{
  "_id": "6a101d1cacfb0bcc41c8a058",
  "Package": "SingleCellExperiment",
  "Version": "1.35.1",
  "Date": "2026-05-14",
  "Title": "S4 Classes for Single Cell Data",
  "Authors@R": "c(\nperson(\"Aaron\", \"Lun\", role=c(\"aut\", \"cph\"), email=\"infinite.monkeys.with.keyboards@gmail.com\"),\nperson(\"Davide\",\"Risso\", role=c(\"aut\",\"cre\", \"cph\"), email=\"risso.davide@gmail.com\"),\nperson(\"Keegan\", \"Korthauer\", role=\"ctb\"),\nperson(\"Kevin\", \"Rue-Albrecht\", role=\"ctb\"),\nperson(\"Luke\", \"Zappia\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7744-8565\", github = \"lazappi\")))",
  "biocViews": "ImmunoOncology, DataRepresentation, DataImport,\nInfrastructure, SingleCell",
  "Description": "Defines a S4 class for storing data from single-cell\nexperiments. This includes specialized methods to store and\nretrieve spike-in information, dimensionality reduction\ncoordinates and size factors for each cell, along with the\nusual metadata for genes and libraries.",
  "License": "GPL-2 | GPL-3",
  "URL": "https://github.com/drisso/SingleCellExperiment",
  "BugReports": "https://github.com/drisso/SingleCellExperiment/issues",
  "VignetteBuilder": "knitr",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-14 02:13:59 UTC",
  "RemoteUrl": "https://github.com/bioc/SingleCellExperiment",
  "RemoteRef": "HEAD",
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  "Packaged": {
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    "User": "root"
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  "Author": "Aaron Lun [aut, cph],\nDavide Risso [aut, cre, cph],\nKeegan Korthauer [ctb],\nKevin Rue-Albrecht [ctb],\nLuke Zappia [ctb] (ORCID: <https://orcid.org/0000-0001-7744-8565>,\ngithub: lazappi)",
  "Maintainer": "Davide Risso <risso.davide@gmail.com>",
  "MD5sum": "351672094e009fc5332eb96bb95187a7",
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  "_created": "2026-05-14T07:46:57.000Z",
  "_published": "2026-05-22T09:08:44.635Z",
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.json",
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  "_exports": [
    "altExp",
    "altExp<-",
    "altExpNames",
    "altExpNames<-",
    "altExps",
    "altExps<-",
    "applySCE",
    "cbind",
    "coerce",
    "colData",
    "colLabels",
    "colLabels<-",
    "colPair",
    "colPair<-",
    "colPairNames",
    "colPairNames<-",
    "colPairs",
    "colPairs<-",
    "combineCols",
    "counts",
    "counts<-",
    "cpm",
    "cpm<-",
    "factorData",
    "factorData<-",
    "featureLoadings",
    "featureLoadings<-",
    "int_colData",
    "int_colData<-",
    "int_elementMetadata",
    "int_elementMetadata<-",
    "int_metadata",
    "int_metadata<-",
    "LinearEmbeddingMatrix",
    "logcounts",
    "logcounts<-",
    "mainExpName",
    "mainExpName<-",
    "normcounts",
    "normcounts<-",
    "objectVersion",
    "parallel_slot_names",
    "rbind",
    "reduced.dim.matrix",
    "reducedDim",
    "reducedDim<-",
    "reducedDimNames",
    "reducedDimNames<-",
    "reducedDims",
    "reducedDims<-",
    "removeAltExps",
    "rowData",
    "rowPair",
    "rowPair<-",
    "rowPairNames",
    "rowPairNames<-",
    "rowPairs",
    "rowPairs<-",
    "rowSubset",
    "rowSubset<-",
    "sampleFactors",
    "sampleFactors<-",
    "show",
    "simplifyToSCE",
    "SingleCellExperiment",
    "sizeFactors",
    "sizeFactors<-",
    "splitAltExps",
    "swapAltExp",
    "tpm",
    "tpm<-",
    "unsplitAltExps",
    "updateObject",
    "weights",
    "weights<-"
  ],
  "_help": [
    {
      "page": "altExps",
      "title": "Alternative Experiment methods",
      "topics": [
        "%",
        "altExp",
        "altExp,SingleCellExperiment,character-method",
        "altExp,SingleCellExperiment,missing-method",
        "altExp,SingleCellExperiment,numeric-method",
        "altExp<-",
        "altExp<-,SingleCellExperiment,character-method",
        "altExp<-,SingleCellExperiment,missing-method",
        "altExp<-,SingleCellExperiment,numeric-method",
        "altExpNames",
        "altExpNames,SingleCellExperiment-method",
        "altExpNames<-",
        "altExpNames<-,SingleCellExperiment,character-method",
        "altExps",
        "altExps,SingleCellExperiment-method",
        "altExps<-",
        "altExps<-,SingleCellExperiment-method",
        "c,SummarizedExperimentByColumn-method",
        "check",
        "complain.",
        "doesn't",
        "Dumping",
        "here,",
        "length,SummarizedExperimentByColumn-method",
        "mainExpName",
        "mainExpName,SingleCellExperiment-method",
        "mainExpName<-",
        "mainExpName<-,SingleCellExperiment,character_OR_NULL-method",
        "methods",
        "names,SummarizedExperimentByColumn-method",
        "names<-,SummarizedExperimentByColumn-method",
        "removeAltExps",
        "SEBC",
        "so",
        "that",
        "the",
        "[,SummarizedExperimentByColumn,ANY,ANY,ANY-method",
        "[<-,SummarizedExperimentByColumn,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "applySCE",
      "title": "Applying over parts of a SingleCellExperiment",
      "topics": [
        "applySCE"
      ]
    },
    {
      "page": "colLabels",
      "title": "Get or set column labels",
      "topics": [
        "colLabels",
        "colLabels,SingleCellExperiment-method",
        "colLabels<-",
        "colLabels<-,SingleCellExperiment-method"
      ]
    },
    {
      "page": "colPairs",
      "title": "Column pair methods",
      "topics": [
        "colPair",
        "colPair,SingleCellExperiment,character-method",
        "colPair,SingleCellExperiment,missing-method",
        "colPair,SingleCellExperiment,numeric-method",
        "colPair<-",
        "colPair<-,SingleCellExperiment,character-method",
        "colPair<-,SingleCellExperiment,missing-method",
        "colPair<-,SingleCellExperiment,numeric-method",
        "colPairNames",
        "colPairNames,SingleCellExperiment-method",
        "colPairNames<-",
        "colPairNames<-,SingleCellExperiment,character-method",
        "colPairs",
        "colPairs,SingleCellExperiment-method",
        "colPairs<-",
        "colPairs<-,SingleCellExperiment-method"
      ]
    },
    {
      "page": "LEM-combine",
      "title": "LEM combining methods",
      "topics": [
        "cbind,LinearEmbeddingMatrix-method",
        "rbind,LinearEmbeddingMatrix-method"
      ]
    },
    {
      "page": "defunct",
      "title": "Defunct methods",
      "topics": [
        "clearSizeFactors",
        "clearSpikes",
        "defunct",
        "isSpike",
        "isSpike<-",
        "sizeFactorNames",
        "spikeNames"
      ]
    },
    {
      "page": "LEM-getset",
      "title": "LinearEmbeddingMatrix getters/setters",
      "topics": [
        "$,LinearEmbeddingMatrix-method",
        "$<-,LinearEmbeddingMatrix-method",
        "as.matrix,LinearEmbeddingMatrix-method",
        "dim,LinearEmbeddingMatrix-method",
        "dimnames,LinearEmbeddingMatrix-method",
        "dimnames<-,LinearEmbeddingMatrix,ANY-method",
        "dimnames<-,LinearEmbeddingMatrix-method",
        "factorData",
        "factorData,LinearEmbeddingMatrix-method",
        "factorData<-",
        "factorData<-,LinearEmbeddingMatrix-method",
        "featureLoadings",
        "featureLoadings,LinearEmbeddingMatrix-method",
        "featureLoadings<-",
        "featureLoadings<-,LinearEmbeddingMatrix-method",
        "sampleFactors",
