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Mapping, quantification and variant analysis of sequencing data

Bioconductor version: Release (3.19)

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>, Yang Liao <yang.liao at> and Gordon K Smyth <smyth at>

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


To install this package, start R (version "4.4") 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 2.18.0
In Bioconductor since BioC 2.8 (R-2.13) (13.5 years)
License GPL (>=3)
Imports grDevices, stats, utils, Matrix
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Depends On Me ExCluster
Imports Me APAlyzer, Damsel, diffUTR, dupRadar, FRASER, ribosomeProfilingQC, scPipe, scruff
Suggests Me autonomics, icetea, singleCellTK, SpliceWiz, tidybulk, MetaScope
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Source Package Rsubread_2.18.0.tar.gz
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macOS Binary (x86_64) Rsubread_2.18.0.tgz
macOS Binary (arm64) Rsubread_2.18.0.tgz
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