Function reference • cogeqc

All functions

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

compare_genome_stats(): Compare user-defined assembly statistics with statistics of NCBI genomes

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 Datasets API

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 oleraceae

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