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  "Title": "Tools for Single Cell Genomics",
  "Description": "A toolkit for quality control, analysis, and exploration\nof single cell RNA sequencing data. 'Seurat' aims to enable\nusers to identify and interpret sources of heterogeneity from\nsingle cell transcriptomic measurements, and to integrate\ndiverse types of single cell data. See Satija R, Farrell J,\nGennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu\nA, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>,\nStuart T, Butler A, et al (2019)\n<doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020)\n<doi:10.1101/2020.10.12.335331> for more details.",
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      "topics": [
        "as.SingleCellExperiment",
        "as.SingleCellExperiment.Seurat"
      ]
    },
    {
      "page": "as.sparse",
      "title": "Cast to Sparse",
      "concept": [
        "objects",
        "utilities"
      ],
      "topics": [
        "as.data.frame.Matrix",
        "as.sparse.H5Group"
      ]
    },
    {
      "page": "Assay-class",
      "title": "The Assay Class",
      "topics": [
        "Assay-class"
      ]
    },
    {
      "page": "AugmentPlot",
      "title": "Augments ggplot2-based plot with a PNG image.",
      "concept": [
        "visualization"
      ],
      "topics": [
        "AugmentPlot"
      ]
    },
    {
      "page": "AutoPointSize",
      "title": "Automagically calculate a point size for ggplot2-based scatter plots",
      "concept": [
        "visualization"
      ],
      "topics": [
        "AutoPointSize"
      ]
    },
    {
      "page": "AverageExpression",
      "title": "Averaged feature expression by identity class",
      "concept": [
        "utilities"
      ],
      "topics": [
        "AverageExpression"
      ]
    },
    {
      "page": "BarcodeInflectionsPlot",
      "title": "Plot the Barcode Distribution and Calculated Inflection Points",
      "concept": [
        "visualization"
      ],
      "topics": [
        "BarcodeInflectionsPlot"
      ]
    },
    {
      "page": "BGTextColor",
      "title": "Determine text color based on background color",
      "concept": [
        "visualization"
      ],
      "topics": [
        "BGTextColor"
      ]
    },
    {
      "page": "CustomPalette",
      "title": "Create a custom color palette",
      "concept": [
        "visualization"
      ],
      "topics": [
        "BlackAndWhite",
        "BlueAndRed",
        "CustomPalette",
        "PurpleAndYellow"
      ]
    },
    {
      "page": "BridgeCellsRepresentation",
      "title": "Construct a dictionary representation for each unimodal dataset",
      "concept": [
        "integration"
      ],
      "topics": [
        "BridgeCellsRepresentation"
      ]
    },
    {
      "page": "BridgeReferenceSet-class",
      "title": "The BridgeReferenceSet Class The BridgeReferenceSet is an output from PrepareBridgeReference",
      "concept": [
        "objects"
      ],
      "topics": [
        "BridgeReferenceSet",
        "BridgeReferenceSet-class"
      ]
    },
    {
      "page": "BuildClusterTree",
      "title": "Phylogenetic Analysis of Identity Classes",
      "concept": [
        "tree"
      ],
      "topics": [
        "BuildClusterTree"
      ]
    },
    {
      "page": "BuildNicheAssay",
      "title": "Construct an assay for spatial niche analysis",
      "concept": [
        "clustering"
      ],
      "topics": [
        "BuildNicheAssay"
      ]
    },
    {
      "page": "CalcPerturbSig",
      "title": "Calculate a perturbation Signature",
      "concept": [
        "mixscape"
      ],
      "topics": [
        "CalcPerturbSig"
      ]
    },
    {
      "page": "CalculateBarcodeInflections",
      "title": "Calculate the Barcode Distribution Inflection",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "CalculateBarcodeInflections"
      ]
    },
    {
      "page": "CaseMatch",
      "title": "Match the case of character vectors",
      "concept": [
        "utilities"
      ],
      "topics": [
        "CaseMatch"
      ]
    },
    {