        "sampleFactors,LinearEmbeddingMatrix-method",
        "sampleFactors<-",
        "sampleFactors<-,LinearEmbeddingMatrix-method"
      ]
    },
    {
      "page": "LinearEmbeddingMatrix",
      "title": "LinearEmbeddingMatrix class",
      "topics": [
        "LinearEmbeddingMatrix",
        "LinearEmbeddingMatrix-class"
      ]
    },
    {
      "page": "LEM-misc",
      "title": "Miscellaneous LEM methods",
      "topics": [
        "show,LinearEmbeddingMatrix-method"
      ]
    },
    {
      "page": "reduced.dim.matrix",
      "title": "The reduced.dim.matrix class",
      "topics": [
        "cbind.reduced.dim.matrix",
        "rbind.reduced.dim.matrix",
        "reduced.dim.matrix",
        "reduced.dim.matrix-class",
        "[.reduced.dim.matrix"
      ]
    },
    {
      "page": "reducedDims",
      "title": "Reduced dimensions methods",
      "topics": [
        "reducedDim",
        "reducedDim,SingleCellExperiment,character-method",
        "reducedDim,SingleCellExperiment,missing-method",
        "reducedDim,SingleCellExperiment,numeric-method",
        "reducedDim<-",
        "reducedDim<-,SingleCellExperiment,character-method",
        "reducedDim<-,SingleCellExperiment,missing-method",
        "reducedDim<-,SingleCellExperiment,numeric-method",
        "reducedDimNames",
        "reducedDimNames,SingleCellExperiment-method",
        "reducedDimNames<-",
        "reducedDimNames<-,SingleCellExperiment,character-method",
        "reducedDims",
        "reducedDims,SingleCellExperiment-method",
        "reducedDims<-",
        "reducedDims<-,SingleCellExperiment-method"
      ]
    },
    {
      "page": "rowPairs",
      "title": "Row pair methods",
      "topics": [
        "c,DualSubset-method",
        "length,DualSubset-method",
        "rowPair",
        "rowPair,SingleCellExperiment,character-method",
        "rowPair,SingleCellExperiment,missing-method",
        "rowPair,SingleCellExperiment,numeric-method",
        "rowPair<-",
        "rowPair<-,SingleCellExperiment,character-method",
        "rowPair<-,SingleCellExperiment,missing-method",
        "rowPair<-,SingleCellExperiment,numeric-method",
        "rowPairNames",
        "rowPairNames,SingleCellExperiment-method",
        "rowPairNames<-",
        "rowPairNames<-,SingleCellExperiment,character-method",
        "rowPairs",
        "rowPairs,SingleCellExperiment-method",
        "rowPairs<-",
        "rowPairs<-,SingleCellExperiment-method",
        "[,DualSubset,ANY,ANY,ANY-method",
        "[<-,DualSubset,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "rowSubset",
      "title": "Get or set the row subset",
      "topics": [
        "rowSubset",
        "rowSubset,SingleCellExperiment-method",
        "rowSubset<-",
        "rowSubset<-,SingleCellExperiment-method"
      ]
    },
    {
      "page": "assays",
      "title": "Named assay getters and setters",
      "topics": [
        "counts",
        "counts,SingleCellExperiment-method",
        "counts<-",
        "counts<-,SingleCellExperiment-method",
        "cpm",
        "cpm,SingleCellExperiment-method",
        "cpm<-",
        "cpm<-,SingleCellExperiment-method",
        "logcounts",
        "logcounts,SingleCellExperiment-method",
        "logcounts<-",
        "logcounts<-,SingleCellExperiment-method",
        "normcounts",
        "normcounts,SingleCellExperiment-method",
        "normcounts<-",
        "normcounts<-,SingleCellExperiment-method",
        "SCE-assays",
        "tpm",
        "tpm,SingleCellExperiment-method",
        "tpm<-",
        "tpm<-,SingleCellExperiment-method",
        "weights",
        "weights,SingleCellExperiment-method",
        "weights<-",
        "weights<-,SingleCellExperiment-method"
