Rsubread

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Rsubread.

Subread Sequence Alignment and Counting for R


Bioconductor version: 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 (!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

Details

biocViews Alignment, ChIPSeq, GeneExpression, GeneFusionDetection, GeneRegulation, GeneticVariability, Genetics, GenomeAnnotation, ImmunoOncology, IndelDetection, MultipleSequenceAlignment, Preprocessing, QualityControl, RNASeq, SNP, SequenceMatching, Sequencing, Software, VariantAnnotation, VariantDetection
Version 1.34.7
In Bioconductor since BioC 2.8 (R-2.13) (13 years)
License GPL-3
Depends
Imports grDevices, stats, utils
System Requirements
URL http://bioconductor.org/packages/Rsubread
See More
Suggests
Linking To
Enhances
Depends On Me 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_1.34.7.tar.gz
Windows Binary Rsubread_1.34.7.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) Rsubread_1.34.7.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 3.9 Source Archive