Rhisat2
R Wrapper for HISAT2 Aligner
Bioconductor version: Release (3.20)
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 | 1.22.0 |
| 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_1.22.0.tar.gz |
| Windows Binary (x86_64) | Rhisat2_1.22.0.zip (64-bit only) |
| macOS Binary (x86_64) | Rhisat2_1.22.0.tgz |
| macOS Binary (arm64) | Rhisat2_1.22.0.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 |