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  "Date": "2026-04-29",
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  "Title": "Single-Cell Analysis Toolkit for Gene Expression Data in R",
  "Description": "A collection of tools for doing various analyses of\nsingle-cell RNA-seq gene expression data, with a focus on\nquality control and visualization.",
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    "normalize",
    "normalizeCounts",
    "numDetectedAcrossCells",
    "numDetectedAcrossFeatures",
    "perCellQCMetrics",
    "perFeatureQCMetrics",
    "plotColData",
    "plotDiffusionMap",
    "plotDots",
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    "plotExpression",
    "plotGroupedHeatmap",
    "plotHeatmap",
    "plotHighestExprs",
    "plotMDS",
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    "plotPCA",
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    "plotPlatePosition",
    "plotReducedDim",
    "plotRLE",
    "plotRowData",
    "plotScater",
    "plotTSNE",
    "plotUMAP",
    "plotXY",
    "projectReducedDim",
    "quickPerCellQC",
    "readSparseCounts",
    "retrieveCellInfo",
    "retrieveFeatureInfo",
    "runColDataPCA",
    "runDiffusionMap",
    "runMDS",
    "runMultiUMAP",
    "runNMF",
    "runPCA",
    "runTSNE",
    "runUMAP",
    "stand_exprs",
    "stand_exprs<-",
    "sumCountsAcrossCells",
    "sumCountsAcrossFeatures",
    "toSingleCellExperiment",
    "uniquifyFeatureNames",
    "updateSCESet"
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      "title": "Get feature annotation information from Biomart",
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        "getBMFeatureAnnos"
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    },
    {
      "page": "bootstraps",
      "title": "Accessor and replacement for bootstrap results in a 'SingleCellExperiment' object",
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        "bootstraps,SingleCellExperiment-method",
        "bootstraps<-",
        "bootstraps<-,SingleCellExperiment,array-method"
      ]
    },
    {
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      "topics": [
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        "calculateMDS,ANY-method",
        "calculateMDS,SingleCellExperiment-method",
        "calculateMDS,SummarizedExperiment-method",
        "runMDS"
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    {
      "page": "runNMF",
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        "calculateNMF,ANY-method",
        "calculateNMF,SingleCellExperiment-method",
        "calculateNMF,SummarizedExperiment-method",
        "runNMF"
      ]
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      "topics": [
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        "calculatePCA,ANY-method",
        "calculatePCA,SingleCellExperiment-method",
        "calculatePCA,SummarizedExperiment-method",
        "runPCA",
        "runPCA,SingleCellExperiment-method"
      ]
    },
    {
      "page": "runTSNE",
      "title": "Perform t-SNE on cell-level data",
      "topics": [
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        "calculateTSNE,ANY-method",
        "calculateTSNE,SingleCellExperiment-method",
        "calculateTSNE,SummarizedExperiment-method",
        "runTSNE"
      ]
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      "title": "Perform UMAP on cell-level data",
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        "calculateUMAP,ANY-method",
        "calculateUMAP,SingleCellExperiment-method",
        "calculateUMAP,SummarizedExperiment-method",
        "runUMAP"
      ]
    },
    {
      "page": "categoricalHlines",
      "title": "Draw horizontal lines by category",
      "topics": [
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        "categoricalHlinesNamed"
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    },
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      "page": "defunct",
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        "defunct",
        "multiplot",
        "normalize,SingleCellExperiment-method",
        "runDiffusionMap"
      ]
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      "title": "Per-PC variance explained by a variable",
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    },
    {
      "page": "getVarianceExplained",
      "title": "Per-gene variance explained by a variable",
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        "getVarianceExplained,ANY-method",
        "getVarianceExplained,SummarizedExperiment-method"
      ]
    },
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        "ggfeatures"
