Rsubread
This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see Rsubread.
Subread sequence alignment for R
Bioconductor version: 3.6
Provides powerful and easy-to-use tools for analyzing next-gen sequencing read data. Includes quality assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers.
Author: Wei Shi and Yang Liao with contributions from Gordon Smyth, 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("Rsubread")):
Installation
To install this package, start R (version "3.4") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, ChIPSeq, GeneExpression, GeneRegulation, GeneticVariability, Genetics, GenomeAnnotation, Preprocessing, QualityControl, RNASeq, SNP, SequenceMatching, Sequencing, Software |
| Version | 1.28.1 |
| 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 |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | samExploreR |
| Imports Me | dupRadar |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Rsubread_1.28.1.tar.gz |
| Windows Binary | |
| Mac OS X 10.11 (El Capitan) | Rsubread_1.28.1.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 3.6 | Source Archive |