| calculate_geneSetRatio | Calculate geneSetRatio per gene per enrichment contrast |
| colorify | Create and/or modify color/gradient palettes |
| colorify_map | Colorify colorRamp between colors mapping to breakpoint values |
| display_palettes | Display R grDevices palettes |
| example_enrichment | An example enrichment |
| example_genelist | An example genelist |
| example_genesets | Example genesets |
| example_genes_overview | An example genes overview |
| example_ppi_data | An example ppi data |
| file_extension | Get file extension |
| filter_enrichment | Filter enrichment |
| get_base_folder | Set base folder |
| get_ppigraph | Get PPI igraph |
| get_string_ppi | Get STRING database Protein-Protein Interactions |
| get_terms_by_keywords | Get term names by searching with (partial) keywords |
| get_visNetwork | Get visNetwork graph |
| goatea_server | Server for goatea package |
| goatea_ui | UI for GOATEA package |
| hexcolor2rgba | Hex code colors to rgba format |
| palette_name_mapping | Palette original name mapping |
| plot_ComplexHeatmap | Plot ComplexHeatmap |
| plot_EnhancedVolcano | Plot EnhancedVolcano |
| plot_genelists_overlap_upsetjs | Visualize genelists gene overlap in an interactive UpSet plot |
| plot_gene_effectsize_ComplexHeatmap | Plot gene2effectsize ComplexHeatmap |
| plot_splitdot | Plot splitdot plot |
| plot_termtree | Plot semantic similarity termtree |
| process_string_input | Process Shiny area input string |
| read_validate_genelist | Read and validate a table with genes (that should be tested in overrepresentation-analysis) for compatibility with this R package#' |
| rename_gene_overview | Rename the gene overview |
| run_genelists_overlap | Create gene overview through overlapping genelists information by overlapping significant genes |
| run_geneset_enrichment | Perform geneset enrichment testing using any supported method |
| scale_values_between | Scale values between given min/max |
| set_significant_N_genes | Set significant and number of genes |
| wrap_hovertip | Wrap Shiny UI element with a hoverable tooltip contained in html div tags |
| wrap_loader | Wrap Shiny UI element with a loading spinner contained in html div tags |