├── .Rbuildignore ├── .gitignore ├── ClustAssess.Rproj ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── ECS.R ├── PAC.R ├── RcppExports.R ├── convert.R ├── generics.R ├── marker-overlap.R ├── shiny-app.R ├── shiny-comparisons.R ├── shiny-feature-stability.R ├── shiny-graph-clustering.R ├── shiny-graph-construction.R ├── shiny-info.R ├── shiny-landing-page.R ├── shiny-sandbox.R ├── shiny-utils.R ├── stability-1-dim-reduction.R ├── stability-2-graph-construction.R ├── stability-3-graph-clustering.R ├── stability-based-parameter-assessment.R └── utils.R ├── README.md ├── _pkgdown.yml ├── cran-comments.md ├── docs ├── 404.html ├── LICENSE-text.html ├── LICENSE.html ├── articles │ ├── ClustAssess.html │ ├── ClustAssess_files │ │ ├── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ │ └── figure-html │ │ │ ├── ecs-1.png │ │ │ ├── ecs-2.png │ │ │ ├── ecs-3.png │ │ │ ├── frust-1.png │ │ │ ├── jsi-1.png │ │ │ ├── pac-1.png │ │ │ ├── pac-2.png │ │ │ └── setup-1.png │ ├── comparing-soft-and-hierarchical.html │ ├── comparing-soft-and-hierarchical_files │ │ ├── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ │ └── figure-html │ │ │ ├── clustering-1.png │ │ │ ├── clustering-2.png │ │ │ ├── clustering-3.png │ │ │ ├── ecs-1.png │ │ │ ├── ecs-2.png │ │ │ ├── ecs-3.png │ │ │ └── setup-1.png │ ├── index.html │ ├── stability-dim-reduction-flexibility.html │ ├── stability-dim-reduction-flexibility_files │ │ ├── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ │ └── figure-html │ │ │ ├── umap_atac-1.png │ │ │ ├── umap_harmony-1.png │ │ │ └── umap_pca-1.png │ ├── stability-pipeline-description.html │ ├── stability-pipeline-description_files │ │ ├── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ │ └── figure-html │ │ │ ├── comps_evo-1.png │ │ │ ├── k_n_part_1-1.png │ │ │ ├── k_n_part_1-2.png │ │ │ ├── k_res_corr_1-1.png │ │ │ ├── k_res_corr_1-2.png │ │ │ ├── n_k_corr-1.png │ │ │ ├── n_neigh_ecs-1.png │ │ │ ├── phenograph_different_plots-1.png │ │ │ ├── qc-1.png │ │ │ ├── qc_violin-1.png │ │ │ ├── qc_violin_post-1.png │ │ │ ├── stab_boxplot-1.png │ │ │ ├── stab_ecs-1.png │ │ │ ├── stab_ecs_inc-1.png │ │ │ ├── stab_mb-1.png │ │ │ ├── unnamed-chunk-10-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── stability-pipeline-shiny.html │ └── stability-pipeline-shiny_files │ │ └── accessible-code-block-0.0.1 │ │ └── empty-anchor.js ├── authors.html ├── deps │ ├── bootstrap-5.3.1 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ └── bootstrap.min.css │ ├── bootstrap-toc-1.0.1 │ │ └── bootstrap-toc.min.js │ ├── clipboard.js-2.0.11 │ │ └── clipboard.min.js │ ├── data-deps.txt │ ├── font-awesome-6.4.2 │ │ ├── css │ │ │ ├── all.css │ │ │ ├── all.min.css │ │ │ ├── v4-shims.css │ │ │ └── v4-shims.min.css │ │ └── webfonts │ │ │ ├── fa-brands-400.ttf │ │ │ ├── fa-brands-400.woff2 │ │ │ ├── fa-regular-400.ttf │ │ │ ├── fa-regular-400.woff2 │ │ │ ├── fa-solid-900.ttf │ │ │ ├── fa-solid-900.woff2 │ │ │ ├── fa-v4compatibility.ttf │ │ │ └── fa-v4compatibility.woff2 │ ├── font-awesome-6.5.2 │ │ ├── css │ │ │ ├── all.css │ │ │ ├── all.min.css │ │ │ ├── v4-shims.css │ │ │ └── v4-shims.min.css │ │ └── webfonts │ │ │ ├── fa-brands-400.ttf │ │ │ ├── fa-brands-400.woff2 │ │ │ ├── fa-regular-400.ttf │ │ │ ├── fa-regular-400.woff2 │ │ │ ├── fa-solid-900.ttf │ │ │ ├── fa-solid-900.woff2 │ │ │ ├── fa-v4compatibility.ttf │ │ │ └── fa-v4compatibility.woff2 │ ├── headroom-0.11.0 │ │ ├── headroom.min.js │ │ └── jQuery.headroom.min.js │ ├── jquery-3.6.0 │ │ ├── jquery-3.6.0.js │ │ ├── jquery-3.6.0.min.js │ │ └── jquery-3.6.0.min.map │ └── search-1.0.0 │ │ ├── autocomplete.jquery.min.js │ │ ├── fuse.min.js │ │ └── mark.min.js ├── index.html ├── katex-auto.js ├── lightswitch.js ├── link.svg ├── news │ └── index.html ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── Clustering-class.html │ ├── Clustering.html │ ├── Rplot001.png │ ├── add_metadata.html │ ├── assess_clustering_stability-1.png │ ├── assess_clustering_stability.html │ ├── assess_feature_stability-1.png │ ├── assess_feature_stability.html │ ├── assess_nn_stability-1.png │ ├── assess_nn_stability.html │ ├── automatic_stability_assessment.html │ ├── calculate_markers.html │ ├── calculate_markers_shiny.html │ ├── choose_stable_clusters.html │ ├── consensus_cluster-1.png │ ├── consensus_cluster.html │ ├── create_clustering,character-method.html │ ├── create_clustering,factor-method.html │ ├── create_clustering,hclust-method.html │ ├── create_clustering,integer-method.html │ ├── create_clustering,matrix-method.html │ ├── create_clustering,numeric-method.html │ ├── create_clustering.html │ ├── create_monocle_default.html │ ├── create_monocle_from_clustassess.html │ ├── create_monocle_from_clustassess_app.html │ ├── create_seurat_object_default.html │ ├── create_seurat_object_from_clustassess_app.html │ ├── element_agreement.html │ ├── element_consistency.html │ ├── element_sim.html │ ├── element_sim_elscore.html │ ├── element_sim_matrix.html │ ├── figures │ │ ├── ClustAssess_app_supp.png │ │ ├── ClustAssess_diagram_all.png │ │ └── ClustAssess_starry_night.png │ ├── getNNmatrix.html │ ├── get_clusters_from_clustassess_object.html │ ├── get_colour_vector_from_palette.html │ ├── get_highest_prune_param.html │ ├── get_highest_prune_param_embedding.html │ ├── get_nn_conn_comps-1.png │ ├── get_nn_conn_comps.html │ ├── index.html │ ├── length-Clustering-method.html │ ├── marker_overlap-1.png │ ├── marker_overlap.html │ ├── merge_partitions.html │ ├── merge_resolutions.html │ ├── pac_convergence-1.png │ ├── pac_convergence.html │ ├── pac_landscape-1.png │ ├── pac_landscape.html │ ├── plot_clust_hierarchical-1.png │ ├── plot_clust_hierarchical.html │ ├── plot_clustering_difference_facet.html │ ├── plot_clustering_overall_stability-1.png │ ├── plot_clustering_overall_stability.html │ ├── plot_clustering_per_value_stability-1.png │ ├── plot_clustering_per_value_stability.html │ ├── plot_connected_comps_evolution-1.png │ ├── plot_connected_comps_evolution.html │ ├── plot_feature_overall_stability_boxplot-1.png │ ├── plot_feature_overall_stability_boxplot.html │ ├── plot_feature_overall_stability_incremental-1.png │ ├── plot_feature_overall_stability_incremental.html │ ├── plot_feature_per_resolution_stability_boxplot-1.png │ ├── plot_feature_per_resolution_stability_boxplot.html │ ├── plot_feature_per_resolution_stability_incremental-1.png │ ├── plot_feature_per_resolution_stability_incremental.html │ ├── plot_feature_stability_ecs_facet-1.png │ ├── plot_feature_stability_ecs_facet.html │ ├── plot_feature_stability_mb_facet-1.png │ ├── plot_feature_stability_mb_facet.html │ ├── plot_k_n_partitions-1.png │ ├── plot_k_n_partitions.html │ ├── plot_k_resolution_corresp-1.png │ ├── plot_k_resolution_corresp.html │ ├── plot_n_neigh_ecs-1.png │ ├── plot_n_neigh_ecs.html │ ├── plot_n_neigh_k_correspondence-1.png │ ├── plot_n_neigh_k_correspondence.html │ ├── print-Clustering-method.html │ ├── server_comparisons.html │ ├── server_dimensionality_reduction.html │ ├── server_graph_clustering.html │ ├── server_graph_construction.html │ ├── server_landing_page.html │ ├── server_sandbox.html │ ├── ui_comparisons.html │ ├── ui_dimensionality_reduction.html │ ├── ui_graph_clustering.html │ ├── ui_graph_construction.html │ ├── ui_landing_page.html │ ├── ui_sandbox.html │ ├── weighted_element_consistency.html │ ├── write_objects.html │ ├── write_shiny_app.Seurat.html │ ├── write_shiny_app.default.html │ └── write_shiny_app.html ├── search.json ├── sitemap.xml └── tutorials │ ├── ._compare-the-selected-comparison.html │ ├── ._dimensionality-reduction.html │ ├── ._graph-clustering.html │ ├── ._graph-construction.html │ ├── ._home-screen.html │ ├── ._index.html │ ├── ._reference-keys.txt │ ├── ._sandbox-tab.html │ ├── ._search_index.json │ ├── compare-the-selected-comparison.html │ ├── dimensionality-reduction.html │ ├── graph-clustering.html │ ├── graph-construction.html │ ├── home-screen.html │ ├── index.html │ ├── reference-keys.txt │ ├── sandbox-tab.html │ └── search_index.json ├── inst └── CITATION ├── man ├── Clustering-class.Rd ├── add_metadata.Rd ├── assess_clustering_stability.Rd ├── assess_feature_stability.Rd ├── assess_nn_stability.Rd ├── automatic_stability_assessment.Rd ├── calculate_markers.Rd ├── calculate_markers_shiny.Rd ├── choose_stable_clusters.Rd ├── consensus_cluster.Rd ├── create_clustering.Rd ├── create_monocle_default.Rd ├── create_monocle_from_clustassess.Rd ├── create_monocle_from_clustassess_app.Rd ├── create_seurat_object_default.Rd ├── create_seurat_object_from_clustassess_app.Rd ├── element_agreement.Rd ├── element_consistency.Rd ├── element_sim.Rd ├── element_sim_elscore.Rd ├── element_sim_matrix.Rd ├── figures │ ├── ClustAssess_app_supp.png │ ├── ClustAssess_diagram_all.png │ └── ClustAssess_starry_night.png ├── getNNmatrix.Rd ├── get_clusters_from_clustassess_object.Rd ├── get_colour_vector_from_palette.Rd ├── get_highest_prune_param.Rd ├── get_highest_prune_param_embedding.Rd ├── get_nn_conn_comps.Rd ├── length-Clustering-method.Rd ├── marker_overlap.Rd ├── merge_partitions.Rd ├── merge_resolutions.Rd ├── pac_convergence.Rd ├── pac_landscape.Rd ├── plot_clust_hierarchical.Rd ├── plot_clustering_difference_facet.Rd ├── plot_clustering_overall_stability.Rd ├── plot_clustering_per_value_stability.Rd ├── plot_connected_comps_evolution.Rd ├── plot_feature_overall_stability_boxplot.Rd ├── plot_feature_overall_stability_incremental.Rd ├── plot_feature_per_resolution_stability_boxplot.Rd ├── plot_feature_per_resolution_stability_incremental.Rd ├── plot_feature_stability_ecs_facet.Rd ├── plot_feature_stability_mb_facet.Rd ├── plot_k_n_partitions.Rd ├── plot_k_resolution_corresp.Rd ├── plot_n_neigh_ecs.Rd ├── plot_n_neigh_k_correspondence.Rd ├── print-Clustering-method.Rd ├── server_comparisons.Rd ├── server_dimensionality_reduction.Rd ├── server_graph_clustering.Rd ├── server_graph_construction.Rd ├── server_landing_page.Rd ├── server_sandbox.Rd ├── ui_comparisons.Rd ├── ui_dimensionality_reduction.Rd ├── ui_graph_clustering.Rd ├── ui_graph_construction.Rd ├── ui_landing_page.Rd ├── ui_sandbox.Rd ├── weighted_element_consistency.Rd ├── write_objects.Rd └── write_shiny_app.Rd ├── src ├── RcppExports.cpp ├── calculate_ecs.cpp ├── calculate_pac.cpp ├── optimise_snn.cpp ├── update_connectivity.cpp └── wilcox.cpp ├── tests ├── testthat.R └── testthat │ └── test-ECS.R └── vignettes ├── ClustAssess.Rmd ├── comparing-soft-and-hierarchical.Rmd ├── stability-dim-reduction-flexibility.Rmd ├── stability-pipeline-description.Rmd └── stability-pipeline-shiny.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Core-Bioinformatics/ClustAssess/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: 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