AnnotationHub

Client to access AnnotationHub resources

Bioconductor version: Release (3.17)

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 "4.3") 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

Details

biocViews	DataImport, GUI, Infrastructure, Software, ThirdPartyClient
Version	3.8.0
In Bioconductor since	BioC 2.12 (R-3.0) (10.5 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, interactiveDisplayBase
Linking To
Suggests	IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub
System Requirements
Enhances	AnnotationHubData
URL
Bug Reports	https://github.com/Bioconductor/AnnotationHub/issues

Depends On Me	adductomicsR, annotation, AnnotationHubData, EpiTxDb.Hs.hg38, EpiTxDb.Mm.mm10, EpiTxDb.Sc.sacCer3, EuPathDB, ExperimentHub, GenomicState, hipathia, ipdDb, LRcell, MetaGxBreast, MetaGxOvarian, NestLink, octad, org.Mxanthus.db, PANTHER.db, phastCons30way.UCSC.hg38, phastCons35way.UCSC.mm39, phyloP35way.UCSC.mm39, rGenomeTracksData, scMultiome, sequencing, sesameData, synaptome.data, tartare, UCSCRepeatMasker
Imports Me	adductData, AHLRBaseDbs, AHMeSHDbs, AHPathbankDbs, AHPubMedDbs, AHWikipathwaysDbs, alpineData, alternativeSplicingEvents.hg19, alternativeSplicingEvents.hg38, annotatr, atena, BiocHubsShiny, BioImageDbs, biscuiteerData, celldex, chipseqDBData, circRNAprofiler, coMethDMR, crisprScoreData, cTRAP, curatedMetagenomicData, curatedTBData, curatedTCGAData, customCMPdb, depmap, dmrseq, DropletTestFiles, easierData, ENmix, EpiCompare, EpiMix, epimutacions, FieldEffectCrc, FlowSorted.Blood.EPIC, FlowSorted.CordBloodCombined.450k, GenomicDistributionsData, GenomicScores, GRaNIE, grasp2db, GSEABenchmarkeR, gwascat, HCAData, HiContactsData, HMP16SData, HMP2Data, iSEEhub, MACSr, mcsurvdata, MerfishData, meshes, metaboliteIDmapping, MetaGxPancreas, MethReg, msigdb, MSnID, NxtIRFcore, OGRE, ontoProc, psichomics, pwOmics, regutools, REMP, restfulSE, RLHub, RLSeq, scanMiRApp, scAnnotatR, scmeth, scpdata, scRNAseq, scTensor, SFEData, SingleCellMultiModal, singleCellTK, spatialLIBD, SpliceWiz, synaptome.db, TabulaMurisSenisData, TCGAWorkflow, TENxBrainData, TENxBUSData, TENxPBMCData, tuberculosis, tximeta, Ularcirc
Suggests Me	AHEnsDbs, AHMassBank, BgeeCall, BiocOncoTK, BioPlex, Chicago, ChIPpeakAnno, CINdex, clusterProfiler, CNVRanger, COCOA, CoSIAdata, crisprViz, CTCF, DNAshapeR, dupRadar, ELMER, ENCODExplorerData, ensembldb, epiNEM, EpiTxDb, epivizrChart, epivizrData, excluderanges, factR, GenomicRanges, Glimma, GOSemSim, gwascatData, HarmonizedTCGAData, HiCool, maser, MetaboAnnotation, MIRA, MSnbase, multicrispr, nullranges, ontoProcData, OrganismDbi, plotgardener, recountmethylation, satuRn, TCGAbiolinks, TCGAutils, VariantAnnotation, xcore
Links To Me
Build Report

Package Archives

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

Source Package	AnnotationHub_3.8.0.tar.gz
Windows Binary	AnnotationHub_3.8.0.zip
macOS Binary (x86_64)	AnnotationHub_3.8.0.tgz
macOS Binary (arm64)	AnnotationHub_3.8.0.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