Rsubread

DOI: 10.18129/B9.bioc.Rsubread    

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

Subread Sequence Alignment and Counting for R

Bioconductor version: Development (3.9)

Alignment, quantification and analysis of second and third generation sequencing data. 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 <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 "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("Rsubread", version = "3.9")

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, Software, VariantAnnotation, VariantDetection
Version 1.33.24
In Bioconductor since BioC 2.8 (R-2.13) (8 years)
License GPL-3
Depends
Imports grDevices, stats, utils
LinkingTo
Suggests
SystemRequirements
Enhances
URL http://bioconductor.org/packages/Rsubread
Depends On Me ExCluster, samExploreR
Imports Me dupRadar
Suggests Me icetea, scPipe, scruff, singleCellTK
Links To Me
Build Report  

Package Archives

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

Source Package Rsubread_1.33.24.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) Rsubread_1.33.24.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 http://bioconductor.org/packages/Rsubread/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: