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SynMut

SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews ExperimentalDesign, Preprocessing, SequenceMatching, Software
Version 1.18.0
In Bioconductor since BioC 3.9 (R-3.6) (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
See More
Suggests BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc, glue
Linking To
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Build Report Build Report

Package Archives

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

Source Package SynMut_1.18.0.tar.gz
Windows Binary SynMut_1.18.0.zip
macOS Binary (x86_64) SynMut_1.18.0.tgz
macOS Binary (arm64) SynMut_1.18.0.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