SynMut
This is the development version of SynMut; for the stable release version, see SynMut.
SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.29.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 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_1.29.0.tar.gz |
| Windows Binary (x86_64) | SynMut_1.29.0.zip |
| macOS Binary (big-sur-x86_64) | SynMut_1.29.0.tgz |
| macOS Binary (sonoma-arm64) | SynMut_1.29.0.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 |