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      "title": "Count the number of non-zero counts per cell or feature",
      "topics": [
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        "nexprs,ANY-method",
        "nexprs,SummarizedExperiment-method"
      ]
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        "exprs,SingleCellExperiment-method,",
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        "fpkm",
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        "fpkm<-,SingleCellExperiment,ANY-method",
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      ]
    },
    {
      "page": "plotDots",
      "title": "Create a dot plot of expression values",
      "topics": [
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      ]
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    {
      "page": "plotExplanatoryPCs",
      "title": "Plot the explanatory PCs for each variable",
      "topics": [
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    },
    {
      "page": "plotExplanatoryVariables",
      "title": "Plot explanatory variables ordered by percentage of variance explained",
      "topics": [
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      ]
    },
    {
      "page": "plotExpression",
      "title": "Plot expression values for all cells",
      "topics": [
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      ]
    },
    {
      "page": "plotGroupedHeatmap",
      "title": "Plot heatmap of group-level expression averages",
      "topics": [
        "plotGroupedHeatmap"
      ]
    },
    {
      "page": "plotHeatmap",
      "title": "Plot heatmap of gene expression values",
      "topics": [
        "plotHeatmap"
      ]
    },
    {
      "page": "plotHighestExprs",
      "title": "Plot the highest expressing features",
      "topics": [
        "plotHighestExprs"
      ]
    },
    {
      "page": "plotPlatePosition",
      "title": "Plot cells in plate positions",
      "topics": [
        "plotPlatePosition"
      ]
    },
    {
      "page": "plotReducedDim",
      "title": "Plot reduced dimensions",
      "topics": [
        "plotReducedDim"
      ]
    },
    {
      "page": "plotRLE",
      "title": "Plot relative log expression",
      "topics": [
        "plotRLE",
        "plotRLE,SingleCellExperiment-method"
      ]
    },
    {
      "page": "plotRowData",
      "title": "Plot row metadata",
      "topics": [
        "plotRowData"
      ]
    },
    {
      "page": "plotScater",
      "title": "Plot an overview of expression for each cell",
      "topics": [
        "plotScater"
      ]
    },
    {
      "page": "plotXY",
      "title": "Plot arbitrary x- and y-coordinates",
      "topics": [
        "plotXY"
      ]
    },
    {
      "page": "projectReducedDim",
      "title": "Project cells into an arbitrary dimensionality reduction space.",
      "topics": [
        "projectReducedDim",
        "projectReducedDim,matrix-method",
        "projectReducedDim,SummarizedExperiment-method"
      ]
    },
    {
      "page": "plot_reddim",
      "title": "Plot specific reduced dimensions",
      "topics": [
        "plotDiffusionMap",
        "plotMDS",
        "plotNMF",
        "plotPCA",
        "plotPCA,SingleCellExperiment-method",
        "plotPCASCE",
        "plotTSNE",
        "plotUMAP",
        "Reduced dimension plots"
      ]
    },
    {
      "page": "retrieveCellInfo",
      "title": "Cell-based data retrieval",
      "topics": [
        "retrieveCellInfo"
      ]
    },
    {
      "page": "retrieveFeatureInfo",
      "title": "Feature-based data retrieval",
      "topics": [
        "retrieveFeatureInfo"
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    },
    {
      "page": "runColDataPCA",
      "title": "Perform PCA on column metadata",
      "topics": [
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      "page": "runMultiUMAP",
      "title": "Multi-modal UMAP",
      "topics": [
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        "calculateMultiUMAP,ANY-method",
        "calculateMultiUMAP,SingleCellExperiment-method",
        "calculateMultiUMAP,SummarizedExperiment-method",
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      "title": "General visualization parameters",
      "topics": [
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    {
      "page": "SCESet",
      "title": "The \"Single Cell Expression Set\" (SCESet) class",
      "topics": [
        "SCESet",
        "SCESet-class"
      ]
    },
    {
      "page": "toSingleCellExperiment",
      "title": "Convert an SCESet object to a SingleCellExperiment object",
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        "updateSCESet"
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