SynMut

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

SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures

Bioconductor version: 3.21

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>

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

Installation

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

SynMut: Designing Synonymous Mutants for DNA Sequences HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ExperimentalDesign, Preprocessing, SequenceMatching, Software

Version 1.24.0

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

License GPL-2

Depends

Imports seqinr, methods, Biostrings, stringr, BiocGenerics

System Requirements

URL https://github.com/Koohoko/SynMut

Bug Reports https://github.com/Koohoko/SynMut/issues

Suggests BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc, glue

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Package Archives

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

Source Package SynMut_1.24.0.tar.gz

Windows Binary (x86_64) SynMut_1.24.0.zip

macOS Binary (x86_64) SynMut_1.24.0.tgz

macOS Binary (arm64) SynMut_1.24.0.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/

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