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>

Citation (from within R, enter citation("AnnotationHub")):

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

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