Identification and classification of duplicated genes


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Documentation for package ‘doubletrouble’ version 1.2.1

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cds_scerevisiae Coding sequences (CDS) of S. cerevisiae
classify_genes Classify genes into unique modes of duplication
classify_gene_pairs Classify duplicate gene pairs based on their modes of duplication
diamond_inter Interspecies DIAMOND output for yeast species
diamond_intra Intraspecies DIAMOND output for S. cerevisiae
find_ks_peaks Find peaks in a Ks distribution with Gaussian Mixture Models
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_ks_peaks Plot histogram of Ks distribution with peaks
scerevisiae_kaks Duplicate pairs and Ka, Ks, and Ka/Ks values for S. cerevisiae
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