.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
exampleDESeqResultsHS   List of example results from DESeq2 for human
exampleDESeqResultsMM   List of example results from DESeq2 in mice
getPathwayDistances     Calculate pairwise distances from a table of
                        pathways and genes
groupedPathwayColours   Colour assignments for grouped pathways
hallmarkDatabaseHS      Table of Hallmark gene sets and their genes
innateDbPPIHS           InnateDB PPI data for humans
innateDbPPIMM           InnateDB PPI data for mice
keggDatabaseHS          Table of KEGG pathways and genes in humans
keggDatabaseMM          Table of KEGG pathways and genes in mice
mappingFileHS           Table of human gene ID mappings
mappingFileMM           Table of mouse 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
pathwayCategoriesHS     Top-level pathway categories for human
pathwayCategoriesMM     Top-level pathway categories for mouse
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
reactomeDatabaseHS      Table of all Reactome pathways and genes for
                        humans
reactomeDatabaseMM      Table of all Reactome pathways and genes for
                        mice
sigoraDatabaseHS        Table of all Sigora pathways and their
                        constituent genes for humans
sigoraDatabaseMM        Table of all Sigora pathways and their
                        constituent genes for mice
sigoraExamplesHS        Sigora enrichment example
sigoraExamplesMM        Sigora enrichment example in mice
