Bioconductor ExperimentData Packages

Bioconductor version: 3.0

Package Maintainer Title
affycompData Harris Jaffee affycomp data
affydata Harris Jaffee Affymetrix Data for Demonstration Purpose
Affyhgu133A2Expr Zhicheng Ji Affymetrix Human Genome U133A 2.0 Array (GPL571) Expression Data Package
Affyhgu133aExpr Zhicheng Ji Affymetrix Human hgu133a Array (GPL96) Expression Data Package
Affyhgu133Plus2Expr Zhicheng Ji Affyhgu133Plus2Expr (GPL570) Expression Data Package
AffymetrixDataTestFiles Henrik Bengtsson Affymetrix data files (CEL, CDF, CHP, EXP, PSI) for testing
Affymoe4302Expr Zhicheng Ji Affymetrix Mouse Genome 430 2.0 Array (GPL1261) Expression Data Package
airway Michael Love SummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014
ALL Robert Gentleman A data package
ALLMLL B. M. Bolstad A subset of arrays from a large acute lymphoblastic leukemia (ALL) study
AmpAffyExample Rafael A. Irizarry Example of Amplified Data
antiProfilesData Hector Corrada Bravo Normal colon and cancer preprocessed affy data for antiProfile building.
ARRmData Jean-Philippe Fortin Example dataset for normalization of Illumina 450k Methylation data
bcellViper Mariano Javier Alvarez Human B-cell transcriptional interactome and normal human B-cell expression data
beadarrayExampleData Mark Dunning Example data for the beadarray package
BeadArrayUseCases Mike Smith Analysing Illumina BeadArray expression data using Bioconductor
beta7 Jean Yang Rodriguez et al. (2004) Differential Gene Expression by Memory/Effector T Helper Cells Bearing the Gut-Homing Receptor Integrin alpha4 beta7.
bladderbatch Jeffrey T. Leek Bladder gene expression data illustrating batch effects
blimaTestingData Vojtech Kulvait Data for testing of the package blima.
breastCancerMAINZ Markus Schroeder, Benjamin Haibe-Kains Gene expression dataset published by Schmidt et al. [2008] (MAINZ).
breastCancerNKI Markus Schroeder, Benjamin Haibe-Kains Genexpression dataset published by van't Veer et al. [2002] and van de Vijver et al. [2002] (NKI).
breastCancerTRANSBIG Markus Schroeder, Benjamin Haibe-Kains Gene expression dataset published by Desmedt et al. [2007] (TRANSBIG).
breastCancerUNT Markus Schroeder, Benjamin Haibe-Kains Gene expression dataset published by Sotiriou et al. [2007] (UNT).
breastCancerUPP Markus Schroeder, Benjamin Haibe-Kains Gene expression dataset published by Miller et al. [2005] (UPP).
breastCancerVDX Markus Schroeder, Benjamin Haibe-Kains Gene expression datasets published by Wang et al. [2005] and Minn et al. [2007] (VDX).
bronchialIL13 Vince Carey time course experiment involving il13
bsseqData Kasper Daniel Hansen Example whole genome bisulfite data for the bsseq package
cancerdata Daniel Kosztyla Development and validation of diagnostic tests from high-dimensional molecular data: Datasets
CCl4 Audrey Kauffmann Carbon Tetrachloride (CCl4) treated hepatocytes
ccTutorial Joern Toedling Data package for ChIP-chip tutorial
ceu1kg VJ Carey CEU (N=60) genotypes from 1000 genomes pilot phase I
ceu1kgv VJ Carey expression + genotype on 79 unrelated CEU individuals
ceuhm3 VJ Carey ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort
cgdv17 VJ Carey Complete Genomics Diversity Panel, chr17 on 46 individuals
ChAMPdata Tiffany Morris Data Packages for ChAMP package
charmData Martin Aryee An example dataset for use with the charm package
cheung2010 Vince Carey resources for genetics of gene expression based on Cheung et al 2010
ChimpHumanBrainData Sean Davis Chimp and human brain data package Ryan P. Welch, Chee Lee, Raymond G. Cavalcante Gene set enrichment analysis for ChIP-seq data
ChIPXpressData George Wu ChIPXpress Pre-built Databases
CLL Robert Gentleman A Package for CLL Gene Expression Data
cMap2data J. Saez-Rodriguez Connectivity Map (version 2) Data
cnvGSAdata Robert Ziman Data used in the vignette of the cnvGSA package
COHCAPanno Charles Warden Annotations for City of Hope CpG Island Analysis Pipeline
colonCA W Sylvia Merk exprSet for Alon et al. (1999) colon cancer data
ConnectivityMap Paul Shannon Functional connections between drugs, genes and diseases as revealed by common gene-expression changes J Fah Sathirapongsasuti Data to support sexually dimorphic and COPD differential analysis for gene expression and methylation.
