AnnotationHub

Client to access AnnotationHub resources

Bioconductor version: Release (3.19)

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 "4.4") and enter:


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

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")

AnnotationHub: Access the AnnotationHub Web Service	HTML	R Script
AnnotationHub: AnnotationHub HOW TO's	HTML	R Script
Troubleshooting The Hubs	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	3.12.0
In Bioconductor since	BioC 2.12 (R-3.0) (11.5 years)
License	Artistic-2.0
Depends	BiocGenerics(>= 0.15.10), BiocFileCache(>= 1.5.1)
Imports	utils, methods, grDevices, RSQLite, BiocManager, BiocVersion, curl, rappdirs, AnnotationDbi(>= 1.31.19), S4Vectors, httr, yaml, dplyr
System Requirements
URL
Bug Reports	https://github.com/Bioconductor/AnnotationHub/issues

Suggests	IRanges, GenomicRanges, GenomeInfoDb, 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	AnnotationHubData, ExperimentHub, LRcell, adductomicsR, hipathia, ipdDb, 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, MetaGxOvarian, NestLink, scMultiome, sesameData, tartare, annotation, sequencing, OSCA.advanced, OSCA.basic, OSCA.workflows, SingleRBook
Imports Me	BiocHubsShiny, DMRcate, EpiMix, GRaNIE, GSEABenchmarkeR, GenomicScores, MACSr, MSnID, MetaboAnnotation, MethReg, Moonlight2R, OGRE, REMP, SpliceWiz, Ularcirc, annotatr, atena, cTRAP, circRNAprofiler, coMethDMR, customCMPdb, dmrseq, epimutacions, epiregulon, gDNAx, gwascat, iSEEhub, meshes, ontoProc, orthos, partCNV, psichomics, pwOmics, regutools, scAnnotatR, scTensor, scanMiRApp, scmeth, singleCellTK, tximeta, AHLRBaseDbs, AHMeSHDbs, AHPathbankDbs, AHPubMedDbs, AHWikipathwaysDbs, alternativeSplicingEvents.hg19, alternativeSplicingEvents.hg38, EPICv2manifest, grasp2db, HPO.db, metaboliteIDmapping, MPO.db, synaptome.db, 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, MetaGxPancreas, MouseAgingData, msigdb, orthosData, RLHub, scpdata, scRNAseq, SFEData, SingleCellMultiModal, spatialLIBD, TabulaMurisSenisData, TENxBrainData, TENxBUSData, TENxPBMCData, tuberculosis, TCGAWorkflow, RNAseqQC, SeedMatchR
Suggests Me	AHMassBank, AlphaMissenseR, BgeeCall, BiocOncoTK, CINdex, CNVRanger, COCOA, ChIPpeakAnno, Chicago, DNAshapeR, ELMER, EpiTxDb, GOSemSim, GenomicRanges, Glimma, HiCool, LRBaseDbi, MIRA, MSnbase, OrganismDbi, TCGAbiolinks, TCGAutils, VariantAnnotation, autonomics, clusterProfiler, crisprViz, dupRadar, ensembldb, epiNEM, epivizrChart, epivizrData, factR, lute, maser, methodical, motifTestR, multicrispr, nullranges, plotgardener, raer, recountmethylation, satuRn, scTensor, simona, tidyCoverage, 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.

Source Package	AnnotationHub_3.12.0.tar.gz
Windows Binary (x86_64)	AnnotationHub_3.12.0.zip
macOS Binary (x86_64)	AnnotationHub_3.12.0.tgz
macOS Binary (arm64)	AnnotationHub_3.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/AnnotationHub
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/AnnotationHub
Bioc Package Browser	https://code.bioconductor.org/browse/AnnotationHub/
Package Short Url	https://bioconductor.org/packages/AnnotationHub/
Package Downloads Report	Download Stats