Package index
-
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