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Rbowtie

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

R bowtie wrapper


Bioconductor version: Development (3.20)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("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")
An introduction to Rbowtie HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Alignment, Sequencing, Software
Version 1.45.0
In Bioconductor since BioC 2.12 (R-3.0) (11 years)
License Artistic-2.0 | file LICENSE
Depends
Imports utils
System Requirements GNU make
URL https://github.com/fmicompbio/Rbowtie
Bug Reports https://github.com/fmicompbio/Rbowtie/issues
See More
Suggests testthat, parallel, BiocStyle, knitr, rmarkdown
Linking To
Enhances
Depends On Me QuasR
Imports Me crisprBowtie, multicrispr, seqpac
Suggests Me crisprDesign, eisaR
Links To Me
Build Report Build Report

Package Archives

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

Source Package Rbowtie_1.45.0.tar.gz
Windows Binary Rbowtie_1.45.0.zip
macOS Binary (x86_64) Rbowtie_1.45.0.tgz
macOS Binary (arm64) Rbowtie_1.45.0.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