      "page": "cc.genes",
      "title": "Cell cycle genes",
      "concept": [
        "data"
      ],
      "topics": [
        "cc.genes"
      ]
    },
    {
      "page": "cc.genes.updated.2019",
      "title": "Cell cycle genes: 2019 update",
      "concept": [
        "data"
      ],
      "topics": [
        "cc.genes.updated.2019"
      ]
    },
    {
      "page": "CCAIntegration",
      "title": "Seurat-CCA Integration",
      "concept": [
        "integration"
      ],
      "topics": [
        "CCAIntegration"
      ]
    },
    {
      "page": "CellCycleScoring",
      "title": "Score cell cycle phases",
      "concept": [
        "utilities"
      ],
      "topics": [
        "CellCycleScoring"
      ]
    },
    {
      "page": "Cells",
      "title": "Get Cell Names",
      "concept": [
        "objects",
        "spatial"
      ],
      "topics": [
        "Cells.SCTModel",
        "Cells.SlideSeq",
        "Cells.STARmap",
        "Cells.VisiumV1"
      ]
    },
    {
      "page": "CellScatter",
      "title": "Cell-cell scatter plot",
      "concept": [
        "visualization"
      ],
      "topics": [
        "CellPlot",
        "CellScatter"
      ]
    },
    {
      "page": "CellSelector",
      "title": "Cell Selector",
      "concept": [
        "visualization"
      ],
      "topics": [
        "CellSelector",
        "FeatureLocator"
      ]
    },
    {
      "page": "CollapseEmbeddingOutliers",
      "title": "Move outliers towards center on dimension reduction plot",
      "concept": [
        "visualization"
      ],
      "topics": [
        "CollapseEmbeddingOutliers"
      ]
    },
    {
      "page": "CollapseSpeciesExpressionMatrix",
      "title": "Slim down a multi-species expression matrix, when only one species is primarily of interenst.",
      "concept": [
        "utilities"
      ],
      "topics": [
        "CollapseSpeciesExpressionMatrix"
      ]
    },
    {
      "page": "ColorDimSplit",
      "title": "Color dimensional reduction plot by tree split",
      "concept": [
        "visualization"
      ],
      "topics": [
        "ColorDimSplit"
      ]
    },
    {
      "page": "CombinePlots",
      "title": "Combine ggplot2-based plots into a single plot",
      "concept": [
        "visualization"
      ],
      "topics": [
        "CombinePlots"
      ]
    },
    {
      "page": "contrast-theory",
      "title": "Get the intensity and/or luminance of a color",
      "concept": [
        "visualization"
      ],
      "topics": [
        "contrast-theory",
        "Intensity",
        "Luminance"
      ]
    },
    {
      "page": "CreateCategoryMatrix",
      "title": "Create one hot matrix for a given label",
      "concept": [
        "utilities"
      ],
      "topics": [
        "CreateCategoryMatrix"
      ]
    },
    {
      "page": "CreateSCTAssayObject",
      "title": "Create a SCT Assay object",
      "concept": [
        "objects"
      ],
      "topics": [
        "CreateSCTAssayObject"
      ]
    },
    {
      "page": "CustomDistance",
      "title": "Run a custom distance function on an input data matrix",
      "concept": [
        "utilities"
      ],
      "topics": [
        "CustomDistance"
      ]
    },
    {
      "page": "DEenrichRPlot",
      "title": "DE and EnrichR pathway visualization barplot",
      "concept": [
        "mixscape"
      ],
      "topics": [
        "DEenrichRPlot"
      ]
    },
    {
      "page": "DietSeurat",
      "title": "Slim down a Seurat object",
      "concept": [
        "objects"
      ],
      "topics": [
        "DietSeurat"
      ]
    },
    {
      "page": "DimHeatmap",
      "title": "Dimensional reduction heatmap",
      "concept": [
        "convenience",
        "visualization"
      ],
      "topics": [
        "DimHeatmap",
        "PCHeatmap"
      ]
    },
    {
      "page": "DimPlot",
      "title": "Dimensional reduction plot",
      "concept": [
        "convenience",
        "visualization"
      ],
      "topics": [
        "DimPlot",
        "ICAPlot",
        "PCAPlot",
        "TSNEPlot",
        "UMAPPlot"
      ]
    },
    {
      "page": "DimReduc-class",
