{
  "_id": "6a1ad29d1d7bb097a09e304b",
  "Package": "ExperimentSubset",
  "Type": "Package",
  "Title": "Manages subsets of data with Bioconductor Experiment objects",
  "Version": "1.23.0",
  "Date": "2021-05-09",
  "Authors@R": "c(person(given=\"Irzam\", family=\"Sarfraz\", email=\"irzam9095@gmail.com\", role=c(\"aut\",\"cre\"),\ncomment = c(ORCID = \"0000-0001-8121-792X\")),\nperson(given=\"Muhammad\", family=\"Asif\", email=\"asif@ntu.edu.pk\", role=c(\"aut\",\"ths\"),\ncomment = c(ORCID = \"0000-0003-1839-2527\")),\nperson(given=c(\"Joshua\",\"D.\"), family=\"Campbell\", email=\"camp@bu.edu\", role=c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-0780-8662\")))",
  "Description": "Experiment objects such as the SummarizedExperiment or\nSingleCellExperiment are data containers for one or more\nmatrix-like assays along with the associated row and column\ndata. Often only a subset of the original data is needed for\ndown-stream analysis. For example, filtering out poor quality\nsamples will require excluding some columns before analysis.\nThe ExperimentSubset object is a container to efficiently\nmanage different subsets of the same data without having to\nmake separate objects for each new subset.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.1.1",
  "biocViews": "Infrastructure, Software, DataImport, DataRepresentation",
  "VignetteBuilder": "knitr",
  "Collate": "'allClasses.R' 'allGenerics.R' 'ExperimentSubset.R'\n'SubsetRangedSummarizedExperiment.R'\n'SubsetSingleCellExperiment.R' 'SubsetSummarizedExperiment.R'\n'SubsetSpatialExperiment.R' 'SubsetTreeSummarizedExperiment.R'",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:54:05 UTC",
  "RemoteUrl": "https://github.com/bioc/ExperimentSubset",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 08:32:00 UTC",
    "User": "root"
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  "Author": "Irzam Sarfraz [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-8121-792X>),\nMuhammad Asif [aut, ths] (ORCID:\n<https://orcid.org/0000-0003-1839-2527>),\nJoshua D. Campbell [aut] (ORCID:\n<https://orcid.org/0000-0003-0780-8662>)",
  "Maintainer": "Irzam Sarfraz <irzam9095@gmail.com>",
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  "_user": "bioc",
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  "_created": "2026-05-30T08:32:00.000Z",
  "_published": "2026-05-30T12:05:49.347Z",
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    "ExperimentSubset",
    "getSubsetAssay",
    "reducedDimNames",
    "reducedDimNames<-",
    "reducedDims<-",
    "setSubsetAssay",
    "subsetAssayCount",
    "subsetAssayNames",
    "subsetColData",
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    "subsetColnames",
    "subsetColnames<-",
    "subsetCount",
    "subsetDim",
    "subsetNames",
    "subsetParent",
    "subsetRowData",
    "subsetRowData<-",
    "subsetRowLinks",
    "subsetRownames",
    "subsetRownames<-",
    "subsetSpatialCoords",
    "subsetSpatialData",
    "subsetSpatialData<-",
    "subsetSummary"
  ],
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    {
      "page": "AssaySubset",
      "title": "AssaySubset constructor",
      "topics": [
        "AssaySubset"
      ]
    },
    {
      "page": "AssaySubset-class",
      "title": "An S4 class to manage subset representation.",
      "topics": [
        ".AssaySubset",
        "AssaySubset-class"
      ]
    },
    {
      "page": "createSubset",
      "title": "Subset creation method for ExperimentSubset objects",
      "topics": [
        "createSubset",
        "createSubset,SubsetRangedSummarizedExperiment-method",
        "createSubset,SubsetSingleCellExperiment-method",
        "createSubset,SubsetSpatialExperiment-method",
        "createSubset,SubsetSummarizedExperiment-method",
        "createSubset,SubsetTreeSummarizedExperiment-method"
      ]
    },
    {
      "page": "ExperimentSubset",
      "title": "ExperimentSubset constructor",
      "topics": [
        "ExperimentSubset"
      ]
    },
    {
      "page": "getSubsetAssay",
      "title": "Get subset assay from an 'ExperimentSubset' object.",
      "topics": [
        "getSubsetAssay",
        "getSubsetAssay,SubsetRangedSummarizedExperiment,character-method",
