Function reference
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cds_scerevisiae - Coding sequences (CDS) of S. cerevisiae
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classify_gene_pairs() - Classify duplicate gene pairs based on their modes of duplication
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classify_genes() - Classify genes into unique modes of duplication
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diamond_inter - Interspecies DIAMOND output for yeast species
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diamond_intra - Intraspecies DIAMOND output for S. cerevisiae
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duplicates2counts() - Get a duplicate count matrix for each genome
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find_ks_peaks() - Find peaks in a Ks distribution with Gaussian Mixture Models
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fungi_kaks - Duplicate pairs and Ka, Ks, and Ka/Ks values for fungi species
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get_anchors_list() - Get a list of anchor pairs for each species
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get_intron_counts() - Get a data frame of intron counts per gene
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get_segmental() - Classify gene pairs derived from segmental duplications
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get_tandem_proximal() - Classify gene pairs derived from tandem and proximal duplications
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get_transposed() - Classify gene pairs originating from transposon-derived duplications
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get_transposed_classes() - Classify TRD genes as derived from either DNA transposons or retrotransposons
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gmax_ks - Duplicate pairs and Ks values for Glycine max
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pairs2kaks() - Calculate Ka, Ks, and Ka/Ks from duplicate gene pairs
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plot_duplicate_freqs() - Plot frequency of duplicates per mode for each species
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plot_ks_distro() - Plot distribution of synonymous substitution rates (Ks)
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plot_ks_peaks() - Plot histogram of Ks distribution with peaks
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plot_rates_by_species() - Plot distributions of substitution rates (Ka, Ks, or Ka/Ks) per species
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split_pairs_by_peak() - Split gene pairs based on their Ks peaks
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yeast_annot - Genome annotation of the yeast species S. cerevisiae and C. glabrata
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yeast_seq - Protein sequences of the yeast species S. cerevisiae and C. glabrata