SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures

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Documentation for package ‘SynMut’ version 1.14.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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