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  "Title": "Spatial Interaction Markers",
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  "Date/Publication": "2026-04-28 13:02:49 UTC",
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    "plot_im_scores",
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        "character"
      ],
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        "array"
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      "page": "dot-calc_IM_scores",
      "title": "Calculate interaction scores for a specific pattern pair",
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      ]
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    {
      "page": "dot-calc_threshold",
      "title": "Compute the threshold for identifying outlier values or hotspots",
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        ".calc_threshold"
      ]
    },
    {
      "page": "dot-find_genes_of_interest",
      "title": ".find_genes_of_interest Identify genes associated with pattern interaction. This function identifies genes exhibiting significantly higher values of testMat in the Interaction region of the two patterns compared to regions with exclusive influence from either pattern. It uses Kruskal-Wallis test followed by posthoc analysis using Dunn's Test to identify the genes.",
      "topics": [
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    },
    {
      "page": "calculate_gene_scores_directed",
      "title": "Calculate interaction scores for all pattern pairs",
      "topics": [
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      "page": "calculate_gene_set_score",
      "title": "calculate_gene_set_score",
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      "page": "calculate_gene_set_specificity",
      "title": "calculate_gene_set_specificity",
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    {
      "page": "calculate_influence",
      "title": "Compute the spatial influence of a spatial feature",
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    {
      "page": "calculate_overlap_directed",
      "title": "calculate_overlap_directed",
      "topics": [
        "calculate_overlap_directed"
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    {
      "page": "calculate_overlap_undirected",
      "title": "calculate_overlap_undirected",
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        "calculate_overlap_undirected"
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    {
      "page": "calculate_thresholds",
      "title": "Compute the thresholds for all columns in a data frame",
      "topics": [
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    {
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      "title": "Curated Genes for example purposes",
      "topics": [
        "curated_genes"
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    },
    {
      "page": "find_all_hotspots",
      "title": "Find hotSpots for all spatial patterns",
      "topics": [
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    },
    {
      "page": "find_hotspots_gmm",
      "title": "Find hotspots for all patterns or influences based on values",
      "topics": [
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    },
    {
      "page": "find_pattern_hotspots",
      "title": "Identify hotspots of spatial pattern influence",
      "concept": [
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    {
      "page": "get_interacting_genes",
      "title": "Calculate Interaction Regions and Associated Genes",
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    {
      "page": "get_pairwise_interacting_genes",
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      "topics": [
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    {
      "page": "get_spatial_features",
      "title": "Load spatial features",
      "topics": [
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    {
      "page": "get_spatial_parameters",
      "title": "Read optimal parameters for spatial kernel density from user input or .json file",
      "topics": [
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    },
    {
      "page": "get_spatial_params_morans_i",
      "title": "Calculate the optimal parameters from spatial kernel density for cell-cell interactions",
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      "page": "load10XCoords",
      "title": "Load 10x Visium Spatial Coordinates",
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      "title": "Load 10X Visium Expression Data",
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    },
    {
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      "page": "plot_spatial_data_over_image",
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      "title": "Plot Ligand-Receptor Interactions from Multiple Source to a Single Target Cell Type",
      "topics": [
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        "Residual Mode vs DE Mode: Differences",
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        "Comparing DE mode to residual mode",
        "Types of Analyses",
        "Residual Mode vs DE Mode: Enrichment",
        "Visualizing SpaceMarkers",
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