NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(camera,EdgeResult)
S3method(camera,LimmaVoomResult)
S3method(kendallW,eSet)
S3method(kendallW,matrix)
S3method(kendallWinfo,matrix)
S3method(print,FisherResult)
S3method(print,FisherResultList)
S3method(print,FishersMethodResult)
export("gsGeneValues<-")
export("gsGenes<-")
export()
export(AnnoBroadGseaRes)
export(AnnoBroadGseaResItem)
export(DGEList)
export(DesignContrast)
export(EdgeObject)
export(GeMS_BASE_URL)
export(GeMS_GENESETS_URL)
export(GeMS_INSERT_URL)
export(GeMS_REMOVE_URL)
export(GeMS_TEST_GENESETS_URL)
export(GeMS_TEST_URL)
export(biosCamera)
export(buildBroadGSEAcomm)
export(camera)
export(cameraDGEListByContrast)
export(cameraLimmaVoomResultsByContrast)
export(cameraTable2graph)
export(designMatrix)
export(doGse)
export(expandCameraTableGenes)
export(factorByNumberInStr)
export(fdrValue)
export(filterBySize)
export(fisherTest)
export(fishersMethod)
export(geneSetPerm)
export(getFDRCol)
export(getJsonResponse)
export(getPvalCol)
export(getSetWithNameFromGeMS)
export(getSetsWithNamesFromGeMS)
export(getSetsWithPropertyFromGeMS)
export(getUserSetsFromGeMS)
export(gsEffectiveSize)
export(gsFisherTestCore)
export(gsGeneCount)
export(gsGeneIndices)
export(gsGeneValues)
export(gsGenes)
export(gsListFisherTestCore)
export(gsName)
export(gsNamespace)
export(gsSize)
export(gseaCoreEnrichGenes)
export(gseaCoreEnrichThr)
export(gseaES)
export(gseaESprofile)
export(gseaFDR)
export(gseaFWER)
export(gseaFingerprint)
export(gseaFingerprintMatrix)
export(gseaNES)
export(gseaNP)
export(gseaResES)
export(gseaResQvalue)
export(gseaScore)
export(gseaScores)
export(hits)
export(insertGmtListToGeMS)
export(insertGmtListToGeMSBody)
export(isGeMSReachable)
export(isSigGeneSet)
export(kendallW)
export(kendallWmat)
export(kmeansGeneset)
export(list2mat)
export(logFCgage)
export(mergeCameraResults)
export(minFDRvalue)
export(minPvalue)
export(myGage)
export(orderByNumberInStr)
export(pValue)
export(parseCameraContributingGenes)
export(parseContributingGenes)
export(parseGSEAdir)
export(parseGenesetsContributingGenes)
export(prettyRonetGenesetNames)
export(printContributingGenes)
export(readCameraResults)
export(readDefaultGenesets)
export(readMPSGmt)
export(readRonetGmt)
export(readSigCameraResults)
export(readSigCameraScoreMatrix)
export(removeFromGeMS)
export(removeFromGeMSBody)
export(ronetGeneSetNamespace)
export(sigGeneSet)
export(sigGeneSetTable)
export(topGeneSetTable)
export(topOrSigGeneSetTable)
export(writeGmt)
export(zscoreDGE)
exportClasses(AnnoBroadGseaRes)
exportClasses(AnnoBroadGseaResItem)
exportClasses(AnnoBroadGseaResList)
exportClasses(BroadGseaResItem)
exportClasses(FisherResult)
exportClasses(FisherResultList)
exportClasses(GeneSetResult)
exportMethods("[")
exportMethods("gsGeneValues<-")
exportMethods("gsGenes<-")
exportMethods(as.data.frame)
exportMethods(fdrValue)
exportMethods(fisherTest)
exportMethods(gsEffectiveSize)
exportMethods(gsGeneIndices)
exportMethods(gsGeneValues)
exportMethods(gsGenes)
exportMethods(gsName)
exportMethods(gsNamespace)
exportMethods(gseaCoreEnrichGenes)
