Rhisat2
R Wrapper for HISAT2 Aligner
Bioconductor version: Release (3.19)
An R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.
Author: Charlotte Soneson [aut, cre]
Maintainer: Charlotte Soneson <charlottesoneson at gmail.com>
Citation (from within R, enter
citation("Rhisat2")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Rhisat2")
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("Rhisat2")
Rhisat2 | HTML | R Script |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | Alignment, Sequencing, Software, SplicedAlignment |
Version | 1.20.0 |
In Bioconductor since | BioC 3.9 (R-3.6) (5.5 years) |
License | GPL-3 |
Depends | R (>= 4.4.0) |
Imports | txdbmaker, SGSeq, GenomicRanges, methods, utils |
System Requirements | GNU make |
URL | https://github.com/fmicompbio/Rhisat2 |
Bug Reports | https://github.com/fmicompbio/Rhisat2/issues |
See More
Suggests | testthat, knitr, rmarkdown, BiocStyle |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | CircSeqAlignTk |
Suggests Me | eisaR, QuasR |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | Rhisat2_1.20.0.tar.gz |
Windows Binary | Rhisat2_1.20.0.zip |
macOS Binary (x86_64) | Rhisat2_1.20.0.tgz |
macOS Binary (arm64) | Rhisat2_1.20.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/Rhisat2 |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Rhisat2 |
Bioc Package Browser | https://code.bioconductor.org/browse/Rhisat2/ |
Package Short Url | https://bioconductor.org/packages/Rhisat2/ |
Package Downloads Report | Download Stats |