calcGseaStat            Calculates GSEA statistics for a given query
                        gene set
calcGseaStatBatchCpp    Calculates GSEA statistic valus for all gene
                        sets in 'selectedStats' list.
collapsePathways        Collapse list of enriched pathways to
                        independent ones.
collapsePathwaysGeseca
                        Collapse list of enriched pathways to
                        independent ones (GESECA version, highly
                        experimental).
collapsePathwaysORA     Collapse list of enriched pathways to
                        independent ones. Version for ORA
                        hypergeometric test.
exampleExpressionMatrix
                        Example of expression values obtained for
                        GSE14308.
examplePathways         Example list of mouse Reactome pathways.
exampleRanks            Example vector of gene-level statistics
                        obtained for Th1 polarization.
fgsea                   Wrapper to run methods for preranked gene set
                        enrichment analysis.
fgseaLabel              Runs label-permuring gene set enrichment
                        analysis.
fgseaMultilevel         Runs preranked gene set enrichment analysis.
fgseaSimple             Runs preranked gene set enrichment analysis.
fgseaSimpleImpl         Runs preranked gene set enrichment analysis for
                        preprocessed input data.
fora                    Simple overrepresentation analysis based on
                        hypergeometric test
geseca                  Runs multilevel Monte-Carlo variant for
                        performing gene sets co-regulation analysis
gesecaSimple            Runs simple variant for performing gene sets
                        co-regulation analysis
gmtPathways             Returns a list of pathways from a GMT file.
mapIdsList              Effeciently converts collection of pathways
                        using AnnotationDbi::mapIds function.
                        Parameters are the sames as for mapIds except
                        for keys, which is assumed to be a list of
                        vectors.
multilevelError         Calculates the expected error for the standard
                        deviation of the P-value logarithm.
multilevelImpl          Calculates P-values for preprocessed data.
plotCoregulationProfile
                        Plots expression profile of a gene set
plotCoregulationProfileReduction
                        Plot a spatial expression profile of a gene set
plotCoregulationProfileSpatial
                        Plot a spatial expression profile of a gene set
plotEnrichment          Plots GSEA enrichment plot. For more
                        flexibility use 'plotEnrichmentData' function.
plotEnrichmentData      Returns data required for doing an enrichment
                        plot.
plotGesecaTable         Plots table of gene set profiles.
plotGseaTable           Plots table of enrichment graphs using ggplot
                        and gridExtra.
reactomePathways        Returns a list of Reactome pathways for given
                        Entrez gene IDs
writeGmtPathways        Write collection of pathways (list of vectors)
                        to a gmt file