      ]
    },
    {
      "page": "combine",
      "title": "Combining or subsetting SingleCellExperiment objects",
      "topics": [
        "cbind,SingleCellExperiment-method",
        "combineCols,SingleCellExperiment-method",
        "rbind,SingleCellExperiment-method",
        "SCE-combine",
        "[,SingleCellExperiment,ANY,ANY,ANY-method",
        "[,SingleCellExperiment,ANY,ANY-method",
        "[,SingleCellExperiment,ANY-method",
        "[<-,SingleCellExperiment,ANY,ANY,SingleCellExperiment-method"
      ]
    },
    {
      "page": "internals",
      "title": "Internal SingleCellExperiment functions",
      "topics": [
        "colData,SingleCellExperiment-method",
        "int_colData",
        "int_colData,SingleCellExperiment-method",
        "int_colData<-",
        "int_colData<-,SingleCellExperiment-method",
        "int_elementMetadata",
        "int_elementMetadata,SingleCellExperiment-method",
        "int_elementMetadata<-",
        "int_elementMetadata<-,SingleCellExperiment-method",
        "int_metadata",
        "int_metadata,SingleCellExperiment-method",
        "int_metadata<-",
        "int_metadata<-,SingleCellExperiment-method",
        "parallel_slot_names,SingleCellExperiment-method",
        "rowData,SingleCellExperiment-method",
        "SCE-internals"
      ]
    },
    {
      "page": "miscellaneous",
      "title": "Miscellaneous SingleCellExperiment methods",
      "topics": [
        "objectVersion",
        "objectVersion,SingleCellExperiment-method",
        "SCE-miscellaneous",
        "show,SingleCellExperiment-method"
      ]
    },
    {
      "page": "simplifyToSCE",
      "title": "Simplify a list to a single SingleCellExperiment",
      "topics": [
        "simplifyToSCE"
      ]
    },
    {
      "page": "SingleCellExperiment",
      "title": "The SingleCellExperiment class",
      "topics": [
        "coerce,RangedSummarizedExperiment,SingleCellExperiment-method",
        "coerce,SummarizedExperiment,SingleCellExperiment-method",
        "SingleCellExperiment",
        "SingleCellExperiment-class"
      ]
    },
    {
      "page": "sizeFactors",
      "title": "Size factor methods",
      "topics": [
        "sizeFactors",
        "sizeFactors,SingleCellExperiment-method",
        "sizeFactors<-,SingleCellExperiment-method"
      ]
    },
    {
      "page": "splitAltExps",
      "title": "Split off alternative features",
      "topics": [
        "splitAltExps"
      ]
    },
    {
      "page": "LEM-subset",
      "title": "LEM subsetting methods",
      "topics": [
        "[,LinearEmbeddingMatrix,ANY,ANY,ANY-method",
        "[,LinearEmbeddingMatrix,ANY,ANY-method",
        "[,LinearEmbeddingMatrix,ANY-method",
        "[<-,LinearEmbeddingMatrix,ANY,ANY,LinearEmbeddingMatrix-method"
      ]
    },
    {
      "page": "swapAltExp",
      "title": "Swap main and alternative Experiments",
      "topics": [
        "swapAltExp"
      ]
    },
    {
      "page": "unsplitAltExps",
      "title": "Unsplit the alternative experiments",
      "topics": [
        "unsplitAltExps"
      ]
    },
    {
      "page": "updateObject",
      "title": "Update a SingleCellExperiment object",
      "topics": [
        "updateObject",
        "updateObject,SingleCellExperiment-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/SingleCellExperiment/raw/HEAD/README.md",
  "_rundeps": [
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    "Biobase",
    "BiocGenerics",
    "DelayedArray",
    "generics",
    "GenomicRanges",
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    "lattice",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "S4Arrays",
    "S4Vectors",
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