Rbowtie

DOI: 10.18129/B9.bioc.Rbowtie    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see Rbowtie.

R bowtie wrapper

Bioconductor version: 3.8

This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.

Author: Florian Hahne, Anita Lerch, Michael B Stadler

Maintainer: Michael Stadler <michael.stadler at fmi.ch>

Citation (from within R, enter citation("Rbowtie")):

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("Rbowtie")

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("Rbowtie")

 

HTML R Script An introduction to Rbowtie
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Alignment, Sequencing, Software
Version 1.22.0
In Bioconductor since BioC 2.12 (R-3.0) (6 years)
License Artistic-1.0 | file LICENSE
Depends
Imports
LinkingTo
Suggests parallel, BiocStyle, knitr, rmarkdown
SystemRequirements GNU make
Enhances
URL
Depends On Me QuasR
Imports Me MACPET
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package Rbowtie_1.22.0.tar.gz
Windows Binary Rbowtie_1.22.0.zip
Mac OS X 10.11 (El Capitan) Rbowtie_1.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Rbowtie
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Rbowtie
Package Short Url http://bioconductor.org/packages/Rbowtie/
Package Downloads Report Download Stats

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