Rsubread

This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see Rsubread.

Rsubread package: high-performance read alignment, quantification and mutation discovery

Bioconductor version: 3.0

This R package provides powerful and easy-to-use tools for analyzing next-gen sequencing read data. Functions of this package include quality assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. This package can be used to anlayze data generated from all major sequencing platforms such as Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers. It supports multiple operating systems incluidng Linux, Mac OS X, FreeBSD and Solaris.

Author: Wei Shi and Yang Liao with contributions from Jenny Zhiyin Dai and Timothy Triche, Jr.

Maintainer: Wei Shi <shi at wehi.edu.au>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Rsubread")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Rsubread")

Details

Package Archives

Follow Installation instructions to use this package in your R session.