Package: SynMut 1.29.0

Haogao Gu

SynMut: SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures

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.

Authors:Haogao Gu [aut, cre], Leo L.M. Poon [led]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SynMut/json (API)

# Install 'SynMut' in R:

install.packages('SynMut', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/koohoko/synmut/issues

On BioConductor:SynMut-1.29.0(bioc 3.24)SynMut-1.28.0(bioc 3.23)

sequencematching experimentaldesign preprocessing

4.30 score 2 stars 10 scripts 364 downloads 15 exports 26 dependencies

Last updated from:b50cc017ec. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	190
linux-devel-x86_64	OK	278
source / vignettes	OK	204
linux-release-x86_64	OK	269
macos-release-arm64	OK	142
macos-oldrel-arm64	OK	125
windows-devel	OK	146
windows-release	OK	167
windows-oldrel	OK	181
wasm-release	OK	148

Exports:codon_dist codon_mimic codon_random codon_to dinu_dist dinu_to get_cu get_dna get_du get_freq get_nu get_region get_rscu input_seq seq_random

Dependencies:ade4 BiocGenerics Biostrings cli crayon generics glue IRanges lattice lifecycle magrittr MASS nlme pixmap Rcpp RcppArmadillo rlang S4Vectors segmented Seqinfo seqinr sp stringi stringr vctrs XVector

SynMut: Tools for Designing Synonymously Mutated Sequences

Rendered fromSynMut.Rmdusingknitr::rmarkdown

Last update: 2019-04-29
Started: 2019-04-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculating the codon usage difference between sequences	codon_dist codon_dist,ANY-method
Mimic a target codon usage bias	codon_mimic codon_mimic,DNAStringSet,DNAStringSet-method codon_mimic,regioned_dna,DNAStringSet-method codon_mimic,regioned_dna,vector-method
Generate random synonymous mutations	codon_random codon_random,DNAStringSet-method codon_random,regioned_dna-method
Maximize or minimize the usage of certain codon.	codon_to codon_to,regioned_dna-method
Calculating the dinucleotide usage difference between sequences	dinu_dist dinu_dist,ANY-method
Maximize or minimize the usage of certain dinucleotide.	dinu_to dinu_to,regioned_dna-method
Get codon usage matrix	get_cu get_cu,DNAStringSet-method get_cu,regioned_dna-method
Get the DNAStringSet data	get_dna get_dna,regioned_dna-method
Get dinucleotide usage matrix	get_du get_du,DNAStringSet-method get_du,regioned_dna-method
Get codon usage frequency of synonymous codons	get_freq get_freq,DNAStringSet-method get_freq,matrix-method get_freq,regioned_dna-method get_freq,vector-method
Get nucleotide usage matrix	get_nu get_nu,DNAStringSet-method get_nu,regioned_dna-method
Get the variable region	get_region get_region,regioned_dna-method
Get Relative Synonymous Codon Usage (rscu) of synonymous codons	get_rscu get_rscu,DNAStringSet-method get_rscu,regioned_dna-method
Import region / constructing regioned_dna object	input_seq input_seq,character-method input_seq,DNAString-method input_seq,DNAStringSet-method
An S4 class to record DNA sequences and variable regions for mutations	regioned_dna-class
Generate 'n' random DNA sequnces of length 'm'	seq_random seq_random,numeric,numeric-method