Movatterモバイル変換

cubar 1.2.0

• 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.

cubar 1.1.0

• Added options for codon-family level analysis (default,subfamily).

• Improved documentation and GitHub workflow.

cubar 1.0.0

• 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 (Thanks@maltesemike forvaluable suggestions and feedback). The false discovery rate iscontrolled by thefdr 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.

cubar 0.6.0

• Add util functions (codon_optimize &codon_diff)
• Fix url failure of gtRNAdb, which caused remove of cubar from cran:(

cubar 0.5.1

• fix a bug inget_cscg that caused an error when theinput codon frequency matrix has a single row.
• finish unit tests for all functions and internal data.

cubar 0.5.0

• fixed a bug inest_trna_weight. Now zero w values werereplaced with geometric mean (rather than the arithmetic mean) ofnon-zero w values.
• fixed unexpected warnings inest_optimal_codons.
• fixed bugs that update input codon table due todata.table reference semantics.
• added a new vignette explaining the mathematical details ofimplementation.

cubar 0.4.2

• adjust formatting
• fix a typo inget_enc code

cubar 0.4.1

• New vignette for mitochondrial codon usage analysis.
• Fix a bug when inget_enc for non-standard geneticcode.

cubar 0.4.0

• Released to CRAN.

cubar 0.3.2

• Initial CRAN submission.