AnnotationHub

DOI: 10.18129/B9.bioc.AnnotationHub    

Client to access AnnotationHub resources

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	AnnotationHub: Access the AnnotationHub Web Service
HTML	R Script	AnnotationHub: AnnotationHub HOW TO's
HTML	R Script	Troubleshooting The Hubs
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, GUI, Infrastructure, Software, ThirdPartyClient
Version	3.4.0
In Bioconductor since	BioC 2.12 (R-3.0) (9.5 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, interactiveDisplayBase, httr, yaml, dplyr
LinkingTo
Suggests	IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub
SystemRequirements
Enhances	AnnotationHubData
URL
BugReports	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, org.Mxanthus.db, PANTHER.db, phastCons30way.UCSC.hg38, ProteomicsAnnotationHubData, rGenomeTracksData, sequencing, sesameData, synaptome.data, tartare, UCSCRepeatMasker
Imports Me	adductData, AHLRBaseDbs, AHMeSHDbs, AHPathbankDbs, AHPubMedDbs, AHWikipathwaysDbs, alpineData, alternativeSplicingEvents.hg19, alternativeSplicingEvents.hg38, annotatr, atena, BioImageDbs, biscuiteerData, celldex, chipseqDBData, circRNAprofiler, coMethDMR, cTRAP, curatedMetagenomicData, curatedTBData, curatedTCGAData, customCMPdb, depmap, dmrseq, DropletTestFiles, easierData, ENmix, EpiCompare, FieldEffectCrc, FlowSorted.Blood.EPIC, FlowSorted.CordBloodCombined.450k, GenomicDistributionsData, GenomicScores, grasp2db, GSEABenchmarkeR, gwascat, HCAData, HMP16SData, HMP2Data, MACSr, mcsurvdata, meshes, metaboliteIDmapping, MetaGxPancreas, MethReg, msigdb, MSnID, NxtIRFcore, OGRE, ontoProc, psichomics, pwOmics, regutools, REMP, restfulSE, RLHub, RLSeq, scanMiRApp, scAnnotatR, scmeth, scpdata, scRNAseq, scTensor, SingleCellMultiModal, spatialLIBD, synaptome.db, TabulaMurisSenisData, TCGAWorkflow, TENxBrainData, TENxBUSData, TENxPBMCData, TSRchitect, tuberculosis, tximeta, Ularcirc
Suggests Me	AHEnsDbs, BgeeCall, BioPlex, Chicago, ChIPpeakAnno, CINdex, clusterProfiler, CNVRanger, COCOA, CTCF, DNAshapeR, dupRadar, ELMER, ENCODExplorerData, ensembldb, epimutacions, epiNEM, EpiTxDb, epivizrChart, epivizrData, excluderanges, GenomicRanges, Glimma, GOSemSim, gwascatData, HarmonizedTCGAData, maser, 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_3.4.0.tar.gz
Windows Binary	AnnotationHub_3.4.0.zip
macOS Binary (x86_64)	AnnotationHub_3.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/AnnotationHub
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/AnnotationHub
Package Short Url	https://bioconductor.org/packages/AnnotationHub/
Package Downloads Report	Download Stats