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Bioconductor ExperimentData Packages

Bioconductor version: Development (3.21)

Package Maintainer Title
adductData Josie Hayes Data from untargeted MS of modifications to Cys34 of serum albumin
affycompData Robert D Shear affycomp data
affydata Robert D Shear 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, PGF, PSI) for Testing
Affymoe4302Expr Zhicheng Ji Affymetrix Mouse Genome 430 2.0 Array (GPL1261) Expression Data Package
airway Michael Love RangedSummarizedExperiment 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 Robert D Shear Example of Amplified Data
AneuFinderData Aaron Taudt WGSCS Data for Demonstration Purposes
antiProfilesData Hector Corrada Bravo Normal colon and cancer preprocessed affy data for antiProfile building.
aracne.networks Federico M. Giorgi, Mariano Alvarez ARACNe-inferred gene networks from TCGA tumor datasets
ARRmData Jean-Philippe Fortin Example dataset for normalization of Illumina 450k Methylation data
AshkenazimSonChr21 Who to complain to Annotated variants on the chromosome 21, human genome 19, Ashkenazim Trio son sample
ASICSdata Gaëlle Lefort Example of 1D NMR spectra data for ASICS package
AssessORFData Deepank Korandla Data and Files for the AssessORF Package
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
BeadSorted.Saliva.EPIC Jonah Fisher Illumina EPIC data on BeadSorted child saliva cells
benchmarkfdrData2019 Stephanie Hicks Data and Benchmarking Results from Korthauer and Kimes et al. (2019)
beta7 Jean Yang Rodriguez et al. (2004) Differential Gene Expression by Memory/Effector T Helper Cells Bearing the Gut-Homing Receptor Integrin alpha4 beta7.
BioImageDbs Satoshi Kume Bio- and biomedical imaging dataset for machine learning and deep learning (for ExperimentHub)
BioPlex Ludwig Geistlinger R-side access to BioPlex protein-protein interaction data
biotmleData Nima Hejazi Example experimental microarray data set for the "biotmle" R package
biscuiteerData "Jacob Morrison" Data Package for Biscuiteer
bladderbatch Jeffrey T. Leek Bladder gene expression data illustrating batch effects
blimaTestingData Vojtech Kulvait Data for testing of the package blima.
BloodCancerMultiOmics2017 Malgorzata Oles "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al. - experimental data and complete analysis
bodymapRat Stephanie Hicks Experimental dataset from the rat BodyMap project
breakpointRdata David Porubsky Strand-seq data for demonstration purposes
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).
brgedata Dolors Pelegri-Siso Exposures, Gene Expression and Methylation data for ilustration purpouses
bronchialIL13 Vince Carey time course experiment involving il13
bsseqData Kasper Daniel Hansen Example whole genome bisulfite data for the bsseq package
bugphyzz Samuel Gamboa A harmonized data resource and software for enrichment analysis of microbial physiologies
cancerdata Daniel Kosztyla Development and validation of diagnostic tests from high-dimensional molecular data: Datasets
CardinalWorkflows Kylie A. Bemis Datasets and workflows for the Cardinal MSI
ccdata Alex Pickering Data for Combination Connectivity Mapping (ccmap) Package
CCl4 Audrey Kauffmann Carbon Tetrachloride (CCl4) treated hepatocytes
celarefData Sarah Williams Processed scRNA data for celaref Vignette - cell labelling by reference
celldex Aaron Lun Index of Reference Cell Type Datasets
CellMapperData Brad Nelms Pre-processed data for use with the CellMapper package
cfToolsData Ran Hu ExperimentHub data for the cfTools package
ChAMPdata Yuan Tian Data Packages for ChAMP package
ChimpHumanBrainData Sean Davis Chimp and human brain data package
chipenrich.data Kai Wang Companion package to chipenrich
ChIPexoQualExample Rene Welch Example data for the ChIPexoQual package, which implements a quality control pipeline for ChIP-exo data
chipseqDBData Aaron Lun Data for the chipseqDB Workflow
ChIPXpressData George Wu ChIPXpress Pre-built Databases
chromstaRData Aaron Taudt ChIP-seq data for Demonstration Purposes
CLL Robert Gentleman A Package for CLL Gene Expression Data
CLLmethylation Malgorzata Oles, Andreas Mock Methylation data of primary CLL samples in PACE project
CluMSIDdata Tobias Depke Data for the CluMSID package
clustifyrdatahub Kent Riemondy External data sets for clustifyr in ExperimentHub
cMap2data J. Saez-Rodriguez Connectivity Map (version 2) Data
cnvGSAdata Joseph Lugo 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
CONFESSdata Diana LOW Example dataset for CONFESS package
ConnectivityMap Paul Shannon Functional connections between drugs, genes and diseases as revealed by common gene-expression changes
COPDSexualDimorphism.data J Fah Sathirapongsasuti Data to support sexually dimorphic and COPD differential analysis for gene expression and methylation.
