Added options for codon-family level analysis (default, subfamily).
Improved documentation and GitHub workflow.
est_optimal_codons and get_fop now work on codon frequency matrix like
other cubar functions.
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 fdr argument.
There were two RSCU columns (RSCU and rscu) in the output of
est_optimal_codons and get_fop. Now only rscu is kept and represents
the RSCU values.
New functions to perform sliding window analysis on codon usage: slide,
slide_codon, slide_apply and slide_plot.
New function to calculate the deviation from proportionality (Dp) of host
tRNA availability: get_dp.
codon_optimize & codon_diff)get_cscg that caused an error when the input codon frequency
matrix has a single row.est_trna_weight. Now zero w values were replaced with
geometric mean (rather than the arithmetic mean) of non-zero w values.est_optimal_codons.data.table reference
semantics.get_enc codeget_enc for non-standard genetic code.