        "getSubsetAssay,SubsetSingleCellExperiment,character-method",
        "getSubsetAssay,SubsetSpatialExperiment,character-method",
        "getSubsetAssay,SubsetSummarizedExperiment,character-method",
        "getSubsetAssay,SubsetTreeSummarizedExperiment,character-method"
      ]
    },
    {
      "page": "reducedDimNames",
      "title": "reducedDimNames",
      "topics": [
        "reducedDimNames",
        "reducedDimNames,ANY-method"
      ]
    },
    {
      "page": "reducedDimNames-set",
      "title": "reducedDimNames<-",
      "topics": [
        "reducedDimNames<-",
        "reducedDimNames<-,ANY-method"
      ]
    },
    {
      "page": "reducedDims-set",
      "title": "reducedDims<-",
      "topics": [
        "reducedDims<-"
      ]
    },
    {
      "page": "reducedDims-set-ANY-method",
      "title": "reducedDims<-",
      "topics": [
        "reducedDims<-,ANY-method"
      ]
    },
    {
      "page": "setSubsetAssay",
      "title": "Method for storing new assays inside subsets in ExperimentSubset objects",
      "topics": [
        "setSubsetAssay",
        "setSubsetAssay,SubsetRangedSummarizedExperiment,character,ANY,character-method",
        "setSubsetAssay,SubsetSingleCellExperiment,character,ANY,character-method",
        "setSubsetAssay,SubsetSpatialExperiment,character,ANY,character-method",
        "setSubsetAssay,SubsetSummarizedExperiment,character,ANY,character-method",
        "setSubsetAssay,SubsetTreeSummarizedExperiment,character,ANY,character-method"
      ]
    },
    {
      "page": "subsetAssayCount",
      "title": "Count method for subset assays in ExperimentSubset objects",
      "topics": [
        "subsetAssayCount",
        "subsetAssayCount,SubsetRangedSummarizedExperiment-method",
        "subsetAssayCount,SubsetSingleCellExperiment-method",
        "subsetAssayCount,SubsetSpatialExperiment-method",
        "subsetAssayCount,SubsetSummarizedExperiment-method",
        "subsetAssayCount,SubsetTreeSummarizedExperiment-method"
      ]
    },
    {
      "page": "subsetAssayNames",
      "title": "Name retrieval method for all subset assays in ExperimentSubset objects",
      "topics": [
        "subsetAssayNames",
        "subsetAssayNames,SubsetRangedSummarizedExperiment-method",
        "subsetAssayNames,SubsetSingleCellExperiment-method",
        "subsetAssayNames,SubsetSpatialExperiment-method",
        "subsetAssayNames,SubsetSummarizedExperiment-method",
        "subsetAssayNames,SubsetTreeSummarizedExperiment-method"
      ]
    },
    {
      "page": "subsetColData",
      "title": "Accessor method for colData from subsets in ExperimentSubset objects",
      "topics": [
        "subsetColData",
        "subsetColData,SubsetRangedSummarizedExperiment,character-method",
        "subsetColData,SubsetSingleCellExperiment,character-method",
        "subsetColData,SubsetSpatialExperiment,character-method",
        "subsetColData,SubsetSummarizedExperiment,character-method",
        "subsetColData,SubsetTreeSummarizedExperiment,character-method",
        "subsetColData<-",
        "subsetColData<-,SubsetRangedSummarizedExperiment,character,DataFrame-method",
        "subsetColData<-,SubsetSingleCellExperiment,character,DataFrame-method",
        "subsetColData<-,SubsetSpatialExperiment,character,DataFrame-method",
        "subsetColData<-,SubsetSummarizedExperiment,character,DataFrame-method",
        "subsetColData<-,SubsetTreeSummarizedExperiment,character,DataFrame-method"
      ]
    },
    {
      "page": "subsetColLinks",
      "title": "Accessor method for colLinks from subsets in ExperimentSubset objects",
      "topics": [
        "subsetColLinks",
        "subsetColLinks,SubsetTreeSummarizedExperiment,character-method"
      ]
    },
    {
      "page": "subsetColnames",
      "title": "subsetColnames",
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        "subsetColnames,SubsetRangedSummarizedExperiment,character-method",
        "subsetColnames,SubsetSingleCellExperiment,character-method",
        "subsetColnames,SubsetSpatialExperiment,character-method",
        "subsetColnames,SubsetSummarizedExperiment,character-method",
        "subsetColnames,SubsetTreeSummarizedExperiment,character-method",
