Rhisat2

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see Rhisat2.

R Wrapper for HISAT2 Aligner


Bioconductor version: 3.12

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 "4.0") 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 1.6.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License GPL-3
Depends R (>= 3.6)
Imports GenomicFeatures, 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 QuasR
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Build Report Build Report

Package Archives

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

Source Package Rhisat2_1.6.0.tar.gz
Windows Binary Rhisat2_1.6.0.zip (64-bit only)
macOS 10.13 (High Sierra) Rhisat2_1.6.0.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
Old Source Packages for BioC 3.12 Source Archive