Rbowtie
This is the released version of Rbowtie; for the devel version, see Rbowtie.
R bowtie wrapper
Bioconductor version: Release (3.23)
This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.
Author: Florian Hahne [aut], Anita Lerch [aut], Michael Stadler [aut, cre]
Maintainer: Michael Stadler <michael.stadler at fmi.ch>
citation("Rbowtie")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Rbowtie")
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("Rbowtie")| An introduction to Rbowtie | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, Sequencing, Software |
| Version | 1.52.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (13.5 years) |
| License | Artistic-2.0 | file LICENSE |
| Depends | |
| Imports | utils |
| System Requirements | GNU make |
| URL | https://github.com/fmicompbio/Rbowtie |
| Bug Reports | https://github.com/fmicompbio/Rbowtie/issues |
See More
| Suggests | testthat, parallel, BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | QuasR |
| Imports Me | crisprBowtie, multicrispr, seqpac |
| Suggests Me | crisprDesign, eisaR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Rbowtie_1.52.0.tar.gz |
| Windows Binary (x86_64) | Rbowtie_1.52.0.zip |
| macOS Binary (big-sur-x86_64) | Rbowtie_1.52.0.tgz |
| macOS Binary (sonoma-arm64) | Rbowtie_1.52.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Rbowtie |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Rbowtie |
| Bioc Package Browser | https://code.bioconductor.org/browse/Rbowtie/ |
| Package Short Url | https://bioconductor.org/packages/Rbowtie/ |
| Package Downloads Report | Download Stats |