{
  "_id": "6aafc5b23d719c1f84081cd7",
  "Package": "MultiAssaySpatialExperiment",
  "Version": "0.99.12",
  "Date": "2026-08-30",
  "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",
  "URL": "https://github.com/Genentech/MultiAssaySpatialExperiment",
  "BugReports": "https://github.com/Genentech/MultiAssaySpatialExperiment/issues",
  "Encoding": "UTF-8",
  "biocViews": "Infrastructure, DataRepresentation, Spatial",
  "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-package.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": "8.1.0",
  "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://bioc.r-universe.dev",
  "Date/Publication": "2026-08-30 21:54:15 UTC",
  "RemoteUrl": "https://github.com/bioc/MultiAssaySpatialExperiment",
  "RemoteRef": "HEAD",
  "RemoteSha": "02ad0731b6263fbe885001b854cccaf2d20b0fe1",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-20 11:29:07 UTC",
    "User": "root"
  },
  "Author": "Patrick Aboyoun [aut, cre],\nGenentech, Inc. [cph]",
  "Maintainer": "Patrick Aboyoun <aboyounp@gene.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "MultiAssaySpatialExperiment_0.99.12.tar.gz",
  "_fileid": "https://r2.ropensci.org/44f95b0dc4d3df570197e3aae916c669883e258e28ca64b0ccffb11bc35be96d",
  "_filesize": 1930341,
  "_sha256": "44f95b0dc4d3df570197e3aae916c669883e258e28ca64b0ccffb11bc35be96d",
  "_expires": "2026-12-29T11:38:24.000Z",
  "_created": "2026-09-20T11:29:07.000Z",
  "_published": "2026-09-20T11:38:26.726Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 8
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/35507736934",
  "_status": "success",
  "_upstream": "https://github.com/bioc/MultiAssaySpatialExperiment",
  "_commit": {
    "id": "02ad0731b6263fbe885001b854cccaf2d20b0fe1",
    "author": "Patrick Aboyoun <aboyoun.patrick@gene.com>",
    "committer": "Patrick Aboyoun <aboyoun.patrick@gene.com>",
    "message": "docs: change \\dontrun{} → \\donttest{} in man page examples\n",
    "time": 1788126855
  },
  "_maintainer": {
    "name": "Patrick Aboyoun",
    "email": "aboyounp@gene.com"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 106070933179,
      "time": 218,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10603928051"
    },
    {
      "job": 106070933123,
      "time": 432,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "10604802410"
    },
    {
      "job": 106070933112,
      "time": 487,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10604787381"
    },
    {
      "job": 106070933152,
      "time": 290,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "10603803279"
    },
    {
      "job": 106070933127,
      "time": 254,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10604227284"
    },
    {
      "job": 106070311049,
      "time": 321,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10604387687"
    },
    {
      "job": 106070933150,
      "time": 208,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10603908117"
    },
    {
      "job": 106070933161,
      "time": 327,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "10604283206"
    },
    {
      "job": 106070933118,
      "time": 330,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "10604522803"
    },
    {
      "job": 106070933165,
      "time": 359,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "10604657583"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "MultiAssayExperiment",
      "role": "Depends"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "MatrixGenerics",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "SpatialExperiment",
      "role": "Imports"
    },
    {
      "package": "sf",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "arrow",
      "role": "Suggests"
    },
    {
      "package": "DropletUtils",
      "role": "Suggests"
    },
    {
      "package": "jsonlite",
      "role": "Suggests"
    },
    {
      "package": "sfarrow",
      "role": "Suggests"
    },
    {
      "package": "terra",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "Matrix",
      "role": "Suggests"
    },
    {
      "package": "RBioFormats",
      "role": "Suggests"
    },
    {
      "package": "SpatialFeatureExperiment",
      "role": "Suggests"
    },
    {
      "package": "spdep",
      "role": "Suggests"
    },
    {
      "package": "zellkonverter",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2026-08",
      "n": 10
    },
    {
      "week": "2026-09",
      "n": 3
    },
    {
      "week": "2026-11",
      "n": 1
    },
    {
      "week": "2026-13",
      "n": 1
    },
    {
      "week": "2026-23",
      "n": 1
    },
    {
      "week": "2026-24",
      "n": 3
    },
    {
      "week": "2026-25",
      "n": 1
    },
    {
      "week": "2026-27",
      "n": 1
    },
    {
      "week": "2026-28",
      "n": 1
    },
    {
      "week": "2026-29",
      "n": 1
    },
    {
      "week": "2026-30",
      "n": 6
    },
    {
      "week": "2026-32",
      "n": 2
    },
    {
      "week": "2026-33",
      "n": 2
    },
    {
      "week": "2026-35",
      "n": 6
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "0.99.12",
      "bioc": "3.24"
    }
  ],
  "_topics": [
    "infrastructure",
    "datarepresentation",
    "spatial"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "aboyounp-gne",