CopyNumber450kData Simon Papillon-Cavanagh Example data for the Illumina Methylation 450k array
COSMIC.67 Julian Gehring COSMIC.67
CRCL18 Claudio Isella CRC cell line dataset
curatedBladderData Markus Riester Bladder Cancer Gene Expression Analysis
curatedCRCData Princy Parsana Colorectal Cancer Gene Expression Analysis
curatedOvarianData Levi Waldron Clinically Annotated Data for the Ovarian Cancer Transcriptome
davidTiling Wolfgang Huber Data and analysis scripts for David, Huber et al. yeast tiling array paper
derfinderData Leonardo Collado-Torres Processed BigWigs from BrainSpan for examples
DeSousa2013 Xin Wang Poor prognosis colon cancer is defined by a molecularly distinct subtype and precursor lesion
DLBCL Marcus Dittrich Diffuse large B-cell lymphoma expression data
DMRcatedata Tim Peters Data Package for DMRcate package
DonaPLLP2013 Joseph D. Barry Supplementary data package for Dona et al. (2013) containing example images and tables
DREAM4 Paul Shannon Synthetic Expression Data for Gene Regulatory Network Inference from the 2009 DREAM4 challenge
dressCheck Vincent Carey data and software for checking Dressman JCO 25(5) 2007
DrugVsDiseasedata J. Saez-Rodriguez Drug versus Disease Data
dsQTL VJ Carey dsQTL, data excerpt from Degner et al. 2012 Nature letter
DvDdata J. Saez-Rodriguez Drug versus Disease Data
dyebiasexamples Philip Lijnzaad Example data for the dyebias package, which implements the GASSCO method.
EatonEtAlChIPseq Patrick Aboyoun ChIP-seq data of ORC-binding sites in Yeast excerpted from Eaton et al. 2010
ecoliLeucine Laurent Gautier Experimental data with Affymetrix E. coli chips
encoDnaseI VJ Carey data provided by UCSC for Cd4 raw measures of DnaseI hypersensitivity
estrogen R. Gentleman 2x2 factorial design exercise for the Bioconductor short course
faahKO Colin A. Smith Saghatelian et al. (2004) FAAH knockout LC/MS data
fabiaData Sepp Hochreiter Data sets for FABIA (Factor Analysis for Bicluster Acquisition)
facopy.annot David Mosen-Ansorena Annotation for the copy number alteration association and enrichment analyses with facopy
facsDorit Florian Hahne DKFZ FACS example data
FANTOM3and4CAGE Vanja Haberle CAGE data from FANTOM3 and FANTOM4 projects
ffpeExampleData Levi Waldron Illumina DASL example microarray data
fibroEset Sylvia Merk exprSet for Karaman et al. (2003) fibroblasts data
fission Michael Love SummarizedExperiment for time course RNA-Seq of fission yeast in response to stress, by Leong et al., Nat Commun 2014.
Fletcher2013a Mauro Castro Gene expression data from breast cancer cells under FGFR2 signalling perturbation.
Fletcher2013b Mauro Castro Master regulators of FGFR2 signalling and breast cancer risk.
flowFitExampleData Davide Rambaldi Example data for the flowFit package
FlowSorted.Blood.450k Andrew E Jaffe Illumina HumanMethylation data on sorted blood cell populations
FlowSorted.DLPFC.450k Andrew E Jaffe Illumina HumanMethylation data on sorted frontal cortex cell populations
flowWorkspaceData Mike Jiang A data package containing two flowJo xml workspaces and associated fcs files for testing the flowWorkspace and openCyto packages.
