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.
Version: 1.1.0 Depends: R (≥ 4.1.0) Imports: Biostrings (≥ 2.60.0), IRanges (≥ 2.34.0), data.table (≥ 1.14.0), ggplot2 (≥ 3.3.5), rlang (≥ 0.4.11) Suggests: knitr, rmarkdown, testthat (≥ 3.0.0) Published: 2024-12-07 DOI: 10.32614/CRAN.package.cubar Author: Hong Zhang [aut, cre], Mengyue Liu [aut], Bu Zi [aut] Maintainer: Hong Zhang <mt1022.dev at gmail.com> BugReports: https://github.com/mt1022/cubar/issues License: MIT + file LICENSE URL: https://github.com/mt1022/cubar, https://mt1022.github.io/cubar/ NeedsCompilation: no Materials: README NEWS CRAN checks: cubar results Documentation: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=cubar to link to this page.
RetroSearch is an open source project built by @garambo | Open a GitHub Issue
Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo
HTML:
3.2
| Encoding:
UTF-8
| Version:
0.7.4