Rsubread
Mapping, quantification and variant analysis of sequencing data
Bioconductor version: Release (3.20)
Alignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). 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 <wei.shi at onjcri.org.au>, Yang Liao <yang.liao at onjcri.org.au> and Gordon K Smyth <smyth at wehi.edu.au>
citation("Rsubread")):
Installation
To install this package, start R (version "4.4") 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 | |
| SubreadUsersGuide.pdf | ||
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, ChIPSeq, GeneExpression, GeneFusionDetection, GeneRegulation, GeneticVariability, Genetics, GenomeAnnotation, ImmunoOncology, IndelDetection, MultipleSequenceAlignment, Preprocessing, QualityControl, RNASeq, SNP, SequenceMatching, Sequencing, SingleCell, Software, VariantAnnotation, VariantDetection |
| Version | 2.20.0 |
| In Bioconductor since | BioC 2.8 (R-2.13) (13.5 years) |
| License | GPL (>=3) |
| Depends | |
| Imports | grDevices, stats, utils, Matrix |
| System Requirements | |
| URL | http://bioconductor.org/packages/Rsubread |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | ExCluster |
| Imports Me | APAlyzer, CleanUpRNAseq, Damsel, diffUTR, dupRadar, FRASER, ribosomeProfilingQC, scPipe, scruff |
| Suggests Me | autonomics, icetea, singleCellTK, SpliceWiz, tidybulk, MetaScope |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Rsubread_2.20.0.tar.gz |
| Windows Binary (x86_64) | Rsubread_2.20.0.zip |
| macOS Binary (x86_64) | Rsubread_2.20.0.tgz |
| macOS Binary (arm64) | Rsubread_2.19.6.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 |