exportMethods(gseaCoreEnrichThr)
exportMethods(gseaES)
exportMethods(gseaESprofile)
exportMethods(gseaFDR)
exportMethods(gseaFWER)
exportMethods(gseaNES)
exportMethods(gseaNP)
exportMethods(hits)
exportMethods(pValue)
importClassesFrom(BioQC,GmtList)
importClassesFrom(Biobase,eSet)
importClassesFrom(ribiosNGS,EdgeResult)
importClassesFrom(ribiosNGS,LimmaVoomResult)
importFrom(BioQC,GmtList)
importFrom(BioQC,`gsNamespace<-`)
importFrom(BioQC,appendGmtList)
importFrom(BioQC,gsDesc)
importFrom(BioQC,gsGenes)
importFrom(BioQC,gsName)
importFrom(BioQC,gsNamespace)
importFrom(BioQC,hasNamespace)
importFrom(BioQC,matchGenes)
importFrom(BioQC,readGmt)
importFrom(Biobase,exprs)
importFrom(XML,xmlAttrs)
importFrom(XML,xmlChildren)
importFrom(XML,xmlName)
importFrom(XML,xmlRoot)
importFrom(XML,xmlTreeParse)
importFrom(dplyr,`%>%`)
importFrom(dplyr,arrange)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,pull)
importFrom(dplyr,ungroup)
importFrom(edgeR,DGEList)
importFrom(edgeR,estimateDisp)
importFrom(edgeR,getDispersion)
importFrom(edgeR,glmFit)
importFrom(edgeR,zscoreNBinom)
importFrom(gage,gage)
importFrom(graph,connComp)
importFrom(igraph,V)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(igraph,layout_in_circle)
importFrom(igraph,make_empty_graph)
importFrom(limma,camera)
importFrom(limma,contrastAsCoef)
importFrom(limma,rankSumTestWithCorrelation)
importFrom(limma,squeezeVar)
importFrom(limma,zscoreT)
importFrom(methods,as)
importFrom(methods,callGeneric)
importFrom(methods,is)
importFrom(methods,new)
importFrom(parallel,detectCores)
importFrom(parallel,mclapply)
importFrom(readr,parse_number)
importFrom(readr,read_tsv)
importFrom(ribiosExpression,DesignContrast)
importFrom(ribiosExpression,contrastMatrix)
importFrom(ribiosExpression,contrastNames)
importFrom(ribiosExpression,designMatrix)
importFrom(ribiosExpression,featureNames)
importFrom(ribiosExpression,phenoData)
importFrom(ribiosIO,readTable)
importFrom(ribiosIO,write_gmt)
importFrom(ribiosNGS,EdgeObject)
importFrom(ribiosNGS,dgeTable)
importFrom(ribiosNGS,dgeTables)
importFrom(ribiosNGS,dgeWithEdgeR)
importFrom(ribiosNGS,dgeWithLimmaVoom)
importFrom(ribiosNGS,fData)
importFrom(ribiosNGS,humanGeneSymbols)
importFrom(ribiosPlot,royalbluegrayred)
importFrom(ribiosUtils,assertFile)
importFrom(ribiosUtils,boundNorm)
importFrom(ribiosUtils,haltifnot)
importFrom(ribiosUtils,jaccardIndex)
importFrom(ribiosUtils,longdf2matrix)
importFrom(ribiosUtils,matchColumn)
importFrom(ribiosUtils,munion)
importFrom(ribiosUtils,pairwiseJaccardIndex)
importFrom(ribiosUtils,putColsFirst)
importFrom(ribiosUtils,sortByCol)
importFrom(ribiosUtils,uniqueNonNA)
importFrom(stats,ave)
importFrom(stats,cor)
importFrom(stats,dist)
importFrom(stats,fisher.test)
importFrom(stats,hclust)
importFrom(stats,kmeans)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,p.adjust)
importFrom(stats,pchisq)
importFrom(stats,pt)
importFrom(stats,qt)
importFrom(stats,sd)
importFrom(stats,var)
importFrom(utils,read.table)
importFrom(utils,write.table)
useDynLib(ribiosGSEA, .registration=TRUE, .fixes=`_ribiosGSEA_`)