frmaExampleData Matthew N. McCall Frma Example Data Simon G. Coetzee Various data sets for use with the FunciSNP package
gageData Weijun Luo Auxillary data for gage package
gaschYHS Vince Carey ExpressionSet for response of yeast to heat shock and other environmental stresses
gatingMLData J. Spidlen Data and XML files for Gating-ML Test suite
gcspikelite Mark Robinson Spike-in data for GC/MS data and methods within flagme
geneLenDataBase Matthew Young, Nadia Davidson Lengths of mRNA transcripts for a number of genomes
GGdata VJ Carey all 90 hapmap CEU samples, 47K expression, 4mm SNP
ggtut VJ Carey support for tutorial on genetics of gene expression ISMB 2011
golubEsets Vince Carey exprSets for golub leukemia data
GSBenchMark Bahman Afsari Gene Set Benchmark
GSVAdata Robert Castelo Data employed in the vignette of the GSVA package
GWASdata Stephanie Gogarten, Adrienne Stilp Data used in the examples and vignettes of the GWASTools package
h5vcData Paul Theodor Pyl Example data for the h5vc package
hapmap100khind Benilton Carvalho Sample data - Hapmap 100K HIND Affymetrix
hapmap100kxba Benilton Carvalho Sample data - Hapmap 100K XBA Affymetrix
hapmap500knsp Benilton Carvalho Sample data - Hapmap 500K NSP Affymetrix
hapmap500ksty Benilton Carvalho Sample data - Hapmap 500K STY Affymetrix
hapmapsnp5 Benilton Carvalho Sample data - Hapmap SNP 5.0 Affymetrix
hapmapsnp6 Benilton Carvalho Sample data - Hapmap SNP 6.0 Affymetrix
harbChIP VJ Carey Experimental Data Package: harbChIP
HD2013SGI Bernd Fischer Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping
healthyFlowData Ariful Azad Healthy dataset used by the flowMatch package
HEEBOdata Agnes Paquet HEEBO set and HEEBO controls.
hgu133abarcodevecs Matthew N. McCall hgu133a data for barcode
hgu133plus2barcodevecs Matthew N. McCall hgu133plus2 data for barcode
hgu2beta7 Bioconductor Package Maintainer A data package containing annotation data for hgu2beta7
HiCDataHumanIMR90 Nicolas Servant Human IMR90 Fibroblast HiC data from Dixon et al. 2012
HiCDataLymphoblast Borbala Mifsud Human lymphoblastoid HiC data from Lieberman-Aiden et al. 2009
Hiiragi2013 Andrzej Oles Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages
HIVcDNAvantWout03 Chris Fraley T cell line infections with HIV-1 LAI (BRU)
hmyriB36 Vincent Carey YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes
HSMMSingleCell Cole Trapnell Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)
humanStemCell R. Gentleman Human Stem Cells time course experiment
Illumina450ProbeVariants.db Tiffany Morris Annotation Package combining variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes
IlluminaDataTestFiles Kasper Daniel Hansen Illumina microarray files (IDAT) for testing
ind1KG VJ Carey Data from 1000 Genomes, NA19240 (female) chr6 excerpt
iontreeData Mingshu Cao Data provided to show the usage of functions in iontree package
ITALICSData Guillem Rigaill ITALICSData
Iyer517 Vince Carey exprSets for Iyer, Eisen et all 1999 Science paper
JASPAR2014 Ge Tan Data package for JASPAR
KEGGandMetacoreDzPathwaysGEO Gaurav Bhatti Disease Datasets from GEO
KEGGdzPathwaysGEO Gaurav Bhatti KEGG Disease Datasets from GEO
kidpack Wolfgang Huber DKFZ kidney package
leeBamViews VJ Carey leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009
leukemiasEset Sara Aibar Leukemia's microarray gene expression data (expressionSet).
LiebermanAidenHiC2009 Felix Klein Selected data from the HiC paper of E. Lieberman-Aiden et al. in Science (2009)
ListerEtAlBSseq Kamal Kishore BS-seq data of H1 and IMR90 cell line excerpted from Lister et al. 2009
lumiBarnes Pan Du Barnes Benchmark Illumina Tissues Titration Data
LungCancerACvsSCCGEO Adi Laurentiu Tarca A lung cancer dataset that can be used with maPredictDSC package for developing outcome prediction models from Affymetrix CEL files.