CopyhelpeR Oscar Krijgsman Helper files for CopywriteR
CopyNeutralIMA Xavier Pastor Hostench Copy Neutral Illumina Methylation Arrays
CoSIAdata Amanda D. Clark VST normalized RNA-Sequencing data with annotations for multiple species samples from Bgee
COSMIC.67 Julian Gehring COSMIC.67
CRCL18 Claudio Isella CRC cell line dataset
crisprScoreData Jean-Philippe Fortin Pre-trained models for the crisprScore package
curatedAdipoArray Mahmoud Ahmed A Curated Microarrays Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Under Genetic and Pharmacological Perturbations
curatedAdipoChIP Mahmoud Ahmed A Curated ChIP-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1)
curatedAdipoRNA Mahmoud Ahmed A Curated RNA-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1)
curatedBladderData Markus Riester Bladder Cancer Gene Expression Analysis
curatedBreastData Katie Planey Curated breast cancer gene expression data with survival and treatment information
curatedCRCData Princy Parsana Colorectal Cancer Gene Expression Analysis
curatedMetagenomicData Lucas schiffer Curated Metagenomic Data of the Human Microbiome
curatedOvarianData Levi Waldron Clinically Annotated Data for the Ovarian Cancer Transcriptome
curatedPCaData Teemu Daniel Laajala Curated Prostate Cancer Data
curatedTBData Xutao Wang Curation of existing tuberculosis transcriptomic studies
curatedTCGAData Marcel Ramos Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
CytoMethIC Jacob Fanale DNA methylation-based classification and regression
DAPARdata Samuel Wieczorek Data accompanying the DAPAR and Prostar packages
davidTiling Wolfgang Huber Data and analysis scripts for David, Huber et al. yeast tiling array paper
depmap Laurent Gatto Cancer Dependency Map Data Package
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
DExMAdata Juan Antonio Villatoro-García Data package for DExMA package
diffloopdata Caleb Lareau Example ChIA-PET Datasets for the diffloop Package
diggitdata Mariano Javier Alvarez Example data for the diggit package
DLBCL Marcus Dittrich Diffuse large B-cell lymphoma expression data
DMRcatedata Tim Peters Data Package for DMRcate
DNAZooData Jacques Serizay DNA Zoo data package
DonaPLLP2013 Joseph D. Barry Supplementary data package for Dona et al. (2013) containing example images and tables
dorothea Pau Badia-i-Mompel Collection Of Human And Mouse TF Regulons
dressCheck Vincent Carey data and software for checking Dressman JCO 25(5) 2007
DropletTestFiles Aaron Lun Test Files for Single-Cell Droplet Utilities
DrugVsDiseasedata J. Saez-Rodriguez Drug versus Disease Data
DuoClustering2018 Angelo Duò Data, Clustering Results and Visualization Functions From Duò et al (2018)
DvDdata J. Saez-Rodriguez Drug versus Disease Data
dyebiasexamples Philip Lijnzaad Example data for the dyebias package, which implements the GASSCO method.
