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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("rtracklayer")
In most cases, you don't need to download the package archive at all.
rtracklayer
|
This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see rtracklayer.
R interface to genome browsers and their annotation tracks
Bioconductor version: 2.9
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, and BigWig 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 (from within R,
enter citation("rtracklayer")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("rtracklayer")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rtracklayer")
| rtracklayer.pdf | ||
| Reference Manual |
Details
| biocViews | Annotation, DataImport, Software, Visualization |
| Version | 1.14.4 |
| In Bioconductor since | BioC 2.2 (R-2.7) (8 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.7.0), methods, RCurl (>= 1.4-2) |
| Imports | XML (>= 1.98-0), IRanges(>= 1.11.34), GenomicRanges(>= 1.5.42), Biostrings(>= 2.21.12), BSgenome(>= 1.15.17), zlibbioc |
| LinkingTo | IRanges |
| Suggests | humanStemCell, microRNA(>= 1.1.1), genefilter, limma, org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, hgu133plus2.db, Rsamtools |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | EatonEtAlChIPseq, GGtools, r3Cseq |
| Imports Me | ChromHeatMap, geneLenDataBase, GenomicFeatures, GGtools, R453Plus1Toolbox, Rsamtools |
| Suggests Me | biovizBase, GenomicFeatures, GenomicRanges, GGtools, ggtut, ind1KG, MotIV, oneChannelGUI, PICS, R453Plus1Toolbox, Ringo, rMAT, TSSi |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | rtracklayer_1.14.4.tar.gz |
| Windows Binary | rtracklayer_1.14.4.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | |
| Mac OS X 10.9 (Mavericks) | |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/rtracklayer/tree/release-2.9 |
| Package Short Url | http://bioconductor.org/packages/rtracklayer/ |
| Package Downloads Report | Download Stats |
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