importClassesFrom("graph", "graphNEL")
importFrom("graph", "numNodes", "numEdges", "nodes")
import("igraph", "GSEABase", "BioNet", "biomaRt", "AnnotationDbi")
importFrom("cellHTS2", "state", "scoreReplicates", "summarizeReplicates", "Data", "Data<-")
importFrom("RankProd", "RP")
exportClasses(
	"GSCA",
	"NWA"
)
export(
	   "aggregatePvals",
	   "annotationConvertor",
	   "biogridDataDownload", 
       "celAnnotationConvertor",
       "cellHTS2OutputStatTests",
       "collectionGsea",
       "drosoAnnotationConvertor",
       "duplicateRemover",
       "FDRcollectionGsea",
       "analyzeGeneSetCollections",
       "GOGeneSets",
       "gseaPlots",
       "gseaScores",
       "gseaScoresBatch",
       "gseaScoresBatchParallel",
       "HTSanalyzeR4cellHTS2",
       "KeggGeneSets",
       "mammalAnnotationConvertor",
       "multiHyperGeoTest",
       "networkAnalysis",
       "networkPlot",
	   "pairwiseGsea",
	   "pairwiseGseaPlot",
	   "pairwisePhenoMannWhit",
       "permutationPvalueCollectionGsea",
       "hyperGeoTest",
       "writeReportHTSA",
	"changes")

exportMethods(
	"analyze",
	"reportAll",
	"plotSubNet",
	"viewSubNet",
	"viewEnrichMap",
	"plotEnrichMap",
	"plotGSEA",
	"viewGSEA",
    "writeHits",	
    "getTopGeneSets",	
    "appendGSTerms",
	"interactome",
	"preprocess",
	"show",
	"summarize",
	"report"
)

