Bioconductor version: Development (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>
To install this package, start R and enter:
To cite this package in a publication, start R and enter:
|R Script||Rsubread Vignette|
|biocViews||Alignment, ChIPSeq, GeneExpression, GeneRegulation, GeneticVariability, Genetics, GenomeAnnotation, Preprocessing, QualityControl, RNASeq, SNP, SequenceMatching, Sequencing, Software|
|In Bioconductor since||BioC 2.8 (R-2.13)|
|Depends On Me|
|Mac OS X 10.6 (Snow Leopard)||Rsubread_1.15.0.tgz|
|Mac OS X 10.9 (Mavericks)|
|Package Downloads Report||Download Stats|
Common Bioconductor workflows include: