse4302frmavecs
Version: 1.1.10
Depends: R (>= 2.10.0)
License: GPL (>= 2)
Title: Vectors used by frma for microarrays of type mouse4302
Description: This package was created by frmaTools version 1.9.1.
biocViews: AnnotationData, AffymetrixChip, mouse4302, Mus_musculus
Author: Matthew N. McCall <mmccall@jhsph.edu>, Rafael A. Irizarry
<rafa@jhu.edu>
Maintainer: Matthew N. McCall <mmccall@jhsph.edu>
MD5sum: 31f0f4306f18580d74596be16c1bedc0
source.ver: src/contrib/mouse4302frmavecs_1.1.10.tar.gz
win.binary.ver: bin/windows/contrib/2.15/mouse4302frmavecs_1.1.10.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: msdata
Version: 0.1.12
Suggests: xcms
License: GPL (>= 2)
Title: Various Mass Spectrometry raw data example files
Description: Ion Trap positive ionization mode data in mzData file
format. Subset from 500-850 m/z and 1190-1310 seconds, incl.
MS2 and MS3, intensity threshold 100.000. Extracts from FTICR
Apex III, m/z 400-450. Subset of UPLC - Bruker micrOTOFq data,
both mzData and mzML.
biocViews: ExperimentData, MassSpectrometryData
Author: Steffen Neumann <sneumann@ipb-halle.de>
Maintainer: Steffen Neumann <sneumann@ipb-halle.de>
MD5sum: 4396c1ce3cf1cc4acaff2efcc8bf134e
source.ver: src/contrib/msdata_0.1.12.tar.gz
win.binary.ver: bin/windows/contrib/2.15/msdata_0.1.12.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: mvoutData
Version: 0.99.9
Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4),
lumi
License: Artistic-2.0
Title: affy and illumina raw data for assessing outlier detector
performance
Description: affy and illumina raw data for assessing outlier detector
performance
biocViews: ExperimentData
Author: VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
MD5sum: 61a59cd7bd16f62d54ed197499d6b996
source.ver: src/contrib/mvoutData_0.99.9.tar.gz
win.binary.ver: bin/windows/contrib/2.15/mvoutData_0.99.9.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: pasillaBamSubset
Version: 0.0.6
Suggests: pasilla
License: LGPL
Title: Subset of BAM files from "Pasilla" experiment
Description: Subset of BAM files untreated1.bam (single-end reads) and
untreated3.bam (paired-end reads) from "Pasilla" experiment
(Pasilla knock-down by Brooks et al., Genome Research 2011).
See the vignette in the pasilla data package for how BAM files
untreated1.bam and untreated3.bam were obtained from the
RNA-Seq read sequence data that is provided by NCBI Gene
Expression Omnibus under accession numbers GSM461176 to
GSM461181. Also contains the DNA sequence for fly chromosome 4
to which the reads can be mapped.
biocViews: ExperimentData, RNAseqData
Author: H. Pages
Maintainer: H. Pages <hpages@fhcrc.org>
MD5sum: 8296c5e83acc2dabb8c13c3fd0c7f8dc
source.ver: src/contrib/pasillaBamSubset_0.0.6.tar.gz
win.binary.ver: bin/windows/contrib/2.15/pasillaBamSubset_0.0.6.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: pasilla
Version: 0.2.15
Depends: DEXSeq, DESeq
Suggests: locfit, edgeR, xtable
License: LGPL
Title: Data package with per-exon and per-gene read counts of RNA-seq
samples of Pasilla knock-down by Brooks et al., Genome Research
2011.
Description: This package provides per-exon and per-gene read counts
computed for selected genes from RNA-seq data that were
presented in the article "Conservation of an RNA regulatory map
between Drosophila and mammals" by Brooks AN, Yang L, Duff MO,
Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR, Genome
Res. 2011 Feb;21(2):193-202, Epub 2010 Oct 4, PMID: 20921232.