      "count": 43,
      "uuid": 171627243
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 468,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 117,
    "source": "https://www.bioconductor.org/packages/stats/bioc/MultiAssaySpatialExperiment"
  },
  "_devurl": "https://github.com/genentech/multiassayspatialexperiment",
  "_searchresults": 9,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/MultiAssaySpatialExperiment.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/genentech/multiassayspatialexperiment",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addImg",
    "aggregateByRegion",
    "annotateWithRegions",
    "buildSpatialMap",
    "cbind",
    "checkSpatialMap",
    "coerce",
    "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": [
        "coerce,List,PointsLayerList-method",
        "coerce,list,PointsLayerList-method",
        "coerce,List,RasterLayerList-method",
        "coerce,list,RasterLayerList-method",
        "coerce,List,ShapesLayerList-method",
        "coerce,list,ShapesLayerList-method",
        "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"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/MultiAssaySpatialExperiment/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocParallel",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "class",
    "classInt",
    "cli",
    "codetools",
    "cpp11",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "dplyr",
    "e1071",
    "fastmap",
    "filelock",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "glue",
    "httr2",
    "IRanges",
    "KernSmooth",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magick",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "MultiAssayExperiment",
    "openssl",
    "pillar",
    "pkgconfig",
    "proxy",
    "purrr",
    "R6",
    "Rcpp",
    "rjson",
    "rlang",
    "RSQLite",
    "s2",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "sf",
    "SingleCellExperiment",
    "snow",
    "SparseArray",
    "SpatialExperiment",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "units",
    "utf8",
    "vctrs",
    "withr",
    "wk",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "MultiAssaySpatialExperiment.Rmd",
      "filename": "MultiAssaySpatialExperiment.html",
      "title": "Introduction to MultiAssaySpatialExperiment",
      "author": "Patrick Aboyoun",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Citing MultiAssaySpatialExperiment",
        "Why another spatial data structure?",
        "When to use MASE",
        "Prerequisites",
        "A worked example",
        "Building the object",
        "Looking at what it holds",
        "Subsetting keeps the links consistent",
        "Annotating and aggregating",
        "Handing the data to other tools",
        "See also",
        "Session info"
      ],
      "created": "2026-08-26 03:48:04",
      "modified": "2026-08-30 15:48:33",
      "commits": 3
    },
    {
      "source": "MultiAssaySpatialExperiment-workflows.Rmd",
      "filename": "MultiAssaySpatialExperiment-workflows.html",
      "title": "Working with MultiAssaySpatialExperiment",
      "author": "Patrick Aboyoun",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Building MASE objects",
        "Optional: lazy Parquet I/O via BiocDuckDB",
        "Minimal MASE",
        "Adding spatial coordinates",
        "Adding spatial shapes",
        "Building from multiple SingleCellExperiment objects",
        "prepMASE and buildSpatialMap",
        "Validation checklist",
        "Subsetting operations",
        "Overview of subsetting operations",
        "Basic subsetting",
        "Subset by specimen",
        "Subset by assay column",
        "Bracket notation",
        "Spatial subsetting",
        "Subset by bounding box",
        "Subset by polygon",
        "Select data from multiple non-contiguous regions",
        "Buffer-based subsets",
        "Spatial annotation and aggregation",
        "Example setup",
        "Annotate with regions",
        "Aggregate by region",
        "Count points per region",
        "Sum expression per region",
        "Mean expression per region",
        "Lower-level spatial joins",
        "Aggregation strategies",
        "Visualizing aggregated data",
        "Labels ↔ shapes interoperability",
        "Rasterization: shapes → labels",
        "Vectorization: labels → shapes",
        "Use cases",
        "See also",
        "Session info"
      ],
      "created": "2026-08-26 03:48:04",
      "modified": "2026-08-30 15:48:33",
      "commits": 3
    },
    {
      "source": "MultiAssaySpatialExperiment-usecases.Rmd",
      "filename": "MultiAssaySpatialExperiment-usecases.html",
      "title": "MultiAssaySpatialExperiment use cases",
      "author": "Patrick Aboyoun",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Part 1: Data import",
        "Reading Xenium data",
        "Basic usage",
        "Options",
        "When to load transcripts",
        "Reading Visium data",
        "Visium HD support",
        "Reading CosMx data",
        "FOV (Field of View) handling",
        "Reading MERSCOPE data (MERFISH)",
        "Choosing a reader",
        "Converting from other Bioconductor classes",
        "From SpatialExperiment",
        "From SpatialFeatureExperiment",
        "Reading multiple samples",
