Man pages for santiago1234/iCodon
iCodon: Designing "ideal" coding (iCodon) sequences for customized expression level
| add_codon_counts | Add codon counts to data |
| codon_distance | Codon distance |
| codones | The genetic code #' codon three letter nucleotide codon |
| count_codons | Count codons in DNA sequence |
| evolution | Generate synonimous mutant variants |
| gc_amino_to_codons_l | Genetic code amino -> codons |
| gc_codons_to_amino | Genetic code codons -> amino acid |
| human_optimality | Codon optimality code for human |
| mrna_stability_model | Predictive model of mRNA stability |
| nucleotide_distance | Nucleotide distance |
| optimizer | Genetic algorithm for mRNA stability optimization |
| optipred | Predictions for endogenous sequences |
| pipe | Pipe operator |
| plot_optimization | Plot optimization path and mRNA stability level |
| predict_stability | Predict mRNA stability functional factory |
| preprocessing_recipe | Data pre-processing pipeline |
| preprocess_secuences | Preprocess sequence for prediction mRNA stability |
| runExample | Run iCodon example |
| run_optimization_shinny | Script to run the optimization in shiny app |
| sample_synonimous_codon | Sample synonymous codons according to the optimality effect |
| sampling_deoptimization | Sampling probabilities (deoptimization) |
| sampling_optimization | Sampling probabilities (optimization) |
| selection | Selection (functional factory) |
| split_by_codons | Split a sequence by codons |
| testing | Testing data |
| test_seq | DNA sequence |
| training | Training data |
| translate | translate DNA sequence to amino acid |
| unscale_decay_to_mouse | Convert scaled decay rate to unscaled versio (half-life) |
| validate_sequence | Check correct input DNA sequence |
| visualize_evolution | Visualiztion tools |
| viz_result_shiny | Visualize optimization results in shiny |
