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  "Package": "SpNeigh",
  "Title": "Spatial Neighborhood Modeling and Differential Expression\nAnalysis for Transcriptomics",
  "Version": "1.1.0",
  "Authors@R": "person(given = \"Jinming\",\nfamily = \"Cheng\",\nemail=\"jinming.cheng@outlook.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-3806-4694\"))",
  "Description": "SpNeigh provides methods for neighborhood-aware analysis\nof spatial transcriptomics data. It supports boundary\ndetection, spatial weighting (centroid- and boundary-based),\nspatially informed differential expression using spline-based\nmodels, and spatial enrichment analysis via the Spatial\nEnrichment Index (SEI). Designed for compatibility with Seurat\nobjects, SpatialExperiment objects and spatial data frames,\nSpNeigh enables interpretable, publication-ready analysis of\nspatial gene expression patterns.",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:06:43 UTC",
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    "computeBoundaryWeights",
    "computeCentroidWeights",
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    "computeSpatialEnrichmentIndex",
    "computeSpatialInteractionMatrix",
    "extractCoords",
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    "getBoundary",
    "getCellsInside",
    "getInnerBoundary",
    "getOuterBoundary",
    "getRingRegion",
    "plotBoundary",
    "plotCellsInside",
    "plotEdge",
    "plotExpression",
    "plotInteractionMatrix",
    "plotRegion",
    "plotSpatialExpression",
    "plotStatsBar",
    "plotStatsPie",
    "plotWeights",
    "removeOutliers",
    "runLimmaDE",
    "runSpatialDE",
    "safeColorPalette",
    "splineDesign",
    "splitBoundaryPolyByAnchor",
    "statsCellsInside",
    "theme_spneigh"
  ],
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      "page": "AddBoundary",
      "title": "Add boundary outlines to a spatial ggplot",
      "topics": [
        "addBoundary"
      ]
    },
    {
      "page": "AddBoundaryPoly",
      "title": "Add boundary polygons or linestrings to a spatial plot",
      "topics": [
        "addBoundaryPoly"
      ]
    },
    {
      "page": "BoundaryPolyToPoints",
      "title": "Convert boundary polygons to boundary point coordinates",
      "topics": [
        "boundaryPolyToPoints"
      ]
    },
    {
      "page": "BuildBoundaryPoly",
      "title": "Convert boundary points into valid polygon geometries",
      "topics": [
        "buildBoundaryPoly"
      ]
    },
    {
      "page": "colors15_cheng",
      "title": "Custom Color Palette",
      "topics": [
        "colors15_cheng"
      ]
    },
    {
      "page": "ComputeBoundaryWeights",
      "title": "Compute spatial weights based on distance to nearest boundary",
      "topics": [
        "computeBoundaryWeights"
      ]
    },
    {
      "page": "ComputeCentroidWeights",
      "title": "Compute spatial weights based on distance to the centroid",
      "topics": [
        "computeCentroidWeights"
      ]
    },
    {
      "page": "ComputeSEI",
      "title": "Compute Spatial Enrichment Index (SEI)",
      "topics": [
        "computeSEI"
      ]
    },
    {
      "page": "ComputeSpatialEnrichmentIndex",
      "title": "Compute Spatial Enrichment Index (SEI) for Each Gene",
      "topics": [
        "computeSpatialEnrichmentIndex"
      ]
    },
    {
      "page": "ComputeSpatialInteractionMatrix",
      "title": "Compute a spatial neighborhood interaction matrix using K-nearest neighbors (KNN)",
      "topics": [
        "computeSpatialInteractionMatrix"
      ]
    },
    {
      "page": "ExtractCoords",
      "title": "Extract spatial coordinates and cluster information",
      "topics": [
        "extractCoords"
      ]
    },
    {
      "page": "FactorNaturalOrder",
      "title": "Create a factor with natural (human-friendly) ordering",
      "topics": [
        "factorNaturalOrder"
      ]
    },
    {
      "page": "GetBoundary",
      "title": "Extract spatial boundary points for a cluster or cell population",
      "topics": [
        "getBoundary"
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    },
    {
      "page": "GetCellsInside",
      "title": "Identify cells located within spatial boundaries or ring regions",
      "topics": [
        "getCellsInside"
      ]
    },
    {
      "page": "GetInnerBoundary",
      "title": "Generate an inner boundary polygon by shrinking an existing boundary inward",
      "topics": [
        "getInnerBoundary"
      ]
    },
    {
      "page": "GetOuterBoundary",
      "title": "Generate an outer or inner boundary polygon by buffering an existing boundary",
      "topics": [
        "getOuterBoundary"
      ]
    },
    {
      "page": "GetRingRegion",
      "title": "Generate ring regions between a boundary and its outer buffer",
      "topics": [
        "getRingRegion"
      ]
    },
    {
      "page": "PlotBoundary",
      "title": "Plot spatial cell coordinates with cluster boundaries",
      "topics": [
        "plotBoundary"
      ]
    },
    {
      "page": "PlotCellsInside",
      "title": "Plot cells located within spatial boundaries or ring regions",
      "topics": [
        "plotCellsInside"
      ]
    },
    {
      "page": "PlotEdge",
      "title": "Plot boundary edges or segmented boundary lines",
      "topics": [
        "plotEdge"
      ]
    },
    {
      "page": "PlotExpression",
      "title": "Plot gene expression across spatial coordinates",
      "topics": [
        "plotExpression"
      ]
    },
    {
      "page": "PlotInteractionMatrix",
      "title": "Plot a heatmap of a row-scaled spatial interaction matrix",
      "topics": [
        "plotInteractionMatrix"
      ]
    },
    {
      "page": "PlotRegion",
      "title": "Plot filled spatial regions inside boundaries or rings",
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      ]
    },
    {
      "page": "PlotSpatialExpression",
      "title": "Plot average gene expression along spatial distance",
      "topics": [
        "plotSpatialExpression"
      ]
    },
    {
      "page": "PlotStatsBar",
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        "plotStatsBar"
      ]
    },
    {
      "page": "PlotStatsPie",
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        "plotStatsPie"
      ]
    },
    {
      "page": "PlotWeights",
      "title": "Plot spatial weights for cells on a spatial plot",
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        "plotWeights"
      ]
    },
    {
      "page": "RemoveOutliers",
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      "page": "theme_spneigh",
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      "source": "SpNeigh.Rmd",
      "filename": "SpNeigh.html",
      "title": "Getting Started with SpNeigh",
      "author": "Jinming Cheng",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Overview of this vignette",
        "Installation",
        "Load packages",
        "Load data",
        "Input: Coordinate data frame and Normalized expression matrix",
        "Alternative input: SpatialExperiment object",
        "Alternative input: Seurat object",
        "Neighborhood analysis for cluster 2 cells",
        "Quick look at the boundaries of one cluster",
        "Detect spatial boundaries",
        "Obtain neighborhood ring regions",
        "Statistics of cells inside rings",
        "Neighborhood interaction of clusters inside rings",
        "DE analysis of cluster 2 cells inside and outside boundaries",
        "Spatial DE analysis of cells in cluster 0 along spatial weights",
        "Compute and plot spatial weights",
        "Perform spatial differential analysis along boundary weights",
        "Spatial enrichment analysis for each gene",
        "Session Info"
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