Rsubread

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see Rsubread.

Subread sequence alignment and counting for R

Bioconductor version: 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 wehi.edu.au>, Yang Liao <liao at wehi.edu.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 "3.5") and enter:


if (!require("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

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) (13 years)
License	GPL-3
Depends
Imports
System Requirements
URL	http://bioconductor.org/packages/release/bioc/html/Rsubread.html

Suggests
Linking To
Enhances
Depends On Me	chipseqDB, ExCluster, samExploreR
Imports Me	dupRadar
Suggests Me	icetea, scPipe, scruff, singleCellTK
Links To Me
Build Report	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 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 3.8	Source Archive