Rbowtie2

This is the released version of Rbowtie2; for the devel version, see Rbowtie2.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6

An R Wrapper for Bowtie2 and AdapterRemoval

Bioconductor version: Release (3.23)

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")):

Zheng Wei, Wei Zhang. Rbowtie2: An R Wrapper for Bowtie2 and AdapterRemoval. doi:10.18129/B9.bioc.Rbowtie2, R package version 2.18.0, https://bioconductor.org/packages/Rbowtie2.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Preprocessing, Sequencing, Software
Version	2.18.0
In Bioconductor since	BioC 3.6 (R-3.4) (9 years)
License	GPL (>= 3)
Depends	R (>= 4.1.0)
Imports	magrittr, Rsamtools
System Requirements	C++11, GNU make, samtools
URL

Suggests	knitr, testthat (>= 3.0.0), rmarkdown
Linking To
Enhances
Depends On Me
Imports Me	CircSeqAlignTk, esATAC, MetaScope, UMI4Cats
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	Rbowtie2_2.18.0.tar.gz
Windows Binary (x86_64)	Rbowtie2_2.18.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	Rbowtie2_2.18.0.tgz
macOS Binary (sonoma-arm64)	Rbowtie2_2.18.0.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