{
  "_id": "6a16a22dacfb0bcc41d81720",
  "Package": "imcExperiment",
  "Title": "Mass Cytometry S4 Class Structure Pipeline for Images",
  "Version": "0.99.0",
  "Authors@R": "person(\"Anthony\", \"Colombo\", email = \"anthonycolombo60@gmail.com\", role=c(\"aut\",\"cre\"))",
  "Maintainer": "Anthony Colombo <anthonycolombo60@gmail.com>",
  "Description": "Containerizes cytometry data and allows for S4 class\nstructure to extend slots related to cell morphology, spatial\ncoordinates, phenotype network information, and unique cellular\nlabeling.",
  "License": "MIT + file LICENSE",
  "biocViews": "Software, WorkflowStep, MultipleComparison",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.1.1",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://arcolombo.r-universe.dev",
  "Date/Publication": "2021-08-18 17:40:39 UTC",
  "RemoteUrl": "https://github.com/arcolombo/imcexperiment",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-27 07:45:14 UTC",
    "User": "root"
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  "Author": "Anthony Colombo [aut, cre]",
  "MD5sum": "61ac6db750848d0d0ac366abb1fd1810",
  "_user": "arcolombo",
  "_type": "src",
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    "email": "anthonycolombo60@gmail.com",
    "login": "arcolombo",
    "description": "daydreamer.",
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  "_dependencies": [
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      "package": "R",
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      "package": "SingleCellExperiment",
      "role": "Depends"
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    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
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  "_selfowned": true,
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  "_updates": [],
  "_tags": [],
  "_topics": [
    "software",
    "workflowstep",
    "multiplecomparison",
    "imc"
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    "name": "Anthony R. Colombo",
    "description": "daydreamer."
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  "_cranurl": true,
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      "date": "2021-08-19"
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    ".checkSpatialDimension",
    "cellIntensity",
    "cellIntensity<-",
    "getCoordinates",
    "getCoordinates<-",
    "getDistance",
    "getDistance<-",
    "getLabel",
    "getMorphology",
    "getMorphology<-",
    "getNeighborhood",
    "getNeighborhood<-",
    "getNetwork",
    "getNetwork<-",
    "imcExperiment",
    "imcExperimentToHyperFrame",
    "percentilenormalize",
    "selectCases",
    "subsetCase"
  ],
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      "name": "data",
      "title": "data",
      "object": "data",
      "file": "data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ImageId",
        "CellId",
        "marker1",
        "marker2",
        "marker3",
        "marker4",
        "marker5",
        "marker6",
        "marker7",
        "marker8",
        "marker9",
        "marker10",
        "marker11",
        "marker12",
        "marker13",
        "marker14",
        "marker15",
        "marker16",
        "marker17",
        "marker18",
        "marker19",
        "marker20",
        "marker21",
        "marker22",
        "marker23",
        "marker24",
        "marker25",
        "marker26",
        "marker27",
        "marker28",
        "marker29",
        "marker30",
        "marker31",
        "marker32",
        "marker33",
        "marker34",
        "Area",
        "Eccentricity",
        "Solidity",
        "Extent",
        "EulerNumber",
        "Perimeter",
        "MajorAxisLength",
        "MinorAxisLength",
        "Orientation",
        "X_position",
        "Y_position",
        "Percent_Touching",
        "Number_Neighbors",
        "neighbour_4_CellId1",
        "neighbour_4_CellId2",
        "neighbour_4_CellId3",
        "neighbour_4_CellId4",
        "neighbour_4_CellId5",
        "neighbour_4_CellId6",
        "neighbour_4_CellId7",
        "neighbour_4_CellId8",
        "neighbour_4_CellId9",
        "neighbour_4_CellId10",
        "Phenograph7851534969",
        "tSNE4148542692_1",
        "tSNE4148542692_2"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "imcdata",
      "title": "imcdata",
      "object": "imcData",
      "file": "imcData.rda",
      "class": [
        "imcExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "dot-checkSpatialDimension",
      "title": "the rows are the panel names, the columns are the single cells,the column are the single cells to match the SCE designs (scRNA)",
      "topics": [
        ".checkSpatialDimension"
      ]
    },
    {
      "page": "dot-imcExperimentToPPP",
      "title": "map to point pattern from imcExperiment class.",
      "topics": [
        ".imcExperimentToPPP"
      ]
    },
    {
      "page": "cellIntensity",
      "title": "finds the intensities getter.",
