This package is for version 3.9 of Bioconductor;
for the stable, up-to-date release version, see
AnnotationHub.
Client to access AnnotationHub resources
Bioconductor version: 3.9
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: Martin Morgan [cre], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb], Lori Shepherd [ctb]
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
Citation (from within R, enter citation("AnnotationHub")):
Installation
To install this package, start R (version "3.6") 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: Creating An AnnotationHub Package
HTML
Details
Version
2.16.1
In Bioconductor since
BioC 2.12 (R-3.0) (11 years)
License
Artistic-2.0
Imports
utils, methods, grDevices, RSQLite, BiocManager, curl, rappdirs,
AnnotationDbi(>= 1.31.19),
S4Vectors,
interactiveDisplayBase, httr, yaml, dplyr
System Requirements
See More
Suggests
IRanges,
GenomicRanges,
GenomeInfoDb,
VariantAnnotation,
Rsamtools,
rtracklayer,
BiocStyle, knitr,
AnnotationForge,
rBiopaxParser, RUnit,
GenomicFeatures,
MSnbase,
mzR,
Biostrings,
SummarizedExperiment,
ExperimentHub,
gdsfmt
Linking To
Depends On Me
adductomicsR,
allenpvc,
annotation,
AnnotationHubData,
curatedMetagenomicData,
EuPathDB,
ExperimentHub,
hipathia,
ipdDb,
MetaGxBreast,
MetaGxOvarian,
MetaGxPancreas,
NestLink,
ProteomicsAnnotationHubData,
RefNet,
sequencing,
sesameData
Imports Me
adductData,
alpineData,
alternativeSplicingEvents.hg19,
alternativeSplicingEvents.hg38,
annotatr,
chipseqDBData,
curatedTCGAData,
dmrseq,
ENCODExplorer,
ENmix,
GenomicScores,
grasp2db,
GSEABenchmarkeR,
HCAData,
HMP16SData,
mcsurvdata,
PathwaySplice,
psichomics,
pwOmics,
REMP,
restfulSE,
scmeth,
scTensor,
TCGAWorkflow,
TENxBrainData,
TENxPBMCData,
TSRchitect,
Ularcirc
Suggests Me
AHEnsDbs,
BgeeCall,
Chicago,
CINdex,
clusterProfiler,
CNVRanger,
COCOA,
DNAshapeR,
dupRadar,
ENCODExplorerData,
ensembldb,
epiNEM,
epivizrChart,
epivizrData,
GenomicRanges,
GOSemSim,
gwascat,
HarmonizedTCGAData,
maser,
MIRA,
MSnbase,
OrganismDbi,
Pbase,
VariantAnnotation
Links To Me
Package Archives
Follow Installation instructions to use this package in your R session.
Source Repository
git clone https://git.bioconductor.org/packages/AnnotationHub
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/AnnotationHub