NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(GeneSetDb,default)
S3method(all.equal,GeneSetDb)
S3method(as.data.frame,GeneSetDb)
S3method(as.list,GeneSetDb)
S3method(fdata,default)
S3method(pdata,default)
S3method(rename_rows,DGEList)
S3method(rename_rows,EList)
S3method(rename_rows,SummarizedExperiment)
S3method(rename_rows,default)
S3method(rename_rows,eSet)
S3method(result,MultiGSEAResult)
S3method(scale_rows,Matrix)
S3method(scale_rows,default)
S3method(scale_rows,matrix)
S3method(scale_rows,sparseMatrix)
export("featureIdType<-")
export("geneSetCollectionURLfunction<-")
export("org<-")
export(GeneSetDb)
export(addCollectionMetadata)
export(addGeneSetMetadata)
export(annotateGeneSetMembership)
export(calculateIndividualLogFC)
export(corplot)
export(eigenWeightedMean)
export(encode_gskey)
export(exampleDgeResult)
export(exampleExpressionSet)
export(exampleGeneSetDF)
export(exampleGeneSetDb)
export(exampleGeneSets)
export(exampleMultiGSEAResult)
export(failWith)
export(geneSetDb)
export(geneSets)
export(geneSetsStats)
export(getGOslimGeneSetDb)
export(getHousekeepingGeneSetDb)
export(getKeggGeneSetDb)
export(getMSigGeneSetDb)
export(getPantherGeneSetDb)
export(getReactomeGeneSetDb)
export(goseq)
export(gsdScore)
export(hasGeneSet)
export(hasGeneSetCollection)
export(incidenceMatrix)
export(iplot)
export(is.active)
export(is.conformed)
export(load_id_xref)
export(logFC)
export(mgheatmap)
export(mgheatmap2)
export(msg)
export(multiGSEA)
export(multiGSEA_methods)
export(ora)
export(p.matrix)
export(pcWeightedMean)
export(plot_ora_bias)
export(remap_identifiers)
export(rename_rows)
export(result)
export(resultNames)
export(results)
export(scale_rows)
export(scoreSingleSamples)
export(species_info)
export(split_gskey)
export(ssGSEA.normalize)
export(tabulateResults)
export(validateInputs)
export(volcanoPlot)
export(volcanoStatsTable)
export(zScore)
export(ztransformPvalues)
exportClasses(GeneSetDb)
exportClasses(MultiGSEAResult)
exportMethods("[")
exportMethods(append)
exportMethods(collectionMetadata)
exportMethods(combine)
exportMethods(conform)
exportMethods(featureIdMap)
exportMethods(featureIdType)
exportMethods(featureIds)
exportMethods(geneSet)
exportMethods(geneSetCollectionURLfunction)
exportMethods(geneSetSummaryByGenes)
exportMethods(geneSetURL)
exportMethods(geneSets)
exportMethods(nrow)
exportMethods(org)
exportMethods(subsetByFeatures)
exportMethods(summarized)
exportMethods(unconform)
import(checkmate)
import(data.table)
import(magrittr)
import(methods)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpparam)
importFrom(ComplexHeatmap,Heatmap)
importFrom(DelayedMatrixStats,rowSds)
importFrom(GSEABase,ENSEMBLIdentifier)
importFrom(GSEABase,EntrezIdentifier)
importFrom(GSEABase,GeneSet)
importFrom(GSEABase,GeneSetCollection)
importFrom(GSEABase,NullIdentifier)
importFrom(GSEABase,geneIdType)
importFrom(GSEABase,geneIds)
importFrom(GSEABase,setName)
importFrom(GSVA,gsva)
importFrom(Matrix,rankMatrix)
importFrom(circlize,colorRamp2)
importFrom(edgeR,camera.DGEList)
importFrom(edgeR,cpm)
importFrom(edgeR,fry.DGEList)
importFrom(edgeR,glmFit)
importFrom(edgeR,glmLRT)
importFrom(edgeR,glmQLFTest)
importFrom(edgeR,glmQLFit)
importFrom(edgeR,glmTreat)
importFrom(edgeR,mroast.DGEList)
importFrom(edgeR,romer.DGEList)
importFrom(edgeR,topTags)
importFrom(ggplot2,aes)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_hex)
importFrom(ggplot2,geom_jitter)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,theme_bw)
importFrom(grDevices,col2rgb)
importFrom(grDevices,rgb)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,hist)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,pairs)
importFrom(graphics,par)
importFrom(graphics,points)
importFrom(graphics,rect)
importFrom(graphics,segments)
importFrom(graphics,smoothScatter)
importFrom(graphics,strwidth)
importFrom(graphics,text)
importFrom(irlba,svdr)
importFrom(limma,barcodeplot)
importFrom(limma,camera)
importFrom(limma,cameraPR)
importFrom(limma,contrasts.fit)
importFrom(limma,eBayes)
importFrom(limma,fry)
importFrom(limma,geneSetTest)
importFrom(limma,kegga)
importFrom(limma,lmFit)
importFrom(limma,mroast)
importFrom(limma,romer)
importFrom(limma,topTable)
importFrom(limma,topTreat)
importFrom(limma,treat)
importFrom(limma,voom)
importFrom(msigdb.data,msigdb_retrieve)
importFrom(plotly,add_lines)
importFrom(plotly,add_markers)
importFrom(plotly,config)
importFrom(plotly,ggplotly)
importFrom(plotly,layout)
importFrom(plotly,plot_ly)
importFrom(plotly,plotly_build)
importFrom(stats,approx)
importFrom(stats,as.dendrogram)
importFrom(stats,as.dist)
importFrom(stats,cor)
importFrom(stats,density)
importFrom(stats,filter)
importFrom(stats,hclust)
importFrom(stats,model.matrix)
importFrom(stats,order.dendrogram)
importFrom(stats,p.adjust)
importFrom(stats,phyper)
importFrom(stats,quantile)
importFrom(stats,runif)
importFrom(stats,setNames)
importFrom(stats,weighted.mean)
importFrom(utils,getFromNamespace)
importFrom(utils,head)
importFrom(utils,packageVersion)
importFrom(utils,read.csv)
importFrom(utils,tail)
importFrom(utils,write.csv)
importFrom(viridis,viridis)
importMethodsFrom(BiocGenerics,append)
importMethodsFrom(BiocGenerics,combine)
importMethodsFrom(BiocGenerics,nrow)