        "Part 2: Real-world workflows",
        "Workflow 1: Xenium + Visium integration",
        "Background",
        "Data preparation",
        "Build MASE object",
        "Exploratory analysis",
        "Do the two assays overlap in space?",
        "Which genes are shared between assays",
        "Spatial annotation: Cell types in Visium spots",
        "Reading the composition result",
        "Spatial aggregation: Summarize Xenium by regions",
        "Comparing expression between the two platforms",
        "Integration insights",
        "Workflow 2: Coordinate transformation and alignment",
        "Converting Visium grid to microns",
        "Applying affine transformations",
        "Landmark-based alignment",
        "Storing transformed coordinates",
        "Checking the alignment visually",
        "Workflow 3: Multi-sample analysis",
        "Workflow 4: Iterative analysis pattern",
        "Summary",
        "See also",
        "Session info"
      ],
      "created": "2026-08-26 03:48:04",
      "modified": "2026-08-30 15:48:33",
      "commits": 3
    },
    {
      "source": "MultiAssaySpatialExperiment-design.Rmd",
      "filename": "MultiAssaySpatialExperiment-design.html",
      "title": "Design of MultiAssaySpatialExperiment",
      "author": "Patrick Aboyoun",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Scope",
        "Anatomy of a MultiAssaySpatialExperiment",
        "What it inherits from MultiAssayExperiment",
        "The spatial layers it adds",
        "The tables that tie observations to space",
        "The relational schema",
        "Session info"
      ],
      "created": "2026-08-26 03:48:04",
      "modified": "2026-08-28 17:07:58",
      "commits": 2
    },
    {
      "source": "MultiAssaySpatialExperiment-cheatsheet.Rmd",
      "filename": "MultiAssaySpatialExperiment-cheatsheet.html",
      "title": "MultiAssaySpatialExperiment Cheatsheet",
      "author": "Patrick Aboyoun",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Summary of the MultiAssaySpatialExperiment API",
        "Constructors",
        "Platform readers",
        "Spatial accessors",
        "Inherited accessors used most often",
        "Subsetting",
        "Spatial operations",
        "Coercion",
        "Combining",
        "Session info"
      ],
      "created": "2026-08-26 03:48:04",
      "modified": "2026-08-28 17:07:58",
      "commits": 2
    }
  ],
  "_score": 6.021189299069938,
  "_indexed": true,
  "_nocasepkg": "multiassayspatialexperiment",
  "_universes": [
    "bioc",
    "genentech"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.12",
      "date": "2026-09-20T11:33:23.000Z",
      "distro": "resolute",
      "commit": "02ad0731b6263fbe885001b854cccaf2d20b0fe1",
      "fileid": "https://r2.ropensci.org/d3b28afa60dae936851765a3565047e7c15e7755f6766384617932bf07afa6a3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35507736934"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.99.12",
      "date": "2026-09-20T11:34:13.000Z",
      "distro": "resolute",
      "commit": "02ad0731b6263fbe885001b854cccaf2d20b0fe1",
      "fileid": "https://r2.ropensci.org/1f2f0ea694f12afc652f750d57ba69fd9c9dd17b3de426aa39feba721d2f9dd2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35507736934"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.12",
      "date": "2026-09-20T11:31:28.000Z",
      "commit": "02ad0731b6263fbe885001b854cccaf2d20b0fe1",
      "fileid": "https://r2.ropensci.org/6fe941508e9d108539de9a8e787d2174bc78cbaf05b704b6b991795ac45b2cdd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35507736934"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.99.12",
      "date": "2026-09-20T11:31:24.000Z",
      "commit": "02ad0731b6263fbe885001b854cccaf2d20b0fe1",
      "fileid": "https://r2.ropensci.org/d70d22016ac2f194921b3e6359cd46a059e9b5dcd175d89f263e55b44cd26cf8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35507736934"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.99.12",
      "date": "2026-09-20T11:33:13.000Z",
      "commit": "02ad0731b6263fbe885001b854cccaf2d20b0fe1",
      "fileid": "https://r2.ropensci.org/a6137546a0841762278f668a50b8a5e9019c219a83ff7611d192420343394b11",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35507736934"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.99.12",
      "date": "2026-09-20T11:31:12.000Z",
      "commit": "02ad0731b6263fbe885001b854cccaf2d20b0fe1",
      "fileid": "https://r2.ropensci.org/2dcfb7928f78be5a9ec0ba4bd12ea9dd057ef5af04d0ef6a5ff5bb88d839c0c6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35507736934"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.99.12",
      "date": "2026-09-20T11:31:36.000Z",
      "commit": "02ad0731b6263fbe885001b854cccaf2d20b0fe1",
      "fileid": "https://r2.ropensci.org/6dfe20b2c7d3ef3fe9809ed4a4f13af8081cdf146b25635c4812e8397ea190f2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35507736934"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.99.12",
      "date": "2026-09-20T11:31:22.000Z",
      "commit": "02ad0731b6263fbe885001b854cccaf2d20b0fe1",
      "fileid": "https://r2.ropensci.org/dc3678dcf22e453dbc56d027bf05ab330cf49ed8afcabdbb3f15da4e93729edc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35507736934"
    }
  ]
}