Rhisat2

R Wrapper for HISAT2 Aligner

Bioconductor version: Release (3.17)

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 "4.3") 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	PDF
NEWS	Text
LICENSE	Text

Details

biocViews	Alignment, Sequencing, Software, SplicedAlignment
Version	1.16.0
In Bioconductor since	BioC 3.9 (R-3.6) (4.5 years)
License	GPL-3
Depends	R (>= 4.2)
Imports	GenomicFeatures, SGSeq, GenomicRanges, methods, utils
Linking To
Suggests	testthat, knitr, rmarkdown, BiocStyle
System Requirements	GNU make
Enhances
URL	https://github.com/fmicompbio/Rhisat2
Bug Reports	https://github.com/fmicompbio/Rhisat2/issues

Depends On Me
Imports Me	CircSeqAlignTk
Suggests Me	eisaR, QuasR
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	Rhisat2_1.16.0.tar.gz
Windows Binary	Rhisat2_1.16.0.zip (64-bit only)
macOS Binary (x86_64)	Rhisat2_1.16.0.tgz
macOS Binary (arm64)	Rhisat2_1.16.0.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