easierData Oscar Lapuente-Santana easier internal data and exemplary dataset from IMvigor210CoreBiologies package
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
EGSEAdata Monther Alhamdoosh Gene set collections for the EGSEA package
ELMER.data Tiago Chedraoui Silva Data for the ELMER package
emtdata Malvika D. Kharbanda An ExperimentHub Package for data sets with an Epithelial to Mesenchymal Transition (EMT)
eoPredData Victor Yuan ExperimentHub package containing model data for predicting preeclampsia status for based on plcaental DNA methylation profile
EpiMix.data Yuanning Zheng Data for the EpiMix package
epimutacionsData Leire Abarrategui Data for epimutacions package
EpipwR.data Jackson Barth EpipwR.data: Reference data for EpipwR
estrogen Wolfgang Huber Microarray dataset that can be used as example for 2x2 factorial designs
etec16s Joseph N. Paulson Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment
ewceData Alan Murphy The ewceData package provides reference data required for ewce
faahKO Steffen Neumann Saghatelian et al. (2004) FAAH knockout LC/MS data
fabiaData Sepp Hochreiter Data sets for FABIA (Factor Analysis for Bicluster Acquisition)
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
FieldEffectCrc Christopher Dampier Tumor, tumor-adjacent normal, and healthy colorectal transcriptomes as SummarizedExperiment objects
FIs Herbert Braselmann, Martin Selmansberger Human Functional Interactions (FIs) for splineTimeR package
fission Michael Love RangedSummarizedExperiment 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
flowPloidyData Tyler Smith Example Flow Cytometry Data
FlowSorted.Blood.450k Andrew E Jaffe Illumina HumanMethylation data on sorted blood cell populations
FlowSorted.Blood.EPIC Lucas A. Salas Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells
FlowSorted.CordBlood.450k Shan V. Andrews Illumina 450k data on sorted cord blood cells
FlowSorted.CordBloodCombined.450k Lucas A. Salas Illumina 450k/EPIC data on FACS and MACS umbilical blood cells
FlowSorted.CordBloodNorway.450k kristina gervin Illumina HumanMethylation data on sorted cord 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, one diva xml workspace and the associated fcs files as well as three GatingSets for testing the flowWorkspace, openCyto and CytoML packages.
fourDNData Jacques Serizay 4DN data package
frmaExampleData Matthew N. McCall Frma Example Data
furrowSeg Joseph Barry Furrow Segmentation
gageData Weijun Luo Auxillary data for gage package
gaschYHS Vince Carey ExpressionSet for response of yeast to heat shock and other environmental stresses
gcspikelite Mark Robinson Spike-in data for GC/MS data and methods within flagme
gDNAinRNAseqData Robert Castelo RNA-seq data with different levels of gDNA contamination
gDRtestData Arkadiusz Gladki gDRtestData - R data package with testing dose response data
geneLenDataBase Federico Marini Lengths of mRNA transcripts for a number of genomes
genomationData Vedran Franke Experimental data for showing functionalities of the genomation package
GenomicDistributionsData Kristyna Kupkova Reference data for GenomicDistributions package
GeuvadisTranscriptExpr Malgorzata Nowicka Data package with transcript expression and bi-allelic genotypes from the GEUVADIS project
GIGSEAdata Shijia Zhu Gene set collections for the GIGSEA package
golubEsets Vince Carey exprSets for golub leukemia data
gpaExample Dongjun Chung Example data for the GPA package (Genetic analysis incorporating Pleiotropy and Annotation)
grndata Pau Bellot Synthetic Expression Data for Gene Regulatory Network Inference
GSBenchMark Bahman Afsari Gene Set Benchmark
GSE103322 Mariano Alvarez GEO accession data GSE103322 as a SingleCellExperiment
GSE13015 Darawan Rinchai GEO accession data GSE13015_GPL6106 as a SummarizedExperiment
GSE159526 Victor Yuan Placental cell DNA methylation data from GEO accession GSE159526
GSE62944 Bioconductor Package Maintainer GEO accession data GSE62944 as a SummarizedExperiment
GSVAdata Robert Castelo Data employed in the vignette of the GSVA package
GWASdata Stephanie Gogarten 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
HarmanData Jason Ross Data for the Harman package
HarmonizedTCGAData Tianle Ma Processed Harmonized TCGA Data of Five Selected Cancer Types
HCAData Federico Marini Accessing The Datasets Of The Human Cell Atlas in R/Bioconductor
HCATonsilData Ramon Massoni-Badosa Provide programmatic access to the tonsil cell atlas datasets
HD2013SGI Mike Smith Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping
HDCytoData Lukas M. Weber Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats
healthyControlsPresenceChecker Davide Chicco Dowloads A Gene Expression Dataset From GEO And Checks If It Contains Data Of Healthy Controls Or Not
healthyFlowData Ariful Azad Healthy dataset used by the flowMatch package
HEEBOdata Agnes Paquet HEEBO set and HEEBO controls.
