Rbowtie

DOI: 10.18129/B9.bioc.Rbowtie    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see Rbowtie.

R bowtie wrapper

Bioconductor version: 3.11

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>

Installation

To install this package, start R (version "4.0") 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	1.28.1
In Bioconductor since	BioC 2.12 (R-3.0) (7.5 years)
License	Artistic-2.0 | file LICENSE
Depends
Imports
LinkingTo
Suggests	parallel, BiocStyle, knitr, rmarkdown
SystemRequirements	GNU make
Enhances
URL
Depends On Me	QuasR
Imports Me	MACPET
Suggests Me	eisaR
Links To Me
Build Report

Package Archives

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

Source Package	Rbowtie_1.28.1.tar.gz
Windows Binary	Rbowtie_1.28.1.zip (64-bit only)
macOS 10.13 (High Sierra)	Rbowtie_1.28.1.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	https://bioconductor.org/packages/Rbowtie/
Package Downloads Report	Download Stats