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cubar
View on CRAN: Click
here
Download and install cubar package within the R console
Install from CRAN:
install.packages("cubar")
Install from Github:
library("remotes")
install_github("cran/cubar") Install by package version:
library("remotes")
install_version("cubar", "1.2.0") Attach the package and use:
library("cubar")
Maintained by
Hong Zhang
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2023-07-17
Latest Update: 2024-12-07
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.
How to cite:
Hong Zhang (2023). cubar: Codon Usage Bias Analysis. R package version 1.2.0, https://cran.r-project.org/web/packages/cubar. Accessed 05 Jun. 2026.
Previous versions and publish date:
Other packages that cited cubar R package
View cubar citation profile
Other R packages that cubar depends,
imports, suggests or enhances
Complete documentation for cubar
Functions, R codes and Examples using
the cubar R package
Some associated functions: aa2codon . check_cds . count_codons . create_codon_table . est_csc . est_optimal_codons . est_rscu . est_trna_weight . get_cai . get_codon_table . get_cscg . get_enc . get_fop . get_gc . get_gc3s . get_gc4d . get_tai . human_mt . plot_ca_pairing . rev_comp . seq_to_codons . show_codon_tables . yeast_cds . yeast_exp . yeast_half_life . yeast_trna_gcn .
Some associated R codes: codon_info.R . codon_weight.R . data.R . gene_index.R . sequences.R . Full cubar package functions and examples
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