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 2.10 of Bioconductor; for the stable, up-to-date release version, see rtracklayer.

R interface to genome browsers and their annotation tracks

Bioconductor version: 2.10

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 (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")

PDF rtracklayer

PDF Reference Manual

Text NEWS

Details

biocViews Annotation, DataImport, Software, Visualization

Version 1.16.3

In Bioconductor since BioC 2.2 (R-2.7) (8 years)

License Artistic-2.0

Depends R (>= 2.10), methods, GenomicRanges

Imports XML (>= 1.98-0), BiocGenerics(>= 0.1.0), IRanges(>= 1.13.14), GenomicRanges(>= 1.7.28), Biostrings(>= 2.23.2), BSgenome(>= 1.23.1), zlibbioc, RCurl (>= 1.4-2), Rsamtools(>= 1.7.3)

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

SystemRequirements

Enhances

URL

Depends On Me EatonEtAlChIPseq, r3Cseq

Imports Me ChromHeatMap, FunciSNP.data, geneLenDataBase, GenomicFeatures, ggbio, Gviz, lumi, R453Plus1Toolbox