SynMut

DOI: 10.18129/B9.bioc.SynMut    

SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures

Bioconductor version: Release (3.10)

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 "3.6") and enter:

if (!requireNamespace("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 1.2.0
In Bioconductor since BioC 3.9 (R-3.6) (0.5 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_1.2.0.tar.gz
Windows Binary SynMut_1.2.0.zip
Mac OS X 10.11 (El Capitan) SynMut_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SynMut
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SynMut
Package Short Url https://bioconductor.org/packages/SynMut/
Package Downloads Report Download Stats

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