{
  "_id": "6a60f38d1fed6d528131bf90",
  "Package": "MultiAssaySpatialExperiment",
  "Version": "0.99.2",
  "Date": "2026-07-22",
  "Title": "Multi-Assay Experiment with Spatial Context",
  "Description": "Extends MultiAssayExperiment with spatial context elements\n(images, labels, points, shapes) for integrative analysis of\nspatially resolved multi-omics data. Supports coercion to and\nfrom SpatialExperiment and SpatialFeatureExperiment.",
  "Authors@R": "c(\nperson(\"Patrick\", \"Aboyoun\", role=c(\"aut\", \"cre\"), email=\"aboyounp@gene.com\"),\nperson(\"Genentech, Inc.\", role=\"cph\")\n)",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "biocViews": "Infrastructure, DataRepresentation",
  "VignetteBuilder": "knitr",
  "Collate": "'SpatialGenerics.R' 'SpatialLayerList-class.R'\n'MultiAssaySpatialExperiment-class.R'\n'MultiAssaySpatialExperiment-SpatialExperiment.R'\n'MultiAssaySpatialExperiment-SpatialFeatureExperiment.R'\n'MultiAssaySpatialExperiment-combine.R'\n'MultiAssaySpatialExperiment-spatialMap.R'\n'MultiAssaySpatialExperiment-helpers.R'\n'MultiAssaySpatialExperiment-read-components.R'\n'MultiAssaySpatialExperiment-read-config.R'\n'MultiAssaySpatialExperiment-read-cosmx.R'\n'MultiAssaySpatialExperiment-read-generics.R'\n'MultiAssaySpatialExperiment-read-helpers.R'\n'MultiAssaySpatialExperiment-read-merscope.R'\n'MultiAssaySpatialExperiment-read-visium.R'\n'MultiAssaySpatialExperiment-read-visiumhd.R'\n'MultiAssaySpatialExperiment-read-xenium.R'\n'MultiAssaySpatialExperiment-subset.R' 'spatial-aggregate.R'\n'spatial-annotate.R' 'spatial-operations.R'\n'spatial-raster-convert.R' 'zzz.R'",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibmagick++-dev gsfonts libicu-dev libssl-dev libproj-dev\nlibsqlite3-dev libudunits2-dev zlib1g-dev",
  "Repository": "https://biocstaging.r-universe.dev",
  "Date/Publication": "2026-07-22 15:54:31 UTC",
  "RemoteUrl": "https://github.com/BiocStaging/MultiAssaySpatialExperiment",
  "RemoteRef": "HEAD",
  "RemoteSha": "1c4601f09049897b3f6ba9294642648059e40368",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-22 16:13:47 UTC",
    "User": "root"
  },
  "Author": "Patrick Aboyoun [aut, cre],\nGenentech, Inc. [cph]",
  "Maintainer": "Patrick Aboyoun <aboyounp@gene.com>",
  "_user": "biocstaging",
  "_type": "src",
  "_file": "MultiAssaySpatialExperiment_0.99.2.tar.gz",
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  "_created": "2026-07-22T16:13:47.000Z",
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    "author": "Patrick Aboyoun <aboyoun.patrick@gene.com>",
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  "_assets": [
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  "_exports": [
    "addImg",
    "aggregateByRegion",
    "annotateWithRegions",
    "buildSpatialMap",
    "cbind",
    "checkSpatialMap",
    "getImg",
    "imgData",
    "imgData<-",
    "imgRaster",
    "imgSource",
    "labelsToShapes",
    "mirrorImg",
    "molecules",
    "MultiAssaySpatialExperiment",
    "PointsLayerList",
    "prepMASE",
    "RasterLayerList",
    "readCosMxMASE",
    "readCSVForMASE",
    "readGeoJSONForMASE",
    "readGeoParquetForMASE",
    "readHDF5ForMASE",
    "readMERSCOPEMASE",
    "readParquetForMASE",
    "readVisiumHDMASE",
    "readVisiumMASE",
    "readXeniumMASE",
    "rmvImg",
    "rotateImg",
    "scaleFactors",
    "ShapesLayerList",
    "shapesToLabels",
    "show",
    "spatialCoords",
    "spatialCoordsNames",
    "spatialImage",
    "spatialImage<-",
    "spatialImageNames",
    "spatialImages",
    "spatialImages<-",
    "spatialJoin",
    "spatialLabel",
    "spatialLabel<-",
    "spatialLabelNames",
    "spatialLabels",
    "spatialLabels<-",
    "spatialMap",
    "spatialMap<-",
    "spatialMatch",
    "spatialOverlaps",
    "spatialPoint",
    "spatialPoint<-",
    "spatialPointNames",
    "spatialPoints",
    "spatialPoints<-",
    "spatialShape",
    "spatialShape<-",
    "spatialShapeNames",
    "spatialShapes",
    "spatialShapes<-",
    "subsetByAssay",
    "subsetByBoundingBox",
    "subsetByColData",
    "subsetByColumn",
    "subsetByPolygon",
    "subsetByRow"
  ],
  "_help": [
    {
      "page": "aggregateByRegion",
      "title": "Aggregate assay values by shape region",
      "topics": [
        "aggregateByRegion",
        "aggregateByRegion,MultiAssaySpatialExperiment-method"
      ]
    },
    {
      "page": "annotateWithRegions",
      "title": "Annotate points with shape regions",
      "topics": [
        "annotateWithRegions",
        "annotateWithRegions,MultiAssaySpatialExperiment-method"
      ]
    },
    {
      "page": "buildSpatialMap",
      "title": "Build a spatialMap table from sampleMap",
      "topics": [
        "buildSpatialMap"
      ]
    },
    {
      "page": "checkSpatialMap",
      "title": "Check spatialMap consistency",
      "topics": [
        "checkSpatialMap"
      ]
    },
    {
      "page": "labelsToShapes",
      "title": "Convert label rasters to polygon shapes",
      "topics": [
        "labelsToShapes"
      ]
    },
    {
      "page": "MultiAssaySpatialExperiment-class",
      "title": "MultiAssaySpatialExperiment objects",
      "topics": [
        "imgData,MultiAssaySpatialExperiment-method",
        "imgData<-,MultiAssaySpatialExperiment,ANY-method",
        "MultiAssaySpatialExperiment",
        "MultiAssaySpatialExperiment-class",
        "show,MultiAssaySpatialExperiment-method",
        "spatialImage,MultiAssaySpatialExperiment-method",
        "spatialImage<-,MultiAssaySpatialExperiment-method",
        "spatialImageNames,MultiAssaySpatialExperiment-method",
        "spatialImages,MultiAssaySpatialExperiment-method",
        "spatialImages<-,MultiAssaySpatialExperiment-method",
        "spatialLabel,MultiAssaySpatialExperiment-method",
        "spatialLabel<-,MultiAssaySpatialExperiment-method",
        "spatialLabelNames,MultiAssaySpatialExperiment-method",
        "spatialLabels,MultiAssaySpatialExperiment-method",
        "spatialLabels<-,MultiAssaySpatialExperiment-method",
        "spatialMap,MultiAssaySpatialExperiment-method",
        "spatialMap<-,MultiAssaySpatialExperiment-method",
        "spatialPoint,MultiAssaySpatialExperiment-method",
        "spatialPoint<-,MultiAssaySpatialExperiment-method",
        "spatialPointNames,MultiAssaySpatialExperiment-method",
        "spatialPoints,MultiAssaySpatialExperiment-method",
        "spatialPoints<-,MultiAssaySpatialExperiment-method",
        "spatialShape,MultiAssaySpatialExperiment-method",
        "spatialShape<-,MultiAssaySpatialExperiment-method",
        "spatialShapeNames,MultiAssaySpatialExperiment-method",
        "spatialShapes,MultiAssaySpatialExperiment-method",
        "spatialShapes<-,MultiAssaySpatialExperiment-method"
      ]
    },
    {
      "page": "MultiAssaySpatialExperiment-combine",
      "title": "MultiAssaySpatialExperiment combining",
      "topics": [
        "c,MultiAssaySpatialExperiment-method",
        "cbind,MultiAssaySpatialExperiment-method",
        "MultiAssaySpatialExperiment-combine"
      ]
    },
    {
      "page": "MultiAssaySpatialExperiment-SpatialExperiment",
      "title": "MultiAssaySpatialExperiment - SpatialExperiment integration",
      "topics": [
        "addImg,MultiAssaySpatialExperiment-method",
        "coerce,MultiAssaySpatialExperiment,SpatialExperiment-method",
        "coerce,SpatialExperiment,MultiAssaySpatialExperiment-method",
        "getImg,MultiAssaySpatialExperiment-method",
        "imgRaster,MultiAssaySpatialExperiment-method",
        "imgSource,MultiAssaySpatialExperiment-method",
        "mirrorImg,MultiAssaySpatialExperiment-method",
        "molecules,MultiAssaySpatialExperiment-method",
        "MultiAssaySpatialExperiment-SpatialExperiment",
        "rmvImg,MultiAssaySpatialExperiment-method",
        "rotateImg,MultiAssaySpatialExperiment-method",
        "scaleFactors,MultiAssaySpatialExperiment-method",
        "spatialCoords,MultiAssaySpatialExperiment-method",
        "spatialCoordsNames,MultiAssaySpatialExperiment-method"
      ]
    },
    {
      "page": "MultiAssaySpatialExperiment-subset",
      "title": "MultiAssaySpatialExperiment subsetting",
      "topics": [
        "MultiAssaySpatialExperiment-subset",
        "subsetByAssay,MultiAssaySpatialExperiment-method",
        "subsetByBoundingBox",
        "subsetByBoundingBox,MultiAssaySpatialExperiment-method",
        "subsetByColData,MultiAssaySpatialExperiment,ANY-method",
        "subsetByColData,MultiAssaySpatialExperiment,character-method",
        "subsetByColumn,MultiAssaySpatialExperiment,ANY-method",
