To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("AnnotationHub")

In most cases, you don't need to download the package archive at all.

AnnotationHub

DOI: 10.18129/B9.bioc.AnnotationHub    

Client to access AnnotationHub resources

Bioconductor version: Release (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 and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("AnnotationHub")

Documentation

HTML R Script AnnotationHub: Access the AnnotationHub Web Service
HTML R Script AnnotationHub: AnnotationHub HOW TO's
HTML R Script AnnotationHub: Creating An AnnotationHub Package
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, GUI, Infrastructure, Software, ThirdPartyClient
Version 2.10.1
In Bioconductor since BioC 2.12 (R-3.0) (4.5 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
LinkingTo
Suggests IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, SummarizedExperiment, ExperimentHub, gdsfmt
SystemRequirements
Enhances AnnotationHubData
URL
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
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
Package Short Url http://bioconductor.org/packages/AnnotationHub/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.6 Source Archive

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