{
  "_id": "6a1bcf5a1d7bb097a0a1402e",
  "Package": "scider",
  "Type": "Package",
  "Title": "Spatial cell-type inter-correlation by density in R",
  "Version": "1.11.0",
  "Authors@R": "c(person(given = \"Mengbo\",family = \"Li\",\nrole = c(\"aut\"),\nemail = \"li.me@wehi.edu.au\",\ncomment = c(ORCID = \"0000-0002-9666-5810\")),\nperson(given = \"Ning\",\nfamily = \"Liu\",\nrole = c(\"aut\"),\nemail = \"liu.n@wehi.edu.au\",\ncomment = c(ORCID = \"0000-0002-9487-9305\")),\nperson(given = \"Quoc Hoang\",\nfamily = \"Nguyen\",\nrole = c(\"aut\"),\nemail = \"nguyen.q@wehi.edu.au\",\ncomment = c(ORCID = \"0009-0007-2828-7567\")),\nperson(given = \"Yunshun\",\nfamily = \"Chen\",\nrole = c(\"aut\", \"cre\"),\nemail = \"yuchen@wehi.edu.au\",\ncomment = c(ORCID = \"0000-0003-4911-5653\")))",
  "Author": "Mengbo Li, Ning Liu, Quoc Hoang Nguyen, Yunshun Chen",
  "Maintainer": "Yunshun Chen <yuchen@wehi.edu.au>",
  "Description": "scider is an user-friendly R package providing functions\nto model the global density of cells in a slide of spatial\ntranscriptomics data. All functions in the package are built\nbased on the SpatialExperiment object, allowing integration\ninto various spatial transcriptomics-related packages from\nBioconductor. After modelling density, the package allows for\nseveral downstream analysis, including colocalization analysis,\nboundary detection analysis and differential density analysis.",
  "biocViews": "Spatial, Transcriptomics",
  "License": "GPL-3 + file LICENSE",
  "URL": "https://github.com/ChenLaboratory/scider,\nhttps://chenlaboratory.github.io/scider/",
  "BugReports": "https://github.com/ChenLaboratory/scider/issues",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:01:50 UTC",
  "RemoteUrl": "https://github.com/bioc/scider",
  "RemoteRef": "HEAD",
  "RemoteSha": "7dcb837f327cfc8ac9f649491c61c04c5e5be2e7",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-29 19:36:53 UTC",
    "User": "root"
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  "MD5sum": "409e3db968b45b45823274f0a37b158c",
  "_user": "bioc",
  "_type": "src",
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  "_created": "2026-05-29T19:36:53.000Z",
  "_published": "2026-05-31T06:04:10.065Z",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
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    "cpp",
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  "_contributors": [
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    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_downloads": {
    "count": 309,
    "source": "https://www.bioconductor.org/packages/stats/bioc/scider"
  },
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  "_pkgdown": "https://chenlaboratory.github.io/scider/",
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
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    "extra/readme.md",
    "extra/scider.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/chenlaboratory/scider",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "allocateCells",
    "corDensity",
    "findNbrsGrid",
    "findNbrsSNN",
    "findNbrsSpatial",
    "findROI",
    "getClusters",
    "getContour",
    "getHVG",
    "getNiche",
    "globalMoran",
    "gridDensity",
    "gridSPE",
    "localMoran",
    "mergeROI",
    "normalizeAssay",
    "plotCellCompo",
    "plotContour",
    "plotCorHeatmap",
    "plotDensCor",
    "plotDensity",
    "plotDots",
    "plotDR",
    "plotGrid",
    "plotImage",
    "plotLISA",
    "plotLISAscatter",
    "plotPCA",
    "plotROI",
    "plotSpatial",
    "plotUMAP",
    "plotViolin",
    "postSelRegion",
    "readProseg",
    "readVisium",
    "readVisiumHD",
    "readXenium",
    "realignVisium",
    "realignVisiumHD",
    "runPCA",
    "runUMAP",
    "selectRegion",
    "spe2PB"
  ],
  "_datasets": [
    {
      "name": "spe",
      "title": "Description of the scider example datasets",
      "object": "xenium_bc_spe",
      "file": "xenium_bc_spe.rda",
      "class": [
        "SpatialExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "sub-SpatialExperiment-ANY-ANY-ANY-method",
      "title": "Subset for grid level analysis",
      "topics": [
        "[,SpatialExperiment,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "allocateCells",
      "title": "Annotate all cells with contour level of cell type-specific density.",
      "topics": [
        "allocateCells"
      ]
    },
    {
      "page": "cellsInRegion",
      "title": "Check which cells are in which regions",
      "topics": [
        "cellsInRegion"
      ]
    },
    {
      "page": "computeDensity",
      "title": "Perform kernel density estimation on SpatialExperiment",
      "topics": [
        "computeDensity"
      ]
    },
    {
      "page": "computeDensityHex",
      "title": "Perform kernel density estimation on SpatialExperiment",
      "topics": [
        "computeDensityHex"
      ]
    },
    {
      "page": "contour2sf",
      "title": "Draw a contour region on some density level",
      "topics": [
        "contour2sf"
      ]
    },
    {
      "page": "coord_hash",
      "title": "Hash two 15-bytes signed integers into one 32-bytes integer.",
      "topics": [
        "coord_hash"
      ]
    },
    {
      "page": "corDensity",
      "title": "Test for density correlation between two cell types.",
      "topics": [
        "corDensity"
      ]
    },
    {
      "page": "findNbrsGrid",
      "title": "Construct a neighbour list from grid coordinates.",
      "topics": [
        "findNbrsGrid"
      ]
    },
    {
      "page": "findNbrsSNN",
      "title": "Construct a SNN neighbour list from assay.",
      "topics": [
        "findNbrsSNN"
      ]
    },
    {
      "page": "findNbrsSpatial",
      "title": "Construct a distance-based neighbour list from cell coordinates.",
      "topics": [
        "findNbrsSpatial"
      ]
    },
    {
      "page": "findROI",
      "title": "Find ROIs based on cell type-specific densities via graph-based method.",
      "topics": [
        "findROI"
      ]
    },
    {
      "page": "getClusters",
      "title": "Cluster cells in spe using graph methods.",
      "topics": [
        "getClusters"
      ]
    },
    {
      "page": "getContour",
      "title": "Get contour from density",
      "topics": [
        "getContour"
      ]
    },
    {
      "page": "getContourRegions",
      "title": "Calculate areas between every two density levels",
      "topics": [
        "getContourRegions"
      ]
    },
    {
      "page": "getHVG",
      "title": "Get top highly variable genes.",
      "topics": [
        "getHVG"
      ]
    },
    {
      "page": "getNiche",
      "title": "Build a niche assay based on the profile of neighbouring cells",
      "topics": [
        "getNiche"
      ]
    },
    {
      "page": "globalMoran",
      "title": "Calculate global Moran for 1 to 2 variables.",
      "topics": [
        "globalMoran"
      ]
    },
    {
      "page": "grid2df",
      "title": "Convert x,y nodes to data.frame of polygons",
      "topics": [
        "grid2df"
      ]
    },
    {
      "page": "grid2sf",
      "title": "Convert x,y nodes to sf polygons",
      "topics": [
        "grid2sf"
      ]
    },
    {
      "page": "gridDensity",
      "title": "Perform kernel density estimation on SpatialExperiment for cell types of interest",
      "topics": [
        "gridDensity"
      ]
    },
    {
      "page": "gridSPE",
      "title": "Summarize a SpatialExperiment object at grid-level",
      "topics": [
        "gridSPE"
      ]
    },
    {
      "page": "localMoran",
      "title": "Calculate local Moran for 1 to 2 variables.",
      "topics": [
        "localMoran"
      ]
    },
    {
      "page": "mergeROI",
      "title": "Manually merge ROIs",
      "topics": [
        "mergeROI"
      ]
    },
    {
      "page": "normalizeAssay",
      "title": "Perform log normalization for counts",
      "topics": [
        "normalizeAssay"
      ]
    },
    {
      "page": "plotCellCompo",
      "title": "Plot cell type composition in each density level of cell of interest.",
      "topics": [
        "plotCellCompo"
      ]
    },
    {
      "page": "plotContour",
      "title": "Plot contour lines.",
      "topics": [