The experiment studied the effect of RNAi knockdown of Pasilla,
the Drosophila melanogaster ortholog of mammalian NOVA1 and
NOVA2, on the transcriptome. The package vignette describes
how the data provided here were derived from the RNA-Seq read
sequence data that is provided by NCBI Gene Expression Omnibus
under accession numbers GSM461176 to GSM461181
biocViews: ExperimentData, RNAseqData
Author: Wolfgang Huber, Alejandro Reyes
Maintainer: Alejandro Reyes <reyes@embl.de>
MD5sum: e15e7e01bfba489f4eed3a8f9b81e5b0
source.ver: src/contrib/pasilla_0.2.15.tar.gz
win.binary.ver: bin/windows/contrib/2.15/pasilla_0.2.15.zip
mac.binary.leopard.ver:
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vignettes: vignettes/pasilla/inst/doc/create_objects.pdf
vignetteTitles: Data preprocessing and creation of the data objects
pasillaGenes and pasillaExons
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/pasilla/inst/doc/create_objects.R
suggestsMe: pasillaBamSubset
Package: pcaGoPromoter.Hs.hg19
Version: 0.99.3
License: GPL (>= 2)
Title: pcaGoPromoter.Hs.hg19 is a data package used by pcaGoPromoter
Description: Contains the data for transciption factors analysis of
organism Homo Sapiens with package pcaGoPromoter
biocViews: AnnotationData, Homo_sapiens
Author: Morten Hansen, <mhansen@sund.ku.dk>
Maintainer: Morten Hansen, <mhansen@sund.ku.dk>
MD5sum: c272b922c542f988295bf26c79c26764
source.ver: src/contrib/pcaGoPromoter.Hs.hg19_0.99.3.tar.gz
win.binary.ver:
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mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: pcaGoPromoter.Mm.mm9
Version: 0.99.3
License: GPL (>= 2)
Title: pcaGoPromoter.Mm.mm9 is a data package used by pcaGoPromoter
Description: Contains the data for transciption factors analysis of
organism Mus musculus with package pcaGoPromoter
biocViews: AnnotationData, Mus_musculus
Author: Morten Hansen, <mhansen@sund.ku.dk>
Maintainer: Morten Hansen, <mhansen@sund.ku.dk>
MD5sum: e636e88d6940809ed0a96681967b5343
source.ver: src/contrib/pcaGoPromoter.Mm.mm9_0.99.3.tar.gz
win.binary.ver:
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mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: pcaGoPromoter.Rn.rn4
Version: 0.99.3
License: GPL (>= 2)
Title: pcaGoPromoter.Rn.rn4 is a data package used by pcaGoPromoter
Description: Contains the data for transciption factors analysis of
organism Rattus norvegicus with package pcaGoPromoter
biocViews: AnnotationData, Rattus_norvegicus
Author: Morten Hansen, <mhansen@sund.ku.dk>
Maintainer: Morten Hansen, <mhansen@sund.ku.dk>
MD5sum: deeebabcd4e8c89b83bec661f3d761af
source.ver: src/contrib/pcaGoPromoter.Rn.rn4_0.99.3.tar.gz
win.binary.ver:
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mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: pd.atdschip.tiling
Version: 0.0.4
Depends: R (>= 2.14.0), methods, RSQLite (>= 0.10.0), oligoClasses (>=
1.15.58), oligo (>= 1.17.3), DBI
Imports: Biostrings (>= 2.21.11), IRanges (>= 1.11.31)
License: Artistic-2.0
Title: Platform Design Info for Affymetrix Atdschip_tiling
Description: Platform Design Info for Affymetrix Atdschip_tiling
biocViews: AnnotationData
Author: Kristof De Beuf
Maintainer: Kristof De Beuf <kristof.debeuf@ugent.be>
MD5sum: 983b90f0eb34efb9a5a0f079cf99c7c7
source.ver: src/contrib/pd.atdschip.tiling_0.0.4.tar.gz
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Package: ppiData
Version: 0.1.18
Depends: graph
Suggests: org.Sc.sgd.db, ppiStats
License: Artistic-2.0
Title: A package that contains the bait to prey directed graphs for
protein-protein interactions.
