Rbowtie

DOI: 10.18129/B9.bioc.Rbowtie    

This is the development version of Rbowtie; for the stable release version, see Rbowtie.

R bowtie wrapper

Bioconductor version: Development (3.14)

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 "4.1") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.33.0
In Bioconductor since BioC 2.12 (R-3.0) (8.5 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 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_1.33.0.tar.gz
Windows Binary Rbowtie_1.33.0.zip
macOS 10.13 (High Sierra) Rbowtie_1.33.0.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

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