      "title": "The DimReduc Class",
      "topics": [
        "DimReduc-class"
      ]
    },
    {
      "page": "DiscretePalette",
      "title": "Discrete colour palettes from pals",
      "concept": [
        "visualization"
      ],
      "topics": [
        "DiscretePalette"
      ]
    },
    {
      "page": "DoHeatmap",
      "title": "Feature expression heatmap",
      "concept": [
        "visualization"
      ],
      "topics": [
        "DoHeatmap"
      ]
    },
    {
      "page": "DotPlot",
      "title": "Dot plot visualization",
      "concept": [
        "visualization"
      ],
      "topics": [
        "DotPlot",
        "SplitDotPlotGG"
      ]
    },
    {
      "page": "ElbowPlot",
      "title": "Quickly Pick Relevant Dimensions",
      "concept": [
        "visualization"
      ],
      "topics": [
        "ElbowPlot"
      ]
    },
    {
      "page": "ExpMean",
      "title": "Calculate the mean of logged values",
      "concept": [
        "utilities"
      ],
      "topics": [
        "ExpMean"
      ]
    },
    {
      "page": "ExpSD",
      "title": "Calculate the standard deviation of logged values",
      "concept": [
        "utilities"
      ],
      "topics": [
        "ExpSD"
      ]
    },
    {
      "page": "ExpVar",
      "title": "Calculate the variance of logged values",
      "concept": [
        "utilities"
      ],
      "topics": [
        "ExpVar"
      ]
    },
    {
      "page": "FastRowScale",
      "title": "Scale and/or center matrix rowwise",
      "concept": [
        "utilities"
      ],
      "topics": [
        "FastRowScale"
      ]
    },
    {
      "page": "FastRPCAIntegration",
      "title": "Perform integration on the joint PCA cell embeddings.",
      "concept": [
        "integration"
      ],
      "topics": [
        "FastRPCAIntegration"
      ]
    },
    {
      "page": "FeaturePlot",
      "title": "Visualize 'features' on a dimensional reduction plot",
      "concept": [
        "visualization"
      ],
      "topics": [
        "FeatureHeatmap",
        "FeaturePlot"
      ]
    },
    {
      "page": "FeatureScatter",
      "title": "Scatter plot of single cell data",
      "concept": [
        "visualization"
      ],
      "topics": [
        "FeatureScatter",
        "GenePlot"
      ]
    },
    {
      "page": "FetchResiduals",
      "title": "Calculate pearson residuals of features not in the scale.data",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "FetchResiduals"
      ]
    },
    {
      "page": "FilterSlideSeq",
      "title": "Filter stray beads from Slide-seq puck",
      "concept": [
        "objects",
        "spatial"
      ],
      "topics": [
        "FilterSlideSeq"
      ]
    },
    {
      "page": "FindAllMarkers",
      "title": "Gene expression markers for all identity classes",
      "concept": [
        "differential_expression"
      ],
      "topics": [
        "FindAllMarkers",
        "FindAllMarkersNode"
      ]
    },
    {
      "page": "FindBridgeIntegrationAnchors",
      "title": "Find integration bridge anchors between query and extended bridge-reference",
      "concept": [
        "integration"
      ],
      "topics": [
        "FindBridgeIntegrationAnchors"
      ]
    },
    {
      "page": "FindBridgeTransferAnchors",
      "title": "Find bridge anchors between query and extended bridge-reference",
      "concept": [
        "integration"
      ],
      "topics": [
        "FindBridgeTransferAnchors"
      ]
    },
    {
      "page": "FindClusters",
      "title": "Cluster Determination",
      "concept": [
        "clustering"
      ],
      "topics": [
        "FindClusters",
        "FindClusters.default",
        "FindClusters.Seurat"
      ]
    },
    {
      "page": "FindConservedMarkers",
      "title": "Finds markers that are conserved between the groups",
      "concept": [
        "differential_expression"
      ],
      "topics": [
        "FindConservedMarkers"
      ]
    },
    {
      "page": "FindIntegrationAnchors",
      "title": "Find integration anchors",
      "concept": [
        "integration"
      ],
