Version 0.99.0 (2026-01-20)
NEW FEATURES
- Added calculate_codon_frequencies() for codon usage analysis
- Added calculate_shannon_entropy() for entropy calculation
- Added calculate_kl_divergence() for comparing codon distributions
- Added calculate_rscu() for Relative Synonymous Codon Usage
- Added calculate_enc() for Effective Number of Codons
- Added read_fasta() for reading FASTA files
- Added extract_known_genes() for extracting genes from GTF/GFF annotations
- Added create_reference_profile() for building organism-specific profiles
- Added sliding_window_scan() for genome-wide entropy scanning
- Added entropy_peak_detection() for identifying low-entropy regions
- Added find_candidate_orfs() for ORF discovery
- Added plot_entropy_profile() for visualization
- Added compare_entropy_profiles() for comparative analysis
- Added plot_candidate_orfs() for candidate ORF visualization
DOCUMENTATION
- Added comprehensive vignette with examples
- Added function documentation with roxygen2
- Added example datasets (chr19.fasta, APOE.fasta)
TESTS
- Added testthat test suite with 20+ tests
- Tests cover all major functions
BUG FIXES
- None (initial release)
DEPRECATED AND DEFUNCT
- None