Rbowtie2

DOI: 10.18129/B9.bioc.Rbowtie2  

An R Wrapper for Bowtie2 and AdapterRemoval

Bioconductor version: Release (3.16)

This package provides an R wrapper of the popular bowtie2 sequencing reads aligner and AdapterRemoval, a convenient tool for rapid adapter trimming, identification, and read merging. The package contains wrapper functions that allow for genome indexing and alignment to those indexes. The package also allows for the creation of .bam files via Rsamtools.

Author: Zheng Wei [aut, cre], Wei Zhang [aut]

Maintainer: Zheng Wei <wzweizheng at qq.com>

Citation (from within R, enter citation("Rbowtie2")):

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("Rbowtie2")

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("Rbowtie2")

 

HTML R Script An Introduction to Rbowtie2
PDF   Reference Manual
Text   NEWS

Details

biocViews Alignment, Preprocessing, Sequencing, Software
Version 2.4.2
In Bioconductor since BioC 3.6 (R-3.4) (5.5 years)
License GPL (>= 3)
Depends R (>= 4.1.0)
Imports magrittr, Rsamtools
LinkingTo
Suggests knitr, testthat (>= 3.0.0), rmarkdown
SystemRequirements C++11, GNU make, samtools
Enhances
URL
Depends On Me
Imports Me CircSeqAlignTk, esATAC, UMI4Cats
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package Rbowtie2_2.4.2.tar.gz
Windows Binary Rbowtie2_2.4.2.zip (64-bit only)
macOS Binary (x86_64) Rbowtie2_2.4.2.tgz
macOS Binary (arm64) Rbowtie2_2.4.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/Rbowtie2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Rbowtie2
Bioc Package Browser https://code.bioconductor.org/browse/Rbowtie2/
Package Short Url https://bioconductor.org/packages/Rbowtie2/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.16 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: