ED1                     Compute Euclidean distance matrix by rows
ED2                     Compute Euclidean distance matrix by columns
ann                     Cell type annotations for data extracted from a
                        publication by Yan et al.
calculate_distance      Calculate a distance matrix
calculate_stability     Calculate the stability index of the obtained
                        clusters when changing 'k'
consensus_matrix        Calculate consensus matrix
consmx                  Consensus matrix computation
estkTW                  Estimate the optimal k for k-means clustering
get_auroc               Calculate the area under the ROC curve for a
                        given gene.
get_biolgy              Wrapper for calculating biological properties
get_de_genes            Find differentially expressed genes
get_marker_genes        Calculate marker genes
get_outl_cells          Find cell outliers in each cluster.
get_processed_dataset   Get processed dataset used by 'SC3' clustering
markers_for_heatmap     Reorder and subset gene markers for plotting on
                        a heatmap
norm_laplacian          Graph Laplacian calculation
organise_de_genes       Get differentiall expressed genes from an
                        object of 'SingleCellExperiment' class
organise_marker_genes   Get marker genes from an object of
                        'SingleCellExperiment' class
prepare_for_svm         A helper function for the SVM analysis
reindex_clusters        Reindex cluster labels in ascending order
sc3                     Run all steps of 'SC3' in one go
sc3_calc_biology        Calculate DE genes, marker genes and cell
                        outliers.
sc3_calc_consens        Calculate consensus matrix.
sc3_calc_dists          Calculate distances between the cells.
sc3_calc_transfs        Calculate transformations of the distance
                        matrices.
sc3_estimate_k          Estimate the optimal number of cluster 'k' for
                        a scRNA-Seq expression matrix
sc3_export_results_xls
                        Write 'SC3' results to Excel file
sc3_interactive         Opens 'SC3' results in an interactive session
                        in a web browser.
sc3_kmeans              'kmeans' clustering of cells.
sc3_plot_cluster_stability
                        Plot stability of the clusters
sc3_plot_consensus      Plot consensus matrix as a heatmap
sc3_plot_de_genes       Plot expression of DE genes of the clusters
                        identified by 'SC3' as a heatmap
sc3_plot_expression     Plot expression matrix used for SC3 clustering
                        as a heatmap
sc3_plot_markers        Plot expression of marker genes identified by
                        'SC3' as a heatmap.
sc3_plot_silhouette     Plot silhouette indexes of the cells
sc3_prepare             Prepare the 'SingleCellExperiment' object for
                        'SC3' clustering.
sc3_run_svm             Run the hybrid 'SVM' approach.
support_vector_machines
                        Run support vector machines ('SVM') prediction
tmult                   Matrix left-multiplied by its transpose
transformation          Distance matrix transformation
yan                     Single cell RNA-Seq data extracted from a
                        publication by Yan et al.