      "topics": [
        "FindIntegrationAnchors"
      ]
    },
    {
      "page": "FindMarkers",
      "title": "Gene expression markers of identity classes",
      "concept": [
        "differential_expression"
      ],
      "topics": [
        "FindMarkers",
        "FindMarkers.Assay",
        "FindMarkers.default",
        "FindMarkers.DimReduc",
        "FindMarkers.SCTAssay",
        "FindMarkers.Seurat",
        "FindMarkersNode"
      ]
    },
    {
      "page": "FindMultiModalNeighbors",
      "title": "Construct weighted nearest neighbor graph",
      "concept": [
        "clustering"
      ],
      "topics": [
        "FindMultiModalNeighbors"
      ]
    },
    {
      "page": "FindNeighbors",
      "title": "(Shared) Nearest-neighbor graph construction",
      "concept": [
        "clustering"
      ],
      "topics": [
        "FindNeighbors",
        "FindNeighbors.Assay",
        "FindNeighbors.default",
        "FindNeighbors.dist",
        "FindNeighbors.Seurat"
      ]
    },
    {
      "page": "FindSpatiallyVariableFeatures",
      "title": "Find spatially variable features",
      "concept": [
        "preprocessing",
        "spatial"
      ],
      "topics": [
        "FindSpatiallyVariableFeatures",
        "FindSpatiallyVariableFeatures.Assay",
        "FindSpatiallyVariableFeatures.default",
        "FindSpatiallyVariableFeatures.Seurat",
        "FindSpatiallyVariableFeatures.StdAssay"
      ]
    },
    {
      "page": "FindSubCluster",
      "title": "Find subclusters under one cluster",
      "concept": [
        "clustering"
      ],
      "topics": [
        "FindSubCluster"
      ]
    },
    {
      "page": "FindTransferAnchors",
      "title": "Find transfer anchors",
      "concept": [
        "integration"
      ],
      "topics": [
        "FindTransferAnchors"
      ]
    },
    {
      "page": "FindVariableFeatures",
      "title": "Find variable features",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "FindVariableFeatures",
        "FindVariableFeatures.Assay",
        "FindVariableFeatures.SCTAssay",
        "FindVariableFeatures.Seurat",
        "FindVariableFeatures.V3Matrix",
        "FindVariableGenes"
      ]
    },
    {
      "page": "FoldChange",
      "title": "Fold Change",
      "concept": [
        "differential_expression"
      ],
      "topics": [
        "FoldChange",
        "FoldChange.Assay",
        "FoldChange.default",
        "FoldChange.DimReduc",
        "FoldChange.SCTAssay",
        "FoldChange.Seurat"
      ]
    },
    {
      "page": "GetAssay",
      "title": "Get an Assay object from a given Seurat object.",
      "concept": [
        "objects"
      ],
      "topics": [
        "GetAssay",
        "GetAssay.Seurat"
      ]
    },
    {
      "page": "GetImage",
      "title": "Get Image Data",
      "concept": [
        "objects",
        "spatial"
      ],
      "topics": [
        "GetImage.SlideSeq",
        "GetImage.STARmap",
        "GetImage.VisiumV1",
        "GetImage.VisiumV2"
      ]
    },
    {
      "page": "GetIntegrationData",
      "title": "Get integration data",
      "concept": [
        "objects"
      ],
      "topics": [
        "GetIntegrationData"
      ]
    },
    {
      "page": "GetResidual",
      "title": "Calculate pearson residuals of features not in the scale.data",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "GetResidual"
      ]
    },
    {
      "page": "GetTissueCoordinates",
      "title": "Get Tissue Coordinates",
      "concept": [
        "objects",
        "spatial"
      ],
      "topics": [
        "GetTissueCoordinates.SlideSeq",
        "GetTissueCoordinates.STARmap",
        "GetTissueCoordinates.VisiumV1",
        "GetTissueCoordinates.VisiumV2"
      ]
    },
    {
      "page": "GetTransferPredictions",
      "title": "Get the predicted identity",
      "concept": [
        "integration"
      ],
      "topics": [
        "GetTransferPredictions"
      ]
    },
    {
      "page": "Graph-class",
      "title": "The Graph Class",
      "topics": [
        "Graph-class"
      ]
    },
    {
      "page": "GroupCorrelation",
