# Generated by roxygen2: do not edit by hand

export(addResamplingCounts)
export(annotePathwayToFather)
export(availableOmicMethods)
export(computeFreqs)
export(computeOmicsIntersections)
export(downloadPathwayRelationFromReactome)
export(getPathwaysModulesSuccess)
export(makeOmics)
export(multiOmicsSurvivalModuleTest)
export(multiOmicsSurvivalPathwayTest)
export(multiOmicsTwoClassModuleTest)
export(multiOmicsTwoClassPathwayTest)
export(multiPathwayModuleReport)
export(multiPathwayReport)
export(plotFrequencies)
export(plotModuleHeat)
export(plotModuleInGraph)
export(plotModuleKM)
export(plotModuleReport)
export(plotMultiPathwayReport)
export(plotPathwayHeat)
export(plotPathwayKM)
export(resamplingModulesSurvival)
export(resamplingModulesTwoClass)
export(resamplingPathwaySurvival)
export(resamplingPathwayTwoClass)
export(runSupertest)
export(selectStablePathwaysModules)
export(showMOSpalette)
export(showModule)
export(showOmics)
export(showPathway)
export(stripModulesFromPathways)
exportMethods(showModule)
exportMethods(showOmics)
exportMethods(showPathway)
import(MultiAssayExperiment)
importClassesFrom(graph,graphNEL)
importClassesFrom(graphite,Pathway)
importFrom(AnnotationDbi,select)
importFrom(ComplexHeatmap,'%v%')
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,draw)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(FactoMineR,estim_ncp)
importFrom(Matrix,diag)
importFrom(NbClust,NbClust)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,DataFrame)
importFrom(SuperExactTest,supertest)
importFrom(checkmate,assertClass)
importFrom(circlize,colorRamp2)
importFrom(corpcor,cov.shrink)
importFrom(coxrobust,coxr)
importFrom(elasticnet,spca)
importFrom(gRbase,coerceGraph)
importFrom(gRbase,is.DAG)
importFrom(gRbase,moralize)
importFrom(gRbase,moralizeMAT)
importFrom(gRbase,rip)
importFrom(gRbase,triangulate)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_polar)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_path)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_polygon)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,ggplot_gtable)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,labs)
importFrom(ggplot2,rel)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplotify,as.ggplot)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,rainbow)
importFrom(graph,nodes)
importFrom(graph,subGraph)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,legend)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,title)
importFrom(graphite,pathwayGraph)
importFrom(grid,gpar)
importFrom(grid,grid.draw)
importFrom(grid,grid.grabExpr)
importFrom(grid,grid.newpage)
importFrom(grid,grid.text)
importFrom(grid,rectGrob)
importFrom(gridExtra,arrangeGrob)
importFrom(igraph,"V<-")
importFrom(igraph,V)
importFrom(igraph,as_ids)
importFrom(igraph,distances)
importFrom(igraph,ego)
importFrom(igraph,graph_from_graphnel)
importFrom(igraph,make_ego_graph)
importFrom(igraph,simplify)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(org.Hs.eg.db,org.Hs.eg.db)
importFrom(pheatmap,pheatmap)
importFrom(qpgraph,qpIPF)
importFrom(reshape,melt)
importFrom(stats,as.formula)
importFrom(stats,cov)
importFrom(stats,cutree)
importFrom(stats,deviance)
importFrom(stats,df.residual)
importFrom(stats,dist)
importFrom(stats,glm)
importFrom(stats,hclust)
importFrom(stats,kruskal.test)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,pchisq)
importFrom(stats,pnorm)
importFrom(stats,poisson)
importFrom(stats,quantile)
importFrom(stats,relevel)
importFrom(stats,reorder)
importFrom(stats,sd)
importFrom(survival,Surv)
importFrom(survival,coxph)
importFrom(survminer,ggsurvplot)
importFrom(survminer,surv_categorize)
importFrom(survminer,surv_cutpoint)
importFrom(survminer,surv_fit)
importFrom(utils,data)
importFrom(utils,head)
importFrom(utils,read.table)