https://github.com/bioconductor-source/synmut
Science Score: 26.0%
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Low similarity (12.9%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- Language: R
- Default Branch: devel
- Size: 1.3 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
SynMut: Tools for Designing Synonymously Mutated Sequences with Different Genomic Signatures
Haogao Gu, Leo L.M. Poon
##### This work was conducted in School of Public Health, The University of Hong Kong under the supervison of Prof. Leo Poon.
Introduction
SynMut designs synonymous mutants for DNA sequences.
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 also works well for desinging mutants with extremely over-/under- represented dinucleotides.
This tool was originally designed for generating recombinant virus sequences in influenza A virus to study the effects of different dinucleotide usage and codon usage, yet the functions provided in this package can be generic to a variety of other biological researches.
Components of the package
Installation
Use the below code to install the package.
```r
Stable version
if (!requireNamespace("BiocManager")) install.packages("BiocManager")
if (!requireNamespace("SynMut")) BiocManager::install("SynMut")
Development version
if (!requireNamespace("devtools")) install.packages("devtools")
if (!requireNamespace("SynMut")) devtools::install_github("Koohoko/SynMut") ```
Example and methods
Details tutorial please refer to the vignette.
The strategies and functionalities of the codom_mimic and dinu_to functions can be found at here.
Find it at Bioconductor
https://bioconductor.org/packages/devel/bioc/html/SynMut.html
Changelog
Changes in version 1.1.5 (2022-06-03) + Enhancement: add other non-standard genetic codes for functions codonrandom, dinuto, codon_mimic.
Changes in version 1.1.4 (2020-11-12) + bug fix: fix for function codon_mimic.
Changes in version 1.1.3 (2019-05-08) + Revise dinu_to.keep algorithm, enhance performance.
Changes in version 1.1.2 (2019-05-08) + Bug fix: "dinuto" ifelse issue in getoptimal_codon.
Changes in version 1.1.1 (2019-05-06) + Bug fix: "dinu_to" fix wrong result with "keep == TRUE" parameter.
Owner
- Name: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
Source code for packages accepted into Bioconductor
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Dependencies
- BiocGenerics * imports
- Biostrings * imports
- methods * imports
- seqinr * imports
- stringr * imports
- BiocManager * suggests
- devtools * suggests
- glue * suggests
- knitr * suggests
- prettydoc * suggests
- rmarkdown * suggests
- testthat * suggests