##Namespace file for SeqGSEA package
import(methods, Biobase, doParallel)
import(DESeq2)
importFrom(biomaRt, getBM, useMart)

export(
    "DENBStat4GSEA",
    "DENBStatPermut4GSEA",
    "DENBTest",
    "DEpermutePval",
    "DSpermute4GSEA",
    "DSpermutePval",
    "DSresultExonTable",
    "DSresultGeneTable",
    "GSEAresultTable",
    "GSEnrichAnalyze",
    "calES",
    "calES.perm",
    "convertEnsembl2Symbol",
    "convertSymbol2Ensembl",
    "estiExonNBstat",
    "estiGeneNBstat",
    "exonID",
    "exonTestability",
    "geneID",
    "geneList",
    "genePermuteScore",
    "geneScore",
    "geneSetDescs",
    "geneSetNames",
    "geneSetSize",
    "geneTestability",
    "genpermuteMat",
    "getGeneCount",
    "label",
    "loadExonCountData",
    "loadGenesets",
    "newGeneSets",
    "newReadCountSet",
    "normES",
    "normFactor",
    "plotES",
    "plotGeneScore",
    "plotSig",
    "plotSigGeneSet",
    "rankCombine",
    "runDESeq",
    "runSeqGSEA",
    "scoreNormalization",
    "signifES",
    "size",
    "subsetByGenes",
    "topDEGenes",
    "topDSExons",
    "topDSGenes",
    "topGeneSets",
    "writeSigGeneSet",
    "writeScores",
    "runSeqGSEA"
)
exportMethods(
    "counts",
    "counts<-",
    "["
)
exportClasses(
    "SeqGeneSet",
    "ReadCountSet" 
)

