AnnotationHub

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see AnnotationHub.

Client to access AnnotationHub resources

Bioconductor version: 3.6

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]

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

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

Installation

To install this package, start R (version "3.4") 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

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, GUI, Infrastructure, Software, ThirdPartyClient

Version 2.10.1

In Bioconductor since BioC 2.12 (R-3.0) (11 years)

License Artistic-2.0

Depends BiocGenerics(>= 0.15.10)

Imports utils, methods, grDevices, RSQLite, BiocInstaller, curl, AnnotationDbi(>= 1.31.19), S4Vectors, interactiveDisplayBase, httr, yaml

System Requirements

URL

Suggests IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, SummarizedExperiment, ExperimentHub, gdsfmt

Linking To

Enhances AnnotationHubData

Depends On Me AnnotationHubData, curatedMetagenomicData, ExperimentHub, ProteomicsAnnotationHubData, RefNet

Imports Me alpineData, alternativeSplicingEvents.hg19, annotatr, curatedTCGAData, ensembldb, GenomicScores, grasp2db, gwascat, PathwaySplice, psichomics, pwOmics, REMP, restfulSE, TSRchitect

Suggests Me AHEnsDbs, Chicago, CINdex, clusterProfiler, DNAshapeR, dupRadar, epiNEM, epivizrData, GenomicRanges, GOSemSim, HarmonizedTCGAData, MSnbase, OrganismDbi, Pbase, VariantAnnotation

Links To Me

Build Report Build Report

Package Archives

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

Source Package AnnotationHub_2.10.1.tar.gz

Windows Binary AnnotationHub_2.10.1.zip

Mac OS X 10.11 (El Capitan) AnnotationHub_2.10.1.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

Old Source Packages for BioC 3.6 Source Archive