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Changelog

Source: NEWS.md

cubar (development version)

cubar 1.2.0

CRAN release: 2025-08-19

  • 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.

cubar 1.1.0

CRAN release: 2024-12-07

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

  • Improved documentation and GitHub workflow.

cubar 1.0.0

CRAN release: 2024-08-01

  • 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.

cubar 0.6.0

CRAN release: 2024-07-04

  • 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 in get_cscg that caused an error when the input codon frequency matrix has a single row.
  • finish unit tests for all functions and internal data.

cubar 0.5.0

CRAN release: 2024-01-09

  • fixed a bug in est_trna_weight. Now zero w values were replaced with geometric mean (rather than the arithmetic mean) of non-zero w values.
  • fixed unexpected warnings in est_optimal_codons.
  • fixed bugs that update input codon table due to data.table reference semantics.
  • added a new vignette explaining the mathematical details of implementation.

cubar 0.4.2

CRAN release: 2023-11-18

  • adjust formatting
  • fix a typo in get_enc code

cubar 0.4.1

  • New vignette for mitochondrial codon usage analysis.
  • Fix a bug when in get_enc for non-standard genetic code.

cubar 0.4.0

CRAN release: 2023-07-17

  • Released to CRAN.

cubar 0.3.2

  • Initial CRAN submission.