        "subsetColnames<-",
        "subsetColnames<-,SubsetRangedSummarizedExperiment,character-method",
        "subsetColnames<-,SubsetSingleCellExperiment,character-method",
        "subsetColnames<-,SubsetSpatialExperiment,character-method",
        "subsetColnames<-,SubsetSummarizedExperiment,character-method",
        "subsetColnames<-,SubsetTreeSummarizedExperiment,character-method"
      ]
    },
    {
      "page": "subsetCount",
      "title": "Subset count method for ExperimentSubset objects",
      "topics": [
        "subsetCount",
        "subsetCount,SubsetRangedSummarizedExperiment-method",
        "subsetCount,SubsetSingleCellExperiment-method",
        "subsetCount,SubsetSpatialExperiment-method",
        "subsetCount,SubsetSummarizedExperiment-method",
        "subsetCount,SubsetTreeSummarizedExperiment-method"
      ]
    },
    {
      "page": "subsetDim",
      "title": "Get dimensions of subsets in ExperimentSubset objects",
      "topics": [
        "subsetDim",
        "subsetDim,SubsetRangedSummarizedExperiment,character-method",
        "subsetDim,SubsetSingleCellExperiment,character-method",
        "subsetDim,SubsetSpatialExperiment,character-method",
        "subsetDim,SubsetSummarizedExperiment,character-method",
        "subsetDim,SubsetTreeSummarizedExperiment,character-method"
      ]
    },
    {
      "page": "subsetNames",
      "title": "Get names of only the subsets in ExperimentSubset objects",
      "topics": [
        "subsetNames",
        "subsetNames,SubsetRangedSummarizedExperiment-method",
        "subsetNames,SubsetSingleCellExperiment-method",
        "subsetNames,SubsetSpatialExperiment-method",
        "subsetNames,SubsetSummarizedExperiment-method",
        "subsetNames,SubsetTreeSummarizedExperiment-method"
      ]
    },
    {
      "page": "subsetParent",
      "title": "Subset parent hierarchy retrieval method for ExperimentSubset objects",
      "topics": [
        "subsetParent",
        "subsetParent,SubsetRangedSummarizedExperiment-method",
        "subsetParent,SubsetSingleCellExperiment-method",
        "subsetParent,SubsetSpatialExperiment-method",
        "subsetParent,SubsetSummarizedExperiment-method",
        "subsetParent,SubsetTreeSummarizedExperiment-method"
      ]
    },
    {
      "page": "SubsetRangedSummarizedExperiment-class",
      "title": "An S4 class for 'RangedSummarizedExperiment' objects with added support for subsets.",
      "topics": [
        ".SubsetRangedSummarizedExperiment",
        "SubsetRangedSummarizedExperiment-class"
      ]
    },
    {
      "page": "subsetRowData",
      "title": "Accessor method for rowData from subsets in ExperimentSubset objects",
      "topics": [
        "subsetRowData",
        "subsetRowData,SubsetRangedSummarizedExperiment,character-method",
        "subsetRowData,SubsetSingleCellExperiment,character-method",
        "subsetRowData,SubsetSpatialExperiment,character-method",
        "subsetRowData,SubsetSummarizedExperiment,character-method",
        "subsetRowData,SubsetTreeSummarizedExperiment,character-method",
        "subsetRowData<-",
        "subsetRowData<-,SubsetRangedSummarizedExperiment,character,DataFrame-method",
        "subsetRowData<-,SubsetSingleCellExperiment,character,DataFrame-method",
        "subsetRowData<-,SubsetSpatialExperiment,character,DataFrame-method",
        "subsetRowData<-,SubsetSummarizedExperiment,character,DataFrame-method",
        "subsetRowData<-,SubsetTreeSummarizedExperiment,character,DataFrame-method"
      ]
    },
    {
      "page": "subsetRowLinks",
      "title": "Accessor method for rowLinks from subsets in ExperimentSubset objects",
      "topics": [
        "subsetRowLinks",
        "subsetRowLinks,SubsetTreeSummarizedExperiment,character-method"
      ]
    },
    {
      "page": "subsetRownames",
      "title": "subsetRownames",
      "topics": [
        "subsetRownames",
        "subsetRownames,SubsetRangedSummarizedExperiment,character-method",
        "subsetRownames,SubsetSingleCellExperiment,character-method",
        "subsetRownames,SubsetSpatialExperiment,character-method",
        "subsetRownames,SubsetSummarizedExperiment,character-method",
        "subsetRownames,SubsetTreeSummarizedExperiment,character-method",