      "title": "Compute the correlation of features broken down by groups with another covariate",
      "concept": [
        "utilities"
      ],
      "topics": [
        "GroupCorrelation"
      ]
    },
    {
      "page": "GroupCorrelationPlot",
      "title": "Boxplot of correlation of a variable (e.g. number of UMIs) with expression data",
      "concept": [
        "visualization"
      ],
      "topics": [
        "GroupCorrelationPlot"
      ]
    },
    {
      "page": "HarmonyIntegration",
      "title": "Harmony Integration",
      "concept": [
        "integration"
      ],
      "topics": [
        "HarmonyIntegration"
      ]
    },
    {
      "page": "HoverLocator",
      "title": "Hover Locator",
      "concept": [
        "visualization"
      ],
      "topics": [
        "HoverLocator"
      ]
    },
    {
      "page": "HTODemux",
      "title": "Demultiplex samples based on data from cell 'hashing'",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "HTODemux"
      ]
    },
    {
      "page": "HTOHeatmap",
      "title": "Hashtag oligo heatmap",
      "concept": [
        "visualization"
      ],
      "topics": [
        "HTOHeatmap"
      ]
    },
    {
      "page": "HVFInfo.SCTAssay",
      "title": "Get Variable Feature Information",
      "concept": [
        "objects"
      ],
      "topics": [
        "HVFInfo.SCTAssay"
      ]
    },
    {
      "page": "IFeaturePlot",
      "title": "Visualize features in dimensional reduction space interactively",
      "concept": [
        "visualization"
      ],
      "topics": [
        "IFeaturePlot"
      ]
    },
    {
      "page": "ImageDimPlot",
      "title": "Spatial Cluster Plots",
      "concept": [
        "spatial",
        "visualization"
      ],
      "topics": [
        "ImageDimPlot"
      ]
    },
    {
      "page": "ImageFeaturePlot",
      "title": "Spatial Feature Plots",
      "concept": [
        "spatial",
        "visualization"
      ],
      "topics": [
        "ImageFeaturePlot"
      ]
    },
    {
      "page": "IntegrateData",
      "title": "Integrate data",
      "concept": [
        "integration"
      ],
      "topics": [
        "IntegrateData"
      ]
    },
    {
      "page": "IntegrateEmbeddings",
      "title": "Integrate low dimensional embeddings",
      "concept": [
        "integration"
      ],
      "topics": [
        "IntegrateEmbeddings",
        "IntegrateEmbeddings.IntegrationAnchorSet",
        "IntegrateEmbeddings.TransferAnchorSet"
      ]
    },
    {
      "page": "IntegrateLayers",
      "title": "Integrate Layers",
      "concept": [
        "integration"
      ],
      "topics": [
        "IntegrateLayers"
      ]
    },
    {
      "page": "IntegrationAnchorSet-class",
      "title": "The IntegrationAnchorSet Class",
      "concept": [
        "objects"
      ],
      "topics": [
        "IntegrationAnchorSet",
        "IntegrationAnchorSet-class"
      ]
    },
    {
      "page": "IntegrationData-class",
      "title": "The IntegrationData Class",
      "concept": [
        "objects"
      ],
      "topics": [
        "IntegrationData",
        "IntegrationData-class"
      ]
    },
    {
      "page": "ISpatialDimPlot",
      "title": "Visualize clusters spatially and interactively",
      "concept": [
        "spatial",
        "visualization"
      ],
      "topics": [
        "ISpatialDimPlot"
      ]
    },
    {
      "page": "ISpatialFeaturePlot",
      "title": "Visualize features spatially and interactively",
      "concept": [
        "spatial",
        "visualization"
      ],
      "topics": [
        "ISpatialFeaturePlot"
      ]
    },
    {
      "page": "JackStraw",
      "title": "Determine statistical significance of PCA scores.",
      "concept": [
        "dimensional_reduction"
      ],
      "topics": [
        "JackStraw"
      ]
    },
    {
      "page": "JackStrawData-class",
      "title": "The JackStrawData Class",
      "topics": [
        "JackStrawData-class"
      ]
    },
    {
      "page": "JackStrawPlot",
      "title": "JackStraw Plot",
      "concept": [
        "visualization"
      ],
      "topics": [
