Rsubread

DOI: 10.18129/B9.bioc.Rsubread    

Mapping, quantification and variant analysis of sequencing data

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	Alignment, ChIPSeq, GeneExpression, GeneFusionDetection, GeneRegulation, GeneticVariability, Genetics, GenomeAnnotation, ImmunoOncology, IndelDetection, MultipleSequenceAlignment, Preprocessing, QualityControl, RNASeq, SNP, SequenceMatching, Sequencing, SingleCell, Software, VariantAnnotation, VariantDetection
Version	2.6.4
In Bioconductor since	BioC 2.8 (R-2.13) (10.5 years)
License	GPL (>=3)
Depends
Imports	grDevices, stats, utils, Matrix
LinkingTo
Suggests
SystemRequirements
Enhances
URL	http://bioconductor.org/packages/Rsubread
Depends On Me	ExCluster, samExploreR
Imports Me	APAlyzer, diffUTR, dupRadar, FRASER, ribosomeProfilingQC, scruff
Suggests Me	autonomics, icetea, scPipe, singleCellTK, tidybulk
Links To Me
Build Report

Package Archives

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

Source Package	Rsubread_2.6.4.tar.gz
Windows Binary	Rsubread_2.6.4.zip
macOS 10.13 (High Sierra)	Rsubread_2.6.4.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Rsubread
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Rsubread
Package Short Url	https://bioconductor.org/packages/Rsubread/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.13	Source Archive