GenomicFeatures
Query the gene models of a given organism/assembly
Bioconductor version: Release (3.20)
Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a small collection of TxDb objects in the form of ready-to-install TxDb packages for the most commonly studied organisms. Additionally, the user can easily make a TxDb object (or package) for the organism/assembly of their choice by using the tools from the txdbmaker package.
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 | 1.58.0 |
| In Bioconductor since | BioC 2.5 (R-2.10) (15 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0), BiocGenerics(>= 0.51.2), 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_1.58.0.tar.gz |
| Windows Binary (x86_64) | GenomicFeatures_1.58.0.zip (64-bit only) |
| macOS Binary (x86_64) | GenomicFeatures_1.58.0.tgz |
| macOS Binary (arm64) | GenomicFeatures_1.57.1.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 |