HelloRangesData Michael Lawrence Data for the HelloRanges tutorial vignette
hgu133abarcodevecs Matthew N. McCall hgu133a data for barcode
hgu133plus2barcodevecs Matthew N. McCall hgu133plus2 data for barcode
hgu133plus2CellScore Nancy Mah CellScore Standard Cell Types Expression Dataset [hgu133plus2]
hgu2beta7 Bioconductor Package Maintainer A data package containing annotation data for hgu2beta7
HiBED Ze Zhang HiBED
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
HiContactsData Jacques Serizay HiContacts companion data package
HighlyReplicatedRNASeq Constantin Ahlmann-Eltze Collection of Bulk RNA-Seq Experiments With Many Replicates
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)
HMP16SData Lucas schiffer 16S rRNA Sequencing Data from the Human Microbiome Project
HMP2Data John Stansfield, Ekaterina Smirnova 16s rRNA sequencing data from the Human Microbiome Project 2
homosapienDEE2CellScore Justin Marsh Example Data Package for CellScore
HSMMSingleCell Cole Trapnell Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)
HumanAffyData Brad Nelms GEO accession GSE64985 and ArrayExpress accession E-MTAB-62 as ExpressionSet objects
humanStemCell R. Gentleman Human Stem Cells time course experiment
IHWpaper Nikos Ignatiadis Reproduce figures in IHW paper
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
imcdatasets Nicolas Damond Collection of publicly available imaging mass cytometry (IMC) datasets
ITALICSData Guillem Rigaill ITALICSData
Iyer517 Vince Carey exprSets for Iyer, Eisen et all 1999 Science paper
JASPAR2014 Ge Tan Data package for JASPAR
JASPAR2016 Ge Tan Data package for JASPAR 2016
JohnsonKinaseData Florian Geier Kinase PWMs based on data published by Johnson et al. 2023 and Yaron-Barir et al. 2024
KEGGandMetacoreDzPathwaysGEO Gaurav Bhatti Disease Datasets from GEO
KEGGdzPathwaysGEO Gaurav Bhatti KEGG Disease Datasets from GEO
kidpack Wolfgang Huber DKFZ kidney package
KOdata Shana White LINCS Knock-Out Data Package
leeBamViews VJ Carey leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009
LegATo Aubrey Odom LegATo: Longitudinal mEtaGenomic Analysis Toolkit
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 Mattia Furlan BS-seq data of H1 and IMR90 cell line excerpted from Lister et al. 2009
LRcellTypeMarkers Wenjing Ma Marker gene information for LRcell R Bioconductor package
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 Michael Lawrence Reads from Two Lung Cancer Cell Lines
lungExpression Robert Scharpf ExpressionSets for Parmigiani et al., 2004 Clinical Cancer Research paper
lydata Alex Pickering Example Dataset for crossmeta Package
M3DExampleData Tallulah Andrews M3Drop Example Data
macrophage Michael Love Human macrophage immune response
MACSdata Qiang Hu Test datasets for the MACSr package
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
marinerData Eric Davis ExperimentHub data for the mariner package
mCSEAdata Jordi Martorell Marugán Data package for mCSEA package
mcsurvdata Adria Caballe Mestres Meta cohort survival data
MEDIPSData Lukas Chavez Example data for MEDIPS and QSEA packages
MEEBOdata Agnes Paquet MEEBO set and MEEBO controls.
