DOI: 10.18129/B9.bioc.Rhisat2  

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

R Wrapper for HISAT2 Aligner

Bioconductor version: Development (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")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



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biocViews Alignment, Sequencing, Software, SplicedAlignment
Version 1.19.1
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
Suggests testthat, knitr, rmarkdown, BiocStyle
SystemRequirements GNU make
URL https://github.com/fmicompbio/Rhisat2
BugReports 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_1.19.1.tar.gz
Windows Binary Rhisat2_1.19.1.zip (64-bit only)
macOS Binary (x86_64) Rhisat2_1.19.1.tgz
macOS Binary (arm64)
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/
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