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("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 | ||
| 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 |