        "subsetByPolygon",
        "subsetByPolygon,MultiAssaySpatialExperiment-method",
        "subsetByRow,MultiAssaySpatialExperiment,ANY-method",
        "subsetByRow,MultiAssaySpatialExperiment,List-method",
        "subsetByRow,MultiAssaySpatialExperiment,list-method",
        "[,MultiAssaySpatialExperiment,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "prepMASE",
      "title": "Prepare components for a MultiAssaySpatialExperiment",
      "topics": [
        "prepMASE"
      ]
    },
    {
      "page": "readCosMxMASE",
      "title": "Read NanoString CosMx SMI Spatial Data",
      "topics": [
        "readCosMxMASE"
      ]
    },
    {
      "page": "readCSVForMASE",
      "title": "Read CSV Files for MASE",
      "topics": [
        "readCSVForMASE",
        "readCSVForMASE,character-method"
      ]
    },
    {
      "page": "readGeoJSONForMASE",
      "title": "Read GeoJSON Files for MASE",
      "topics": [
        "readGeoJSONForMASE",
        "readGeoJSONForMASE,character-method"
      ]
    },
    {
      "page": "readGeoParquetForMASE",
      "title": "Read GeoParquet Files for MASE",
      "topics": [
        "readGeoParquetForMASE",
        "readGeoParquetForMASE,character-method"
      ]
    },
    {
      "page": "readHDF5ForMASE",
      "title": "Read HDF5 Files for MASE",
      "topics": [
        "readHDF5ForMASE",
        "readHDF5ForMASE,character,character-method"
      ]
    },
    {
      "page": "readMERSCOPEMASE",
      "title": "Read Vizgen MERSCOPE Spatial Data",
      "topics": [
        "readMERSCOPEMASE"
      ]
    },
    {
      "page": "readParquetForMASE",
      "title": "Read Parquet Files for MASE",
      "topics": [
        "readParquetForMASE",
        "readParquetForMASE,character-method"
      ]
    },
    {
      "page": "readVisiumHDMASE",
      "title": "Read 10x Genomics Visium HD Spatial Data",
      "topics": [
        "readVisiumHDMASE"
      ]
    },
    {
      "page": "readVisiumMASE",
      "title": "Read 10x Genomics Visium Spatial Data",
      "topics": [
        "readVisiumMASE"
      ]
    },
    {
      "page": "readXeniumMASE",
      "title": "Read 10x Genomics Xenium Spatial Data",
      "topics": [
        "readXeniumMASE"
      ]
    },
    {
      "page": "shapesToLabels",
      "title": "Rasterize polygon shapes to a label image",
      "topics": [
        "shapesToLabels"
      ]
    },
    {
      "page": "spatial-accessors",
      "title": "Access spatial element slots",
      "topics": [
        "spatial-accessors",
        "spatialImage",
        "spatialImage<-",
        "spatialImageNames",
        "spatialImages",
        "spatialImages<-",
        "spatialLabel",
        "spatialLabel<-",
        "spatialLabelNames",
        "spatialLabels",
        "spatialLabels<-",
        "spatialMap",
        "spatialMap<-",
        "spatialPoint",
        "spatialPoint<-",
        "spatialPointNames",
        "spatialPoints",
        "spatialPoints<-",
        "spatialShape",
        "spatialShape<-",
        "spatialShapeNames",
        "spatialShapes",
        "spatialShapes<-"
      ]
    },
    {
      "page": "spatialJoin",
      "title": "Spatial join between spatial layer tables",
      "topics": [
        "spatialJoin",
        "spatialJoin,DataFrame,DataFrame-method"
      ]
    },
    {
      "page": "SpatialLayerList-class",
      "title": "Spatial layer list objects",
      "topics": [
        "PointsLayerList",
        "PointsLayerList-class",
        "RasterLayerList",
        "RasterLayerList-class",
        "ShapesLayerList",
        "ShapesLayerList-class",
        "show,PointsLayerList-method",
        "show,RasterLayerList-method",
        "show,ShapesLayerList-method",
        "SpatialLayerList-class"
      ]
    },
    {
      "page": "spatialMatch",
      "title": "Spatial match for DataFrame",
      "topics": [
        "spatialMatch",
        "spatialMatch,DataFrame,DataFrame-method"
      ]
    },
    {
      "page": "spatialOverlaps",
      "title": "Spatial overlap predicate for DataFrame",
      "topics": [
        "spatialOverlaps",
        "spatialOverlaps,DataFrame-method"
      ]
    }
  ],
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      "source": "Introduction.Rmd",
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