      "topics": [
        "cellIntensity",
        "cellIntensity,imcExperiment-method",
        "cellIntensity<-",
        "cellIntensity<-,imcExperiment,matrix-method"
      ]
    },
    {
      "page": "data",
      "title": "data",
      "topics": [
        "data"
      ]
    },
    {
      "page": "getCoordinates",
      "title": "finds the spatial coords, getter.",
      "topics": [
        "getCoordinates",
        "getCoordinates,imcExperiment-method",
        "getCoordinates<-,imcExperiment,matrix-method"
      ]
    },
    {
      "page": "getCoordinates-set",
      "title": "Sets the coordinate positions of each cell (matrix), columns are X,Y positions.",
      "topics": [
        "getCoordinates<-"
      ]
    },
    {
      "page": "getDistance-set",
      "title": "re-assigns the distance matrix (rows are cells)",
      "topics": [
        "getDistance<-"
      ]
    },
    {
      "page": "getMorphology-set",
      "title": "re-assigns morphological features can be stored (matrix) rows are cells and columns are Area, etc.",
      "topics": [
        "getMorphology<-"
      ]
    },
    {
      "page": "getNeighborhood",
      "title": "finds the neighborhood information.",
      "topics": [
        "getNeighborhood",
        "getNeighborhood,imcExperiment-method",
        "getNeighborhood<-",
        "getNeighborhood<-,imcExperiment,matrix-method"
      ]
    },
    {
      "page": "getNetwork-set",
      "title": "re-assigns the network assignment (matrix)",
      "topics": [
        "getNetwork<-"
      ]
    },
    {
      "page": "imcdata",
      "title": "imcdata",
      "topics": [
        "imcdata"
      ]
    },
    {
      "page": "imcExperiment",
      "title": "Initializes a imcExperiment and performs some rudimentary checks. Many of the arguments CAN be NULL; determination of which is required is done at run-time.  A imcExperiment must contain at least the expressions and spatial/coordinate assays.",
      "topics": [
        "imcExperiment"
      ]
    },
    {
      "page": "imcExperiment-class",
      "title": "a summarized experiment of IMC runs, dimensions of the spatial and intensity data are regulated.#'",
      "topics": [
        ".imcExperiment",
        "getDistance",
        "getDistance,imcExperiment-method",
        "getDistance<-,imcExperiment,matrix-method",
        "getLabel",
        "getLabel,imcExperiment-method",
        "getMorphology",
        "getMorphology,imcExperiment-method",
        "getMorphology<-,imcExperiment,matrix-method",
        "getNetwork",
        "getNetwork,imcExperiment-method",
        "getNetwork<-,imcExperiment,data.frame-method",
        "imcExperiment-class",
        "imcExperiment-method",
        "spatial"
      ]
    },
    {
      "page": "imcExperimentToHyperFrame",
      "title": "map to point pattern from imcExperiment class.",
      "topics": [
        "imcExperimentToHyperFrame"
      ]
    },
    {
      "page": "percentilenormalize",
      "title": "given a matrix of intensity counts, perform min/max norm.",
      "topics": [
        "percentilenormalize"
      ]
    },
    {
      "page": "selectCases",
      "title": "subsets the imcExperiment to a case along with all slots for a selected multiple ROIs.",
      "topics": [
        "selectCases",
        "selectCases,imcExperiment-method"
      ]
    },
    {
      "page": "subsetCase",
      "title": "subsets the imcExperiment to a case along with all slots for a single ROI, using for distance analysis",
      "topics": [
        "subsetCase",
        "subsetCase,imcExperiment-method"
      ]
    }
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  "_rundeps": [
    "abind",
    "Biobase",
    "BiocGenerics",
    "DelayedArray",
    "deldir",
    "generics",
    "GenomicRanges",
    "IRanges",
    "lattice",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "polyclip",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "SingleCellExperiment",
    "SparseArray",
    "spatstat.data",
    "spatstat.geom",
    "spatstat.univar",
    "spatstat.utils",
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    "XVector"
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      "source": "example.Rmd",
      "filename": "example.html",
      "title": "imcExperiment: containerization of IMC data",
      "author": "Anthony Colombo",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Heatmap plotting script (helper)",
        "example",
        "Accessors, and setters",
        "From histoCAT to R",
        "PCA demo analysis",
        "IMC container and Phenograph cluster neighborhood",
        "histoCAT analysis",
        "Access unique cell ID",
        "Distance computations speedily",
        "Changing class from IMC to SummarizedExperiment",
        "IMC and flowSet conversions",
        "Diffcyt package tutorial (extra)"
      ],
      "created": "2020-03-03 16:43:58",
      "modified": "2021-08-18 17:06:22",
      "commits": 11
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