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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("AnnotationHub")
In most cases, you don't need to download the package archive at all.
AnnotationHub
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see AnnotationHub.
Client to access AnnotationHub resources
Bioconductor version: 3.3
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("https://bioconductor.org/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 | How to create new AnnotationHub resources |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, GUI, Infrastructure, Software, ThirdPartyClient |
| Version | 2.4.2 |
| In Bioconductor since | BioC 2.12 (R-3.0) (3.5 years) |
| License | Artistic-2.0 |
| Depends | BiocGenerics(>= 0.15.10) |
| Imports | utils, methods, grDevices, RSQLite, BiocInstaller, AnnotationDbi(>= 1.31.19), S4Vectors, interactiveDisplayBase, httr |
| LinkingTo | |
| Suggests | IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, SummarizedExperiment |
| SystemRequirements | |
| Enhances | AnnotationHubData |
| URL | |
| Depends On Me | AnnotationHubData, ProteomicsAnnotationHubData, RefNet |
| Imports Me | ensembldb, grasp2db, gwascat, pwOmics |
| Suggests Me | Chicago, CINdex, clusterProfiler, DNAshapeR, dupRadar, GenomicRanges, OrganismDbi, Pbase, VariantAnnotation |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | AnnotationHub_2.4.2.tar.gz |
| Windows Binary | AnnotationHub_2.4.2.zip |
| Mac OS X 10.9 (Mavericks) | AnnotationHub_2.4.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/AnnotationHub/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/AnnotationHub/ |
| Package Downloads Report | Download Stats |
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