# Generated by roxygen2: do not edit by hand

export(assess_orthogroups)
export(assess_synnet)
export(assess_synnet_list)
export(busco_is_installed)
export(calculate_H)
export(compare_genome_stats)
export(compare_orthogroups)
export(fit_sft)
export(get_genome_stats)
export(list_busco_datasets)
export(plot_busco)
export(plot_duplications)
export(plot_genes_in_ogs)
export(plot_genome_stats)
export(plot_og_overlap)
export(plot_og_sizes)
export(plot_orthofinder_stats)
export(plot_species_specific_ogs)
export(plot_species_tree)
export(read_busco)
export(read_orthofinder_stats)
export(read_orthogroups)
export(run_busco)
importFrom(Biostrings,writeXStringSet)
importFrom(ggbeeswarm,geom_quasirandom)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_alpha_identity)
importFrom(ggplot2,scale_color_identity)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_gradient)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylim)
importFrom(ggtree,geom_tiplab)
importFrom(ggtree,get_taxa_name)
importFrom(ggtree,ggtree)
importFrom(ggtree,xlim)
importFrom(graphics,hist)
importFrom(igraph,degree)
importFrom(igraph,graph_from_data_frame)
importFrom(igraph,transitivity)
importFrom(igraph,vcount)
importFrom(jsonlite,read_json)
importFrom(methods,is)
importFrom(patchwork,wrap_plots)
importFrom(reshape2,melt)
importFrom(rlang,.data)
importFrom(scales,label_number)
importFrom(stats,as.dist)
importFrom(stats,ecdf)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,quantile)
importFrom(stats,reshape)
importFrom(utils,read.csv)
importFrom(utils,tail)
