Package index
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calculate_shannon_entropy() - Calculate Shannon Entropy
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calculate_kl_divergence() - Calculate Kullback-Leibler Divergence
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compare_entropy_profiles() - Compare Entropy Profiles
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entropy_peak_detection() - Detect Entropy Peaks
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calculate_codon_frequencies() - Calculate Codon Frequencies
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calculate_rscu() - Calculate Relative Synonymous Codon Usage (RSCU)
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calculate_enc() - Calculate the Effective Number of Codons (ENC)
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find_orfs_in_sequence() - Find ORFs in Sequence
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find_candidate_orfs() - Find Candidate ORFs
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plot_candidate_orfs() - Plot Candidate ORFs
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plot_entropy_profile() - Plot Entropy Profile
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plot_codon_usage_panel() - Plot Codon Usage Bias and RSCU in a Unified Panel
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extract_known_genes() - Extract Known Genes from GTF/GFF File
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create_reference_profile() - Create Reference Codon Profile
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sliding_window_scan() - Sliding Window Entropy Scan
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translate_codons() - Translate Codons to Amino Acids
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.adjust_codon_length() - Ensure Sequence Length is Divisible by 3
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.get_all_codons() - Get All Possible Codons
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.get_window_coords() - Sliding Window Iterator
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.parse_gtf_line() - Parse GTF Line
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.validate_dna() - Validate DNA Sequence
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read_fasta() - Read FASTA File
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.get_codon_aa_map() - Mapping amino acids to their corresponding codons
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codon_frequency_df() - Convert Codon Frequency Vector to Tidy Data Frame
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GeneScout-extdata - Example FASTA and GTF files bundled with GeneScout