AnnotationHub

This is thereleased version of AnnotationHub; for the devel version, seeAnnotationHub.

Client to access AnnotationHub resources

DOI: 10.18129/B9.bioc.AnnotationHub

Bioconductor version: Release (3.22)

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, entercitation("AnnotationHub")):

Installation

To install this package, start R (version "4.5") and enter:

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

For older versions of R, please refer to the appropriateBioconductor 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	4.0.0
In Bioconductor since	BioC 2.12 (R-3.0) (12.5 years)
License	Artistic-2.0
Depends	BiocGenerics(>= 0.15.10),BiocFileCache(>= 2.99.3)
Imports	utils, methods, grDevices,RSQLite,BiocManager,BiocVersion,curl,rappdirs,AnnotationDbi(>= 1.31.19),S4Vectors,httr2,yaml,dplyr,BiocBaseUtils
System Requirements
URL
Bug Reports	https://github.com/Bioconductor/AnnotationHub/issues

Suggests	IRanges,Seqinfo,GenomeInfoDb,GenomicRanges,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	adductomicsR,AnnotationHubData,ExperimentHub,ipdDb,LRcell,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,hpAnnot,org.Mxanthus.db,phastCons30way.UCSC.hg38,phastCons35way.UCSC.mm39,phyloP35way.UCSC.mm39,rGenomeTracksData,synaptome.data,UCSCRepeatMasker,MetaGxBreast,NestLink,scMultiome,sesameData,tartare,annotation,sequencing, OSCA.advanced, OSCA.basic, OSCA.workflows, SingleRBook
Imports Me	annotatr,atena,BiocHubsShiny,BUSpaRse,circRNAprofiler,coMethDMR,cTRAP,customCMPdb,DeconvoBuddies,DMRcate,dmrseq,EpiCompare,EpiMix,epimutacions,epiregulon,gDNAx,GenomicScores,GRaNIE,GSEABenchmarkeR,gwascat,iSEEhub,MACSr,meshes,MetaboAnnotation,methodical,MethReg,Moonlight2R,MSnID,OGRE,ontoProc,orthos,partCNV,psichomics,regutools,REMP,scanMiRApp,scAnnotatR,scmeth,scTensor,shinyDSP,singleCellTK,SpliceWiz,TENET,tximeta,Ularcirc,xCell2,AHLRBaseDbs,AHMeSHDbs,AHPathbankDbs,AHPubMedDbs,AHWikipathwaysDbs,alternativeSplicingEvents.hg19,alternativeSplicingEvents.hg38,CENTREannotation,EPICv2manifest,grasp2db,HPO.db,metaboliteIDmapping,MPO.db,synaptome.db,TENET.AnnotationHub,adductData,BioImageDbs,biscuiteerData,celldex,chipseqDBData,crisprScoreData,curatedMetagenomicData,curatedPCaData,curatedTBData,curatedTCGAData,depmap,DoReMiTra,DropletTestFiles,easierData,FieldEffectCrc,FlowSorted.Blood.EPIC,FlowSorted.CordBloodCombined.450k,GenomicDistributionsData,HCAData,HiBED,HiContactsData,HMP16SData,HMP2Data,mcsurvdata,MerfishData,MetaGxPancreas,MouseAgingData,msigdb,orthosData,ProteinGymR,scpdata,scRNAseq,SFEData,SingleCellMultiModal,spatialLIBD,TabulaMurisSenisData,TENxBrainData,TENxBUSData,TENxPBMCData,tuberculosis,RNAseqQC
Suggests Me	AHMassBank,AlphaMissenseR,autonomics,BgeeCall,Chicago,ChIPpeakAnno,clusterProfiler,CNVRanger,COCOA,crisprViz,DNAshapeR,dupRadar,ELMER,ensembldb,epiNEM,EpiTxDb,epivizrChart,epivizrData,GenomicRanges,Glimma,GOSemSim,LRBaseDbi,maser,MIRA,motifTestR,MSnbase,multicrispr,muscat,nullranges,OrganismDbi,peakCombiner,plotgardener,raer,recountmethylation,satuRn,simona,TCGAbiolinks,TCGAutils,tidyCoverage,VariantAnnotation,xcore,AHEnsDbs,CTCF,ENCODExplorerData,excluderanges,gwascatData,ontoProcData,org.Hbacteriophora.eg.db,BioPlex,ChIPDBData,CoSIAdata,HarmonizedTCGAData,homosapienDEE2CellScore,locuszoomr
Links To Me
Build Report	Build Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source Package	AnnotationHub_4.0.0.tar.gz
Windows Binary (x86_64)	AnnotationHub_3.99.6.zip
macOS Binary (x86_64)	AnnotationHub_4.0.0.tgz
macOS Binary (arm64)	AnnotationHub_4.0.0.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

Movatterモバイル変換

Menu