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Bioconductor - 3.22 ExperimentData Packages
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 Nicholas Cooley 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 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 MaÅgorzata OleÅ "Drug-perturbation-based stratification of blood cancer" by Dietrich S, OleÅ 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 machine learning models 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-GarcÃa 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 Wolfgang Huber 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 humanHippocampus2024 Christine Hou Access to SRT and snRNA-seq data from spatial_HPC project 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 muSpaData Peiying Cai Multi-sample multi-group spatially resolved transcriptomic 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 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 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 TENET.ExperimentHub Rhie Lab at the University of Southern California Experiment data for the TENET package 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 MigdaÅ 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)
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