Package: cubar
Title: Codon Usage Bias Analysis
Version: 1.2.0
Authors@R: c(
    person(given = "Hong",
           family = "Zhang",
           role = c("aut", "cre"),
           email = "mt1022.dev@gmail.com",
           comment = c(ORCID = "0000-0002-4064-9432")),
    person(given = "Mengyue",
           family = "Liu",
           role = c("aut")),
    person(given = "Bu",
           family = "Zi",
           role = c("aut")))
Description: A suite of functions for rapid and flexible analysis of codon 
    usage bias. It provides in-depth analysis at the codon level, including 
    relative synonymous codon usage (RSCU), tRNA weight calculations, machine 
    learning predictions for optimal or preferred codons, and visualization of 
    codon-anticodon pairing. Additionally, it can calculate various gene-
    specific codon indices such as codon adaptation index (CAI), effective 
    number of codons (ENC), fraction of optimal codons (Fop), tRNA adaptation 
    index (tAI), mean codon stabilization coefficients (CSCg), and GC contents 
    (GC/GC3s/GC4d). It also supports both standard and non-standard genetic 
    code tables found in NCBI, as well 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
Imports: Biostrings (>= 2.60.0), IRanges (>= 2.34.0), data.table (>=
        1.14.0), ggplot2 (>= 3.3.5), rlang (>= 0.4.11)
Depends: R (>= 4.1.0)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), reticulate
VignetteBuilder: knitr
RoxygenNote: 7.3.2
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2025-08-01 13:26:15 UTC; mt1022
Author: Hong Zhang [aut, cre] (ORCID: <https://orcid.org/0000-0002-4064-9432>),
  Mengyue Liu [aut],
  Bu Zi [aut]
Maintainer: Hong Zhang <mt1022.dev@gmail.com>
Repository: CRAN
Date/Publication: 2025-08-19 07:30:02 UTC
Built: R 4.5.3; ; 2026-04-25 18:25:46 UTC; windows