        "plotContour"
      ]
    },
    {
      "page": "plotContourRegion",
      "title": "Visualising an sf object (for internal use only at the moment)",
      "topics": [
        "plotContourRegion"
      ]
    },
    {
      "page": "plotCorHeatmap",
      "title": "Plot model statistics using heatmap.",
      "topics": [
        "plotCorHeatmap"
      ]
    },
    {
      "page": "plotDensCor",
      "title": "Plot density correlation between two cell types",
      "topics": [
        "plotDensCor"
      ]
    },
    {
      "page": "plotDensity",
      "title": "Plot grid-based density.",
      "topics": [
        "plotDensity"
      ]
    },
    {
      "page": "plotDots",
      "title": "Dot plot of gene expression by groups",
      "topics": [
        "plotDots"
      ]
    },
    {
      "page": "plotDR",
      "title": "Plot reduced dimensions.",
      "topics": [
        "plotDR",
        "plotPCA",
        "plotUMAP"
      ]
    },
    {
      "page": "plotGrid",
      "title": "Plot grid from metadata.",
      "topics": [
        "plotGrid"
      ]
    },
    {
      "page": "plotImage",
      "title": "Plot background image of spe",
      "topics": [
        "plotImage"
      ]
    },
    {
      "page": "plotLISA",
      "title": "Plotting LISA (e.g. moran)",
      "topics": [
        "plotLISA"
      ]
    },
    {
      "page": "plotLISAscatter",
      "title": "Scatterplot for local moran's I",
      "topics": [
        "plotLISAscatter"
      ]
    },
    {
      "page": "plotROI",
      "title": "Plot ROIs on spatial.",
      "topics": [
        "plotROI"
      ]
    },
    {
      "page": "plotSpatial",
      "title": "Plot cells based on spatial coordinates.",
      "topics": [
        "plotSpatial"
      ]
    },
    {
      "page": "plotViolin",
      "title": "Violin plot using genes or cell data",
      "topics": [
        "plotViolin"
      ]
    },
    {
      "page": "postSelRegion",
      "title": "Merge sel_region from the selectRegion function to SpatialExperiment.",
      "topics": [
        "postSelRegion"
      ]
    },
    {
      "page": "readProseg",
      "title": "Read Proseg V2 output into spe",
      "topics": [
        "readProseg"
      ]
    },
    {
      "page": "readVisium",
      "title": "Read Visium output into spe",
      "topics": [
        "readVisium"
      ]
    },
    {
      "page": "readVisiumHD",
      "title": "Read VisiumHD output into spe",
      "topics": [
        "readVisiumHD"
      ]
    },
    {
      "page": "readXenium",
      "title": "Read Xenium output into spe",
      "topics": [
        "readXenium"
      ]
    },
    {
      "page": "realignVisium",
      "title": "Scale and straighten out Visium coordinates",
      "topics": [
        "realignVisium"
      ]
    },
    {
      "page": "realignVisiumHD",
      "title": "Scale and straighten out VisiumHD coordinates",
      "topics": [
        "realignVisiumHD"
      ]
    },
    {
      "page": "runPCA",
      "title": "Fast PCA using irlba.",
      "topics": [
        "runPCA"
      ]
    },
    {
      "page": "runUMAP",
      "title": "UMAP using uwot. Parameters are set to be similar to Seurat's",
      "topics": [
        "runUMAP"
      ]
    },
    {
      "page": "selectRegion",
      "title": "Select region of interest from plot",
      "topics": [
        "selectRegion"
      ]
    },
    {
      "page": "spe2PB",
      "title": "Given a 'SpatialExperiment' data object, create pseudo-bulk samples using the colData information and return a DGEList object",
      "topics": [
        "spe2PB"
      ]
    },
    {
      "page": "update_bound",
      "title": "Update the x,y limits of a plot",
      "topics": [
        "update_bound"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/scider/raw/HEAD/README.md",
  "_rundeps": [
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    "arrow",
    "askpass",
    "assertthat",
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    "beachmat",
    "BH",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "biocmake",
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