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AnnotationHub

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

Client to access AnnotationHub resources


Bioconductor version: Development (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")

# 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")
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 3.11.1
In Bioconductor since BioC 2.12 (R-3.0) (11 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
See More
Suggests IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, CompoundDb, keras, ensembldb, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub
Linking To
Enhances AnnotationHubData
Depends On Me adductomicsR, AlphaMissense.v2023.hg19, AlphaMissense.v2023.hg38, annotation, AnnotationHubData, cadd.v1.6.hg19, cadd.v1.6.hg38, 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, alternativeSplicingEvents.hg19, alternativeSplicingEvents.hg38, annotatr, atena, BiocHubsShiny, BioImageDbs, biscuiteerData, celldex, chipseqDBData, circRNAprofiler, coMethDMR, crisprScoreData, cTRAP, curatedMetagenomicData, curatedPCaData, curatedTBData, curatedTCGAData, customCMPdb, depmap, dmrseq, DropletTestFiles, easierData, ENmix, EpiCompare, EpiMix, epimutacions, FieldEffectCrc, FlowSorted.Blood.EPIC, FlowSorted.CordBloodCombined.450k, gDNAx, GenomicDistributionsData, GenomicScores, GRaNIE, grasp2db, GSEABenchmarkeR, gwascat, HCAData, HiBED, HiContactsData, HMP16SData, HMP2Data, HPO.db, iSEEhub, MACSr, mcsurvdata, MerfishData, meshes, MetaboAnnotation, metaboliteIDmapping, MetaGxPancreas, MethReg, Moonlight2R, MPO.db, msigdb, MSnID, OGRE, ontoProc, orthos, orthosData, partCNV, 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, AlphaMissenseR, 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, lute, maser, methodical, MIRA, MSnbase, multicrispr, nullranges, ontoProcData, OrganismDbi, plotgardener, raer, recountmethylation, satuRn, simona, TCGAbiolinks, TCGAutils, tidyCoverage, VariantAnnotation, xcore
Links To Me
Build Report Build Report

Package Archives

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

Source Package AnnotationHub_3.11.1.tar.gz
Windows Binary AnnotationHub_3.11.1.zip
macOS Binary (x86_64) AnnotationHub_3.11.1.tgz
macOS Binary (arm64) AnnotationHub_3.11.1.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