        "JackStrawPlot"
      ]
    },
    {
      "page": "JointPCAIntegration",
      "title": "Seurat-Joint PCA Integration",
      "concept": [
        "integration"
      ],
      "topics": [
        "JointPCAIntegration"
      ]
    },
    {
      "page": "L2CCA",
      "title": "L2-Normalize CCA",
      "concept": [
        "dimensional_reduction"
      ],
      "topics": [
        "L2CCA"
      ]
    },
    {
      "page": "L2Dim",
      "title": "L2-normalization",
      "concept": [
        "dimensional_reduction"
      ],
      "topics": [
        "L2Dim"
      ]
    },
    {
      "page": "LabelClusters",
      "title": "Label clusters on a ggplot2-based scatter plot",
      "concept": [
        "visualization"
      ],
      "topics": [
        "LabelClusters"
      ]
    },
    {
      "page": "LabelPoints",
      "title": "Add text labels to a ggplot2 plot",
      "concept": [
        "visualization"
      ],
      "topics": [
        "Labeler",
        "LabelPoints"
      ]
    },
    {
      "page": "LeverageScore",
      "title": "Leverage Score Calculation",
      "concept": [
        "sketching"
      ],
      "topics": [
        "LeverageScore",
        "LeverageScore.Assay",
        "LeverageScore.default",
        "LeverageScore.Seurat",
        "LeverageScore.StdAssay"
      ]
    },
    {
      "page": "LinkedPlots",
      "title": "Visualize spatial and clustering (dimensional reduction) data in a linked, interactive framework",
      "concept": [
        "spatial",
        "visualization"
      ],
      "topics": [
        "LinkedDimPlot",
        "LinkedFeaturePlot",
        "LinkedPlot",
        "LinkedPlots"
      ]
    },
    {
      "page": "Load10X_Spatial",
      "title": "Load a 10x Genomics Visium Spatial Experiment into a 'Seurat' object",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "Load10X_Spatial"
      ]
    },
    {
      "page": "LoadAnnoyIndex",
      "title": "Load the Annoy index file",
      "concept": [
        "utilities"
      ],
      "topics": [
        "LoadAnnoyIndex"
      ]
    },
    {
      "page": "LoadCurioSeeker",
      "title": "Load Curio Seeker data",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "LoadCurioSeeker"
      ]
    },
    {
      "page": "LoadSTARmap",
      "title": "Load STARmap data",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "LoadSTARmap"
      ]
    },
    {
      "page": "ReadXenium",
      "title": "Read and Load 10x Genomics Xenium in-situ data",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "LoadXenium",
        "ReadXenium"
      ]
    },
    {
      "page": "LocalStruct",
      "title": "Calculate the local structure preservation metric",
      "concept": [
        "integration"
      ],
      "topics": [
        "LocalStruct"
      ]
    },
    {
      "page": "LogNormalize",
      "title": "Normalize Raw Data",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "LogNormalize",
        "LogNormalize.data.frame",
        "LogNormalize.default",
        "LogNormalize.V3Matrix"
      ]
    },
    {
      "page": "LogVMR",
      "title": "Calculate the variance to mean ratio of logged values",
      "concept": [
        "utilities"
      ],
      "topics": [
        "LogVMR"
      ]
    },
    {
      "page": "MappingScore",
      "title": "Metric for evaluating mapping success",
      "concept": [
        "integration"
      ],
      "topics": [
        "MappingScore",
        "MappingScore.AnchorSet",
        "MappingScore.default"
      ]
    },
    {
      "page": "MapQuery",
      "title": "Map query cells to a reference",
      "concept": [
        "integration"
      ],
      "topics": [
        "MapQuery"
      ]
    },
    {
      "page": "merge.SCTAssay",
      "title": "Merge SCTAssay objects",
      "concept": [
        "objects"
      ],
      "topics": [
        "merge.SCTAssay"
      ]
    },
    {
      "page": "MetaFeature",
      "title": "Aggregate expression of multiple features into a single feature",
      "concept": [
        "utilities"
      ],
      "topics": [
        "MetaFeature"
      ]
    },
    {
      "page": "MinMax",
