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Bioconductor - AnnotationHub (development version)

AnnotationHub

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

Client to access AnnotationHub resources

Bioconductor version: Development (3.22)

This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with 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("AnnotationHub")): Installation

To install this package, start R (version "4.5") and enter:


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

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

BiocManager::install("AnnotationHub")

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("AnnotationHub")

Details biocViews DataImport, GUI, Infrastructure, Software, ThirdPartyClient Version 3.99.6 In Bioconductor since BioC 2.12 (R-3.0) (12.5 years) License Artistic-2.0 Depends BiocGenerics(>= 0.15.10), BiocFileCache(>= 2.99.3) Imports utils, methods, grDevices, RSQLite, BiocManager, BiocVersion, curl, rappdirs, AnnotationDbi(>= 1.31.19), S4Vectors, httr2, yaml, dplyr System Requirements URL Bug Reports https://github.com/Bioconductor/AnnotationHub/issues See More Suggests IRanges, Seqinfo, GenomeInfoDb, GenomicRanges, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, txdbmaker, MSnbase, mzR, Biostrings, CompoundDb, keras, ensembldb, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub Linking To Enhances AnnotationHubData Depends On Me adductomicsR, AnnotationHubData, ExperimentHub, hipathia, ipdDb, LRcell, octad, AlphaMissense.v2023.hg19, AlphaMissense.v2023.hg38, cadd.v1.6.hg19, cadd.v1.6.hg38, EpiTxDb.Hs.hg38, EpiTxDb.Mm.mm10, EpiTxDb.Sc.sacCer3, EuPathDB, GenomicState, org.Mxanthus.db, phastCons30way.UCSC.hg38, phastCons35way.UCSC.mm39, phyloP35way.UCSC.mm39, rGenomeTracksData, synaptome.data, UCSCRepeatMasker, MetaGxBreast, NestLink, scMultiome, sesameData, tartare, annotation, sequencing, OSCA.advanced, OSCA.basic, OSCA.workflows, SingleRBook Imports Me annotatr, atena, BiocHubsShiny, circRNAprofiler, coMethDMR, cTRAP, customCMPdb, DeconvoBuddies, DMRcate, dmrseq, EpiCompare, EpiMix, epimutacions, epiregulon, gDNAx, GenomicScores, GRaNIE, GSEABenchmarkeR, gwascat, iSEEhub, MACSr, meshes, MetaboAnnotation, methodical, MethReg, Moonlight2R, MSnID, OGRE, ontoProc, orthos, partCNV, psichomics, regutools, REMP, scanMiRApp, scAnnotatR, scmeth, scTensor, shinyDSP, SpliceWiz, TENET, tximeta, Ularcirc, xCell2, AHLRBaseDbs, AHMeSHDbs, AHPathbankDbs, AHPubMedDbs, AHWikipathwaysDbs, alternativeSplicingEvents.hg19, alternativeSplicingEvents.hg38, EPICv2manifest, grasp2db, HPO.db, metaboliteIDmapping, MPO.db, synaptome.db, TENET.AnnotationHub, adductData, BioImageDbs, biscuiteerData, celldex, chipseqDBData, crisprScoreData, curatedMetagenomicData, curatedPCaData, curatedTBData, curatedTCGAData, depmap, DropletTestFiles, easierData, FieldEffectCrc, FlowSorted.Blood.EPIC, FlowSorted.CordBloodCombined.450k, GenomicDistributionsData, HCAData, HiBED, HiContactsData, HMP16SData, HMP2Data, mcsurvdata, MerfishData, MouseAgingData, msigdb, orthosData, ProteinGymR, scpdata, scRNAseq, SFEData, SingleCellMultiModal, spatialLIBD, TabulaMurisSenisData, TENxBrainData, TENxBUSData, TENxPBMCData, tuberculosis, RNAseqQC Suggests Me AHMassBank, AlphaMissenseR, autonomics, BgeeCall, Chicago, ChIPpeakAnno, CINdex, clusterProfiler, CNVRanger, COCOA, crisprViz, DNAshapeR, dupRadar, ELMER, ensembldb, epiNEM, EpiTxDb, epivizrChart, epivizrData, factR, GenomicRanges, Glimma, GOSemSim, HiCool, LRBaseDbi, lute, maser, MIRA, motifTestR, MSnbase, multicrispr, nullranges, OrganismDbi, plotgardener, raer, recountmethylation, satuRn, simona, TCGAbiolinks, TCGAutils, tidyCoverage, VariantAnnotation, xcore, AHEnsDbs, CTCF, ENCODExplorerData, excluderanges, gwascatData, ontoProcData, BioPlex, CoSIAdata, HarmonizedTCGAData, homosapienDEE2CellScore, GeneSelectR, locuszoomr Links To Me Build Report Build Report Package Archives

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

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