Description: This package contains the directed graphs for protein
interaction data as derived from Y2H and APMS as well as the
code used to obtain the y2h data from IntAct Repository.
biocViews: ExperimentData
Author: Tony Chiang
Maintainer: Tony Chiang <tchiang@fhcrc.org>
MD5sum: 5950fc41e0a8e2735a11fbc2b6c6517c
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Package: pumadata
Version: 1.99.4
Depends: R (>= 2.10.0), affy (>= 1.23.4), Biobase (>= 2.5.5), puma
License: LGPL
Title: Various data sets for use with the puma package
Description: This is a simple data package including various data sets
derived from the estrogen data for use with the puma
(Propagating Uncertainty in Microarray Analysis) package.
biocViews: ExperimentData
Author: Richard Pearson
Maintainer: Richard Pearson <richard.pearson@well.ox.ac.ukk>
URL: http://umber.sbs.man.ac.uk/resources/puma
MD5sum: 14910e60fb36b75b99206ed3f9d482d1
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vignettes: vignettes/pumadata/inst/doc/pumadata.pdf
vignetteTitles: pumadata User Guide
hasREADME: FALSE
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Rfiles: vignettes/pumadata/inst/doc/pumadata.R
Package: rheumaticConditionWOLLBOLD
Version: 1.0.2
Depends: R (>= 2.10.0)
Suggests: genefilter, Biobase, hgu133plus2.db
License: Artistic-2.0
Title: Normalized gene expression dataset published by Wollbold et al.
[2009] (WOLLBOLD).
Description: Normalized gene expression data from rheumatic diseases
from study published by Wollbold et al. in 2009, provided as an
eSet.
biocViews: ExperimentData, Rheumatic diseases,Arthritis,
Osteoarthritis, GeneExpression, Microarray
Author: Alejandro Quiroz-Zarate, John Quackenbush
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URL: http://compbio.dfci.harvard.edu/
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hasREADME: FALSE
hasNEWS: FALSE
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Package: serumStimulation
Version: 0.99.3
Depends: R (>= 2.10)
License: GPL (>= 2)
Title: serumStimulation is a data package which is used by examples in
package pcaGoPromoter
Description: Contains 13 micro array data results from a serum
stimulation experiment
biocViews: ExperimentData
Author: Morten Hansen, <mhansen@sund.ku.dk>
Maintainer: Morten Hansen, <mhansen@sund.ku.dk>
MD5sum: 64383a692c1c87ab53e67d1bff192dba
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hasREADME: FALSE
hasNEWS: FALSE
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Package: simpIntLists
Version: 0.99.3
License: GPL (>= 2)
Title: The package contains BioGRID interactions for various organisms
in a simple format
Description: The package contains BioGRID interactions for
arabidopsis(thale cress), c.elegans, fruit fly, human, mouse,
yeast( budding yeast ) and S.pombe (fission yeast) . Entrez
ids, official names and unique ids can be used to find
proteins. The format of interactions are lists. For each
gene/protein, there is an entry in the list with "name"
containing name of the gene/protein and "interactors"
containing the list of genes/proteins interacting with it.
