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  "Title": "From geospatial to spatial omics",
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  "Authors@R": "c(person(\"Lambda\", \"Moses\", email = \"dl3764@columbia.edu\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-7092-9427\")),\nperson(\"Alik\", \"Huseynov\",\ncomment = c(ORCID = \"0000-0002-1438-4389\"),\nrole = \"aut\"),\nperson(\"Kayla\", \"Jackson\", email = \"kaylajac@caltech.edu\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0001-6483-0108\")),\nperson(\"Laura\", \"Luebbert\", email = \"lauraluebbert@caltech.edu\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-1379-2927\")),\nperson(\"Lior\", \"Pachter\", email = \"lpachter@caltech.edu\",\nrole = c(\"aut\", \"rev\"),\ncomment = c(ORCID = \"0000-0002-9164-6231\")))",
  "Description": "SpatialFeatureExperiment (SFE) is a new S4 class for\nworking with spatial single-cell genomics data. The voyager\npackage implements basic exploratory spatial data analysis\n(ESDA) methods for SFE. Univariate methods include univariate\nglobal spatial ESDA methods such as Moran's I, permutation\ntesting for Moran's I, and correlograms. Bivariate methods\ninclude Lee's L and cross variogram. Multivariate methods\ninclude MULTISPATI PCA and multivariate local Geary's C\nrecently developed by Anselin. The Voyager package also\nimplements plotting functions to plot SFE data and ESDA\nresults.",
  "License": "Artistic-2.0",
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  "biocViews": "GeneExpression, Spatial, Transcriptomics, Visualization",
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  "URL": "https://github.com/pachterlab/voyager",
  "BugReports": "https://github.com/pachterlab/voyager/issues",
  "Collate": "'AllGenerics.R' 'res2df.R' 'SFEMethod-class.R'\n'SFEMethod-bivariate.R' 'SFEMethod-multivariate.R'\n'SFEMethod-spdep.R' 'bivariate.R' 'data.R' 'featureData.R'\n'geom_spi.R' 'gstat.R' 'listSFEMethods.R' 'multivariate.R'\n'plot-non-spatial.R' 'plot-transcripts.R'\n'plot-univar-downstream.R' 'plot.R' 'plotLocalResult.R'\n'plotSpatialReducedDim.R' 'spatial-misc.R'\n'univariate-downstream.R' 'univariate-internal.R'\n'univariate.R' 'utils.R'",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:59:10 UTC",
  "RemoteUrl": "https://github.com/bioc/Voyager",
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  "Packaged": {
    "Date": "2026-05-29 09:59:35 UTC",
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  "Author": "Lambda Moses [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-7092-9427>),\nAlik Huseynov [aut] (ORCID: <https://orcid.org/0000-0002-1438-4389>),\nKayla Jackson [aut] (ORCID: <https://orcid.org/0000-0001-6483-0108>),\nLaura Luebbert [aut] (ORCID: <https://orcid.org/0000-0003-1379-2927>),\nLior Pachter [aut, rev] (ORCID:\n<https://orcid.org/0000-0002-9164-6231>)",
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    "plotDimLoadings",
    "plotGeometry",
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    "plotLocalResult",
    "plotMoranMC",
    "plotRowDataFreqpoly",
    "plotRowDataHistogram",
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    "plotTxBin2D",
    "plotVariogram",
    "plotVariogramMap",
    "reducedDimMoransI",
    "reducedDimUnivariate",
    "reorganize_fun",
    "runBivariate",
    "runMoransI",
    "runMultivariate",
    "runUnivariate",
    "SFEMethod",
    "spatialReducedDim",
    "use_graph",
    "use_matrix"
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      "fields": [],
      "table": false,
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      "title": "Bivariate spatial statistics",
      "concept": [
        "Spatial statistics"
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        "calculateBivariate,ANY-method",
        "calculateBivariate,SpatialFeatureExperiment-method",
        "runBivariate"
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      "concept": [
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      ],
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        "calculateMultivariate,ANY,character-method",
        "calculateMultivariate,ANY,SFEMethod-method",
        "calculateMultivariate,SpatialFeatureExperiment,ANY-method",
        "runMultivariate"
      ]
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      "title": "Univariate spatial stiatistics",
      "concept": [
        "Spatial statistics"
      ],
      "topics": [
        "annotGeometryMoransI",
        "annotGeometryUnivariate",
        "calculateMoransI",
        "calculateMoransI,ANY-method",
        "calculateMoransI,SpatialFeatureExperiment-method",
        "calculateUnivariate",
        "calculateUnivariate,ANY,character-method",
        "calculateUnivariate,ANY,SFEMethod-method",
        "calculateUnivariate,SpatialFeatureExperiment,ANY-method",
        "colDataMoransI",
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        "runUnivariate"
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      "concept": [
        "Downstream analyses of univariate spatial results"
