{ "_id": "6a16c652acfb0bcc41d888eb", "Package": "cubar", "Title": "Codon Usage Bias Analysis", "Version": "1.2.0.9000", "Authors@R": "c(\nperson(given = \"Hong\",\nfamily = \"Zhang\",\nrole = c(\"aut\", \"cre\"),\nemail = \"mt1022.dev@gmail.com\",\ncomment = c(ORCID = \"0000-0002-4064-9432\")),\nperson(given = \"Mengyue\",\nfamily = \"Liu\",\nrole = c(\"aut\")),\nperson(given = \"Bu\",\nfamily = \"Zi\",\nrole = c(\"aut\")))", "Description": "A suite of functions for rapid and flexible analysis of\ncodon usage bias. It provides in-depth analysis at the codon\nlevel, including relative synonymous codon usage (RSCU), tRNA\nweight calculations, machine learning predictions for optimal\nor preferred codons, and visualization of codon-anticodon\npairing. Additionally, it can calculate various gene- specific\ncodon indices such as codon adaptation index (CAI), effective\nnumber of codons (ENC), fraction of optimal codons (Fop), tRNA\nadaptation index (tAI), mean codon stabilization coefficients\n(CSCg), and GC contents (GC/GC3s/GC4d). It also supports both\nstandard and non-standard genetic code tables found in NCBI, as\nwell as custom genetic code tables.", "License": "MIT + file LICENSE", "URL": "https://github.com/mt1022/cubar, https://mt1022.github.io/cubar/", "BugReports": "https://github.com/mt1022/cubar/issues", "Encoding": "UTF-8", "LazyData": "true", "LazyDataCompression": "bzip2", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://mt1022.r-universe.dev", "Date/Publication": "2025-10-29 01:44:45 UTC", "RemoteUrl": "https://github.com/mt1022/cubar", "RemoteRef": "HEAD", "RemoteSha": "350b29549e13dbfd95f9599af544e7fdc1fe885e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-27 10:20:37 UTC", "User": "root" }, "Author": "Hong Zhang [aut, cre] (ORCID: ),\nMengyue Liu [aut],\nBu Zi [aut]", "Maintainer": "Hong Zhang ", "MD5sum": "1f105ad1389b0c0d27a5969284a3351f", "_user": "mt1022", "_type": "src", "_file": 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"tojson": false } ], "_help": [ { "page": "aa2codon", "title": "amino acids to codons", "topics": [ "aa2codon" ] }, { "page": "ca_pairs", "title": "Generate codon-anticodon pairing relationship", "topics": [ "ca_pairs" ] }, { "page": "check_cds", "title": "Quality control and preprocessing of coding sequences", "topics": [ "check_cds" ] }, { "page": "codon_diff", "title": "Differential codon usage analysis", "topics": [ "codon_diff" ] }, { "page": "codon_optimize", "title": "Optimize codon usage in coding sequences", "topics": [ "codon_optimize" ] }, { "page": "count_codons", "title": "Count codon frequencies in coding sequences", "topics": [ "count_codons" ] }, { "page": "create_codon_table", "title": "Create custom codon table from amino acid-codon mapping", "topics": [ "create_codon_table" ] }, { "page": "est_aau", "title": "Estimate Amino Acid Usage Frequencies of CDSs.", "topics": [ "est_aau" ] }, { "page": "est_csc", "title": "Estimate Codon Stabilization Coefficient", "topics": 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