AnnotationScatterPlot   Visualiation of a custom annotation over
                        nonlinear dimensionality reduction
CalcSilhInfo            Estimating optimal K using silhouette
ClusteringScatterPlot   Visualize the clustering over nonliner
                        dimensionality reduction
DownOverSampling        Down- and oversample data
FindAllGeneMarkers      identification of gene markers for all clusters
FindGeneMarkers         Identification of gene markers for a cluster or
                        two arbitrary combinations of clusters
GeneHeatmap             Heatmap visualization of the gene markers
                        identified by FindAllGeneMarkers
GeneScatterPlot         Visualize gene expression over nonlinear
                        dimensionality reduction
HierarchicalClustering
                        Hierarchical clustering using the Ward's method
LogisticRegression      Clustering projection using logistic regression
                        from the LiblineaR R package
MergeClusters           Merge clusters
PCAElbowPlot            Elbow plot of the standard deviations of the
                        principal components
PrepareILoReg           Prepare 'SingleCellExperiment' object for
                        'ILoReg' analysis
RenameAllClusters       Renaming all clusters at once
RenameCluster           Renaming one cluster
RunICP                  Iterative Clustering Projection (ICP)
                        clustering
RunPCA                  PCA transformation of the joint probability
                        matrix
RunParallelICP          Run ICP runs parallerly
RunTSNE                 Barnes-Hut implementation of t-Distributed
                        Stochastic Neighbor Embedding (t-SNE)
RunUMAP                 Uniform Manifold Approximation and Projection
                        (UMAP)
SelectKClusters         Selecting K clusters from hierarchical
                        clustering
SelectTopGenes          Select top or bottom N genes based on a
                        selection criterion
SilhouetteCurve         Silhouette curve
VlnPlot                 Gene expression visualization using violin
                        plots
pbmc3k_500              A toy dataset with 500 cells downsampled from
                        the pbmc3k dataset.
