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  "Title": "Integrating SpatialExperiment with Simple Features in sf",
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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(\"Lior\", \"Pachter\", email = \"lpachter@caltech.edu\",\nrole = c(\"aut\", \"ths\"),\ncomment = c(ORCID = \"0000-0002-9164-6231\")))",
  "Description": "A new S4 class integrating Simple Features with the R\npackage sf to bring geospatial data analysis methods based on\nvector data to spatial transcriptomics. Also implements\nmanagement of spatial neighborhood graphs and geometric\noperations. This pakage builds upon SpatialExperiment and\nSingleCellExperiment, hence methods for these parent classes\ncan still be used.",
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  "Collate": "'AllGenerics.R' 'utils.R' 'SFE-class.R' 'aggregate.R'\n'align.R' 'annotGeometries.R' 'cbind.R' 'changeSampleIDs.R'\n'coerce.R' 'data.R' 'debris.R' 'df2sf.R' 'dimGeometries.R'\n'featureData.R' 'formatTxSpots.R' 'geometry_operation.R'\n'graph_wrappers.R' 'image.R' 'int_dimData.R'\n'internal-Voyager.R' 'listw2sparse.R' 'localResults.R' 'read.R'\n'reexports.R' 'rotateMinRect.R' 'saveRDS.R' 'spatialGraphs.R'\n'split.R' 'subset.R' 'tissue_boundary.R' 'transformation.R'\n'updateObject.R' 'validity.R' 'zzz.R'",
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  "URL": "https://pachterlab.github.io/SpatialFeatureExperiment",
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  "Date/Publication": "2026-04-28 12:59:09 UTC",
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      ],
      "topics": [
        "BioFormatsImage-getters",
        "isFull",
        "isFull,BioFormatsImage-method",
        "origin",
        "origin,BioFormatsImage-method",
        "transformation",
        "transformation,BioFormatsImage-method"
      ]
    },
    {
      "page": "cbind-SpatialFeatureExperiment-method",
      "title": "Concatenate SpatialFeatureExperiment objects",
      "concept": [
        "Non-spatial operations"
      ],
      "topics": [
        "cbind,SpatialFeatureExperiment-method"
      ]
    },
    {
      "page": "changeSampleIDs",
      "title": "Change sample IDs",
      "concept": [
        "Utilities"
      ],
      "topics": [
        "changeSampleIDs"
      ]
    },
    {
      "page": "colFeatureData",
      "title": "Get global spatial analysis results and metadata of colData, rowData, and geometries",
      "concept": [
        "Getters and setters"
      ],
      "topics": [
        "colFeatureData",
        "geometryFeatureData",
        "reducedDimFeatureData",
        "rowFeatureData"
      ]
    },
    {
      "page": "colGeometries",
      "title": "Column geometry getters and setters",
      "concept": [
        "Getters and setters"
      ],
      "topics": [
        "cellSeg",
        "cellSeg<-",
        "centroids",
        "centroids<-",
        "colGeometries",
        "colGeometries<-",
        "colGeometry",
        "colGeometry<-",
        "colGeometryNames",
        "colGeometryNames<-",
        "nucSeg",
        "nucSeg<-",
        "ROIPoly",
        "ROIPoly<-",
        "spotPoly",
        "spotPoly<-"
      ]
    },
    {
      "page": "containsOutOfMemoryData-SpatialFeatureExperiment-method",
      "title": "Whether an SFE object contains out of memory data",
      "concept": [
        "Utilities"
      ],
      "topics": [
        "containsOutOfMemoryData,SpatialFeatureExperiment-method"
      ]
    },
    {
      "page": "crop",
      "title": "Crop an SFE object with a geometry",
      "concept": [
        "Geometric operations"
      ],
      "topics": [
        "crop"
      ]
    },
    {
      "page": "cropImg",
      "title": "Crop images",
      "concept": [
        "Image methods",
        "image methods"
      ],
      "topics": [
        "cropImg",
        "cropImg,BioFormatsImage-method",
        "cropImg,ExtImage-method",
        "cropImg,SpatRasterImage-method"
      ]
    },
    {
      "page": "df2sf",
      "title": "From ordinary data frame to sf to construct SFE object",
      "concept": [
        "Utilities"
      ],
      "topics": [
        "df2sf"
      ]
    },
    {
      "page": "dim-BioFormatsImage-method",
      "title": "Find dimension of BioFormatsImage",
      "concept": [
        "Image methods",
        "image methods"
      ],
      "topics": [
        "dim,BioFormatsImage-method"
      ]
    },
    {
      "page": "dim-ExtImage-method",
      "title": "Find dimensions of ExtImage",
      "concept": [
        "Image methods",
        "image methods"
      ],
      "topics": [
        "dim,ExtImage-method"
      ]
    },
    {
      "page": "dimGeometries",
      "title": "Dimension geometry methods",
      "concept": [
        "Getters and setters"
      ],
      "topics": [
        "dimGeometries",
        "dimGeometries,SpatialFeatureExperiment-method",
        "dimGeometries<-",
        "dimGeometries<-,SpatialFeatureExperiment-method",
        "dimGeometry",
        "dimGeometry,SpatialFeatureExperiment-method",
        "dimGeometry<-",
        "dimGeometry<-,SpatialFeatureExperiment-method",
        "dimGeometryNames",
        "dimGeometryNames,SpatialFeatureExperiment-method",
        "dimGeometryNames<-",
        "dimGeometryNames<-,SpatialFeatureExperiment,numeric,character-method"
      ]
    },
    {
      "page": "ext",
      "title": "Get and set extent of image objects",
      "concept": [
        "Image methods",
        "image methods"
      ],
      "topics": [
        "ext",
        "ext,BioFormatsImage-method",
        "ext,ExtImage-method",
        "ext,SpatRasterImage-method",
        "ext<-,BioFormatsImage,numeric-method",
        "ext<-,ExtImage,numeric-method",
        "ext<-,SpatRasterImage,numeric-method"
      ]
    },
    {
      "page": "ExtImage",
      "title": "Use the EBImage 'Image' class in SFE objects",
      "concept": [
        "Image classes"
      ],
      "topics": [
        "ExtImage",
        "ExtImage-class",
        "show,ExtImage-method"
      ]
    },
    {
      "page": "findDebrisCells",
      "title": "Identify cells in small bits outside the main piece of tissue",
      "concept": [
        "Preprocessing and QC"
      ],
      "topics": [
        "findDebrisCells",
        "findDebrisCells,matrix-method",
        "findDebrisCells,sf-method",
        "findDebrisCells,sfc-method",
        "findDebrisCells,SpatialExperiment-method"
      ]
    },
    {
      "page": "findSpatialNeighbors",
      "title": "Find spatial neighborhood graph",
      "concept": [
        "Spatial neighborhood graph"
      ],
      "topics": [
        "findSpatialNeighbors",
        "findSpatialNeighbors,SpatialFeatureExperiment-method"
      ]
    },
    {
      "page": "findVisiumGraph",
      "title": "Find spatial neighborhood graphs for Visium spots",
      "concept": [
        "Spatial neighborhood graph"
      ],
      "topics": [
        "findVisiumGraph"
      ]
    },
    {
      "page": "findVisiumHDGraph",
      "title": "Find Visium HD spatial neighborhood graph",
      "concept": [
        "Spatial neighborhood graph"
      ],
      "topics": [
        "findVisiumHDGraph"
      ]
    },
    {
      "page": "formatTxSpots",
      "title": "Read and process transcript spots geometry for SFE",
      "concept": [
        "Transcript spots"
      ],
      "topics": [
        "addTxSpots",
        "formatTxSpots"
      ]
    },
    {
      "page": "formatTxTech",
      "title": "Read and process transcript spots for specific commercial technologies",
      "concept": [
        "Transcript spots"
      ],
      "topics": [
        "addTxTech",
        "formatTxTech"
      ]
    },
    {
      "page": "gdalParquetAvailable",
      "title": "Check if Parquet GDAL driver is available",
      "concept": [
        "Utilities"
      ],
      "topics": [
        "gdalParquetAvailable"
      ]
    },
    {
      "page": "getParams",
      "title": "Get parameters used in spatial methods",
      "concept": [
        "Getters and setters"
      ],
      "topics": [
        "getParams"
      ]
    },
    {
      "page": "getPixelSize",
      "title": "Get physical size of pixels",
      "concept": [
        "Utilities"
      ],
      "topics": [
        "getPixelSize"
      ]
    },
    {
      "page": "getTechTxFields",
      "title": "Get relevant fields and file paths for transcript spots",
      "concept": [
        "Utilities"
      ],
      "topics": [
        "getTechTxFields"
      ]
    },
    {
      "page": "getTissueBoundaryConcave",
      "title": "Get tissue boundary from concave hull of cell geometries",
      "concept": [
        "Preprocessing and QC"
      ],
      "topics": [
        "getTissueBoundaryConcave",
        "getTissueBoundaryConcave,sf-method",
        "getTissueBoundaryConcave,sfc-method",
        "getTissueBoundaryConcave,SpatialFeatureExperiment-method"
      ]
    },
    {
      "page": "getTissueBoundaryImg",
      "title": "Get tissue boundary from histology image",
      "concept": [
        "Preprocessing and QC"
      ],
      "topics": [
        "getTissueBoundaryImg"
      ]
    },
    {
      "page": "imageIDs",
      "title": "Show all image_ids in the SFE object",
      "concept": [
        "Utilities"
      ],
      "topics": [
        "imageIDs"
      ]
    },
    {
      "page": "Img-set-SpatialExperiment-method",
      "title": "Image setter",
      "concept": [
        "Image methods"
      ],
      "topics": [
        "Img<-",
        "Img<-,SpatialExperiment-method"
      ]
    },
    {
      "page": "imgRaster",
      "title": "Get the image from *Image class",
      "concept": [
        "Image methods",
        "image methods"
      ],
      "topics": [
        "imgRaster",
        "imgRaster,BioFormatsImage-method",
        "imgRaster,ExtImage-method",
        "imgRaster,SpatRasterImage-method"
      ]
    },
    {
      "page": "imgSource",
      "title": "Source of images that are on disk",
      "concept": [
        "Image methods",
        "image methods"
      ],
      "topics": [
        "imgSource",
        "imgSource,BioFormatsImage-method",
        "imgSource,ExtImage-method",
        "imgSource,SpatRasterImage-method"
      ]
    },
    {
      "page": "localResults",
      "title": "Get and set results from local spatial statistics",
      "concept": [
        "Getters and setters"
      ],
      "topics": [
        "localResult",
        "localResult,SpatialFeatureExperiment-method",
        "localResult<-",
        "localResult<-,SpatialFeatureExperiment-method",
        "localResultAttrs",
        "localResultAttrs,SpatialFeatureExperiment-method",
        "localResultFeatures",
        "localResultFeatures,SpatialFeatureExperiment-method",
        "localResultNames",
        "localResultNames,SpatialFeatureExperiment-method",
        "localResultNames<-",
        "localResultNames<-,SpatialFeatureExperiment,character-method",
        "localResults",
        "localResults,SpatialFeatureExperiment-method",
        "localResults<-",
        "localResults<-,SpatialFeatureExperiment-method"
      ]
    },
    {
      "page": "mirrorImg",
      "title": "Mirror/flip images",
      "concept": [
        "Image affine transformation",
        "image methods"
      ],
      "topics": [
        "mirrorImg",
        "mirrorImg,BioFormatsImage-method",
        "mirrorImg,ExtImage-method",
        "mirrorImg,SpatRasterImage-method"
      ]
    },
    {
      "page": "multi_listw2sparse",
      "title": "Convert multiple listw graphs into a single sparse adjacency matrix",
      "concept": [
        "Utilities"
      ],
      "topics": [
        "multi_listw2sparse"
      ]
    },
    {
      "page": "read10xVisiumSFE",
      "title": "Read 10X Visium data as SpatialFeatureExperiment",
      "concept": [
        "Read data into SFE"
      ],
      "topics": [
        "read10xVisiumSFE"
      ]
    },
    {
      "page": "readCosMX",
      "title": "Read CosMX data into SFE",
