Added functions to analyze amino acid usage.
Added new options IDT and CodonTransformer for codon optimizationand SpliceAI for splice site detection.
Added supported for tRNA weights from tAI package.
New vignette for codon optimization.
Fixed bugs in tAI calculation.
Separated codon-anticodon pairing calculation andvisualization.
Improved documentation for all functions.
Miscellaneous bug fixes and code restructuring.
Added options for codon-family level analysis (default,subfamily).
Improved documentation and GitHub workflow.
est_optimal_codons andget_fop now workon codon frequency matrix like other cubar functions.
codon optimization can be done at both family(amino acid) orsubfamily level now and optimal codons can be estimated for each levelusing either codon bias or gene expression levels (Thanksfdr argument.
There were two RSCU columns (RSCU andrscu) in the output ofest_optimal_codons andget_fop. Now onlyrscu is kept and representsthe RSCU values.
New functions to perform sliding window analysis on codon usage:slide,slide_codon,slide_applyandslide_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 theinput codon frequency matrix has a single row.est_trna_weight. Now zero w values werereplaced with geometric mean (rather than the arithmetic mean) ofnon-zero w values.est_optimal_codons.data.table reference semantics.get_enc codeget_enc for non-standard geneticcode.