coRdon

coRdon analyzes codon usage in unannotated or KEGG/COG annotated DNA sequences to calculate codon usage bias measures, predict gene expressivity, and perform gene set enrichment analysis.

Key Features:

• Codon usage bias calculation: Computes different measures of codon usage bias from DNA sequences.
• Gene expressivity prediction: Calculates codon usage-based predictors of gene expressivity.
• Gene set enrichment analysis: Performs enrichment analysis for KEGG/COG annotated sequences.
• Visualization: Implements several methods for visualization of codon usage and enrichment analysis results.

Scientific Applications:

• Codon usage analysis: Analyzes codon usage patterns in unannotated or KEGG/COG annotated DNA sequences.
• Functional annotation analysis: Performs gene set enrichment analysis using KEGG and COG annotations.

Methodology:

The package calculates codon usage bias measures and codon usage-based predictors of gene expressivity, and performs gene set enrichment analysis for annotated sequences.