GenomicFeatures
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see GenomicFeatures.
Conveniently import and query gene models
Bioconductor version: 3.16
A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.
Author: M. Carlson [aut], H. Pagès [aut, cre], P. Aboyoun [aut], S. Falcon [aut], M. Morgan [aut], D. Sarkar [aut], M. Lawrence [aut], V. Obenchain [aut], S. Arora [ctb], J. MacDonald [ctb], M. Ramos [ctb], S. Saini [ctb], P. Shannon [ctb], L. Shepherd [ctb], D. Tenenbaum [ctb], D. Van Twisk [ctb]
Maintainer: H. Pagès <hpages.on.github at gmail.com>
citation("GenomicFeatures")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GenomicFeatures")
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("GenomicFeatures")| Making and Utilizing TxDb Objects | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software |
| Version | 1.50.4 |
| In Bioconductor since | BioC 2.5 (R-2.10) (14.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0), BiocGenerics(>= 0.1.0), S4Vectors(>= 0.17.29), IRanges(>= 2.13.23), GenomeInfoDb(>= 1.34.7), GenomicRanges(>= 1.31.17), AnnotationDbi(>= 1.41.4) |
| Imports | methods, utils, stats, tools, DBI, RSQLite (>= 2.0), RCurl, XVector(>= 0.19.7), Biostrings(>= 2.47.6), BiocIO, rtracklayer(>= 1.51.5), biomaRt(>= 2.17.1), Biobase(>= 2.15.1) |
| System Requirements | |
| URL | https://bioconductor.org/packages/GenomicFeatures |
| Bug Reports | https://github.com/Bioconductor/GenomicFeatures/issues |
See More
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GenomicFeatures_1.50.4.tar.gz |
| Windows Binary | GenomicFeatures_1.50.4.zip |
| macOS Binary (x86_64) | GenomicFeatures_1.50.4.tgz |
| macOS Binary (arm64) | GenomicFeatures_1.50.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GenomicFeatures |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GenomicFeatures |
| Bioc Package Browser | https://code.bioconductor.org/browse/GenomicFeatures/ |
| Package Short Url | https://bioconductor.org/packages/GenomicFeatures/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.16 | Source Archive |