Package: GeneGA 1.57.0
Zhenpeng Li
GeneGA: Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm
R based Genetic algorithm for gene expression optimization by considering both mRNA secondary structure and codon usage bias, GeneGA includes the information of highly expressed genes of almost 200 genomes. Meanwhile, Vienna RNA Package is needed to ensure GeneGA to function properly.
Authors:
GeneGA_1.57.0.tar.gz
GeneGA_1.57.0.zip(r-4.5)GeneGA_1.57.0.zip(r-4.4)GeneGA_1.57.0.zip(r-4.3)
GeneGA_1.57.0.tgz(r-4.4-any)GeneGA_1.57.0.tgz(r-4.3-any)
GeneGA_1.57.0.tar.gz(r-4.5-noble)GeneGA_1.57.0.tar.gz(r-4.4-noble)
GeneGA_1.57.0.tgz(r-4.4-emscripten)GeneGA_1.57.0.tgz(r-4.3-emscripten)
GeneGA.pdf |GeneGA.html✨
GeneGA/json (API)
| # Install 'GeneGA' in R: |
| install.packages('GeneGA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- wSet - Codon Adaptation Index (CAI) w tables
On BioConductor:GeneGA-1.57.0(bioc 3.21)GeneGA-1.56.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:29ef0d44e5. Checks:ERROR: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Dec 29 2024 |
| R-4.5-win | ERROR | Dec 29 2024 |
| R-4.5-linux | ERROR | Dec 29 2024 |
| R-4.4-win | ERROR | Dec 29 2024 |
| R-4.4-mac | ERROR | Dec 29 2024 |
| R-4.3-win | ERROR | Dec 29 2024 |
| R-4.3-mac | ERROR | Dec 29 2024 |
Exports:GeneCodonGeneFoldGAGeneGAplotGeneGAshow
Dependencies:ade4hashlatticeMASSnlmepixmapRcppRcppArmadillosegmentedseqinrsp
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Designing gene based on mRNA secondary structure and codon usage bias using Genetic algorithm, GeneGA includes the information of highly expressed genes of almost 200 genomes. | GeneGA-package |
| Optimizing the codon usage of gene by replacing less usage codons with the most preference used codons or replacing the most preference used codons with less usage codons. | GeneCodon |
| the function optimizes gene merely considering mRNA secondary structure. | GeneFoldGA |
| Class "GeneFoldGA" | GeneFoldGA-class show,GeneFoldGA-method |
| the function optimizes gene expression based on both mRNA secondary structure and codon usage bias | GeneGA |
| Class "GeneGA" | GeneGA-class show,GeneGA-method |
| plotGeneGA methods of GeneGA and GeneFoldGA objects | plotGeneGA plotGeneGA,GeneFoldGA-method plotGeneGA,GeneGA-method plotGeneGA-methods plotGeneGA.GeneFoldGA plotGeneGA.GeneGA |
| Codon Adaptation Index (CAI) w tables | wSet |