slide_codon

<code>slide_codon</code> generates a data.table with start, center, and end columns
 for a sliding window analysis of codons.

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

Mengyue Liu

Bu Zi

slide_codon function

<dl><dt>seq</dt>
<dd>DNAString, the sequence</dd>
<dt>step</dt>
<dd>integer, the step size</dd>
<dt>before</dt>
<dd>integer, the number of codons before the center of a window</dd>
<dt>after</dt>
<dd>integer, the number of codons after the center of a window</dd></dl>

Arguments

sliding window of codons — slide_codon

<dl>

<dt>seq</dt>
<dd>DNAString, the sequence</dd>


<dt>step</dt>
<dd>integer, the step size</dd>


<dt>before</dt>
<dd>integer, the number of codons before the center of a window</dd>


<dt>after</dt>
<dd>integer, the number of codons after the center of a window</dd>

</dl>

slide_codon: sliding window of codons

Description

Usage

Value

Arguments

Examples