ClustAssess
Tools for Assessing Clustering

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API for ClustAssess
Tools for Assessing Clustering

Global functions
Clustering Man page
Clustering-class Man page
add_env_variable Source code
add_metadata Man page Source code
are_identical_memberships Source code
assess_clustering_stability Man page Source code
assess_feature_stability Man page Source code
assess_nn_stability Man page Source code
assess_nn_stability_pca Source code
assess_nn_stability_umap Source code
automatic_stability_assessment Man page Source code
boxplot_settings Source code
calculate_dist Source code
calculate_markers Man page Source code
calculate_markers_shiny Man page Source code
calculate_pac_cpp Source code
calculate_ppr_with_power_iteration Source code
choose_stable_clusters Man page Source code
clustering_functions Source code
color_c_plot Source code
color_ggplot Source code
color_plot Source code
color_plot2 Source code
compar_annotation_info Source code
compar_distribution_info Source code
compar_enrichment_info Source code
compar_heatmap_gene_info Source code
compar_info Source code
compar_markers_info Source code
compar_metadata_jsi_info Source code
compar_violin_info Source code
computeSNN Source code
consensus_cluster Man page Source code
corrected_L1 Source code
corrected_l1_mb Source code
corrected_l1_mb_ Source code
corrected_l1_mb_very_old Source code
create_clu2elm_dict Source code
create_clu2elm_dict_hierarchical Source code
create_clustering Man page
create_clustering,Matrix-method Man page
create_clustering,character-method Man page
create_clustering,factor-method Man page
create_clustering,hclust-method Man page
create_clustering,integer-method Man page
create_clustering,matrix-method Man page
create_clustering,numeric-method Man page
create_clustering_list Source code
create_elm2clu_dict_hierarchical Source code
create_elm2clu_dict_overlapping Source code
create_flat_disjoint_clustering Source code
create_flat_overlapping_clustering Source code
create_monocle_default Man page Source code
create_monocle_from_clustassess Man page Source code
create_monocle_from_clustassess_app Man page Source code
create_seurat_object Source code
create_seurat_object_default Man page Source code
create_seurat_object_from_clustassess_app Man page Source code
disjointECS Source code
disjointECSaverage Source code
dist_path Source code
download_plot_handler Source code
download_plot_modal Source code
dr_choice_info Source code
dr_comparison_info Source code
dr_individual_ecc_info Source code
dr_individual_incremental_info Source code
dr_overall_ecc_info Source code
dr_overall_incremental_info Source code
dr_title_info Source code
element_agreement Man page Source code
element_agreement_flat_disjoint Source code
element_consistency Man page Source code
element_sim Man page Source code
element_sim_elscore Man page Source code
element_sim_matrix Man page Source code
element_sim_matrix_flat_disjoint Source code
empty_ggplot Source code
expression_ggplot Source code
fill_ggplot Source code
find_groups_in_cluster Source code
gclust_choice_info Source code
gclust_distro_overall_boxplot_info Source code
gclust_distro_res_boxplot_info Source code
gclust_info Source code
gclust_k_corresp_info Source code
gclust_k_stab_info Source code
gear_download Source code
gear_overall Source code
gear_umaps Source code
gene_name_transformation Source code
generate_breaks Source code
generate_colours Source code
getNNmatrix Man page Source code
get_clusters_from_clustassess_app Source code
get_clusters_from_clustassess_object Man page Source code
get_count_features Source code
get_dim_reduction_from_clustassess_app Source code
get_env_var Source code
get_expression_matrix_from_clustassess_app Source code
get_highest_prune_param Man page Source code
get_highest_prune_param_embedding Man page Source code
get_info_from_clustassess_app Source code
get_linkage_dist Source code
get_metadata_from_clustassess_app Source code
get_n_strong_components Source code
get_nn_conn_comps Man page Source code
get_nn_conn_comps_pca Source code
get_nn_conn_comps_umap Source code
get_sparse_transition_matrix Source code
grouped_boxplot_dataframe Source code
grouped_boxplot_list Source code
identify_cluster_markers Source code
is_package_installed Source code
jaccard_index Source code Source code
leiden_clustering Source code
length,Clustering-method Man page
make_cielg_hierarchical Source code
make_cielg_overlapping Source code
marker_overlap Man page Source code
mask_ggplot Source code
merge_identical_partitions Source code
merge_partitions Man page Source code
merge_partitions_ecs Source code
merge_resolutions Man page Source code
metadata_ggplot Source code
metadata_plot Source code
