Rbowtie

DOI: 10.18129/B9.bioc.Rbowtie    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see Rbowtie.

R bowtie wrapper

Bioconductor version: 3.15

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 "4.2") and enter:

if (!require("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	1.36.0
In Bioconductor since	BioC 2.12 (R-3.0) (9.5 years)
License	Artistic-2.0 | file LICENSE
Depends
Imports
LinkingTo
Suggests	testthat, parallel, BiocStyle, knitr, rmarkdown
SystemRequirements	GNU make
Enhances
URL	https://github.com/fmicompbio/Rbowtie
BugReports	https://github.com/fmicompbio/Rbowtie/issues
Depends On Me	QuasR
Imports Me	crisprBowtie, MACPET, multicrispr
Suggests Me	eisaR
Links To Me
Build Report

Package Archives

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

Source Package	Rbowtie_1.36.0.tar.gz
Windows Binary	Rbowtie_1.36.0.zip
macOS Binary (x86_64)	Rbowtie_1.36.0.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	https://bioconductor.org/packages/Rbowtie/
Package Downloads Report	Download Stats