| .eruptionBreaks | INTERNAL Create manual breaks/labels for volcano plots |
| .plotFoldChangeLegend | INTERNAL Construct heatmap legend |
| .runSigora | INTERNAL Wrapper around Sigora's enrichment function |
| .truncNeatly | INTERNAL Break long strings at spaces |
| eruption | Create a volcano plot of RNA-Seq results |
| exampleDESeqResults | List of example results from DESeq2 |
| getPathwayDistances | Calculate pairwise distances from a table of pathways and genes |
| groupedPathwayColours | Colour assignments for grouped pathways |
| hallmarkDatabase | Table of Hallmark gene sets and their genes |
| innateDbPPI | InnateDB PPI data |
| keggDatabase | Table of KEGG pathways and genes |
| mappingFile | Table of human gene ID mappings |
| pathnetCreate | Create a pathway network from enrichment results and a pathway interaction foundation |
| pathnetFoundation | Create the foundation for pathway networks using pathway distances |
| pathnetGGraph | Visualize enriched Reactome pathways as a static network |
| pathnetVisNetwork | Visualize enriched Reactome pathways as an interactive network |
| pathwayCategories | Top-level pathway categories |
| pathwayEnrichment | Test significant DE genes for enriched pathways |
| pathwayPlots | Plot pathway enrichment results |
| plotFoldChange | Create a heatmap of fold changes to visualize RNA-Seq results |
| ppiBuildNetwork | Construct a PPI network from input genes and InnateDB's database |
| ppiCleanNetwork | Clean GraphML or JSON input |
| ppiEnrichNetwork | Test a PPI network for enriched pathways |
| ppiExtractSubnetwork | Extract a subnetwork based on pathway genes |
| ppiPlotNetwork | Plot an undirected PPI network using ggraph |
| ppiRemoveSubnetworks | INTERNAL Find and return the largest subnetwork |
| reactomeDatabase | Table of all Reactome pathways and genes |
| sigoraDatabase | Table of all Sigora pathways and their constituent genes |
| sigoraExamples | Sigora enrichment example |