Rbowtie2

DOI: 10.18129/B9.bioc.Rbowtie2    

This is the development version of Rbowtie2; for the stable release version, see Rbowtie2.

An R Wrapper for Bowtie2 and AdapterRemoval

Bioconductor version: Development (3.15)

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

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

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 2.1.0
In Bioconductor since BioC 3.6 (R-3.4) (4 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 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_2.1.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) Rbowtie2_2.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Rbowtie2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Rbowtie2
Package Short Url https://bioconductor.org/packages/Rbowtie2/
Package Downloads Report Download Stats

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