cubar

1.2.0

Codon Usage Bias Analysis

0packages depend

3.6Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Hong ZhangFirst published 2023-07-177 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("cubar", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("mt1022/cubar")

Development version from mt1022/cubar. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-cubar

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 5.1 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.22

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 703 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 42%

Downloads

3.6K

CRAN downloads in the past year

Rank #11,852 · ~10/day · ~300/mo

Releases R versions

Daily download trend is not available in this view yet.

27530 days

85490 days

3.6K1 year

Compare downloads with other packages →

Also on173 r2u

Repository

GitHub ↗ mt1022/cubar

10Stars

3Forks

1Open issues

0Open PRs

8Releases

232Commits

3Contributors

bioinformaticscodon-usagemachine-learningr-packagesequence-analysis

232 commits · Last activity 2025-10-29 · 0% stars, 30d

Stars over time

2024-08-25 · 72026-07-07 · 10

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/mt1022/cubar on 2026-07-31.

Continuous integration (1)

GitHub Actions

CRAN release process (3)

cran-comments.mdrevdep/CRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (5)

Biostrings IRanges data.table (>= 1.14.0)ggplot2 rlang

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown testthat reticulate

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Hong Zhang

Author, Maintainer

Authors (3)

Hong Zhang

Author, Maintainer

Mengyue Liu

Author · added in 1.1.0

Bu Zi

Author · added in 0.6.0

Package Timeline

7 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.2.0Latest
2025-08-19 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.1.0
2024-12-07 · diff ↗
1.0.0
2024-08-01 · diff ↗
0.6.0
2024-07-04 · diff ↗
unarchivedReturned to CRAN
2024-07-04
archivedRemoved from CRAN
2024-07-02
policy violation On Internet access
R
R 4.4.0 released · 2024-04-24
0.5.0
2024-01-09 · diff ↗
0.4.2
2023-11-18 · diff ↗
0.4.0
2023-07-17
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-07-17
Total releases: 7 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 2.4 MB / 7 files
Download size: 2.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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