Rsubread

DOI: 10.18129/B9.bioc.Rsubread    

This is the development version of Rsubread; for the stable release version, see Rsubread.

Subread sequence alignment and counting for R

Bioconductor version: Development (3.8)

Rsubread is a toolbox developed for the analyses of second and third generation sequencing data. It can be used for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. It can be applied to all major sequencing techologies and is suitable for the analysis of both short and long reads.

Author: Wei Shi and Yang Liao with contributions from Gordon K 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>

Citation (from within R, enter citation("Rsubread")):

Installation

To install this package, start R and enter:

if (!require("BiocManager"))
    install.packages("BiocManager")
BiocManager::install("Rsubread", version = "devel")

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 SubreadUsersGuide.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews Alignment, ChIPSeq, GeneExpression, GeneRegulation, GeneticVariability, Genetics, GenomeAnnotation, Preprocessing, QualityControl, RNASeq, SNP, SequenceMatching, Sequencing, Software
Version 1.31.6
In Bioconductor since BioC 2.8 (R-2.13) (7.5 years)
License GPL-3
Depends
Imports
LinkingTo
Suggests
SystemRequirements
Enhances
URL http://bioconductor.org/packages/release/bioc/html/Rsubread.html
Depends On Me chipseqDB, samExploreR
Imports Me dupRadar
Suggests Me icetea, scPipe, singleCellTK
Build Report  

Package Archives

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

Source Package Rsubread_1.31.6.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) Rsubread_1.31.6.tgz
Source Repository git clone https://git.bioconductor.org/packages/Rsubread
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Rsubread
Package Short Url http://bioconductor.org/packages/Rsubread/
Package Downloads Report Download Stats

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