Man pages for almeidasilvaf/cogeqc
Systematic quality checks on comparative genomics analyses
| assess_orthogroups | Assess orthogroup inference based on functional annotation |
| assess_synnet | Assess synteny network based on graph properties |
| assess_synnet_list | Assess list of synteny networks as in 'assess_synnet' |
| batch_summary | BUSCO summary output for batch mode |
| busco_is_installed | Check if BUSCO is installed |
| calculate_H | Calculate homogeneity scores for orthogroups |
| cogeqc-package | cogeqc: Systematic quality checks on comparative genomics... |
| compare_genome_stats | Compare user-defined assembly statistics with statistics of... |
| compare_orthogroups | Compare inferred orthogroups to a reference set |
| fit_sft | Goodness of fit test for the scale-free topology model |
| get_genome_stats | Get summary statistics for genomes on NCBI using the NCBI... |
| interpro_ath | Intepro annotation for Arabidopsis thaliana's genes |
| interpro_bol | Intepro annotation for Brassica oleraceae's genes |
| list_busco_datasets | List BUSCO data sets |
| og | Orthogroups between Arabidopsis thaliana and Brassica... |
| plot_busco | Plot BUSCO summary output |
| plot_duplications | Plot species-specific duplications |
| plot_genes_in_ogs | Plot percentage of genes in orthogroups for each species |
| plot_genome_stats | Plot statistics on genome assemblies on the NCBI |
| plot_og_overlap | Plot pairwise orthogroup overlap between species |
| plot_og_sizes | Plot orthogroup sizes per species |
| plot_orthofinder_stats | Plot a panel with a summary of Orthofinder stats |
| plot_species_specific_ogs | Plot number of species-specific orthogroups |
| plot_species_tree | Plot species tree |
| read_busco | Read and parse BUSCO's summary report |
| read_orthofinder_stats | Read and parse Orthofinder summary statistics |
| read_orthogroups | Read and parse orthogroups file created by OrthoFinder |
| run_busco | Run BUSCO assessment of assembly and annotation quality |
| synnet | Synteny network for Brassica oleraceae, B. napus, and B. rapa |
| tree | Species tree for model species |
