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ExperimentHub

This is the development version of ExperimentHub; for the stable release version, see ExperimentHub.

Client to access ExperimentHub resources


Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews DataImport, GUI, Infrastructure, Software, ThirdPartyClient
Version 2.11.1
In Bioconductor since BioC 3.4 (R-3.3) (7.5 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
See More
Suggests knitr, BiocStyle, rmarkdown, HubPub, GenomicAlignments
Linking To
Enhances ExperimentHubData
Depends On Me adductomicsR, BeadSorted.Saliva.EPIC, benchmarkfdrData2019, biscuiteerData, bodymapRat, CellMapperData, clustifyrdatahub, CoSIA, CoSIAdata, crisprScoreData, curatedAdipoChIP, DMRcatedata, EpiMix.data, ewceData, FlowSorted.Blood.EPIC, FlowSorted.CordBloodCombined.450k, HDCytoData, HiContactsData, HighlyReplicatedRNASeq, HumanAffyData, iSEEhub, LRcell, mcsurvdata, MetaGxBreast, MetaGxOvarian, MetaGxPancreas, multiWGCNAdata, muscData, NanoporeRNASeq, NestLink, nullrangesData, ObMiTi, octad, octad.db, restfulSEData, RNAmodR.Data, scMultiome, scpdata, SeqSQC, sesameData, SimBenchData, SpatialDatasets, spatialDmelxsim, STexampleData, tartare, TENxVisiumData, TENxXeniumData, VectraPolarisData, WeberDivechaLCdata
Imports Me adductData, BiocHubsShiny, BioImageDbs, BloodGen3Module, CBNplot, celldex, cfToolsData, chipseqDBData, CLLmethylation, coMethDMR, CopyNeutralIMA, CTdata, curatedMetagenomicData, curatedPCaData, curatedTBData, curatedTCGAData, depmap, DMRcate, DropletTestFiles, DuoClustering2018, easierData, emtdata, ENmix, EpiMix, epimutacions, ExperimentHubData, FieldEffectCrc, gDNAinRNAseqData, GenomicDistributionsData, GSEABenchmarkeR, HarmonizedTCGAData, HCAData, HCATonsilData, HMP16SData, HMP2Data, hpar, imcdatasets, LRcellTypeMarkers, m6Aboost, MACSr, marinerData, MatrixQCvis, MerfishData, methodical, MethReg, methylclock, methylclockData, MethylSeqData, microbiomeDataSets, MouseGastrulationData, MouseThymusAgeing, MsDataHub, msigdb, NxtIRFdata, orthos, orthosData, PhyloProfile, PhyloProfileData, preciseTADhub, raerdata, restfulSE, RLHub, scRNAseq, SFEData, signatureSearch, signatureSearchData, SingleCellMultiModal, singleCellTK, SingleMoleculeFootprintingData, spatialLIBD, TabulaMurisData, TabulaMurisSenisData, TENxBrainData, TENxBUSData, TENxPBMCData, tuberculosis, TumourMethData, xcoredata
Suggests Me ANF, AnnotationHub, bambu, Banksy, BioPlex, celaref, celarefData, CellMapper, curatedAdipoArray, DEqMS, DESpace, dreamlet, ELMER, epimutacionsData, genomicInstability, GSE103322, GSE13015, GSE159526, GSE62944, HDF5Array, lute, mariner, missMethyl, MsBackendRawFileReader, multiWGCNA, muscat, nullranges, quantiseqr, rawrr, recountmethylation, SingleMoleculeFootprinting, smokingMouse, SPOTlight, standR, TCGAbiolinks, TENxIO, tissueTreg, Voyager, xcore
Links To Me
Build Report Build Report

Package Archives

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

Source Package ExperimentHub_2.11.1.tar.gz
Windows Binary ExperimentHub_2.11.1.zip (64-bit only)
macOS Binary (x86_64) ExperimentHub_2.11.1.tgz
macOS Binary (arm64) ExperimentHub_2.11.1.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