Rbowtie2
An R Wrapper for Bowtie2 and AdapterRemoval
Bioconductor version: Release (3.20)
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("Rbowtie2")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | Alignment, Preprocessing, Sequencing, Software |
| Version | 2.12.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (7 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, UMI4Cats, MetaScope |
| 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_2.12.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | Rbowtie2_2.12.0.tgz |
| macOS Binary (arm64) | Rbowtie2_2.11.0.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 |