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Mapping, quantification and variant analysis of sequencing data

Bioconductor version: Release (3.18)

Alignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads.

Author: Wei Shi, Yang Liao and Gordon K Smyth with contributions from Jenny Dai

Maintainer: Wei Shi <wei.shi at onjcri.org.au>, Yang Liao <yang.liao at onjcri.org.au> and Gordon K Smyth <smyth at wehi.edu.au>

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


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


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:

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


biocViews Alignment, ChIPSeq, GeneExpression, GeneFusionDetection, GeneRegulation, GeneticVariability, Genetics, GenomeAnnotation, ImmunoOncology, IndelDetection, MultipleSequenceAlignment, Preprocessing, QualityControl, RNASeq, SNP, SequenceMatching, Sequencing, SingleCell, Software, VariantAnnotation, VariantDetection
Version 2.16.1
In Bioconductor since BioC 2.8 (R-2.13) (13 years)
License GPL (>=3)
Imports grDevices, stats, utils, Matrix
System Requirements
URL http://bioconductor.org/packages/Rsubread
See More
Linking To
Depends On Me ExCluster
Imports Me APAlyzer, diffUTR, dupRadar, FRASER, ribosomeProfilingQC, scPipe, scruff
Suggests Me autonomics, icetea, MetaScope, singleCellTK, SpliceWiz, tidybulk
Links To Me
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Package Archives

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

Source Package Rsubread_2.16.1.tar.gz
Windows Binary Rsubread_2.16.1.zip
macOS Binary (x86_64) Rsubread_2.16.1.tgz
macOS Binary (arm64) Rsubread_2.16.1.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 3.18 Source Archive