GenomicFeatures
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see GenomicFeatures.
Conveniently import and query gene models
Bioconductor version: 3.13
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, H. Pagès, P. Aboyoun, S. Falcon, M. Morgan, D. Sarkar, M. Lawrence, V. Obenchain
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
citation("GenomicFeatures")
):
Installation
To install this package, start R (version "4.1") 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 | R Script | |
Reference Manual | ||
NEWS | Text |
Details
biocViews | Annotation, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software |
Version | 1.44.2 |
In Bioconductor since | BioC 2.5 (R-2.10) (14.5 years) |
License | Artistic-2.0 |
Depends | BiocGenerics(>= 0.1.0), S4Vectors(>= 0.17.29), IRanges(>= 2.13.23), GenomeInfoDb(>= 1.25.7), 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_1.44.2.tar.gz |
Windows Binary | GenomicFeatures_1.44.2.zip |
macOS 10.13 (High Sierra) | GenomicFeatures_1.44.2.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 3.13 | Source Archive |