Package index
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aa2codon - amino acids to codons
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check_cds() - Quality control of CDS
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codon_diff() - Differential codon usage analysis
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codon_optimize() - Optimize codons
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count_codons() - Count occurrences of different codons
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create_codon_table() - create custom codon table from a data frame
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est_csc() - Estimate Codon Stabilization Coefficient
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est_optimal_codons() - Estimate optimal codons
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est_rscu() - Estimate RSCU
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est_trna_weight() - Estimate tRNA weight w
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get_cai() - Calculate CAI
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get_codon_table() - get codon table by NCBI gene code ID
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get_cscg() - Mean Codon Stabilization Coefficients
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get_dp() - Deviation from Proportionality
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get_enc() - Calculate ENC
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get_fop() - Fraction of optimal codons (Fop)
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get_gc() - GC contents
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get_gc3s() - GC contents at synonymous 3rd codon positions
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get_gc4d() - GC contents at 4-fold degenerate sites
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get_tai() - Calculate TAI
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human_mt - human mitochondrial CDS sequences
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plot_ca_pairing() - Plot codon-anticodon pairing relationship
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rev_comp() - Reverse complement
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seq_to_codons() - Convert CDS to codons
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show_codon_tables() - show available codon tables
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slide() - slide window interval generator
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slide_apply() - apply a cub index to a sliding window
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slide_codon() - sliding window of codons
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slide_plot() - plot sliding window codon usage
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yeast_cds - yeast CDS sequences
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yeast_exp - yeast mRNA expression levels
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yeast_half_life - Half life of yeast mRNAs
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yeast_trna - yeast tRNA sequences
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yeast_trna_gcn - yeast tRNA gene copy numbers (GCN)