biocViews: ExperimentData
Author: Kircicegi Korkmaz, Volkan Atalay, Rengul Cetin-Atalay
Maintainer: Kircicegi Korkmaz <e102771@ceng.metu.edu.tr>
MD5sum: 61a217cd004afd4d9f469dd275e0bd56
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vignettes: vignettes/simpIntLists/inst/doc/simpIntLists.pdf
vignetteTitles: simpIntLists
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/simpIntLists/inst/doc/simpIntLists.R
Package: stemHypoxia
Version: 0.99.2
Depends: R (>= 2.14.1)
License: GPL (>=2)
Title: Differentiation of Human Embryonic Stem Cells under Hypoxia gene
expression dataset by Prado-Lopez et al. (2010)
Description: Expression profiling using microarray technology to prove
if 'Hypoxia Promotes Efficient Differentiation of Human
Embryonic Stem Cells to Functional Endothelium' by Prado-Lopez
et al. (2010) Stem Cells 28:407-418. Full data available at
Gene Expression Omnibus series GSE37761.
biocViews: ExperimentData, Cancer, GeneExpression, Microarray
Author: Cristobal Fresno and Elmer A. Fernandez
Maintainer: Cristobal Fresno <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
MD5sum: 4f7ac05ef4de5b50a40a0eedb3ee699c
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hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
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Package: stjudem
Version: 1.2.8
Depends: R (>= 2.10), utils
License: LGPL (>= 2)
Title: Microarray Data from Yeoh et al. in MACAT format
Description: This is a microarray data set on acute lymphoblastic
leukemia, published in 2002 (Yeoh et al.Cancer Cell 2002). The
experiments were conducted in the St.Jude Children's Research
Hospital, Memphis, Tenessee, USA. The raw data was preprocessed
by variance stabilizing normalization (Huber et al.) on probe
and subsequent summarization of probe expression values into
probe set expression values using median polish.
biocViews: ExperimentData
Author: Benjamin Georgi, Matthias Heinig, Sebastian Schmeier, Joern
Toedling
Maintainer: Joern Toedling <toedling@ebi.ac.uk>
MD5sum: e8e9f98e898724957958894ec39ee220
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hasREADME: FALSE
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hasINSTALL: FALSE
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Package: synapterdata
Version: 0.99.3
Depends: R (>= 2.10), synapter (>= 0.99.6)
License: GPL-2
Title: Data accompanying the synapter package
Description: Data independant acquisition of UPS1 protein mix in an E.
coli background obtained on a Waters Synapt G2 instrument.
biocViews: ExperimentData, MassSpectrometry, MassSpectrometryData,
Proteomics
Author: Laurent Gatto and Pavel V. Shliaha
Maintainer: Laurent Gatto <lg390@cam.ac.uk>
MD5sum: ffd5e483ef866b7b1520fbfbc9a7f09a
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hasREADME: FALSE
hasNEWS: TRUE
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Package: tinesath1cdf
Version: 1.0.8
License: Artistic-2.0
Title: tinesath1cdf
Description: A package containing an environment represeting the
newcdf/tinesATH1.cdf.cdf file.
biocViews: AnnotationData, AffymetrixChip, ath1121501,
Arabidopsis_thaliana
Author: Tine Casneuf
Maintainer: Tine Casneuf <tine@ebi.ac.uk>
MD5sum: e4046e640954166a6126ef2ae9c0a347
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dependsOnMe: XhybCasneuf
Package: tinesath1probe
Version: 1.0.8
Depends: R (>= 1.6), AnnotationDbi (>= 1.11.9)
License: LGPL
Title: Probe sequence data for microarrays of type tinesath1
Description: This package was automatically created by package
matchprobes version 1.4.0. The probe sequence data was obtained
from http://www.affymetrix.com.
biocViews: AnnotationData, AffymetrixChip, tinesath1,
Arabidopsis_thaliana
Author: The Bioconductor Project www.bioconductor.org
Maintainer: Tine Casneuf <tine@ebi.ac.uk>
MD5sum: f891c02f8996f19880f133c0f792ac8c
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Package: tweeDEseqCountData
Version: 1.0.8
Depends: Biobase, R (>= 2.10)
License: GPL (>=2)
Title: RNA-seq count data employed in the vignette of the tweeDEseq
package
Description: RNA-seq count data from Pickrell et al. (2010) employed to
illustrate the use of the Poisson-Tweedie family of
distributions with the tweeDEseq package.
