Systematic quality checks on comparative genomics analyses


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Documentation for package ‘cogeqc’ version 1.11.0

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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