RbowtieCuda
This is the development version of RbowtieCuda; for the stable release version, see RbowtieCuda.
An R Wrapper for nvBowtie and nvBWT, a rewritten version of Bowtie2 for cuda
Bioconductor version: Development (3.24)
This package provides an R wrapper for the popular Bowtie2 sequencing read aligner, optimized to run on NVIDIA graphics cards. It includes wrapper functions that enable both genome indexing and alignment to the generated indexes, ensuring high performance and ease of use within the R environment.
Author: c(Jacopo Pantaleoni [aut], Nuno Subtil [aut], Samuel Simon Sanchez [aut], Franck RICHARD [aut, cre], role = c("aut", "cre"))
Maintainer: Franck RICHARD <franck.richard at winstars.net>
citation("RbowtieCuda")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("RbowtieCuda")
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("RbowtieCuda")| An Introduction to RbowtieCuda | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| INSTALL | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, Coverage, Preprocessing, Sequencing, Software |
| Version | 1.5.3 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | BSD_3_clause + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | methods |
| System Requirements | C++20, GNU make, cmake, CUDA Toolkit(>=10), MSVC, libthrust-dev, libcub-dev, gcc, g++ |
| URL | https://github.com/FranckRICHARD01/RbowtieCuda https://belacqua-labo.ovh/bioinformatic/RbowtieCuda |
| Bug Reports | https://github.com/FranckRICHARD01/RbowtieCuda/issues |
See More
| Suggests | knitr, rmarkdown, RUnit, BiocGenerics |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RbowtieCuda_1.5.3.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/RbowtieCuda |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RbowtieCuda |
| Bioc Package Browser | https://code.bioconductor.org/browse/RbowtieCuda/ |
| Package Short Url | https://bioconductor.org/packages/RbowtieCuda/ |
| Package Downloads Report | Download Stats |