| _version_ | 1866902050449653760 |
|---|---|
| author | Liu, Mengyue Zi, Bu Zhang, Hebin Zhang, Hong |
| author_facet | Liu, Mengyue Zi, Bu Zhang, Hebin Zhang, Hong |
| contents | <ul> <li><p><code>est_optimal_codons</code> and <code>get_fop</code> now work on codon frequency matrices like other cubar functions.</p> </li> <li><p>codon optimization can be done at both family(amino acid) or subfamily level now and optimal codons can be estimated for each level using either codon bias or gene expression levels (Thanks @maltesemike for valuable suggestions and feedback). The false discovery rate is controlled by the <code>fdr</code> argument.</p> </li> <li><p>There were two RSCU columns (<code>RSCU</code> and <code>rscu</code>) in the output of <code>est_optimal_codons</code> and <code>get_fop</code>. Now only <code>rscu</code> is kept and represents the RSCU values.</p> </li> <li><p>New functions to perform sliding window analysis on codon usage: <code>slide</code>, <code>slide_codon</code>, <code>slide_apply</code> and <code>slide_plot</code>.</p> </li> <li><p>New function to calculate the deviation from proportionality (Dp) of host tRNA availability: <code>get_dp</code>.</p> </li> </ul> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_13148855 |
| institution | Zenodo |
| language | |
| publishDate | 2024 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | cubar: a versatile package for codon usage bias analysis in R Liu, Mengyue Zi, Bu Zhang, Hebin Zhang, Hong <ul> <li><p><code>est_optimal_codons</code> and <code>get_fop</code> now work on codon frequency matrices like other cubar functions.</p> </li> <li><p>codon optimization can be done at both family(amino acid) or subfamily level now and optimal codons can be estimated for each level using either codon bias or gene expression levels (Thanks @maltesemike for valuable suggestions and feedback). The false discovery rate is controlled by the <code>fdr</code> argument.</p> </li> <li><p>There were two RSCU columns (<code>RSCU</code> and <code>rscu</code>) in the output of <code>est_optimal_codons</code> and <code>get_fop</code>. Now only <code>rscu</code> is kept and represents the RSCU values.</p> </li> <li><p>New functions to perform sliding window analysis on codon usage: <code>slide</code>, <code>slide_codon</code>, <code>slide_apply</code> and <code>slide_plot</code>.</p> </li> <li><p>New function to calculate the deviation from proportionality (Dp) of host tRNA availability: <code>get_dp</code>.</p> </li> </ul> |
| title | cubar: a versatile package for codon usage bias analysis in R |
| url | https://doi.org/10.5281/zenodo.13148855 |