Identification and classification of duplicated genes

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Documentation for package ‘doubletrouble’ version 1.2.5

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
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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
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