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  "Description": "A set of tools for evaluating clustering robustness using\nproportion of ambiguously clustered pairs (Senbabaoglu et al.\n(2014) <doi:10.1038/srep06207>), as well as similarity across\nmethods and method stability using element-centric clustering\ncomparison (Gates et al. (2019)\n<doi:10.1038/s41598-019-44892-y>). Additionally, this package\nenables stability-based parameter assessment for graph-based\nclustering pipelines typical in single-cell data analysis.",
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  "Repository": "https://core-bioinformatics.r-universe.dev",
  "Date/Publication": "2025-05-27 18:15:47 UTC",
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  "Author": "Andi Munteanu [aut, cre],\nArash Shahsavari [aut],\nRafael Kollyfas [ctb],\nMiguel Larraz Lopez de Novales [aut],\nLiviu Ciortuz [ctb],\nIrina Mohorianu [aut]",
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    "get_clusters_from_clustassess_object",
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    "plot_clustering_overall_stability",
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    "plot_feature_per_resolution_stability_incremental",
    "plot_feature_stability_ecs_facet",
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    "plot_k_resolution_corresp",
    "plot_n_neigh_ecs",
    "plot_n_neigh_k_correspondence",
    "server_comparisons",
    "server_dimensionality_reduction",
    "server_graph_clustering",
    "server_graph_construction",
    "server_landing_page",
    "server_sandbox",
    "ui_comparisons",
    "ui_dimensionality_reduction",
    "ui_graph_clustering",
    "ui_graph_construction",
    "ui_landing_page",
    "ui_sandbox",
    "weighted_element_consistency",
    "write_objects",
    "write_shiny_app"
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      "page": "add_metadata",
      "title": "Add metadata to ClustAssess ShinyApp",
      "topics": [
        "add_metadata"
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      "page": "assess_clustering_stability",
      "title": "Assessment of Stability for Graph Clustering",
      "topics": [
        "assess_clustering_stability"
      ]
    },
    {
      "page": "assess_feature_stability",
      "title": "Assess the stability for configurations of feature types and sizes",
      "topics": [
        "assess_feature_stability"
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    },
    {
      "page": "assess_nn_stability",
      "title": "Assess the stability for Graph Building Parameters",
      "topics": [
        "assess_nn_stability"
      ]
    },
    {
      "page": "automatic_stability_assessment",
      "title": "Assessment of Stability for Graph Clustering",
      "topics": [
        "automatic_stability_assessment"
      ]
    },
    {
      "page": "calculate_markers",
      "title": "Calculate markers",
      "topics": [
        "calculate_markers"
      ]
    },
    {
      "page": "calculate_markers_shiny",
      "title": "Calculate markers - Shiny",
      "topics": [
        "calculate_markers_shiny"
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      "page": "choose_stable_clusters",
      "title": "Choose stable clusters based on ECC and frequency",
      "topics": [
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      ]
    },
    {
      "page": "consensus_cluster",
      "title": "Consensus Clustering and Proportion of Ambiguously Clustered Pairs",
      "topics": [
        "consensus_cluster"
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    },
    {
      "page": "create_monocle_default",
      "title": "Create monocle object",
      "topics": [
        "create_monocle_default"
      ]
    },
    {
      "page": "create_monocle_from_clustassess",
      "title": "Create monocle object from a ClustAssess object",
      "topics": [
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    },
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      "page": "create_monocle_from_clustassess_app",
      "title": "Create monocle object from a ClustAssess shiny app",
      "topics": [
        "create_monocle_from_clustassess_app"
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      "title": "Create Seurat object",
      "topics": [
        "create_seurat_object_default"
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    },
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      "page": "create_seurat_object_from_clustassess_app",
      "title": "Create Seurat object from a ClustAssess shiny app",
      "topics": [
        "create_seurat_object_from_clustassess_app"
      ]
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      "page": "element_agreement",
      "title": "Element-Wise Average Agreement Between a Set of Clusterings",
      "topics": [
        "element_agreement"
      ]
    },
    {
      "page": "element_consistency",
      "title": "Element-Wise Consistency Between a Set of Clusterings",
      "topics": [
        "element_consistency"
      ]
    },
    {
      "page": "element_sim",
      "title": "The Element-Centric Clustering Similarity",
      "topics": [
        "element_sim"
      ]
    },
    {
      "page": "element_sim_elscore",
      "title": "The Element-Centric Clustering Similarity for each Element",
      "topics": [
        "element_sim_elscore"
      ]
    },
    {
      "page": "element_sim_matrix",
      "title": "Pairwise Comparison of Clusterings",
      "topics": [
        "element_sim_matrix"
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    },
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      "title": "Extract config-specific clusters from a ClustAssess object",
      "topics": [
        "get_clusters_from_clustassess_object"
      ]
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      "page": "get_colour_vector_from_palette",
      "title": "Get the vector of colours from a palette",
      "topics": [
        "get_colour_vector_from_palette"
      ]
    },
    {
      "page": "get_highest_prune_param",
      "title": "Calculate the highest pruning parameter for the SNN graph given NN matrix",
      "topics": [
        "get_highest_prune_param"
      ]
    },
    {
      "page": "get_highest_prune_param_embedding",
      "title": "Calculate the highest pruning parameter for the SNN graph given Embedding",
      "topics": [
        "get_highest_prune_param_embedding"
      ]
    },
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      "page": "get_nn_conn_comps",
      "title": "Relationship Between Nearest Neighbours and Connected Components",
      "topics": [
        "get_nn_conn_comps"
      ]
    },
    {
      "page": "getNNmatrix",
      "title": "Computes the NN adjacency matrix given the neighbours",
      "topics": [
        "getNNmatrix"
      ]
    },
    {
      "page": "marker_overlap",
      "title": "Cell-Wise Marker Gene Overlap",
      "topics": [
        "marker_overlap"
      ]
    },
    {
      "page": "merge_partitions",
      "title": "Merge Partitions",
      "topics": [
        "merge_partitions"
      ]
    },
    {
      "page": "merge_resolutions",
      "title": "Merge Partitions from different Resolutions",
      "topics": [
        "merge_resolutions"
      ]
    },
    {
      "page": "pac_convergence",
      "title": "PAC Convergence Plot",
      "topics": [
        "pac_convergence"
      ]
    },
    {
      "page": "pac_landscape",
      "title": "PAC Landscape Plot",
      "topics": [
        "pac_landscape"
      ]
    },
    {
      "page": "plot_clust_hierarchical",
      "title": "Hierarchical relationship between partitions with different number of clusters",
      "topics": [
        "plot_clust_hierarchical"
      ]
    },
    {
      "page": "plot_clustering_difference_facet",
      "title": "Clustering Method Stability Facet Plot",
      "topics": [
        "plot_clustering_difference_facet"
      ]
    },
    {
      "page": "plot_clustering_overall_stability",
      "title": "Clustering Method Overall Stability Boxplot",
      "topics": [
        "plot_clustering_overall_stability"
      ]
    },
    {
      "page": "plot_clustering_per_value_stability",
      "title": "Clustering Method per value Stability Boxplot",
      "topics": [
        "plot_clustering_per_value_stability"
      ]
    },
    {
      "page": "plot_connected_comps_evolution",
      "title": "Relationship Between Number of Nearest Neighbours and Graph Connectivity",
      "topics": [
        "plot_connected_comps_evolution"
      ]
    },
    {
      "page": "plot_feature_overall_stability_boxplot",
      "title": "Overall Feature Stability Boxplot",
      "topics": [
        "plot_feature_overall_stability_boxplot"
      ]
    },
    {
      "page": "plot_feature_overall_stability_incremental",
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