Package: cubar 1.0.0.9000
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:
cubar_1.0.0.9000.tar.gz
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cubar_1.0.0.9000.tgz(r-4.4-any)cubar_1.0.0.9000.tgz(r-4.3-any)
cubar_1.0.0.9000.tar.gz(r-4.5-noble)cubar_1.0.0.9000.tar.gz(r-4.4-noble)
cubar_1.0.0.9000.tgz(r-4.4-emscripten)cubar_1.0.0.9000.tgz(r-4.3-emscripten)
cubar.pdf |cubar.html✨
cubar/json (API)
NEWS
| # 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
- aa2codon - Amino acids to codons
- human_mt - Human mitochondrial CDS sequences
- yeast_cds - Yeast CDS sequences
- yeast_exp - Yeast mRNA expression levels
- yeast_half_life - Half life of yeast mRNAs
- yeast_trna - Yeast tRNA sequences
- yeast_trna_gcn - Yeast tRNA gene copy numbers
bioinformaticscodon-usagemachine-learningsequence-analysis
Last updated 1 months agofrom:13a8d306ff. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 06 2024 |
| R-4.5-win | OK | Sep 06 2024 |
| R-4.5-linux | OK | Sep 06 2024 |
| R-4.4-win | OK | Sep 06 2024 |
| R-4.4-mac | OK | Sep 06 2024 |
| R-4.3-win | OK | Sep 06 2024 |
| R-4.3-mac | OK | Sep 06 2024 |
Exports:check_cdscodon_diffcodon_optimizecount_codonscreate_codon_tableest_cscest_optimal_codonsest_rscuest_trna_weightget_caiget_codon_tableget_cscgget_dpget_encget_fopget_gcget_gc3sget_gc4dget_taiplot_ca_pairingrev_compseq_to_codonsshow_codon_tablesslideslide_applyslide_codonslide_plot
Dependencies:askpassBiocGenericsBiostringsclicolorspacecrayoncurldata.tablefansifarverGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpkgconfigR6RColorBrewerrlangS4VectorsscalessystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
