yeast_exp

Yeast mRNA FPKM determined from rRNA-depleted (RiboZero) total RNA-Seq libraries. RUN1_0_WT and RUN2_0_WT (0 min after RNA Pol II repression) were averaged and used here.

datasets

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

yeast_exp function

a data.frame with 6717 rows and three columns:<dl>
<dt>gene_id</dt>
<dd>gene ID</dd><dt>gene_name</dt>
<dd>gene name</dd><dt>fpkm</dt>
<dd>mRNA expression level in Fragments per kilobase per million reads</dd>
</dl>

Format

yeast mRNA expression levels — yeast_exp

a data.frame with 6717 rows and three columns:<dl>
<dt>gene_id</dt>
<dd>gene ID</dd>

<dt>gene_name</dt>
<dd>gene name</dd>

<dt>fpkm</dt>
<dd>mRNA expression level in Fragments per kilobase per million reads</dd>


</dl>

yeast_exp: yeast mRNA expression levels

Description

Usage

Arguments

Format

References

Examples