# Generated by roxygen2: do not edit by hand

export(calcCounts)
export(calcMedians)
export(calcMediansByClusterMarker)
export(calcMediansBySampleMarker)
export(createContrast)
export(createDesignMatrix)
export(createFormula)
export(diffcyt)
export(generateClusters)
export(plotHeatmap)
export(prepareData)
export(testDA_GLMM)
export(testDA_edgeR)
export(testDA_voom)
export(testDS_LMM)
export(testDS_limma)
export(topClusters)
export(topTable)
export(transformData)
importFrom(ComplexHeatmap,'+.AdditiveUnit')
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,anno_text)
importFrom(ComplexHeatmap,columnAnnotation)
importFrom(ComplexHeatmap,draw)
importFrom(ComplexHeatmap,max_text_width)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(FlowSOM,BuildMST)
importFrom(FlowSOM,BuildSOM)
importFrom(FlowSOM,ReadInput)
importFrom(FlowSOM,metaClustering_consensus)
importFrom(S4Vectors,'metadata<-')
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(SummarizedExperiment,'assays<-')
importFrom(SummarizedExperiment,'colData<-')
importFrom(SummarizedExperiment,'rowData<-')
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(circlize,colorRamp2)
importFrom(dplyr,group_by)
importFrom(dplyr,summarize)
importFrom(dplyr,tally)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,estimateDisp)
importFrom(edgeR,glmFit)
importFrom(edgeR,glmLRT)
importFrom(edgeR,topTags)
importFrom(flowCore,exprs)
importFrom(flowCore,flowFrame)
importFrom(flowCore,flowSet)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(graphics,plot)
importFrom(grid,gpar)
importFrom(limma,contrasts.fit)
importFrom(limma,duplicateCorrelation)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,plotSA)
importFrom(limma,topTable)
importFrom(limma,voom)
importFrom(lme4,glmer)
importFrom(lme4,lmer)
importFrom(magrittr,'%>%')
importFrom(methods,as)
importFrom(methods,is)
importFrom(multcomp,glht)
importFrom(reshape2,acast)
importFrom(reshape2,melt)
importFrom(stats,as.formula)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,p.adjust)
importFrom(stats,quantile)
importFrom(tidyr,complete)
importFrom(utils,head)
