AnnotationHub
This is the released version of AnnotationHub; for the devel version, see AnnotationHub.
Client to access AnnotationHub resources
Bioconductor version: Release (3.23)
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 <maintainer at bioconductor.org>
citation("AnnotationHub")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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: AnnotationHub HOW TO's | HTML | R Script |
| Troubleshooting The Hubs | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, GUI, Infrastructure, Software, ThirdPartyClient |
| Version | 4.2.2 |
| In Bioconductor since | BioC 2.12 (R-3.0) (13.5 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 | https://github.com/Bioconductor/AnnotationHub/issues |
See More
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | AnnotationHub_4.2.2.tar.gz |
| Windows Binary (x86_64) | AnnotationHub_4.2.2.zip |
| macOS Binary (big-sur-x86_64) | AnnotationHub_4.2.2.tgz |
| macOS Binary (sonoma-arm64) | AnnotationHub_4.2.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/AnnotationHub |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/AnnotationHub |
| Bioc Package Browser | https://code.bioconductor.org/browse/AnnotationHub/ |
| Package Short Url | https://bioconductor.org/packages/AnnotationHub/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |