Identification and classification of duplicated genes
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Documentation for package ‘doubletrouble’ version 1.0.0
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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 |
| classify_ssd_pairs | Classify small-scale duplication-derived gene pairs into subcategories |
| 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_transposed | Get transposed duplicate pairs |
| get_wgd_pairs | Get gene pairs derived from whole-genome and small-scale duplications |
| 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 |