Rbowtie

DOI: 10.18129/B9.bioc.Rbowtie  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see Rbowtie.

R bowtie wrapper

Bioconductor version: 3.17

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 [aut], Anita Lerch [aut], Michael Stadler [aut, cre]

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

Installation

To install this package, start R (version "4.3") 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	1.40.0
In Bioconductor since	BioC 2.12 (R-3.0) (10.5 years)
License	Artistic-2.0 | file LICENSE
Depends
Imports	utils
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, multicrispr, seqpac
Suggests Me	crisprDesign, eisaR
Links To Me
Build Report

Package Archives

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

Source Package	Rbowtie_1.40.0.tar.gz
Windows Binary	Rbowtie_1.40.0.zip (64-bit only)
macOS Binary (x86_64)	Rbowtie_1.40.0.tgz
macOS Binary (arm64)	Rbowtie_1.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Rbowtie
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Rbowtie
Bioc Package Browser	https://code.bioconductor.org/browse/Rbowtie/
Package Short Url	https://bioconductor.org/packages/Rbowtie/
Package Downloads Report	Download Stats