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Rsubread

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

Mapping, quantification and variant analysis of sequencing data


Bioconductor version: Development (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 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")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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, GeneFusionDetection, GeneRegulation, GeneticVariability, Genetics, GenomeAnnotation, ImmunoOncology, IndelDetection, MultipleSequenceAlignment, Preprocessing, QualityControl, RNASeq, SNP, SequenceMatching, Sequencing, SingleCell, Software, VariantAnnotation, VariantDetection
Version 2.17.1
In Bioconductor since BioC 2.8 (R-2.13) (13 years)
License GPL (>=3)
Depends
Imports grDevices, stats, utils, Matrix
System Requirements
URL http://bioconductor.org/packages/Rsubread
See More
Suggests
Linking To
Enhances
Depends On Me ExCluster
Imports Me APAlyzer, diffUTR, dupRadar, FRASER, ribosomeProfilingQC, scPipe, scruff
Suggests Me autonomics, icetea, MetaScope, singleCellTK, SpliceWiz, tidybulk
Links To Me
Build Report Build Report

Package Archives

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

Source Package Rsubread_2.17.1.tar.gz
Windows Binary Rsubread_2.17.1.zip
macOS Binary (x86_64) Rsubread_2.17.1.tgz
macOS Binary (arm64) Rsubread_2.17.1.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