export(stoufferTest)
export(scorePval)
export(runGOseq)
export(runSpinglass)
export(runBioNet)
export(plotModule)
export(highScores)
export(extractScores)
export(extractModules)
export(extractGOseq)
export(searchGOseq)
export(removeModification)
export(plotDensityPval)
export(plotCompareScores)
export(normalizePval)
export(makePvalueObject)
export(makePvalueAnnotation)
export(extractModSummary)
export(extractModification)
export(extractExpression)
export(convertGeneIds)
export(annotateModification)
export(annotateExpression)
export(addShadowText)
importFrom("goseq", goseq)
importFrom("goseq", nullp)
importFrom("scales", rescale)
importFrom("Hmisc",cut2)
importFrom("plyr", join)
importClassesFrom("igraph")
importFrom("igraph", simplify,clusters,
            as_adjacency_matrix,
           graph_from_adjacency_matrix,
           induced_subgraph, V, E,
           igraph.from.graphNEL,igraph.to.graphNEL,
           layout_in_circle,layout_with_fr,vcount,
           cluster_spinglass, 'V<-', 'E<-')

import("GenomicRanges")
import("AnnotationDbi")
import("org.Hs.eg.db")
import("ggplot2")
import("Biobase")
import("methods")
import("geneLenDataBase")
importFrom("S4Vectors", queryHits)
importFrom("IRanges", IRanges)
importFrom("KEGGREST",keggLink, keggList) 
importFrom("reactome.db", reactomeEXTID2PATHID, reactomePATHID2NAME)
importFrom("BioNet",runFastHeinz, subNetwork, rmSelfLoops)
import("tools")
importFrom("grDevices", "colorRampPalette", "dev.cur", "dev.new",
             "dev.off", "palette", "pdf", "xy.coords")
importFrom("graphics", "axis", "box", "legend", "lines", "par", "plot",
             "plot.new", "plot.window", "points", "polygon", "strheight",
             "strwidth", "text", "title")
importFrom("stats", "cor", "density", "dist", "pbinom", "pchisq",
             "pnorm", "qchisq", "qnorm", "sd", "weighted.mean",
             "wilcox.test")
importFrom("utils", "data")