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All functions

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