Rsubread

DOI: 10.18129/B9.bioc.Rsubread    

Subread sequence alignment for R

Bioconductor version: Release (3.6)

Provides powerful and easy-to-use tools for analyzing next-gen sequencing read data. Includes 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. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers.

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

Maintainer: Wei Shi <shi at wehi.edu.au>, Yang Liao <liao at wehi.edu.au> and Gordon K Smyth <smyth 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")

 

PDF	R Script	Rsubread Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, ChIPSeq, GeneExpression, GeneRegulation, GeneticVariability, Genetics, GenomeAnnotation, Preprocessing, QualityControl, RNASeq, SNP, SequenceMatching, Sequencing, Software
Version	1.28.1
In Bioconductor since	BioC 2.8 (R-2.13) (7 years)
License	GPL-3
Depends
Imports
LinkingTo
Suggests
SystemRequirements
Enhances
URL	http://bioconductor.org/packages/release/bioc/html/Rsubread.html
Depends On Me	samExploreR
Imports Me	dupRadar
Suggests Me
Build Report

Package Archives

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

Source Package	Rsubread_1.28.1.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)	Rsubread_1.28.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Rsubread
Package Short Url	http://bioconductor.org/packages/Rsubread/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive