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  "Description": "Spatial transcriptomic technologies have helped to resolve\nthe connection between gene expression and the 2D orientation\nof tissues relative to each other. However, the limited\nsingle-cell resolution makes it difficult to highlight the most\nimportant molecular interactions in these tissues.\nSpaceMarkers, R/Bioconductor software, can help to find\nmolecular interactions, by identifying genes associated with\nlatent space interactions in spatial transcriptomics.",
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      "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.",
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      "topics": [
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        "calculate_gene_scores_directed,ANY-method",
        "calculate_gene_scores_directed,SpaceMarkersExperiment-method"
      ]
    },
    {
      "page": "calculate_gene_set_score",
      "title": "calculate_gene_set_score",
      "topics": [
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        "calculate_gene_set_score,ANY-method",
        "calculate_gene_set_score,SpaceMarkersExperiment-method"
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      "page": "calculate_gene_set_specificity",
      "title": "calculate_gene_set_specificity",
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        "calculate_gene_set_specificity,ANY-method",
        "calculate_gene_set_specificity,SpaceMarkersExperiment-method"
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    {
      "page": "calculate_influence",
      "title": "Compute the spatial influence of a spatial feature",
      "topics": [
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        "calculate_influence,data.frame-method",
        "calculate_influence,SpaceMarkersExperiment-method"
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      "page": "calculate_lr_scores",
      "title": "calculate_lr_scores",
      "topics": [
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        "calculate_lr_scores,ANY-method",
        "calculate_lr_scores,SpaceMarkersExperiment-method"
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      "page": "calculate_overlap_directed",
      "title": "calculate_overlap_directed",
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        "calculate_overlap_directed,data.frame-method",
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      "page": "calculate_overlap_undirected",
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      "page": "calculate_thresholds",
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      "page": "create_lr_dataframe",
      "title": "Combine LR / ligand / receptor score matrices into a long table",
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      "page": "curated_genes",
      "title": "Curated Genes for example purposes",
      "topics": [
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      "page": "directed_scores",
      "title": "Access directed interaction scores on a SpaceMarkersExperiment",
      "topics": [
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        "directed_scores<-",
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      "page": "find_all_hotspots",
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      "page": "find_hotspots_gmm",
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      "page": "find_pattern_hotspots",
      "title": "Identify hotspots of spatial pattern influence",
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      "page": "get_im_scores",
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      "page": "get_interacting_genes",
      "title": "Calculate Interaction Regions and Associated Genes",
      "concept": [
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      "page": "get_pairwise_interacting_genes",
      "title": "get_pairwise_interacting_genes",
      "concept": [
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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",
      "topics": [
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      "page": "hotspots",
      "title": "Access hotspot assignments on a SpaceMarkersExperiment",
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        "hotspots<-",
        "hotspots<-,SpaceMarkersExperiment-method"
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      "page": "influence_map",
      "title": "Access the per-spot influence map on a SpaceMarkersExperiment",
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      "page": "interactions",
      "title": "Access pairwise interaction results on a SpaceMarkersExperiment",
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      "page": "load_anndata",
      "title": "Load an AnnData file as a SpaceMarkersExperiment",
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      "page": "load10X",
      "title": "Load 10X Visium data as a SpaceMarkersExperiment",
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    {
      "page": "load10XCoords",
      "title": "Load 10x Visium Spatial Coordinates",
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      "page": "load10XExpr",
      "title": "Load 10X Visium Expression Data",
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      "page": "lr_scores",
      "title": "Access ligand-receptor scores on a SpaceMarkersExperiment",
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      "page": "lrdf",
      "title": "Curated Ligand-receptor interaction genes A list of vectors with genes associated with ligand-receptor interactions from CellChat database",
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      "page": "optParams",
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      "page": "overlap_map",
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      "page": "overlap_scores",
      "title": "Access pattern overlap scores on a SpaceMarkersExperiment",
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