rtracklayer
This is the released version of rtracklayer; for the devel version, see rtracklayer.
R interface to genome annotation files and the UCSC genome browser
Bioconductor version: Release (3.23)
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 <lawremi at gmail.com>
citation("rtracklayer")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.72.0 |
| In Bioconductor since | BioC 2.2 (R-2.7) (18.5 years) |
| License | Artistic-2.0 + file LICENSE |
| Depends | R (>= 3.5), 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), Seqinfo, Biostrings(>= 2.77.2), 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_1.72.0.tar.gz |
| Windows Binary (x86_64) | rtracklayer_1.72.0.zip |
| macOS Binary (big-sur-x86_64) | rtracklayer_1.72.0.tgz |
| macOS Binary (sonoma-arm64) | rtracklayer_1.72.0.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 |