MerfishData Ludwig Geistlinger Collection of public MERFISH datasets
MetaGxBreast Benjamin Haibe-Kains Transcriptomic Breast Cancer Datasets
MetaGxOvarian Benjamin Haibe-Kains Transcriptomic Ovarian Cancer Datasets
MetaGxPancreas Benjamin Haibe-Kains Transcriptomic Pancreatic Cancer Datasets
metaMSdata Yann Guitton Example CDF data for the metaMS package
MetaScope Aubrey Odom Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data
MethylAidData M. van Iterson MethylAid-summarized data for 2800 Illumina 450k array samples and 2620 EPIC array samples
methylclockData Dolors Pelegri-Siso Data for methylclock package
MethylSeqData Peter Hickey Collection of Public DNA Methylation Sequencing Datasets
MicrobiomeBenchmarkData Samuel Gamboa Datasets for benchmarking in microbiome research
microbiomeDataSets Leo Lahti Experiment Hub based microbiome datasets
microRNAome Matthew N. McCall SummarizedExperiment for the microRNAome project
minfiData Kasper Daniel Hansen Example data for the Illumina Methylation 450k array
minfiDataEPIC Kasper Daniel Hansen Example data for the Illumina Methylation EPIC array
minionSummaryData Mike Smith Summarised MinION sequencing data published by Ashton et al. 2015
miRcompData Matthew N. McCall Data used in the miRcomp package
miRNATarget Y-h. Taguchi gene target tabale of miRNA for human/mouse used for MiRaGE package
MMDiffBamSubset Gabriele Schweikert Example ChIP-Seq data for the MMDiff package
MOFAdata Britta Velten Data package for Multi-Omics Factor Analysis (MOFA)
mosaicsExample Dongjun Chung Example data for the mosaics package, which implements MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data for transcription factor binding and histone modification
mouse4302barcodevecs Matthew N. McCall mouse4302 data for barcode
MouseAgingData Tram Nguyen Multi-omics data access for studies investigating the effects of aging
MouseGastrulationData Jonathan Griffiths Single-Cell -omics Data across Mouse Gastrulation and Early Organogenesis
MouseThymusAgeing Mike Morgan Single-cell Transcriptomics Data of the Ageing Mouse Thymus
msd16s Joseph N. Paulson Healthy and moderate to severe diarrhea 16S expression data
msdata Steffen Neumann, Laurent Gatto Various Mass Spectrometry raw data example files
msigdb Dharmesh D. Bhuva An ExperimentHub Package for the Molecular Signatures Database (MSigDB)
MSMB Wolfgang Huber Data sets for the book 'Modern Statistics for Biology'
msPurityData Thomas N. Lawson Fragmentation spectral libraries and data to test the msPurity package
msqc1 Christian Panse Sigma mix MSQC1 data
mtbls2 Steffen Neumann MetaboLights MTBLS2: Comparative LC/MS-based profiling of silver nitrate-treated Arabidopsis thaliana leaves of wild-type and cyp79B2 cyp79B3 double knockout plants. Böttcher et al. (2004)
MUGAExampleData Daniel Gatti Example {M}ouse {U}niversal {G}enotyping {A}rray data for genome reconstruction and quantitative trait locus mapping.
muleaData Eszter Ari Genes Sets for Functional Enrichment Analysis with the 'mulea' R Package
multiWGCNAdata Dario Tommasini Data Package for multiWGCNA
muscData Helena L. Crowell Multi-sample multi-group scRNA-seq data
mvoutData VJ Carey affy and illumina raw data for assessing outlier detector performance
NanoporeRNASeq Ying Chen Nanopore RNA-Seq Example data
nanotubes Malte Thodberg Mouse nanotube CAGE data
NCIgraphData Laurent Jacob Data for the NCIgraph software package
NestLink Lennart Opitz NestLink an R data package to guide through Engineered Peptide Barcodes for In-Depth Analyzes of Binding Protein Ensembles
NetActivityData Carlos Ruiz-Arenas Data required for getting the gene set scores with NetActivity 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
nullrangesData Michael Love ExperimentHub datasets for the nullranges package
NxtIRFdata Alex Chit Hei Wong Data for NxtIRF
ObMiTi Omar Elashkar Ob/ob Mice Data on Normal and High Fat Diet
oct4 Michael Love Conditional knockdown of OCT4 in mouse ESCs
octad.db E. Chekalin Open Cancer TherApeutic Discovery (OCTAD) database
OMICsPCAdata Subhadeep Das Supporting data for package OMICsPCA
OnassisJavaLibs Eugenia Galeota OnassisJavaLibs, java libraries to run conceptmapper and semantic similarity
optimalFlowData Hristo Inouzhe optimalFlowData
orthosData Panagiotis Papasaikas Data for the orthos package
parathyroidSE Michael Love RangedSummarizedExperiment 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 Hervé Pagès Subset of BAM files from "Pasilla" experiment
PasillaTranscriptExpr Malgorzata Nowicka Data package with transcript expression obtained with kallisto from pasilla knock-down RNA-Seq data from Brooks et al.
