ExperimentHub

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see ExperimentHub.

Client to access ExperimentHub resources

Bioconductor version: 3.19

This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated metadata, tags and date of modification. The client creates and manages a local cache of files retrieved enabling quick and reproducible access.

Author: Bioconductor Package Maintainer [cre], Martin Morgan [aut], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb], Valerie Oberchain [ctb], Kayla Morrell [ctb], Lori Shepherd [aut]

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("ExperimentHub")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ExperimentHub")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ExperimentHub")

ExperimentHub: Access the ExperimentHub Web Service	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, GUI, Infrastructure, Software, ThirdPartyClient
Version	2.12.0
In Bioconductor since	BioC 3.4 (R-3.3) (8 years)
License	Artistic-2.0
Depends	methods, BiocGenerics(>= 0.15.10), AnnotationHub(>= 3.3.6), BiocFileCache(>= 1.5.1)
Imports	utils, S4Vectors, BiocManager, rappdirs
System Requirements
URL
Bug Reports	https://github.com/Bioconductor/ExperimentHub/issues

Suggests	knitr, BiocStyle, rmarkdown, HubPub, GenomicAlignments
Linking To
Enhances	ExperimentHubData
Depends On Me	LRcell, SeqSQC, adductomicsR, iSEEhub, octad, BeadSorted.Saliva.EPIC, benchmarkfdrData2019, biscuiteerData, bodymapRat, CellMapperData, clustifyrdatahub, CoSIAdata, crisprScoreData, curatedAdipoChIP, CytoMethIC, DMRcatedata, EpiMix.data, ewceData, FlowSorted.Blood.EPIC, FlowSorted.CordBloodCombined.450k, HDCytoData, HiContactsData, HighlyReplicatedRNASeq, HumanAffyData, mcsurvdata, MetaGxBreast, MetaGxOvarian, MetaGxPancreas, multiWGCNAdata, muscData, NanoporeRNASeq, NestLink, nullrangesData, ObMiTi, octad.db, restfulSEData, RNAmodR.Data, scMultiome, scpdata, sesameData, SimBenchData, SpatialDatasets, spatialDmelxsim, STexampleData, tartare, TENxVisiumData, TENxXeniumData, VectraPolarisData, WeberDivechaLCdata
Imports Me	BiocHubsShiny, BloodGen3Module, CBNplot, CTdata, DMRcate, EpiMix, ExperimentHubData, GSEABenchmarkeR, MACSr, MatrixQCvis, MethReg, Moonlight2R, MsDataHub, PhyloProfile, coMethDMR, epimutacions, epiregulon, hpar, m6Aboost, methodical, methylclock, orthos, signatureSearch, singleCellTK, adductData, BioImageDbs, celldex, cfToolsData, chipseqDBData, CLLmethylation, curatedMetagenomicData, curatedPCaData, curatedTBData, curatedTCGAData, depmap, DropletTestFiles, DuoClustering2018, easierData, emtdata, FieldEffectCrc, gDNAinRNAseqData, GenomicDistributionsData, HarmonizedTCGAData, HCAData, HCATonsilData, HMP16SData, HMP2Data, homosapienDEE2CellScore, imcdatasets, JohnsonKinaseData, LRcellTypeMarkers, marinerData, MerfishData, methylclockData, MethylSeqData, microbiomeDataSets, MouseAgingData, MouseGastrulationData, MouseThymusAgeing, msigdb, NxtIRFdata, orthosData, PhyloProfileData, preciseTADhub, raerdata, RLHub, scaeData, scRNAseq, SFEData, signatureSearchData, SingleCellMultiModal, SingleMoleculeFootprintingData, spatialLIBD, TabulaMurisData, TabulaMurisSenisData, TENxBrainData, TENxBUSData, TENxPBMCData, tuberculosis, TumourMethData, xcoredata
Suggests Me	ANF, AnnotationHub, Banksy, CellMapper, DESpace, ELMER, HDF5Array, MsBackendRawFileReader, SPOTlight, SingleMoleculeFootprinting, TCGAbiolinks, TENxIO, Voyager, bambu, celaref, dreamlet, genomicInstability, lute, mariner, missMethyl, multiWGCNA, muscat, nullranges, quantiseqr, rawDiag, rawrr, recountmethylation, standR, xcore, BioPlex, celarefData, curatedAdipoArray, epimutacionsData, GSE103322, GSE13015, GSE159526, GSE62944, muleaData, smokingMouse, SubcellularSpatialData, tissueTreg, TransOmicsData
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ExperimentHub_2.12.0.tar.gz
Windows Binary (x86_64)	ExperimentHub_2.12.0.zip
macOS Binary (x86_64)	ExperimentHub_2.12.0.tgz
macOS Binary (arm64)	ExperimentHub_2.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ExperimentHub
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ExperimentHub
Bioc Package Browser	https://code.bioconductor.org/browse/ExperimentHub/
Package Short Url	https://bioconductor.org/packages/ExperimentHub/
Package Downloads Report	Download Stats