Systematic quality checks on comparative genomics analyses

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Documentation for package ‘cogeqc’ version 1.11.0

• 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