      "concept": [
        "Read data into SFE"
      ],
      "topics": [
        "readCosMX"
      ]
    },
    {
      "page": "readSelectTx",
      "title": "Read transcript spots of select genes",
      "concept": [
        "Transcript spots"
      ],
      "topics": [
        "addSelectTx",
        "readSelectTx"
      ]
    },
    {
      "page": "readVisiumHD",
      "title": "Read Visium HD data",
      "concept": [
        "Read data into SFE"
      ],
      "topics": [
        "readVisiumHD"
      ]
    },
    {
      "page": "readVizgen",
      "title": "Read Vizgen MERFISH output as SpatialFeatureExperiment",
      "concept": [
        "Read data into SFE"
      ],
      "topics": [
        "readVizgen"
      ]
    },
    {
      "page": "readXenium",
      "title": "Read 10X Xenium output as SpatialFeatureExperiment",
      "concept": [
        "Read data into SFE"
      ],
      "topics": [
        "readXenium"
      ]
    },
    {
      "page": "reexports",
      "title": "Functions re-exported from other packages",
      "topics": [
        "colData",
        "colData<-",
        "counts",
        "getImg",
        "imgData",
        "logcounts",
        "reducedDim",
        "reexports",
        "rmvImg",
        "rowData",
        "spatialCoords",
        "spatialCoords<-",
        "spatialCoordsNames"
      ]
    },
    {
      "page": "removeEmptySpace",
      "title": "Remove empty space",
      "concept": [
        "Geometric operations"
      ],
      "topics": [
        "removeEmptySpace"
      ]
    },
    {
      "page": "rotateImg",
      "title": "Rotate image",
      "concept": [
        "Image affine transformation",
        "image methods"
      ],
      "topics": [
        "rotateImg",
        "rotateImg,BioFormatsImage-method",
        "rotateImg,ExtImage-method",
        "rotateImg,SpatRasterImage-method"
      ]
    },
    {
      "page": "rotateMinRect",
      "title": "Rotate the tissue to reduce empty space in plots",
      "concept": [
        "Geometric operations"
      ],
      "topics": [
        "rotateMinRect",
        "rotateMinRect,matrix-method",
        "rotateMinRect,sf-method",
        "rotateMinRect,sfc-method",
        "rotateMinRect,SpatialFeatureExperiment-method"
      ]
    },
    {
      "page": "rowGeometries",
      "title": "Row geometry getters and setters",
      "concept": [
        "Getters and setters"
      ],
      "topics": [
        "rowGeometries",
        "rowGeometries<-",
        "rowGeometry",
        "rowGeometry<-",
        "rowGeometryNames",
        "rowGeometryNames<-",
        "txSpots",
        "txSpots<-"
      ]
    },
    {
      "page": "sampleIDs",
      "title": "Get all unique sample IDs",
      "concept": [
        "Utilities"
      ],
      "topics": [
        "sampleIDs"
      ]
    },
    {
      "page": "saveRDS-SpatialFeatureExperiment-method",
      "title": "Save SpatialFeatureExperiment as RDS file",
      "concept": [
        "Utilities"
      ],
      "topics": [
        "saveRDS,SpatialFeatureExperiment-method"
      ]
    },
    {
      "page": "scaleImg",
      "title": "Scale image",
      "concept": [
        "Image affine transformation",
        "image methods"
      ],
      "topics": [
        "scaleImg",
        "scaleImg,AlignedSpatialImage-method",
        "scaleImg,BioFormatsImage-method"
      ]
    },
    {
      "page": "SFE-image",
      "title": "Methods for handling image-related data",
      "concept": [
        "Image methods",
        "image methods"
      ],
      "topics": [
        "addImg,SpatialFeatureExperiment-method",
        "affineImg,SpatialFeatureExperiment-method",
        "mirrorImg,SpatialFeatureExperiment-method",
        "rotateImg,SpatialFeatureExperiment-method",
        "scaleImg,SpatialFeatureExperiment-method",
        "SFE-image",
        "translateImg,SpatialFeatureExperiment-method",
        "transposeImg,SpatialFeatureExperiment-method"
      ]
    },
    {
      "page": "SFE-transform",
