get_aau

Calculate Amino Acid Usage Frequencies of each CDS.

A suite of functions for rapid and flexible analysis of codon
usage bias. It provides in-depth analysis at the codon level, including
relative synonymous codon usage (RSCU), tRNA weight calculations, machine
learning predictions for optimal or preferred codons, and visualization of
codon-anticodon pairing. Additionally, it can calculate various gene-
specific codon indices such as codon adaptation index (CAI), effective
number of codons (ENC), fraction of optimal codons (Fop), tRNA adaptation
index (tAI), mean codon stabilization coefficients (CSCg), and GC contents
(GC/GC3s/GC4d). It also supports both standard and non-standard genetic
code tables found in NCBI, as well as custom genetic code tables.

Hong Zhang

cubar

Codon Usage Bias Analysis

get_aau function

<dl><dt>cf</dt>
<dd>matrix of codon frequencies as calculated by `count_codons()`.</dd>
<dt>codon_table</dt>
<dd>a table of genetic code derived from <code>get_codon_table</code> or
<code>create_codon_table</code>.</dd></dl>

Arguments

Amino Acid Usage — get_aau

<dl>

<dt>cf</dt>
<dd>matrix of codon frequencies as calculated by `count_codons()`.</dd>


<dt>codon_table</dt>
<dd>a table of genetic code derived from <code>get_codon_table</code> or
<code>create_codon_table</code>.</dd>

</dl>

get_aau: Amino Acid Usage

Description

Usage

Value

Arguments

Examples