{
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  "Type": "Package",
  "Package": "SpaceMarkers",
  "Title": "Spatial Interaction Markers",
  "Version": "2.3.1",
  "Authors@R": "c(\nperson(given = \"Atul\", family = \"Deshpande\", email = \"adeshpande@jhu.edu\", role = c(\"aut\", \"cre\"), comment = c(ORCID=\"0000-0001-5144-6924\")),\nperson(given = \"Orian\", family = \"Stapleton\", email = \"ostaple1@jh.edu\", role = \"aut\"),\nperson(given = \"Ludmila\", family = \"Danilova\", email = \"ldanilo1@jhmi.edu\", role = \"ctb\"),\nperson(given = \"Dmitrijs\", family = \"Lvovs\", email = \"dlvovs1@jh.edu\", role = \"ctb\", comment = c(ORCID = \"0009-0003-2152-6853\"))\n)",
  "BugReports": "https://github.com/DeshpandeLab/SpaceMarkers/issues",
  "URL": "https://github.com/DeshpandeLab/SpaceMarkers",
  "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.",
  "biocViews": "SingleCell, GeneExpression, Software, Spatial,\nTranscriptomics",
  "VignetteBuilder": "knitr",
  "Collate": "'AllClasses.R' 'AllGenerics.R' 'SpaceMarkers.R'\n'SpaceMarkersExperiment-methods.R' 'data.R'\n'findGenesOfInterest.R' 'getInteractingGenes.R'\n'getSpatialParameters.R' 'hdutils.R' 'plotLRCircos.R'\n'preprocessing.R' 'test-helper.R' 'utils.R'",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-29 03:41:10 UTC",
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  "Author": "Atul Deshpande [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-5144-6924>),\nOrian Stapleton [aut],\nLudmila Danilova [ctb],\nDmitrijs Lvovs [ctb] (ORCID: <https://orcid.org/0009-0003-2152-6853>)",
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  "_exports": [
    "add_features",
    "analysis_type",
    "analysis_type<-",
    "assay",
    "assays",
    "calculate_gene_scores_directed",
    "calculate_gene_set_score",
    "calculate_gene_set_specificity",
    "calculate_influence",
    "calculate_lr_scores",
    "calculate_overlap_directed",
    "calculate_overlap_undirected",
    "calculate_thresholds",
    "colData",
    "create_lr_dataframe",
    "directed_scores",
    "directed_scores<-",
    "find_all_hotspots",
    "find_hotspots_gmm",
    "find_pattern_hotspots",
    "get_im_scores",
    "get_interacting_genes",
    "get_pairwise_interacting_genes",
    "get_spatial_features",
    "get_spatial_parameters",
    "get_spatial_params_morans_i",
    "hotspots",
    "hotspots<-",
    "imgRaster",
    "influence_map",
    "influence_map<-",
    "interactions",
    "interactions<-",
    "load_anndata",
    "load10X",
    "load10XCoords",
    "load10XExpr",
    "lr_scores",
    "lr_scores<-",
    "overlap_map",
    "overlap_scores",
    "overlap_scores<-",
    "params",
    "plot_cell_interaction_circos",
    "plot_im_scores",
    "plot_overlap_scores",
    "plot_source_to_target_circos",
    "plot_spatial",
    "plot_spatial_data_over_image",
    "plot_target_from_sources_circos",
    "rowData",
    "save_anndata",
    "SpaceMarkers",
    "SpaceMarkersExperiment",
    "spatial_params",
    "spatial_params<-",
    "spatial_patterns",
    "spatial_patterns<-",
    "spatialCoords",
    "undirected_scores",
    "undirected_scores<-"
  ],
  "_datasets": [
    {
      "name": "curated_genes",
      "title": "Curated Genes for example purposes",
      "object": "curated_genes",
      "file": "curated_genes.rda",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "optParams",
      "title": "Optimal paramters of 5 patterns from CoGAPS.",
      "object": "optParams",
      "file": "optParams.rda",
      "class": [
        "matrix",
        "array"
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      "fields": [
        "Pattern_1",
        "Pattern_5"
      ],
      "rows": 2,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "dot-calc_IM_scores",
      "title": "Calculate interaction scores for a specific pattern pair",
      "topics": [
        ".calc_IM_scores"
      ]
    },
    {
      "page": "dot-calc_threshold",
      "title": "Compute the threshold for identifying outlier values or hotspots",
      "topics": [
        ".calc_threshold"
      ]
    },
    {
      "page": "dot-directed_SpaceMarkers",
      "title": "Directed SpaceMarkers workflow",
      "topics": [
        ".directed_SpaceMarkers"
      ]
    },
    {
      "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": [
        ".find_genes_of_interest"
      ]
    },
    {
      "page": "dot-pick_image",
      "title": ".pick_image",
      "topics": [
        ".pick_image"
      ]
    },
    {
      "page": "dot-row_t_test",
      "title": "Perform row-wise t-tests from scratch",
      "topics": [
        ".row_t_test"
      ]
    },
    {
      "page": "dot-undirected_SpaceMarkers",
      "title": "Undirected SpaceMarkers workflow",
      "topics": [
        ".undirected_SpaceMarkers"
      ]
    },
    {
      "page": "add_features",
      "title": "Add spatial features to a SpaceMarkersExperiment",
      "topics": [
        "add_features"
      ]
    },
    {
      "page": "analysis_type",
      "title": "Access or set the analysis type on a SpaceMarkersExperiment",
      "topics": [
        "analysis_type",
        "analysis_type,SpaceMarkersExperiment-method",
        "analysis_type<-",
        "analysis_type<-,SpaceMarkersExperiment-method"
      ]
    },
    {
      "page": "as-SingleCellExperiment-SpaceMarkersExperiment",
      "title": "Coercion from SingleCellExperiment to SpaceMarkersExperiment",
      "topics": [
        "as-SingleCellExperiment-SpaceMarkersExperiment"
      ]
    },
    {
      "page": "as-SpatialExperiment-SpaceMarkersExperiment",
      "title": "Coercion from SpatialExperiment to SpaceMarkersExperiment",
      "topics": [
        "as-SpatialExperiment-SpaceMarkersExperiment"
      ]
    },
    {
      "page": "calculate_gene_scores_directed",
      "title": "Calculate interaction scores for all pattern pairs",
      "topics": [
        "calculate_gene_scores_directed",
        "calculate_gene_scores_directed,ANY-method",
        "calculate_gene_scores_directed,SpaceMarkersExperiment-method"
      ]
    },
    {
      "page": "calculate_gene_set_score",
      "title": "calculate_gene_set_score",
      "topics": [
        "calculate_gene_set_score",
        "calculate_gene_set_score,ANY-method",
        "calculate_gene_set_score,SpaceMarkersExperiment-method"
      ]
    },
    {
      "page": "calculate_gene_set_specificity",
      "title": "calculate_gene_set_specificity",
      "topics": [
        "calculate_gene_set_specificity",
        "calculate_gene_set_specificity,ANY-method",
        "calculate_gene_set_specificity,SpaceMarkersExperiment-method"
      ]
    },
    {
      "page": "calculate_influence",
      "title": "Compute the spatial influence of a spatial feature",
      "topics": [
        "calculate_influence",
        "calculate_influence,data.frame-method",
        "calculate_influence,SpaceMarkersExperiment-method"
      ]
    },
    {
      "page": "calculate_lr_scores",
      "title": "calculate_lr_scores",
      "topics": [
        "calculate_lr_scores",
        "calculate_lr_scores,ANY-method",
        "calculate_lr_scores,SpaceMarkersExperiment-method"
      ]
    },
    {
      "page": "calculate_overlap_directed",
      "title": "calculate_overlap_directed",
      "topics": [
        "calculate_overlap_directed",
        "calculate_overlap_directed,data.frame-method",
        "calculate_overlap_directed,SpaceMarkersExperiment-method"
      ]
    },
    {
      "page": "calculate_overlap_undirected",
      "title": "calculate_overlap_undirected",
      "topics": [
        "calculate_overlap_undirected",
        "calculate_overlap_undirected,data.frame-method",
        "calculate_overlap_undirected,SpaceMarkersExperiment-method"
      ]
    },
    {
      "page": "calculate_thresholds",
      "title": "Compute the thresholds for all columns in a data frame",
      "topics": [
        "calculate_thresholds"
      ]
    },
    {
      "page": "create_lr_dataframe",
