CYT-class               Class 'CYT'
CytoTree-package        Visualization and analyzation for flow
                        cytometry data
Rphenograph             RphenoGraph clustering
buildTree               buildTree
constraintMatrix        constraintMatrix
correctBatchCYT         correctBatchCYT
createCYT               create an CYT object
defLeafCells            definition of leaf cells
defRootCells            definition of root cells
fetchCell               Fetching cellls of CYT
fetchClustMeta          Fetching clusters' metadata of CYT
fetchPlotMeta           Fetching plot metadata of CYT
find_neighbors          K Nearest Neighbour Search
gatingMatrix            Apply gating on the matrix data
plot2D                  Visualization of 2D data of CYT
plot3D                  Visualization of 3D data of CYT
plotBranchHeatmap       Visualization heatmap of branch data of CYT
plotCluster             Visualization of cluster data of CYT
plotClusterHeatmap      Visualization heatmap of cluster data of CYT
plotHeatmap             Visualization heatmap of data of CYT
plotMarkerDensity       plotMarkerDensity
plotPieCluster          Visualization pie plot of cluster data of CYT
plotPieTree             plot MST pie of CYT
plotPseudotimeDensity   plot Pseudotime density of CYT
plotPseudotimeTraj      plotPseudotimeTraj
plotTrajHeatmap         Visualization heatmap of intermediate cells of
                        CYT
plotTree                plot MST of CYT
plotViolin              Visualization violin plot of CYT
processingCluster       processingCluster
runClara                runClara
runCluster              Specific Clustering Method Toolkits
runDiff                 Calculate differential expression markers
runDiffusionMap         Calculate diffusion map in CYT
runExprsExtract         Extract the expression data from a FCS file
                        with preprocessing
runExprsMerge           Merge the expression matrix from multiple FCS
                        files with preprocessing
runFastPCA              Calculate principal components in CYT
runHclust               runHclust
runKNN                  Calculate k-nearest neighbors of CYT
runKmeans               runKmeans
runMclust               runMclust
runPhenograph           RphenoGraph clustering
runPseudotime           Calculation of Pseudotime
runSOM                  calculation SOM in CYT object
runTSNE                 Calculate t-Distributed Stochastic Neighbor
                        Embedding in CYT
runUMAP                 Calculating UMAP
runWalk                 Walk between root cells and leaf cells
subsetCYT               subset CYT object
updateClustMeta         Update clusters' meta information of CYT
updatePlotMeta          Update plot meta information of CYT
