Package: cubar 1.2.0.9000

cubar: Codon Usage Bias Analysis

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.

Authors:Hong Zhang [aut, cre], Mengyue Liu [aut], Bu Zi [aut]

cubar_1.2.0.9000.tar.gz
cubar_1.2.0.9000.zip(r-4.7-any)cubar_1.2.0.9000.zip(r-4.6-any)cubar_1.2.0.9000.zip(r-4.5-any)
cubar_1.2.0.9000.tgz(r-4.6-any)cubar_1.2.0.9000.tgz(r-4.5-any)
cubar_1.2.0.9000.tar.gz(r-4.7-any)cubar_1.2.0.9000.tar.gz(r-4.6-any)
cubar_1.2.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cubar/json (API)

# Install 'cubar' in R:
install.packages('cubar', repos = c('https://mt1022.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mt1022/cubar/issues

Pkgdown/docs site:https://mt1022.github.io

Datasets:

On CRAN:

Conda:

bioinformaticscodon-usagemachine-learningsequence-analysis

6.02 score 12 stars 29 scripts 477 downloads 31 exports 26 dependencies

Last updated from:350b29549e. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK170
source / vignettesOK258
linux-releaseOK162
macos-releaseOK233
macos-oldrelOK216
windows-develOK112
windows-releaseOK121
windows-oldrelOK95
wasm-releaseOK138

Exports:ca_pairscheck_cdscodon_diffcodon_optimizecount_codonscreate_codon_tableest_aauest_cscest_optimal_codonsest_rscuest_trna_weightextract_trna_gcnget_aauget_caiget_codon_tableget_cscgget_dpget_encget_fopget_gcget_gc3sget_gc4dget_taiplot_ca_pairsrev_compseq_to_codonsshow_codon_tablesslideslide_applyslide_codonslide_plot

Dependencies:BiocGenericsBiostringsclicpp11crayondata.tablefarvergenericsggplot2gluegtableIRangesisobandlabelinglifecycleR6RColorBrewerrlangS4VectorsS7scalesSeqinfovctrsviridisLitewithrXVector

Codon optimization
Introduction | Evironment setup | Optimization strategies | "naive" method | "IDT" method | "CodonTransformer" method | Splice site detection | Recommendations | References
Rendered fromcodon_optimization.Rmdusingknitr::rmarkdown

Last update: 2025-08-01
Started: 2025-07-01

Get started
Sequences and the Genetic Code | Codon usage indices | Effective Number of Codons (ENC) | Fraction of optimal codons (Fop) | Codon Adaptation Index (CAI) | tRNA Adaptation Index (tAI) | Indices that require additional data | Correlation between indices | Utilities | Test of differential usage | Codon usage optimization | Sliding-window analysis | FAQ
Rendered fromcubar.Rmdusingknitr::rmarkdown

Last update: 2025-07-01
Started: 2023-12-26

Non-standard genetic code
Introduction | Main analysis
Rendered fromnon_standard_genetic_code.Rmdusingknitr::rmarkdown

Last update: 2024-07-29
Started: 2023-11-21

Readme and manuals

Help Manual

Help pageTopics
amino acids to codonsaa2codon
Generate codon-anticodon pairing relationshipca_pairs
Quality control and preprocessing of coding sequencescheck_cds
Differential codon usage analysiscodon_diff
Optimize codon usage in coding sequencescodon_optimize
Count codon frequencies in coding sequencescount_codons
Create custom codon table from amino acid-codon mappingcreate_codon_table
Estimate Amino Acid Usage Frequencies of CDSs.est_aau
Estimate Codon Stabilization Coefficientest_csc
Identify optimal codons using statistical modelingest_optimal_codons
Estimate Relative Synonymous Codon Usage (RSCU)est_rscu
Estimate tRNA weights for TAI calculationest_trna_weight
Extract tRNA gene copy numbers from nature tRNA sequencesextract_trna_gcn
Amino Acid Usageget_aau
Calculate Codon Adaptation Index (CAI)get_cai
Retrieve codon table by NCBI genetic code IDget_codon_table
Mean Codon Stabilization Coefficientsget_cscg
Deviation from Proportionalityget_dp
Calculate effective number of codons (ENC)get_enc
Calculate fraction of optimal codons (Fop)get_fop
Calculate GC content of coding sequencesget_gc
GC contents at synonymous 3rd codon positionsget_gc3s
GC contents at 4-fold degenerate sitesget_gc4d
Calculate tRNA Adaptation Index (TAI)get_tai
human mitochondrial CDS sequenceshuman_mt
Plot codon-anticodon pairing relationshipplot_ca_pairs
Generate reverse complement sequencesrev_comp
Convert a coding sequence to a codon vectorseq_to_codons
Display available genetic code tablesshow_codon_tables
Generate sliding window intervalsslide
apply a cub index to a sliding windowslide_apply
Generate sliding windows for codon-level analysisslide_codon
plot sliding window codon usageslide_plot
yeast CDS sequencesyeast_cds
yeast mRNA expression levelsyeast_exp
Half life of yeast mRNAsyeast_half_life
yeast tRNA sequencesyeast_trna
yeast tRNA gene copy numbers (GCN)yeast_trna_gcn