Package: SynMut 1.23.0

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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NEWS

# 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-1.23.0(bioc 3.21)SynMut-1.22.0(bioc 3.20)

sequencematching experimentaldesign preprocessing

4.30 score 2 stars 1 scripts 156 downloads 15 exports 37 dependencies

Last updated 2 months agofrom:460f81507c. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 30 2024
R-4.5-win	OK	Nov 30 2024
R-4.5-linux	OK	Nov 30 2024
R-4.4-win	OK	Nov 30 2024
R-4.4-mac	OK	Nov 30 2024
R-4.3-win	OK	Nov 30 2024
R-4.3-mac	OK	Nov 30 2024

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 askpass BiocGenerics Biostrings cli crayon curl generics GenomeInfoDb GenomeInfoDbData glue httr IRanges jsonlite lattice lifecycle magrittr MASS mime nlme openssl pixmap R6 Rcpp RcppArmadillo rlang S4Vectors segmented seqinr sp stringi stringr sys UCSC.utils vctrs XVector zlibbioc

SynMut: Tools for Designing Synonymously Mutated Sequences

Haogao Gu, Leo L.M. Poon, School of Public Health, The University of Hong Kong

Rendered fromSynMut.Rmdusingknitr::rmarkdownon Nov 30 2024.

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