NAMESPACE

# Generated by roxygen2: do not edit by hand

export(Rphenograph)
export(addMetaData)
export(buildTree)
export(changeMarker)
export(constraintMatrix)
export(correctBatchCYT)
export(createCYT)
export(defLeafCells)
export(defRootCells)
export(fetchCell)
export(fetchClustMeta)
export(fetchPlotMeta)
export(find_neighbors)
export(gatingMatrix)
export(plot2D)
export(plot3D)
export(plotBranchHeatmap)
export(plotCluster)
export(plotClusterHeatmap)
export(plotHeatmap)
export(plotMarkerDensity)
export(plotPieCluster)
export(plotPieTree)
export(plotPseudotimeDensity)
export(plotPseudotimeTraj)
export(plotTrajHeatmap)
export(plotTree)
export(plotViolin)
export(processingCluster)
export(runClara)
export(runCluster)
export(runDiff)
export(runDiffusionMap)
export(runExprsExtract)
export(runExprsMerge)
export(runFastPCA)
export(runHclust)
export(runKNN)
export(runKmeans)
export(runMclust)
export(runPhenograph)
export(runPseudotime)
export(runSOM)
export(runTSNE)
export(runUMAP)
export(runWalk)
export(subsetCYT)
export(updateClustMeta)
export(updatePlotMeta)
exportClasses(CYT)
exportMethods(show)
import(BiocNeighbors)
import(FlowSOM)
import(Matrix)
import(Rcpp)
import(Rtsne)
import(destiny)
import(flowUtils)
import(ggplot2)
import(gmodels)
import(limma)
import(matrixStats)
import(pheatmap)
import(prettydoc)
import(scatterpie)
import(scatterplot3d)
import(umap)
importClassesFrom(destiny,DPT)
importClassesFrom(destiny,DiffusionMap)
importClassesFrom(flowCore,transformList)
importClassesFrom(methods,ANY)
importClassesFrom(methods,character)
importClassesFrom(methods,formula)
importClassesFrom(methods,logical)
importClassesFrom(methods,matrix)
importClassesFrom(methods,missing)
importFrom(FlowSOM,SOM)
importFrom(RANN,nn2)
importFrom(cluster,clara)
importFrom(flowCore,arcsinhTransform)
importFrom(flowCore,biexponentialTransform)
importFrom(flowCore,compensate)
importFrom(flowCore,estimateLogicle)
importFrom(flowCore,logicleTransform)
importFrom(flowCore,parameters)
importFrom(flowCore,read.FCS)
importFrom(flowCore,transformList)
importFrom(gmodels,fast.prcomp)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,rainbow)
importFrom(grid,current.viewport)
importFrom(grid,get.gpar)
importFrom(grid,gpar)
importFrom(grid,grid.points)
importFrom(grid,grid.polygon)
importFrom(grid,grid.rect)
importFrom(grid,unit)
importFrom(igraph,as_data_frame)
importFrom(igraph,cluster_louvain)
importFrom(igraph,distances)
importFrom(igraph,graph.adjacency)
importFrom(igraph,graph.data.frame)
importFrom(igraph,layout.kamada.kawai)
importFrom(igraph,layout_as_tree)
importFrom(igraph,membership)
importFrom(igraph,minimum.spanning.tree)
importFrom(igraph,modularity)
importFrom(igraph,shortest_paths)
importFrom(igraph,simplify)
importFrom(mclust,Mclust)
importFrom(mclust,mclustBIC)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(stats,IQR)
importFrom(stats,aggregate)
importFrom(stats,cutree)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,kmeans)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,predict)
importFrom(stats,quantile)
importFrom(stats,rnorm)
importFrom(stringr,fixed)
importFrom(stringr,str_replace_all)
importFrom(sva,ComBat)
importMethodsFrom(Biobase,"pData<-")
importMethodsFrom(Biobase,"sampleNames<-")
importMethodsFrom(Biobase,exprs)
importMethodsFrom(Biobase,pData)
importMethodsFrom(Biobase,phenoData)
importMethodsFrom(Biobase,sampleNames)
importMethodsFrom(flowCore,transform)
useDynLib(CytoTree)