      "title": "Combine LR / ligand / receptor score matrices into a long table",
      "topics": [
        "create_lr_dataframe"
      ]
    },
    {
      "page": "curated_genes",
      "title": "Curated Genes for example purposes",
      "topics": [
        "curated_genes"
      ]
    },
    {
      "page": "directed_scores",
      "title": "Access directed interaction scores on a SpaceMarkersExperiment",
      "topics": [
        "directed_scores",
        "directed_scores,SpaceMarkersExperiment-method",
        "directed_scores<-",
        "directed_scores<-,SpaceMarkersExperiment-method"
      ]
    },
    {
      "page": "find_all_hotspots",
      "title": "Find hotSpots for all spatial patterns",
      "topics": [
        "find_all_hotspots",
        "find_all_hotspots,data.frame-method",
        "find_all_hotspots,SpaceMarkersExperiment-method"
      ]
    },
    {
      "page": "find_hotspots_gmm",
      "title": "Find hotspots for all patterns or influences based on values",
      "topics": [
        "find_hotspots_gmm",
        "find_hotspots_gmm,data.frame-method",
        "find_hotspots_gmm,SpaceMarkersExperiment-method"
      ]
    },
    {
      "page": "find_pattern_hotspots",
      "title": "Identify hotspots of spatial pattern influence",
      "concept": [
        "getIntGenes"
      ],
      "topics": [
        "find_pattern_hotspots"
      ]
    },
    {
      "page": "get_im_scores",
      "title": "get_im_scores",
      "topics": [
        "get_im_scores",
        "get_im_scores,list-method",
        "get_im_scores,SpaceMarkersExperiment-method"
      ]
    },
    {
      "page": "get_interacting_genes",
      "title": "Calculate Interaction Regions and Associated Genes",
      "concept": [
        "getIntGenes"
      ],
      "topics": [
        "get_interacting_genes"
      ]
    },
    {
      "page": "get_pairwise_interacting_genes",
      "title": "get_pairwise_interacting_genes",
      "concept": [
        "getIntGenes"
      ],
      "topics": [
        "get_pairwise_interacting_genes",
        "get_pairwise_interacting_genes,ANY-method",
        "get_pairwise_interacting_genes,SpaceMarkersExperiment-method"
      ]
    },
    {
      "page": "get_spatial_features",
      "title": "Load spatial features",
      "topics": [
        "get_spatial_features"
      ]
    },
    {
      "page": "get_spatial_parameters",
      "title": "Read optimal parameters for spatial kernel density from user input or .json file",
      "topics": [
        "get_spatial_parameters"
      ]
    },
    {
      "page": "get_spatial_params_morans_i",
      "title": "Calculate the optimal parameters from spatial kernel density for cell-cell interactions",
      "topics": [
        "get_spatial_params_morans_i"
      ]
    },
    {
      "page": "hotspots",
      "title": "Access hotspot assignments on a SpaceMarkersExperiment",
      "topics": [
        "hotspots",
        "hotspots,SpaceMarkersExperiment-method",
        "hotspots<-",
        "hotspots<-,SpaceMarkersExperiment-method"
      ]
    },
    {
      "page": "influence_map",
      "title": "Access the per-spot influence map on a SpaceMarkersExperiment",
      "topics": [
        "influence_map",
        "influence_map,SpaceMarkersExperiment-method",
        "influence_map<-",
        "influence_map<-,SpaceMarkersExperiment-method"
      ]
    },
    {
      "page": "interactions",
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      "title": "Access ligand-receptor scores on a SpaceMarkersExperiment",
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      "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_scores",
      "title": "Access pattern overlap scores on a SpaceMarkersExperiment",
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      "title": "Access analysis hyperparameters on a SpaceMarkersExperiment",
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      "title": "Main dispatcher for SpaceMarkers",
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