biocViews: HighThroughputSequencingData, RNAseqData
Author: Juan R Gonzalez <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
MD5sum: e96ac3facd8bbb0ae025b3222df015d5
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Package: waveTilingData
Version: 0.99.1
Depends: R (>= 2.14.0)
License: GPL (>= 2)
Title: waveTiling Example Data
Description: Experiment and Annotation Data files used by the examples
/ vignette in the waveTiling package
biocViews: Microarray, AnnotationData, ExperimentData
Author: Kristof De Beuf <kristof.debeuf@ugent.be>
Maintainer: Kristof De Beuf <kristof.debeuf@ugent.be>
MD5sum: 7ca49b9b0866fb9f055daba0b5ab9782
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hasREADME: FALSE
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Package: yeastCC
Version: 1.2.17
Depends: Biobase (>= 2.5.5)
License: Artistic-2.0
Title: Spellman et al. (1998) and Pramila/Breeden (2006) yeast cell
cycle microarray data
Description: ExpressionSet for Spellman et al. (1998) yeast cell cycle
microarray experiment
biocViews: ExperimentData, Yeast
Author: Sandrine Dudoit <sandrine@stat.berkeley.edu>
Maintainer: Sandrine Dudoit <sandrine@stat.berkeley.edu>
MD5sum: fca4de526434f2ffaadb521f81b1b0d5
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vignettes: vignettes/yeastCC/inst/doc/Spellmanetal.pdf
vignetteTitles: Spellmanetal.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: yeastExpData
Version: 0.9.21
Depends: R (>= 2.4), graph (>= 1.9.26)
Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db
License: GPL
Title: Yeast Experimental Data
Description: A collection of different sets of experimental data from
yeast.
biocViews: ExperimentData, Yeast
Author: R. Gentleman
Maintainer: R. Gentleman <rgentlem@fhcrc.org>
MD5sum: 37841cd9eefdeba570802612d89aa0f8
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vignettes: vignettes/yeastExpData/inst/doc/yeastExample.pdf
vignetteTitles: Yeast PPI Example
hasREADME: FALSE
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hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/yeastExpData/inst/doc/yeastExample.R
Package: yeastGSData
Version: 0.1.9
License: Artistic-2.0
Title: Yeast Gold Standard Data
Description: A collection of so-called gold (and other) standard data
sets
biocViews: ExperimentData, Yeast
Author: R. Gentleman
Maintainer: R. Gentleman <rgentlem@fhcrc.org>
MD5sum: 7e876c35b0101516e3d797934d5e7466
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hasREADME: FALSE
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Package: yeastNagalakshmi
Version: 0.99.5
License: Artistic-2.0
Title: Yeast genome RNA sequencing data based on Nagalakshmi et. al.
Description: The yeast genome data was retrieved from the sequence read
archive, aligned with bwa, and converted to BAM format with
samtools.
biocViews: ExperimentData, Yeast, ChIPseqData
Author: Martin Morgan <mtmorgan@fhcrc.org>
Maintainer: Bioconductor Package Maintainer
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MD5sum: fdf8215605e5acc2c6fa0de321bd9482
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Package: yeastRNASeq
Version: 0.0.7
Depends: R (>= 2.4)
Suggests: Biobase, ShortRead, IRanges
License: GPL
Title: Yeast RNA-Seq Experimental Data from Lee et al. 2008
Description: A selection of RNA-Seq data from a yeast transcriptome
experiment.
biocViews: ExperimentData, Yeast, RNAseqData
Author: James H. Bullard and Kasper D. Hansen
Maintainer: J. Bullard <bullard@stat.berkeley.edu>
MD5sum: c88abd3b8e2b7c8d1b0eb1e9ecf471e2
source.ver: src/contrib/yeastRNASeq_0.0.7.tar.gz
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vignetteTitles: An overview of yeastRNASeq
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