add_metadata            Add metadata to ClustAssess ShinyApp
assess_clustering_stability
                        Assessment of Stability for Graph Clustering
assess_feature_stability
                        Assess the stability for configurations of
                        feature types and sizes
assess_nn_stability     Assess the stability for Graph Building
                        Parameters
automatic_stability_assessment
                        Assessment of Stability for Graph Clustering
calculate_markers       Calculate markers
calculate_markers_shiny
                        Calculate markers - Shiny
choose_stable_clusters
                        Choose stable clusters based on ECC and
                        frequency
consensus_cluster       Consensus Clustering and Proportion of
                        Ambiguously Clustered Pairs
create_monocle_default
                        Create monocle object
create_monocle_from_clustassess
                        Create monocle object from a ClustAssess object
create_monocle_from_clustassess_app
                        Create monocle object from a ClustAssess shiny
                        app
create_seurat_object_default
                        Create Seurat object
create_seurat_object_from_clustassess_app
                        Create Seurat object from a ClustAssess shiny
                        app
element_agreement       Element-Wise Average Agreement Between a Set of
                        Clusterings
element_consistency     Element-Wise Consistency Between a Set of
                        Clusterings
element_sim             The Element-Centric Clustering Similarity
element_sim_elscore     The Element-Centric Clustering Similarity for
                        each Element
element_sim_matrix      Pairwise Comparison of Clusterings
getNNmatrix             Computes the NN adjacency matrix given the
                        neighbours
get_clusters_from_clustassess_object
                        Extract config-specific clusters from a
                        ClustAssess object
get_colour_vector_from_palette
                        Get the vector of colours from a palette
get_highest_prune_param
                        Calculate the highest pruning parameter for the
                        SNN graph given NN matrix
get_highest_prune_param_embedding
                        Calculate the highest pruning parameter for the
                        SNN graph given Embedding
get_nn_conn_comps       Relationship Between Nearest Neighbours and
                        Connected Components
marker_overlap          Cell-Wise Marker Gene Overlap
merge_partitions        Merge Partitions
merge_resolutions       Merge Partitions from different Resolutions
pac_convergence         PAC Convergence Plot
pac_landscape           PAC Landscape Plot
plot_clust_hierarchical
                        Hierarchical relationship between partitions
                        with different number of clusters
plot_clustering_difference_facet
                        Clustering Method Stability Facet Plot
plot_clustering_overall_stability
                        Clustering Method Overall Stability Boxplot
plot_clustering_per_value_stability
                        Clustering Method per value Stability Boxplot
plot_connected_comps_evolution
                        Relationship Between Number of Nearest
                        Neighbours and Graph Connectivity
plot_feature_overall_stability_boxplot
                        Overall Feature Stability Boxplot
plot_feature_overall_stability_incremental
                        Overall Feature Stability Incremental Boxplot
plot_feature_per_resolution_stability_boxplot
                        Per resolution Feature Stability Boxplot
plot_feature_per_resolution_stability_incremental
                        Per resolution - Feature Stability Incremental
                        Boxplot
plot_feature_stability_ecs_facet
                        Feature Stability - EC Consistency Facet Plot
plot_feature_stability_mb_facet
                        Feature Stability - Cluster Membership Facet
                        Plot
plot_k_n_partitions     Relationship Between the Number of Clusters and
                        the Number of Unique Partitions
plot_k_resolution_corresp
                        Correspondence Between Resolution and the
                        Number of Clusters
plot_n_neigh_ecs        Graph construction parameters - ECC facet
plot_n_neigh_k_correspondence
                        Relationship Between Number of Nearest
                        Neighbours and Number of Clusters
server_comparisons      Server - Comparison module
server_dimensionality_reduction
                        Server - Dimensionality reduction module
server_graph_clustering
                        Server - Graph clustering module
server_graph_construction
                        Server - Graph construction module
server_landing_page     Server - Landing page module
server_sandbox          Server - Sandbox module
ui_comparisons          UI - Comparison module
ui_dimensionality_reduction
                        UI - Dimensionality reduction module
ui_graph_clustering     UI - Graph clustering module
ui_graph_construction   UI - Graph construction module
ui_landing_page         UI - Landing page module
ui_sandbox              UI - Sandbox module
weighted_element_consistency
                        Weighted Element-Centric Consistency
write_objects           Write the objects for the ClustAssess ShinyApp
write_shiny_app         Create the ClustAssess ShinyApp