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      "topics": [
        "clusterCorrelograms"
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    },
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      "title": "Find clusters on the Moran plot",
      "concept": [
        "Downstream analyses of univariate spatial results"
      ],
      "topics": [
        "clusterMoranPlot"
      ]
    },
    {
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      "title": "Cluster variograms of multiple features",
      "concept": [
        "Downstream analyses of univariate spatial results"
      ],
      "topics": [
        "clusterVariograms"
      ]
    },
    {
      "page": "ditto_colors",
      "title": "Colorblind friendly palette from dittoSeq",
      "topics": [
        "ditto_colors"
      ]
    },
    {
      "page": "ElbowPlot",
      "title": "Plot the elbow plot or scree plot for PCA",
      "topics": [
        "ElbowPlot"
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    {
      "page": "getDivergeRange",
      "title": "Get beginning and end of palette to center a divergent palette",
      "topics": [
        "getDivergeRange"
      ]
    },
    {
      "page": "listSFEMethods",
      "title": "List all spatial methods in Voyager package",
      "concept": [
        "Spatial statistics"
      ],
      "topics": [
        "listSFEMethods"
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    {
      "page": "moranBounds",
      "title": "Compute the bounds of Moran's I given spatial neighborhood graph",
      "concept": [
        "Spatial statistics"
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      "topics": [
        "moranBounds"
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    },
    {
      "page": "moranPlot",
      "title": "Use ggplot to plot the moran.plot results",
      "concept": [
        "Plot spatial analysis results"
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      "topics": [
        "moranPlot"
      ]
    },
    {
      "page": "multispati_rsp",
      "title": "A faster implementation of MULTISPATI PCA",
      "concept": [
        "Internal spatial statistics functions"
      ],
      "topics": [
        "multispati_rsp"
      ]
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    {
      "page": "plotBivariate",
      "title": "Plot expression of two genes or features with bivariate palette",
      "concept": [
        "Spatial plotting"
      ],
      "topics": [
        "plotBivariate"
      ]
    },
    {
      "page": "plotCellBin2D",
      "title": "Plot cell density as 2D histogram",
      "concept": [
        "Spatial plotting"
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      "topics": [
        "plotCellBin2D"
      ]
    },
    {
      "page": "plotColDataFreqpoly",
      "title": "Plot frequency polygons for colData and rowData columns",
      "topics": [
        "plotColDataFreqpoly",
        "plotRowDataFreqpoly"
      ]
    },
    {
      "page": "plotColDataHistogram",
      "title": "Plot histograms for colData and rowData columns",
      "topics": [
        "plotColDataHistogram",
        "plotRowDataHistogram"
      ]
    },
    {
      "page": "plotColGraph",
      "title": "Plot spatial graphs",
      "concept": [
        "Spatial plotting"
      ],
      "topics": [
        "plotAnnotGraph",
        "plotColGraph"
      ]
    },
    {
      "page": "plotCorrelogram",
      "title": "Plot correlogram",
      "concept": [
        "Plot spatial analysis results"
      ],
      "topics": [
        "plotCorrelogram"
      ]
    },
    {
      "page": "plotCrossVariogram",
      "title": "Plot cross variogram",
      "concept": [
        "Plot spatial analysis results"
      ],
      "topics": [
        "plotCrossVariogram"
      ]
    },
    {
      "page": "plotCrossVariogramMap",
      "title": "Plot cross variogram map",
      "concept": [
        "Plot spatial analysis results"
      ],
      "topics": [
        "plotCrossVariogramMap"
      ]
    },
    {
      "page": "plotDimLoadings",
      "title": "Plot top PC loadings of genes",
      "topics": [
        "plotDimLoadings"
      ]
    },
    {
      "page": "plotGeometry",
      "title": "Plot geometries without coloring",
      "concept": [
        "Spatial plotting"
      ],
      "topics": [
        "plotGeometry"
      ]
    },
    {
      "page": "plotImage",
      "title": "Show image without plotting geometries",
      "concept": [
        "Spatial plotting"
      ],
      "topics": [
        "plotImage"
      ]
    },
    {
      "page": "plotLocalResult",
      "title": "Plot local results",
      "concept": [
        "Plot spatial analysis results"
      ],
      "topics": [
        "plotLocalResult"
      ]
    },
    {
      "page": "plotMoranMC",
      "title": "Plot Moran/Geary Monte Carlo results",
      "concept": [
        "Plot spatial analysis results"
      ],
      "topics": [
        "plotMoranMC"
      ]
    },
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