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  "Package": "RegionalST",
  "Type": "Package",
  "Title": "Investigating regions of interest and performing regional cell\ntype-specific analysis with spatial transcriptomics data",
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  "Authors@R": "person(given = \"Ziyi\", \nfamily = \"Li\",\nrole=c(\"aut\", \"cre\"),\nemail=\"zli16@mdanderson.org\")",
  "Description": "This package analyze spatial transcriptomics data through\ncross-regional cell type-specific analysis. It selects regions\nof interest (ROIs) and identifys cross-regional cell\ntype-specific differential signals. The ROIs can be selected\nusing automatic algorithm or through manual selection. It\nfacilitates manual selection of ROIs using a shiny application.",
  "License": "GPL-3",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:01:15 UTC",
  "RemoteUrl": "https://github.com/bioc/RegionalST",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
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  "Author": "Ziyi Li [aut, cre]",
  "Maintainer": "Ziyi Li <zli16@mdanderson.org>",
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      "tojson": true
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      "file": "pathways_kegg.rda",
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      "table": false,
      "tojson": true
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    {
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      "title": "REACTOME database",
      "object": "pathways_reactome",
      "file": "pathways_reactome.rda",
      "class": [
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      "table": false,
      "tojson": true
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      "page": "DoGSEA",
      "title": "Perform GSEA analysis for cross-regional DE genes",
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    {
      "page": "DrawDotplot",
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      "topics": [
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    },
    {
      "page": "DrawRegionProportion",
      "title": "Draw regional cell type distribution with cell type annotation information",
      "topics": [
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      ]
    },
    {
      "page": "DrawRegionProportion_withProp",
      "title": "Draw regional cell type distribution with cellular proportion information",
      "topics": [
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    },
    {
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      "title": "Example single cell experiment for input",
      "topics": [
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      ]
    },
    {
      "page": "exampleRes",
      "title": "Example DE output",
      "topics": [
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      ]
    },
    {
      "page": "FindRegionalCells",
      "title": "Identify regional cells given centers and radiuses",
      "topics": [
        "FindRegionalCells"
      ]
    },
    {
      "page": "GetCellTypeSpecificDE_withProp",
      "title": "Identify cross-regional cell type-specific differential analysis with proportion",
      "topics": [
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    },
    {
      "page": "GetCrossRegionalDE_raw",
      "title": "Identify cross-regional differential analysis",
      "topics": [
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      ]
    },
    {
      "page": "GetCrossRegionalDE_withProp",
      "title": "Identify cross-regional differential analysis with proportion",
      "topics": [
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    {
      "page": "GetOneRadiusEntropy",
      "title": "Computer the entropy for a fixed radius",
      "topics": [
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    },
    {
      "page": "GetOneRadiusEntropy_withProp",
      "title": "Computer the entropy for a fixed radius with cell type proportion",
      "topics": [
        "GetOneRadiusEntropy_withProp"
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    {
      "page": "getProportion",
      "title": "Define an accessor method for Proportion_CARD",
      "topics": [
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      ]
    },
    {
      "page": "ManualSelectCenter",
      "title": "Manually select top ROIs",
      "topics": [
        "ManualSelectCenter"
      ]
    },
    {
      "page": "mySpatialPreprocess",
      "title": "Perform Preprocessing for spatial data (tailored from BayesSpace function)",
      "topics": [
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    },
    {
      "page": "pathways_hallmark",
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      "topics": [
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      "topics": [
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      "page": "PlotOneSelectedCenter",
      "title": "Plot one selected ROI",
      "topics": [
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    {
      "page": "RankCenterByEntropy",
      "title": "Automatically rank ROI centers based on entropy",
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    {
      "page": "RankCenterByEntropy_withProp",
      "title": "Automatically rank ROI centers based on entropy with proportions",
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  "_vignettes": [
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      "source": "RegionalST.Rmd",
      "filename": "RegionalST.html",
      "title": "Understanding Intrasample Heterogeneity from ST data with RegionalST",
      "author": "Ziyi Li",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Install RegionalST",
        "Preparing your data for RegionalST through BayesSpace",
        "Analysis with the incorporation of cell type proportions",
        "Obtain cell deconvolution proportions",
        "Load example dataset",
        "Identify Regions of Interest (ROIs) with incorporation of proportions",
        "Automatic ROI selection",
        "Manual ROI selection",
        "Draw cell type proportions for the selected ROIs",
        "Perform Cross-regional Differential Analysis with proportions",
        "Perform Cross-regional Cell Type-Specific Differential Analysis with proportions and self-defined regions",
        "Analysis with cell type information",
        "Obtain cell type labels",
        "Identify Regions of Interest (ROIs) with cell type information",
        "Automatic selection of the ROIs",
        "Manual ROI selection with cell type information",
        "Perform Cross-regional Differential Analysis with cell type information",
        "Pathway GSEA analysis based on the cross-regional DEs",
        "Session info"
      ],
      "created": "2023-05-02 21:00:36",
      "modified": "2024-11-11 14:58:27",
      "commits": 6
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