Bioconductor - AnnotationHub
Bioconductor 3.22
Software Packages
AnnotationHub
AnnotationHub
This is the
released
version of AnnotationHub; for the devel version, see
AnnotationHub
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
Citation (from within R, enter
citation("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 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
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) (13 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
See More
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
knowYourCG
MACSr
meshes
MetaboAnnotation
methodical
MethReg
Moonlight2R
MSnID
OGRE
ontoProc
orthos
partCNV
psichomics
regutools
REMP
scanMiRApp
scAnnotatR
scmeth
scTensor
shinyDSP
singleCellTK
SpliceWiz
TEKRABber
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
factR
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
easyEWAS
locuszoomr
Links To Me
Build Report
Build Report
Package Archives
Follow
Installation
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
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