Rbowtie

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see Rbowtie.

R bowtie wrapper

Bioconductor version: 3.21

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] ORCID iD ORCID: 0000-0002-2269-4934

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

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

Installation

To install this package, start R (version "4.5") 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")

An introduction to Rbowtie HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Sequencing, Software

Version 1.48.0

In Bioconductor since BioC 2.12 (R-3.0) (12.5 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

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_1.48.0.tar.gz

Windows Binary (x86_64) Rbowtie_1.48.0.zip (64-bit only)

macOS Binary (x86_64) Rbowtie_1.48.0.tgz

macOS Binary (arm64) Rbowtie_1.48.0.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