rtracklayer
R interface to genome annotation files and the UCSC genome browser
Bioconductor version: Release (3.19)
Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.
Author: Michael Lawrence, Vince Carey, Robert Gentleman
Maintainer: Michael Lawrence <michafla at gene.com>
citation("rtracklayer")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("rtracklayer")
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("rtracklayer")
rtracklayer | R Script | |
Reference Manual | ||
NEWS | Text | |
INSTALL | Text | |
LICENSE | Text |
Details
biocViews | Annotation, DataImport, Software, Visualization |
Version | 1.64.0 |
In Bioconductor since | BioC 2.2 (R-2.7) (16.5 years) |
License | Artistic-2.0 + file LICENSE |
Depends | R (>= 3.5.0), methods, GenomicRanges(>= 1.37.2) |
Imports | XML (>= 1.98-0), BiocGenerics(>= 0.35.3), S4Vectors(>= 0.23.18), IRanges(>= 2.13.13), XVector(>= 0.19.7), GenomeInfoDb(>= 1.15.2), Biostrings(>= 2.47.6), zlibbioc, curl, httr, Rsamtools(>= 1.31.2), GenomicAlignments(>= 1.15.6), BiocIO, tools, restfulr (>= 0.0.13) |
System Requirements | |
URL |
See More
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | rtracklayer_1.64.0.tar.gz |
Windows Binary | rtracklayer_1.64.0.zip |
macOS Binary (x86_64) | rtracklayer_1.64.0.tgz |
macOS Binary (arm64) | rtracklayer_1.64.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/rtracklayer |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/rtracklayer |
Bioc Package Browser | https://code.bioconductor.org/browse/rtracklayer/ |
Package Short Url | https://bioconductor.org/packages/rtracklayer/ |
Package Downloads Report | Download Stats |