.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