PathNetData Ludwig Geistlinger Experimental data for the PathNet package
PCHiCdata Mikhail Spivakov Promoter Capture Hi-C data
pd.atdschip.tiling Kristof De Beuf Platform Design Info for Affymetrix Atdschip_tiling
pepDat Renan Sauteraud Peptide microarray data package
PepsNMRData Manon Martin Datasets for the PepsNMR package
PhyloProfileData Vinh Tran Data package for phylogenetic profile analysis using PhyloProfile tool
plotgardenerData Nicole Kramer Datasets and test data files for the plotgardener package
prebsdata Karolis Uziela Data for 'prebs' package
preciseTADhub Mikhail Dozmorov Pre-trained random forest models obtained using preciseTAD
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 Lisa Breckels Data accompanying the pRoloc package
prostateCancerCamcap Mark Dunning Prostate Cancer Data
prostateCancerGrasso Mark Dunning Prostate Cancer Data
prostateCancerStockholm Mark Dunning Prostate Cancer Data
prostateCancerTaylor Mark Dunning Prostate Cancer Data
prostateCancerVarambally Mark Dunning Prostate Cancer Data
ProteinGymR Tram Nguyen Programmatic access to ProteinGym datasets in R/Bioconductor
ptairData camille Roquencourt PTR-TOF-MS volatolomics raw datasets from exhaled air and cell culture headspace
PtH2O2lipids James Collins P. tricornutum HPLC-ESI-MS Lipid Data from van Creveld et al. (2015)
pumadata Xuejun liu Various data sets for use with the puma package
PWMEnrich.Dmelanogaster.background Diego Diez D. melanogaster background for PWMEnrich
PWMEnrich.Hsapiens.background Diego Diez H. sapiens background for PWMEnrich
PWMEnrich.Mmusculus.background Diego Diez M. musculus background for PWMEnrich
QDNAseq.hg19 Daoud Sie QDNAseq bin annotation for hg19
QDNAseq.mm10 Daoud Sie Bin annotation mm10
qPLEXdata Kamal Kishore Developer Data accompanying qPLEXanalyzer package
QUBICdata Yu Zhang Data employed in the vignette of the QUBIC package
raerdata Kent Riemondy A collection of datasets for use with raer package
rcellminerData Augustin Luna, Vinodh Rajapakse, Fathi Elloumi rcellminerData: Molecular Profiles and Drug Response for the NCI-60 Cell Lines
RcisTarget.hg19.motifDBs.cisbpOnly.500bp Sara Aibar RcisTarget motif databases for human (hg19) - Subset of 4.6k motifs
ReactomeGSA.data Johannes Griss Companion data package for the ReactomeGSA package
RegParallel Kevin Blighe Standard regression functions in R enabled for parallel processing over large data-frames
RforProteomics Laurent Gatto Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication
RGMQLlib Simone Pallotta RGMQLlib, java libraries to run GMQL scala API
rheumaticConditionWOLLBOLD Alejandro Quiroz-Zarate Normalized gene expression dataset published by Wollbold et al. [2009] (WOLLBOLD).
