This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Rsubread.
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")
):
To install this package, start R (version "3.6") 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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("Rsubread")
R Script | Rsubread Vignette | |
SubreadUsersGuide.pdf | ||
Reference Manual | ||
Text | NEWS |
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) (8.5 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 |
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 |
Package Short Url | https://bioconductor.org/packages/Rsubread/ |
Package Downloads Report | Download Stats |
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