myContTable Source code
numerical_ppr_scores Source code
only_legend_metadata_plot Source code
only_legend_plot Source code
pac_convergence Man page Source code
pac_landscape Man page Source code
plot_clustering_difference_facet Man page Source code
plot_clustering_overall_stability Man page Source code
plot_clustering_per_value_stability Man page Source code
plot_connected_comps_evolution Man page Source code
plot_feature_overall_stability_boxplot Man page Source code
plot_feature_overall_stability_incremental Man page Source code
plot_feature_per_resolution_stability_boxplot Man page Source code
plot_feature_per_resolution_stability_incremental Man page Source code
plot_feature_stability_ecs_facet Man page Source code
plot_feature_stability_mb_facet Man page Source code
plot_k_n_partitions Man page Source code
plot_k_resolution_corresp Man page Source code
plot_n_neigh_ecs Man page Source code
plot_n_neigh_k_correspondence Man page Source code
ppr_partition Source code
print,Clustering-method Man page
process_clustering_arguments Source code
process_umap_arguments Source code
pruneSNN Source code
rank_configs Source code
render_plot_by_height Source code
rescale_path Source code
server_cell_annotation Source code
server_colour_picker Source code
server_comparison_enrichment Source code
server_comparison_gene_heatmap Source code
server_comparison_gene_panel Source code
server_comparison_jsi Source code
server_comparison_markers Source code
server_comparison_markers_panels Source code
server_comparison_metadata_panel Source code
server_comparison_violin_gene Source code
server_comparisons Man page Source code
server_dimensionality_choice Source code
server_dimensionality_distribution Source code
server_dimensionality_reduction Man page Source code
server_dimensionality_stability Source code
server_graph_clustering Man page Source code
server_graph_clustering_choice Source code
server_graph_clustering_k_stab Source code
server_graph_clustering_overall_boxplot Source code
server_graph_clustering_per_value_boxplot Source code
server_graph_clustering_per_value_umap Source code
server_graph_construction Man page Source code
server_landing_page Man page Source code
server_sandbox Man page Source code
server_sandbox_config_choice Source code
server_sandbox_gene_panel_left Source code
server_sandbox_gene_panel_right Source code
server_sandbox_jsi Source code
server_sandbox_metadata_panel_left Source code
server_sandbox_metadata_panel_right Source code
seurat_clustering Source code
shadowtext Source code
shiny_ggplot_clustering_overall_stability Source code
shiny_ggplot_clustering_per_value_stability Source code
shiny_ggplot_k_n_partitions Source code
shiny_ggplot_k_resolution_corresp Source code
shiny_plot_clustering_overall_stability Source code
shiny_plot_clustering_per_value_stability Source code
shiny_plot_clustering_per_value_stability_old Source code
shiny_plot_feature_stability_boxplot Source code
shiny_plot_feature_stability_incremental Source code
shiny_plot_k_n_partitions Source code
shiny_plot_k_res Source code
stable_config_info Source code
ui_cell_annotation Source code
ui_cell_annotation_element Source code
ui_colour_picker Source code
ui_comparison_enrichment Source code
ui_comparison_gene_heatmap Source code
ui_comparison_gene_panel Source code
ui_comparison_jsi_panel Source code
ui_comparison_markers Source code
ui_comparison_markers_panel Source code
ui_comparison_metadata_panel Source code
ui_comparison_violin_gene Source code
ui_comparisons Man page Source code
ui_dimensionality_choice Source code
ui_dimensionality_distribution_plots Source code
ui_dimensionality_reduction Man page Source code
ui_dimensionality_stability Source code
ui_graph_clustering Man page Source code
ui_graph_clustering_choice Source code
ui_graph_clustering_k_stab Source code
ui_graph_clustering_overall_boxplot Source code
ui_graph_clustering_per_value_boxplot Source code
ui_graph_clustering_per_value_umap Source code
ui_graph_construction Man page Source code
ui_landing_page Man page Source code
ui_sandbox Man page Source code
ui_sandbox_config_choice Source code
ui_sandbox_gene_panel Source code
ui_sandbox_jsi_panel Source code
ui_sandbox_metadata_panel Source code
update_connectivity_cpp Source code
update_gears_width Source code
update_seurat_object Source code
update_sliders Source code
voting_scheme_ggplot Source code
weighted_element_consistency Man page Source code
wilcox_test Source code
write_objects Man page Source code
write_shiny_app Man page Source code
write_shiny_app.Seurat Man page Source code
write_shiny_app.default Man page Source code
ClustAssess documentation built on April 3, 2025, 9:34 p.m.

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