# Systematic quality checks on comparative genomics analyses

## Documentation for package ‘cogeqc’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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