Rhisat2

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see Rhisat2.

R Wrapper for HISAT2 Aligner

Bioconductor version: 3.21

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] ORCID iD ORCID: 0000-0003-3833-2169

Maintainer: Charlotte Soneson <charlottesoneson at gmail.com>

Citation (from within R, enter citation("Rhisat2")):

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Sequencing, Software, SplicedAlignment

Version 1.24.0

In Bioconductor since BioC 3.9 (R-3.6) (6.5 years)

License GPL-3

Depends R (>= 4.4.0)

Imports txdbmaker, SGSeq, GenomicRanges, methods, utils

System Requirements GNU make

URL https://github.com/fmicompbio/Rhisat2

Bug Reports https://github.com/fmicompbio/Rhisat2/issues

Suggests testthat, knitr, rmarkdown, BiocStyle

Linking To

Enhances

Depends On Me

Imports Me CircSeqAlignTk

Suggests Me eisaR, QuasR

Links To Me

Build Report Build Report

Package Archives

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

Source Package Rhisat2_1.24.0.tar.gz

Windows Binary (x86_64) Rhisat2_1.24.0.zip (64-bit only)

macOS Binary (x86_64) Rhisat2_1.24.0.tgz

macOS Binary (arm64) Rhisat2_1.24.0.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