Added functions to analyze amino acid usage.
Added new options IDT and CodonTransformer for codon optimization and 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 and visualization.
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 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.
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