SynMut

DOI: 10.18129/B9.bioc.SynMut  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SynMut.

SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures

Bioconductor version: 3.16

There are increasing demands on designing virus mutants with specific dinucleotide or codon composition. This tool can take both dinucleotide preference and/or codon usage bias into account while designing mutants. It is a powerful tool for in silico designs of DNA sequence mutants.

Author: Haogao Gu [aut, cre], Leo L.M. Poon [led]

Maintainer: Haogao Gu <hggu at connect.hku.hk>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SynMut")

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("SynMut")

 

HTML	R Script	SynMut: Designing Synonymous Mutants for DNA Sequences
PDF		Reference Manual
Text		NEWS

Details

biocViews	ExperimentalDesign, Preprocessing, SequenceMatching, Software
Version	1.14.0
In Bioconductor since	BioC 3.9 (R-3.6) (4 years)
License	GPL-2
Depends
Imports	seqinr, methods, Biostrings, stringr, BiocGenerics
LinkingTo
Suggests	BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc, glue
SystemRequirements
Enhances
URL	https://github.com/Koohoko/SynMut
BugReports	https://github.com/Koohoko/SynMut/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	SynMut_1.14.0.tar.gz
Windows Binary	SynMut_1.14.0.zip
macOS Binary (x86_64)	SynMut_1.14.0.tgz
macOS Binary (arm64)	SynMut_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SynMut
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SynMut
Bioc Package Browser	https://code.bioconductor.org/browse/SynMut/
Package Short Url	https://bioconductor.org/packages/SynMut/
Package Downloads Report	Download Stats