Rsubread

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see Rsubread.

Subread sequence alignment and counting for R


Bioconductor version: 3.7

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 it 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 (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Rsubread")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("Rsubread")
Rsubread Vignette PDF R Script
SubreadUsersGuide.pdf PDF
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, ChIPSeq, GeneExpression, GeneRegulation, GeneticVariability, Genetics, GenomeAnnotation, Preprocessing, QualityControl, RNASeq, SNP, SequenceMatching, Sequencing, Software
Version 1.30.9
In Bioconductor since BioC 2.8 (R-2.13) (13 years)
License GPL-3
Depends
Imports
System Requirements
URL http://bioconductor.org/packages/release/bioc/html/Rsubread.html
See More
Suggests
Linking To
Enhances
Depends On Me chipseqDB, samExploreR
Imports Me dupRadar
Suggests Me singleCellTK
Links To Me
Build Report Build Report

Package Archives

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

Source Package Rsubread_1.30.9.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) Rsubread_1.30.9.tgz
Source Repository git clone https://git.bioconductor.org/packages/Rsubread
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Rsubread
Bioc Package Browser https://code.bioconductor.org/browse/Rsubread/
Package Short Url https://bioconductor.org/packages/Rsubread/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive