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Rhisat2

This is the development version of Rhisat2; for the stable release version, see Rhisat2.

R Wrapper for HISAT2 Aligner

Bioconductor version: Development (3.18)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.17.0
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
See More
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_1.17.0.tar.gz
Windows Binary Rhisat2_1.17.0.zip
macOS Binary (x86_64) Rhisat2_1.17.0.tgz
macOS Binary (arm64) Rhisat2_1.17.0.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