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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("Rsubread")
In most cases, you don't need to download the package archive at all.
Rsubread
Rsubread package: high-performance read alignment, quantification and mutation discovery
Bioconductor version: 3.0
This R package provides powerful and easy-to-use tools for analyzing next-gen sequencing read data. Functions of this package include 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. This package can be used to anlayze data generated from all major sequencing platforms such as Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers. It supports multiple operating systems incluidng Linux, Mac OS X, FreeBSD and Solaris.
Author: Wei Shi and Yang Liao with contributions from Jenny Zhiyin Dai and Timothy Triche, Jr.
Maintainer: Wei Shi <shi at wehi.edu.au>
Citation (from within R,
enter citation("Rsubread")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("Rsubread")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("Rsubread")
| R Script | Rsubread Vignette | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Alignment, ChIPSeq, GeneExpression, GeneRegulation, GeneticVariability, Genetics, GenomeAnnotation, Preprocessing, QualityControl, RNASeq, SNP, SequenceMatching, Sequencing, Software |
| Version | 1.16.1 |
| In Bioconductor since | BioC 2.8 (R-2.13) |
| License | GPL-3 |
| Depends | |
| Imports | |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | http://bioconductor.org/packages/release/bioc/html/Rsubread.html |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | Rsubread_1.16.1.tar.gz |
| Windows Binary | |
| Mac OS X 10.6 (Snow Leopard) | Rsubread_1.16.1.tgz |
| Mac OS X 10.9 (Mavericks) | Rsubread_1.16.1.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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