SynMut

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see SynMut.

SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures


Bioconductor version: 3.11

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 "4.0") 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 1.4.0
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
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package SynMut_1.4.0.tar.gz
Windows Binary SynMut_1.4.0.zip
macOS 10.13 (High Sierra) SynMut_1.4.0.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
Old Source Packages for BioC 3.11 Source Archive