export(

SPIA, DEGraph, Clipper, TBS, PWEA, TAPPA, TopologyGSA,
res, topo.sig, degtable,
convertIdentifiersByVector,
AdjacencyMatrix2Pathway, graphNEL2Pathway,
reduceGraph
)
S3method(print, topResult)
S3method(topo.sig, topResult)
S3method(degtable, topResult)
S3method(res, topResult)
S3method(summary, topResult)
S3method(plot,topResult)

import(graphite, gRbase, graph, locfit)
importFrom(DESeq2, DESeqDataSetFromMatrix, DESeq, results, estimateSizeFactors, estimateDispersions, nbinomWaldTest, varianceStabilizingTransformation)
importFrom(GenomicRanges, assay, colData, "colData<-")

importFrom(igraph, shortest.paths,igraph.from.graphNEL, get.all.shortest.paths)
importFrom(R.utils, reassignInPackage)
importFrom(edgeR,DGEList, calcNormFactors)


importFrom(DESeq, newCountDataSet, estimateSizeFactors, estimateDispersions)
importFrom(fields, image.plot)
importFrom(TeachingDemos, shadowtext)
importFrom(limma,  lmFit, makeContrasts, contrasts.fit, eBayes, decideTests, topTable, voom) 
importMethodsFrom(graph, edgeData, edgeDataDefaults)

importFrom(SPIA, spia)
importFrom(clipper, pathQ, easyClip, cliqueMeanTest, cliqueVarianceTest)
importFrom(topologyGSA, pathway.mean.test, pathway.var.test, clique.mean.test, clique.var.test)