      "title": "Affine transfortaion of SFE object in histological space",
      "concept": [
        "Geometric operations"
      ],
      "topics": [
        "affine",
        "mirror",
        "rotate",
        "scale",
        "SFE-transform",
        "translate",
        "transpose"
      ]
    },
    {
      "page": "show-SpatialFeatureExperiment-method",
      "title": "Print method for SpatialFeatureExperiment",
      "concept": [
        "SpatialFeatureExperiment class"
      ],
      "topics": [
        "show,SpatialFeatureExperiment-method"
      ]
    },
    {
      "page": "SpatialFeatureExperiment",
      "title": "Constructor of SpatialFeatureExperiment object",
      "concept": [
        "SpatialFeatureExperiment class"
      ],
      "topics": [
        "SpatialFeatureExperiment"
      ]
    },
    {
      "page": "SpatialFeatureExperiment-class",
      "title": "The SpatialFeatureExperiment class",
      "concept": [
        "SpatialFeatureExperiment class"
      ],
      "topics": [
        "SpatialFeatureExperiment-class"
      ]
    },
    {
      "page": "SpatialFeatureExperiment-coercion",
      "title": "SpatialFeatureExperiment coercion methods",
      "concept": [
        "SpatialFeatureExperiment class"
      ],
      "topics": [
        "SpatialFeatureExperiment-coercion",
        "toSpatialFeatureExperiment",
        "toSpatialFeatureExperiment,Seurat-method",
        "toSpatialFeatureExperiment,SingleCellExperiment-method",
        "toSpatialFeatureExperiment,SpatialExperiment-method"
      ]
    },
    {
      "page": "SpatialFeatureExperiment-subset",
      "title": "Subsetting SpatialFeatureExperiment objects",
      "concept": [
        "Non-spatial operations"
      ],
      "topics": [
        "SpatialFeatureExperiment-subset",
        "[,SpatialFeatureExperiment,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "spatialGraphs",
      "title": "Spatial graph methods",
      "concept": [
        "Getters and setters"
      ],
      "topics": [
        "annotGraph",
        "annotGraph<-",
        "annotGraphNames",
        "annotGraphNames<-",
        "annotGraphs",
        "annotGraphs<-",
        "colGraph",
        "colGraph<-",
        "colGraphNames",
        "colGraphNames<-",
        "colGraphs",
        "colGraphs<-",
        "rowGraph",
        "rowGraph<-",
        "rowGraphNames",
        "rowGraphNames<-",
        "rowGraphs",
        "rowGraphs<-",
        "spatialGraph",
        "spatialGraph,SpatialFeatureExperiment-method",
        "spatialGraph<-",
        "spatialGraph<-,SpatialFeatureExperiment-method",
        "spatialGraphNames",
        "spatialGraphNames,SpatialFeatureExperiment,numeric-method",
        "spatialGraphNames<-",
        "spatialGraphNames<-,SpatialFeatureExperiment,numeric,ANY,character-method",
        "spatialGraphs",
        "spatialGraphs,SpatialFeatureExperiment-method",
        "spatialGraphs<-",
        "spatialGraphs<-,SpatialFeatureExperiment-method"
      ]
    },
    {
      "page": "SpatRasterImage",
      "title": "SpatRaster representation of images in SFE objects",
      "concept": [
        "Image classes"
      ],
      "topics": [
        "show,SpatRasterImage-method",
        "SpatRasterImage",
        "SpatRasterImage-class"
      ]
    },
    {
      "page": "splitByCol",
      "title": "Split SFE object with categorical vector or geometry",
      "concept": [
        "Geometric operations"
      ],
      "topics": [
        "splitByCol",
        "splitByCol,SpatialFeatureExperiment,list-method",
        "splitByCol,SpatialFeatureExperiment,sf-method",
        "splitByCol,SpatialFeatureExperiment,sfc-method",
        "splitContiguity",
        "splitSamples"
      ]
    },
    {
      "page": "splitComponent",
      "title": "Split by graph component",
      "concept": [
        "Geometric operations"
      ],
      "topics": [
        "splitComponent",
        "splitComponent,sf-method",
        "splitComponent,sfc-method",
        "splitComponent,SpatialFeatureExperiment-method"
