GenomicFeatures
Conveniently import and query gene models
Bioconductor version: Release (3.19)
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 "4.4") 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")
Obtaining and Utilizing TxDb Objects | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | Annotation, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software |
Version | 1.56.0 |
In Bioconductor since | BioC 2.5 (R-2.10) (15 years) |
License | Artistic-2.0 |
Depends | R (>= 3.5.0), BiocGenerics(>= 0.1.0), S4Vectors(>= 0.17.29), IRanges(>= 2.37.1), GenomeInfoDb(>= 1.35.8), GenomicRanges(>= 1.55.2), AnnotationDbi(>= 1.41.4) |
Imports | methods, utils, stats, DBI, XVector, Biostrings, rtracklayer |
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_1.56.0.tar.gz |
Windows Binary (x86_64) | GenomicFeatures_1.56.0.zip (64-bit only) |
macOS Binary (x86_64) | GenomicFeatures_1.56.0.tgz |
macOS Binary (arm64) | GenomicFeatures_1.56.0.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 |