        "subsetRownames<-",
        "subsetRownames<-,SubsetRangedSummarizedExperiment,character-method",
        "subsetRownames<-,SubsetSingleCellExperiment,character-method",
        "subsetRownames<-,SubsetSpatialExperiment,character-method",
        "subsetRownames<-,SubsetSummarizedExperiment,character-method",
        "subsetRownames<-,SubsetTreeSummarizedExperiment,character-method"
      ]
    },
    {
      "page": "SubsetSingleCellExperiment-class",
      "title": "An S4 class for 'SingleCellExperiment' objects with added support for subsets.",
      "topics": [
        ".SubsetSingleCellExperiment",
        "SubsetSingleCellExperiment-class"
      ]
    },
    {
      "page": "subsetSpatialCoords",
      "title": "Accessor method for spatialCoords from subsets in ExperimentSubset objects",
      "topics": [
        "subsetSpatialCoords",
        "subsetSpatialCoords,SubsetSpatialExperiment,character-method"
      ]
    },
    {
      "page": "subsetSpatialData",
      "title": "Accessor method for spatialData from subsets in ExperimentSubset objects",
      "topics": [
        "subsetSpatialData",
        "subsetSpatialData,SubsetSpatialExperiment,character-method",
        "subsetSpatialData<-",
        "subsetSpatialData<-,SubsetSpatialExperiment,character,data.frame-method"
      ]
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      "page": "SubsetSpatialExperiment-class",
      "title": "An S4 class for 'SpatialExperiment' objects with added support for subsets.",
      "topics": [
        ".SubsetSpatialExperiment",
        "SubsetSpatialExperiment-class"
      ]
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      "page": "SubsetSummarizedExperiment-class",
      "title": "An S4 class for 'SummarizedExperiment' objects with added support for subsets.",
      "topics": [
        ".SubsetSummarizedExperiment",
        "SubsetSummarizedExperiment-class"
      ]
    },
    {
      "page": "subsetSummary",
      "title": "Method for displaying 'child-parent' link structure of subsets in ExperimentSubset objects",
      "topics": [
        "subsetSummary",
        "subsetSummary,SubsetRangedSummarizedExperiment-method",
        "subsetSummary,SubsetSingleCellExperiment-method",
        "subsetSummary,SubsetSpatialExperiment-method",
        "subsetSummary,SubsetSummarizedExperiment-method",
        "subsetSummary,SubsetTreeSummarizedExperiment-method"
      ]
    },
    {
      "page": "SubsetTreeSummarizedExperiment-class",
      "title": "An S4 class for 'TreeSummarizedExperiment' objects with added support for subsets.",
      "topics": [
        ".SubsetTreeSummarizedExperiment",
        "SubsetTreeSummarizedExperiment-class"
      ]
    }
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    "yulab.utils"
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      "source": "ExperimentSubset.Rmd",
      "filename": "ExperimentSubset.html",
      "title": "ExperimentSubset: Manages subsets of data with Bioconductor Experiment objects",
      "author": "Irzam Sarfraz, Muhammad Asif, Joshua D. Campbell",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Motivation",
        "A Brief Description",
        "Overview of the ExperimentSubset class",
        "Core methods of ExperimentSubset class",
        "ExperimentSubset constructor",
        "createSubset",
        "setSubsetAssay and getSubsetAssay",
        "subsetSummary",
        "Additional helper methods",
        "subsetColData & subsetRowData",
        "Overridden methods for ExperimentSubset class",
        "assay-get & assay-set inherited methods",
        "Using the ExperimentSubset object: A toy example",
        "Using the ExperimentSubset object: An example with real single cell RNA-seq data",
        "Supported Input Object Classes",
        "Methods for ExperimentSubset",
        "Implementation Details",
        "Inherited parent object",
        "Additional subsets slot",
        "subsetName",
        "rowIndices",
        "colIndices",
        "parentAssay",
        "internalAssay",
        "Session Information"
      ],
      "created": "2020-08-17 09:38:43",
      "modified": "2021-03-06 05:01:11",
      "commits": 13
    }
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