DOI: 10.18129/B9.bioc.Rsubread    

Subread sequence alignment and counting for R

Bioconductor version: Release (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, Yang Liao and Gordon K Smyth with contributions from Jenny Dai and Timothy Triche, Jr.

Maintainer: Wei Shi <shi at>, Yang Liao <liao at> and Gordon K Smyth <smyth at wehi.EDU.AU>

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


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
BiocManager::install("Rsubread", version = "3.8")

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


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



PDF R Script Rsubread Vignette
PDF SubreadUsersGuide.pdf
PDF   Reference Manual
Text   NEWS


biocViews Alignment, ChIPSeq, GeneExpression, GeneRegulation, GeneticVariability, Genetics, GenomeAnnotation, ImmunoOncology, Preprocessing, QualityControl, RNASeq, SNP, SequenceMatching, Sequencing, Software
Version 1.32.4
In Bioconductor since BioC 2.8 (R-2.13) (8 years)
License GPL-3
Depends On Me chipseqDB, ExCluster, samExploreR
Imports Me dupRadar
Suggests Me icetea, scPipe, scruff, singleCellTK
Links To Me
Build Report  

Package Archives

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

Source Package Rsubread_1.32.4.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) Rsubread_1.32.4.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats
Old Source Packages for BioC 3.8 Source Archive

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