LungCancerLines Cory Barr Reads from Two Lung Cancer Cell Lines
lungExpression Robert Scharpf ExpressionSets for Parmigiani et al., 2004 Clinical Cancer Research paper
MafDb.ALL.wgs.phase1.release.v3.20101123 Robert Castelo Minimum allele frequency data from the 1000 Genomes project
MafDb.ESP6500SI.V2.SSA137.dbSNP138 Robert Castelo Minimum allele frequency data from NHLBI ESP
mammaPrintData Luigi Marchionni RGLists from the Glas and Buyse breast cancer studies
maqcExpression4plex Benilton Carvalho Sample Expression Data - MAQC / HG18 - NimbleGen
MAQCsubset VJ Carey Experimental Data Package: MAQCsubset
MAQCsubsetAFX Laurent Gatto MAQC data subset for the Affymetrix platform
MAQCsubsetILM Laurent Gatto MAQC data subset for the Illumina platform
MEDIPSData Lukas Chavez Example data for the MEDIPS package.
MEEBOdata Agnes Paquet MEEBO set and MEEBO controls.
metaMSdata Ron Wehrens Example CDF data for the metaMS package
minfiData Kasper Daniel Hansen Example data for the Illumina Methylation 450k array
miRNATarget Y-h. Taguchi gene target tabale of miRNA for human/mouse used for MiRaGE package
mitoODEdata Gregoire Pau Experimental data associated to the paper "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay" (submitted).
MMDiffBamSubset Gabriele Schweikert Example ChIP-Seq data for the MMDiff package
mosaicsExample Dongjun Chung Example data for the mosaics package, which implements MOSAiCS, a statistical framework to analyze one-sample or two-sample ChIP-seq data
mouse4302barcodevecs Matthew N. McCall mouse4302 data for barcode
MSBdata Wolfgang Huber Data sets for the book 'Modern Statistics for Biology'
msd16s Joseph N. Paulson Healthy and moderate to severe diarrhea 16S expression data
msdata Steffen Neumann Various Mass Spectrometry raw data example files
MUGAExampleData Daniel Gatti Example {M}ouse {U}niversal {G}enotyping {A}rray data for genome reconstruction and quantitative trait locus mapping.
Mulder2012 Xin Wang Predicting functional networks and modules of chromatin factors controlling adult stem cell fate from RNA interference screens
mvoutData VJ Carey affy and illumina raw data for assessing outlier detector performance
NCIgraphData Laurent Jacob Data for the NCIgraph software package
Neve2006 VJ Carey expression and CGH data on breast cancer cell lines
NGScopyData Xiaobei Zhao Subset of BAM files of human tumor and pooled normal sequencing data (Zhao et al. 2014) for the NGScopy package
parathyroid Michael Love RNA-Seq data of primary cultures of parathyroid tumors by Haglund et al., J Clin Endocrinol Metab 2012.
parathyroidSE Michael Love SummarizedExperiment for RNA-Seq of primary cultures of parathyroid tumors by Haglund et al., J Clin Endocrinol Metab 2012.
pasilla Alejandro Reyes 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.
pasillaBamSubset H. Pages Subset of BAM files from "Pasilla" experiment
PathNetData Jason B. Smith Experimental data for the PathNet package
pcaGoPromoter.Hs.hg19 Morten Hansen, pcaGoPromoter.Hs.hg19 is a data package used by pcaGoPromoter
pcaGoPromoter.Mm.mm9 Morten Hansen, pcaGoPromoter.Mm.mm9 is a data package used by pcaGoPromoter
pcaGoPromoter.Rn.rn4 Morten Hansen, pcaGoPromoter.Rn.rn4 is a data package used by pcaGoPromoter
pd.atdschip.tiling Kristof De Beuf Platform Design Info for Affymetrix Atdschip_tiling
pepDat Renan Sauteraud Peptide microarray data package
phastCons100way.UCSC.hg19 Robert Castelo UCSC phastCons conservation scores
ppiData Bioconductor Package Maintainer A package that contains the bait to prey directed graphs for protein-protein interactions.
prebsdata Karolis Uziela Data for 'prebs' package
PREDAsampledata Francesco Ferrari expression and copy number data on clear cell renal carcinoma samples
ProData Xiaochun Li SELDI-TOF data of Breast cancer samples
pRolocdata Laurent Gatto Data accompanying the pRoloc package
pumadata Richard Pearson Various data sets for use with the puma package
PWMEnrich.Dmelanogaster.background Robert Stojnic D. melanogaster background for PWMEnrich
PWMEnrich.Hsapiens.background Robert Stojnic H. sapiens background for PWMEnrich
PWMEnrich.Mmusculus.background Robert Stojnic M. musculus background for PWMEnrich
RforProteomics Laurent Gatto Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication
rheumaticConditionWOLLBOLD Alejandro Quiroz-Zarate Normalized gene expression dataset published by Wollbold et al. [2009] (WOLLBOLD).
RIPSeekerData Alejandro Reyes test data for RIPSeeker
RMassBankData Michael Stravs, Emma Schymanski Test dataset for RMassBank
RNAinteractMAPK Bernd Fischer Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi
RNAseqData.HNRNPC.bam.chr14 H. Pages Aligned reads from RNAseq experiment: Transcription profiling by high throughput sequencing of HNRNPC knockdown and control HeLa cells
RnaSeqTutorial Nicolas Delhomme RNA-Seq Tutorial (EBI Cambridge UK, October 2011)
RRBSdata Katja Hebestreit An RRBS data set with 12 samples and 10,000 simulated DMRs.
rRDPData Michael Hahsler Database for the Default RDP Classifier
RUVnormalizeData Laurent Jacob Gender data for the RUVnormalize package
seqc Yang Liao and Wei Shi RNA-seq data generated from SEQC (MAQC-III) study
seqCNA.annot David Mosen-Ansorena Annotation for the copy number analysis of deep sequencing cancer data with seqCNA
serumStimulation Morten Hansen, serumStimulation is a data package which is used by examples in package pcaGoPromoter
seventyGeneData Luigi Marchionni ExpressionSets from the van't Veer and Van de Vijver breast cancer studies
shinyMethylData Jean-Philippe Fortin Example dataset of input data for shinyMethyl
simpIntLists Kircicegi Korkmaz The package contains BioGRID interactions for various organisms in a simple format
SNAData Denise Scholtens Social Networks Analysis Data Examples
SNAGEEdata David Venet SNAGEE data
SomatiCAData Mengjie Chen An example cancer whole genome sequencing data for the SomatiCA package
SomaticCancerAlterations Julian Gehring Somatic Cancer Alterations
SpikeIn Rafael A. Irizarry Affymetrix Spike-In Experiment Data
SpikeInSubset Rafael A. Irizarry Part of Affymetrix's Spike-In Experiment Data
stemHypoxia Cristobal Fresno Differentiation of Human Embryonic Stem Cells under Hypoxia gene expression dataset by Prado-Lopez et al. (2010)
stjudem Joern Toedling Microarray Data from Yeoh et al. in MACAT format
synapterdata Laurent Gatto Data accompanying the synapter package
TargetScoreData Yue Li TargetScoreData
TargetSearchData Alvaro Cuadros-Inostroza Henning Redestig, Matt Hannah Example GC-MS data for TargetSearch Package
TBX20BamSubset D. Bindreither Subset of BAM files from the "TBX20" experiment
TCGAcrcmiRNA Claudio Isella TCGA CRC 450 miRNA dataset
TCGAcrcmRNA Claudio Isella TCGA CRC 450 mRNA dataset
TCGAMethylation450k Sean Davis The Cancer Genome Atlas Illumina 450k methylation example data
tinesath1cdf Tine Casneuf tinesath1cdf
tinesath1probe Tine Casneuf Probe sequence data for microarrays of type tinesath1
tweeDEseqCountData Juan R Gonzalez RNA-seq count data employed in the vignette of the tweeDEseq package
waveTilingData Kristof De Beuf waveTiling Example Data
XhybCasneuf Tineke Casneuf EBI/PSB cross-hybridisation study package
yeastCC Sandrine Dudoit Spellman et al. (1998) and Pramila/Breeden (2006) yeast cell cycle microarray data
yeastExpData R. Gentleman Yeast Experimental Data
yeastGSData R. Gentleman Yeast Gold Standard Data
yeastNagalakshmi Bioconductor Package Maintainer Yeast genome RNA sequencing data based on Nagalakshmi et. al.
yeastRNASeq J. Bullard Yeast RNA-Seq Experimental Data from Lee et al. 2008
yri1kgv VJ Carey expression + genotype on 79 unrelated YRI individuals
zebrafishRNASeq Davide Risso Zebrafish RNA-Seq Experimental Data from Ferreira et al. (2014)

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