cubar - Release v1.2.0

What's Changed

• New vignette on codon optimization
• Fix bugs in functions, add functions on amino acid usage and sequence sequence optimization, and add tests by @creaturemoon in https://github.com/mt1022/cubar/pull/13
• Add functions on codon-anticodon pairs and fix bugs in tAI calculations by @creaturemoon in https://github.com/mt1022/cubar/pull/17
• Add functions on amino acid usage and modify the format of the code by @creaturemoon in https://github.com/mt1022/cubar/pull/18
• Integrate IDT, CodonTransformer, SpliceAI and tAI package weights by @creaturemoon in https://github.com/mt1022/cubar/pull/19
• Add details on the output of the functions by @creaturemoon in https://github.com/mt1022/cubar/pull/20

Full Changelog: https://github.com/mt1022/cubar/compare/v1.1.0...v1.2.0

- R
Published by mt1022 7 months ago

cubar - Release v1.1.0

What's Changed

• Function update by @creaturemoon in https://github.com/mt1022/cubar/pull/8
• fix typo by @creaturemoon in https://github.com/mt1022/cubar/pull/9

New Contributors

• @creaturemoon made their first contribution in https://github.com/mt1022/cubar/pull/8

Full Changelog: https://github.com/mt1022/cubar/compare/v1.0.0...v1.1.0

- R
Published by mt1022 about 1 year ago

cubar - Release v1.0.0

• est_optimal_codons and get_fop now work on codon frequency matrices 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.

- R
Published by mt1022 over 1 year ago

cubar - v0.6.0

Full Changelog: https://github.com/mt1022/cubar/compare/v0.5.1...v0.6.0

- R
Published by mt1022 over 1 year ago

cubar - Release v0.5.1

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

Full Changelog: https://github.com/mt1022/cubar/compare/v0.5.0...v0.5.1

- R
Published by mt1022 almost 2 years ago

cubar - Release v0.5.0

• 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 about the mathematical details of implementation.

- R
Published by mt1022 about 2 years ago

cubar -

• New vignette for mitochondrial codon usage analysis.
• Fix a bug when in get_enc for non-standard genetic code.
• Formatting vignettes.
• New sample data human_mt for human mitochondrial protein CDS sequences.

- R
Published by mt1022 over 2 years ago

cubar - cubar 0.4.0

- R
Published by mt1022 over 2 years ago