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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 (3.19)

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 "4.4") and enter:


if (!require("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")
An Introduction to Rbowtie2 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, Preprocessing, Sequencing, Software
Version 2.9.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL (>= 3)
Depends R (>= 4.1.0)
Imports magrittr, Rsamtools
System Requirements C++11, GNU make, samtools
URL
See More
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

Package Archives

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

Source Package Rbowtie2_2.9.0.tar.gz
Windows Binary Rbowtie2_2.9.0.zip (64-bit only)
macOS Binary (x86_64) Rbowtie2_2.9.0.tgz
macOS Binary (arm64) Rbowtie2_2.9.0.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