RITANdata Michael Zimmermann This package contains reference annotation and network data sets
RMassBankData Michael Stravs, Emma Schymanski Test dataset for RMassBank
RNAmodR.Data Felix G.M. Ernst Example data for the RNAmodR package
RNAseqData.HNRNPC.bam.chr14 Hervé Pagès Aligned reads from RNAseq experiment: Transcription profiling by high throughput sequencing of HNRNPC knockdown and control HeLa cells
RnaSeqSampleSizeData Shilin Zhao RnaSeqSampleSizeData
RnBeads.hg19 RnBeadsAnnotationCreator RnBeads.hg19
RnBeads.hg38 RnBeads Team RnBeads.hg38
RnBeads.mm10 RnBeads Team RnBeads.mm10
RnBeads.mm9 RnBeadsAnnotationCreator RnBeads.mm9
RnBeads.rn5 RnBeadsAnnotationCreator RnBeads.rn5
RRBSdata Katja Hebestreit An RRBS data set with 12 samples and 10,000 simulated DMRs
rRDPData Michael Hahsler Databases for the Default RDP Classifier
RTCGA.clinical Marcin Kosinski Clinical datasets from The Cancer Genome Atlas Project
RTCGA.CNV Marcin Kosinski CNV (Copy-number variation) datasets from The Cancer Genome Atlas Project
RTCGA.methylation Marcin Kosinski Methylation datasets from The Cancer Genome Atlas Project
RTCGA.miRNASeq Marcin Kosinski miRNASeq datasets from The Cancer Genome Atlas Project
RTCGA.mRNA Marcin Kosinski mRNA datasets from The Cancer Genome Atlas Project
RTCGA.mutations Marcin Kosinski Mutations datasets from The Cancer Genome Atlas Project
RTCGA.PANCAN12 Marcin Kosinski PanCan 12 from Genome Cancer Browser
RTCGA.rnaseq Marcin Kosinski Rna-seq datasets from The Cancer Genome Atlas Project
RTCGA.RPPA Marcin Kosinski RPPA datasets from The Cancer Genome Atlas Project
RUVnormalizeData Laurent Jacob Gender data for the RUVnormalize package
sampleClassifierData Khadija El Amrani Pre-processed data for use with the sampleClassifier package
SBGNview.data Weijun Luo Supporting datasets for SBGNview package
scaeData Ahmad Al Ajami Data Package for SingleCellAlleleExperiment
scanMiRData Pierre-Luc Germain miRNA Affinity models for the scanMiR package
scATAC.Explorer Arrian Gibson-Khademi A Collection of Single-cell ATAC Sequencing Datasets and Corresponding Metadata
SCLCBam Oscar Krijgsman Sequence data from chromosome 4 of a small-cell lung tumor
scMultiome Xiaosai Yao Collection of Public Single-Cell Multiome (scATAC + scRNAseq) Datasets
scpdata Christophe Vanderaa Single-Cell Proteomics Data Package
scRNAseq Aaron Lun Collection of Public Single-Cell RNA-Seq Datasets
scTHI.data Michele Ceccarelli The package contains examples of single cell data used in vignettes and examples of the scTHI package; data contain both tumor cells and immune cells from public dataset of glioma
seq2pathway.data Arjun Kinstlick data set for R package seq2pathway
seqc Yang Liao and Wei Shi RNA-seq data generated from SEQC (MAQC-III) study
serumStimulation Morten Hansen, serumStimulation is a data package which is used by examples in package pcaGoPromoter
sesameData Wanding Zhou Supporting Data for SeSAMe Package
seventyGeneData Luigi Marchionni ExpressionSets from the van't Veer and Van de Vijver breast cancer studies
SFEData Lambda Moses Example SpatialFeatureExperiment datasets
shinyMethylData Jean-Philippe Fortin Example dataset of input data for shinyMethyl
signatureSearchData Brendan Gongol Datasets for signatureSearch package
SimBenchData Yue Cao SimBenchData: a collection of 35 single-cell RNA-seq data covering a wide range of data characteristics
simpIntLists Kircicegi Korkmaz The package contains BioGRID interactions for various organisms in a simple format
Single.mTEC.Transcriptomes Alejandro Reyes Single Cell Transcriptome Data and Analysis of Mouse mTEC cells
SingleCellMultiModal Marcel Ramos Integrating Multi-modal Single Cell Experiment datasets
SingleMoleculeFootprintingData Guido Barzaghi Data supporting the SingleMoleculeFootprinting pkg
smokingMouse Daianna Gonzalez-Padilla Provides access to smokingMouse project data
SNAData Denise Scholtens Social Networks Analysis Data Examples
SNAGEEdata David Venet SNAGEE data
SNPhoodData Christian Arnold Additional and more complex example data for the SNPhood package
SomatiCAData Mengjie Chen An example cancer whole genome sequencing data for the SomatiCA package
SomaticCancerAlterations Julian Gehring Somatic Cancer Alterations
SpatialDatasets Ellis Patrick Collection of spatial omics datasets
spatialDmelxsim Michael Love Spatial allelic expression counts for fly cross embryo
spatialLIBD Leonardo Collado-Torres spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
SpikeIn Robert D Shear Affymetrix Spike-In Experiment Data
SpikeInSubset Robert D Shear Part of Affymetrix's Spike-In Experiment Data
spqnData Yi Wang Data for the spqn package
stemHypoxia Cristobal Fresno Differentiation of Human Embryonic Stem Cells under Hypoxia gene expression dataset by Prado-Lopez et al. (2010)
STexampleData Lukas M. Weber Collection of spatial transcriptomics datasets in SpatialExperiment Bioconductor format
SubcellularSpatialData Dharmesh D. Bhuva Annotated spatial transcriptomics datasets from 10x Xenium, NanoString CosMx and BGI STOmics.