      ]
    },
    {
      "page": "st_any_pred",
      "title": "Simple geometry predicates",
      "concept": [
        "Geometric operations"
      ],
      "topics": [
        "st_any_intersects",
        "st_any_pred",
        "st_n_intersects",
        "st_n_pred"
      ]
    },
    {
      "page": "toExtImage",
      "title": "Convert images to ExtImage",
      "concept": [
        "Image classes"
      ],
      "topics": [
        "toExtImage",
        "toExtImage,BioFormatsImage-method",
        "toExtImage,SpatRasterImage-method"
      ]
    },
    {
      "page": "toSpatRasterImage",
      "title": "Convert images to SpatRasterImage",
      "concept": [
        "Image classes"
      ],
      "topics": [
        "toSpatRasterImage",
        "toSpatRasterImage,BioFormatsImage-method",
        "toSpatRasterImage,ExtImage-method"
      ]
    },
    {
      "page": "translateImg",
      "title": "Translate/shift image in space",
      "concept": [
        "Image affine transformation",
        "image methods"
      ],
      "topics": [
        "translateImg",
        "translateImg,BioFormatsImage-method",
        "translateImg,ExtImage-method",
        "translateImg,SpatRasterImage-method"
      ]
    },
    {
      "page": "transposeImg",
      "title": "Transpose images",
      "concept": [
        "Image affine transformation",
        "image methods"
      ],
      "topics": [
        "transposeImg",
        "transposeImg,BioFormatsImage-method",
        "transposeImg,ExtImage-method",
        "transposeImg,SpatRasterImage-method"
      ]
    },
    {
      "page": "unit-SpatialFeatureExperiment-method",
      "title": "Get unit of a SpatialFeatureExperiment",
      "concept": [
        "SpatialFeatureExperiment class"
      ],
      "topics": [
        "unit",
        "unit,SpatialFeatureExperiment-method"
      ]
    },
    {
      "page": "updateObject",
      "title": "Update a SpatialFeatureExperiment object",
      "concept": [
        "SpatialFeatureExperiment class"
      ],
      "topics": [
        "SFEVersion",
        "updateObject",
        "updateObject,SpatialFeatureExperiment-method"
      ]
    },
    {
      "page": "visium_row_col",
      "title": "Row and columns of Visium barcodes on the slide",
      "concept": [
        "Utilities"
      ],
      "topics": [
        "visium_row_col"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/SpatialFeatureExperiment/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "assorthead",
    "backports",
    "base64enc",
    "beachmat",
    "BH",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "biocmake",
    "BiocNeighbors",
    "BiocParallel",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "boot",
    "bslib",
    "cachem",
    "checkmate",
    "class",
    "classInt",
    "cli",
    "coda",
    "codetools",
    "cpp11",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "DelayedMatrixStats",
    "deldir",
    "digest",
    "dir.expiry",
    "dplyr",
    "dqrng",
    "DropletUtils",
    "e1071",
    "EBImage",
    "edgeR",
    "evaluate",
    "fastmap",
    "fftwtools",
    "filelock",
    "fontawesome",
    "formatR",
    "Formula",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "geometries",
    "glue",
    "h5mread",
    "HDF5Array",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httr2",
    "insight",
    "IRanges",
    "jpeg",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "lambda.r",
    "lattice",
    "LearnBayes",
    "lifecycle",
    "limma",
    "locfit",
    "magick",
    "magrittr",
    "marginaleffects",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "multcomp",
    "mvtnorm",
    "nlme",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "proxy",
    "purrr",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rappdirs",
    "Rcpp",
    "RCurl",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "rjson",
    "rlang",
    "rmarkdown",
    "RSQLite",
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