Rhisat2

DOI: 10.18129/B9.bioc.Rhisat2    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Rhisat2.

R Wrapper for HISAT2 Aligner

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Rhisat2
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Alignment, Sequencing, Software, SplicedAlignment
Version	1.0.3
In Bioconductor since	BioC 3.9 (R-3.6) (< 6 months)
License	GPL-3
Depends	R (>= 3.6)
Imports	GenomicFeatures, SGSeq, GenomicRanges, methods, utils
LinkingTo
Suggests	testthat, knitr, rmarkdown, BiocStyle
SystemRequirements	GNU make
Enhances
URL	https://github.com/fmicompbio/Rhisat2
BugReports	https://github.com/fmicompbio/Rhisat2/issues
Depends On Me
Imports Me	QuasR
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	Rhisat2_1.0.3.tar.gz
Windows Binary	Rhisat2_1.0.3.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	Rhisat2_1.0.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Rhisat2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Rhisat2
Package Short Url	https://bioconductor.org/packages/Rhisat2/
Package Downloads Report	Download Stats