SVM2CRMdata Guidantonio Malagoli Tagliazucchi An example dataset for use with the SVM2CRM package
synapterdata Laurent Gatto Data accompanying the synapter package
systemPipeRdata Thomas Girke systemPipeRdata: Workflow templates and sample data
TabulaMurisData Charlotte Soneson 10x And SmartSeq2 Data From The Tabula Muris Consortium
TabulaMurisSenisData Charlotte Soneson Bulk and single-cell RNA-seq data from the Tabula Muris Senis project
TargetScoreData Yue Li TargetScoreData
TargetSearchData Alvaro Cuadros-Inostroza Example GC-MS data for TargetSearch Package
tartare Christian Panse Raw ground spectra recorded on Thermo Fisher Scientific mass spectrometers
TBX20BamSubset D. Bindreither Subset of BAM files from the "TBX20" experiment
TCGAbiolinksGUI.data Tiago Chedraoui Silva Data for the TCGAbiolinksGUI package
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
TCGAWorkflowData Tiago Chedraoui Silva Data for TCGA Workflow
TENxBrainData Bioconductor Package Maintainer Data from the 10X 1.3 Million Brain Cell Study
TENxBUSData Lambda Moses Single cell dataset from 10x in BUS format
TENxPBMCData Stephanie Hicks PBMC data from 10X Genomics
TENxVisiumData Helena L. Crowell Visium spatial gene expression data by 10X Genomics
TENxXeniumData Matineh Rahmatbakhsh Collection of Xenium spatial data by 10X genomics
timecoursedata Nelle Varoquaux A data package for timecourse RNA-seq and microarray gene expression data sets
TimerQuant Joseph Barry Timer Quantification
tinesath1cdf Tine Casneuf tinesath1cdf
tinesath1probe Tine Casneuf Probe sequence data for microarrays of type tinesath1
tissueTreg Charles Imbusch TWGBS and RNA-seq data from tissue T regulatory cells from mice
TMExplorer Erik Christensen A Collection of Tumour Microenvironment Single-cell RNA Sequencing Datasets and Corresponding Metadata
tofsimsData Lorenz Gerber Import, process and analysis of ToF-SIMS imaging data
topdownrdata Sebastian Gibb Example Files for the topdownr R Package
TransOmicsData Di Xiao A collection of trans-omics datasets across various biological systems
tuberculosis Lucas Schiffer Tuberculosis Gene Expression Data for Machine Learning
TumourMethData Richard Heery A Collection of DNA Methylation Datasets for Human Tumour Samples and Matching Normal Samples
tweeDEseqCountData Dolors Pelegri-Siso RNA-seq count data employed in the vignette of the tweeDEseq package
tximportData Michael Love tximportData
VariantToolsData Michael Lawrence Data for the VariantTools tutorial
VectraPolarisData Wrobel Julia Vectra Polaris and Vectra 3 multiplex single-cell imaging data
vulcandata Federico M. Giorgi VirtUaL ChIP-Seq data Analysis using Networks, dummy dataset
WeberDivechaLCdata Lukas M. Weber Spatially-resolved transcriptomics and single-nucleus RNA-sequencing data from the locus coeruleus (LC) in postmortem human brain samples
WES.1KG.WUGSC Yuchao Jiang Whole Exome Sequencing (WES) of chromosome 22 401st to 500th exon from the 1000 Genomes (1KG) Project by the Washington University Genome Sequencing Center (WUGSC).
WGSmapp Rujin Wang Mappability tracks of Whole-genome Sequencing from the ENCODE Project
xcoredata Maciej Migdał data package for xcore
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
zebrafishRNASeq Davide Risso Zebrafish RNA-Seq Experimental Data from Ferreira et al. (2014)