      "title": "Apply a ceiling and floor to all values in a matrix",
      "concept": [
        "utilities"
      ],
      "topics": [
        "MinMax"
      ]
    },
    {
      "page": "MixingMetric",
      "title": "Calculates a mixing metric",
      "concept": [
        "integration"
      ],
      "topics": [
        "MixingMetric"
      ]
    },
    {
      "page": "MixscapeHeatmap",
      "title": "Differential expression heatmap for mixscape",
      "concept": [
        "mixscape"
      ],
      "topics": [
        "MixscapeHeatmap"
      ]
    },
    {
      "page": "MixscapeLDA",
      "title": "Linear discriminant analysis on pooled CRISPR screen data.",
      "concept": [
        "mixscape"
      ],
      "topics": [
        "MixscapeLDA"
      ]
    },
    {
      "page": "ModalityWeights-class",
      "title": "The ModalityWeights Class",
      "concept": [
        "objects"
      ],
      "topics": [
        "ModalityWeights",
        "ModalityWeights-class"
      ]
    },
    {
      "page": "MULTIseqDemux",
      "title": "Demultiplex samples based on classification method from MULTI-seq (McGinnis et al., bioRxiv 2018)",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "MULTIseqDemux"
      ]
    },
    {
      "page": "Neighbor-class",
      "title": "The Neighbor Class",
      "topics": [
        "Neighbor-class"
      ]
    },
    {
      "page": "NNPlot",
      "title": "Highlight Neighbors in DimPlot",
      "concept": [
        "visualization"
      ],
      "topics": [
        "NNPlot"
      ]
    },
    {
      "page": "NNtoGraph",
      "title": "Convert Neighbor class to an asymmetrical Graph class",
      "concept": [
        "integration"
      ],
      "topics": [
        "NNtoGraph"
      ]
    },
    {
      "page": "NormalizeData",
      "title": "Normalize Data",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "NormalizeData",
        "NormalizeData.Assay",
        "NormalizeData.Seurat",
        "NormalizeData.V3Matrix"
      ]
    },
    {
      "page": "PCASigGenes",
      "title": "Significant genes from a PCA",
      "concept": [
        "dimensional_reduction"
      ],
      "topics": [
        "PCASigGenes"
      ]
    },
    {
      "page": "PercentAbove",
      "title": "Calculate the percentage of a vector above some threshold",
      "concept": [
        "utilities"
      ],
      "topics": [
        "PercentAbove"
      ]
    },
    {
      "page": "PercentageFeatureSet",
      "title": "Calculate the percentage of all counts that belong to a given set of features",
      "concept": [
        "utilities"
      ],
      "topics": [
        "PercentageFeatureSet"
      ]
    },
    {
      "page": "PlotClusterTree",
      "title": "Plot clusters as a tree",
      "concept": [
        "visualization"
      ],
      "topics": [
        "PlotClusterTree"
      ]
    },
    {
      "page": "PlotPerturbScore",
      "title": "Function to plot perturbation score distributions.",
      "concept": [
        "mixscape"
      ],
      "topics": [
        "PlotPerturbScore"
      ]
    },
    {
      "page": "PolyDimPlot",
      "title": "Polygon DimPlot",
      "concept": [
        "visualization"
      ],
      "topics": [
        "PolyDimPlot"
      ]
    },
    {
      "page": "PolyFeaturePlot",
      "title": "Polygon FeaturePlot",
      "concept": [
        "spatial",
        "visualization"
      ],
      "topics": [
        "PolyFeaturePlot"
      ]
    },
    {
      "page": "PredictAssay",
      "title": "Predict value from nearest neighbors",
      "concept": [
        "integration"
      ],
      "topics": [
        "PredictAssay"
      ]
    },
    {
      "page": "PrepareBridgeReference",
      "title": "Prepare the bridge and reference datasets",
      "concept": [
        "integration"
      ],
      "topics": [
        "PrepareBridgeReference"
      ]
    },
    {
      "page": "PrepLDA",
      "title": "Function to prepare data for Linear Discriminant Analysis.",
      "concept": [
        "mixscape"
      ],
      "topics": [
        "PrepLDA"
      ]
    },
    {
      "page": "PrepSCTFindMarkers",
      "title": "Prepare object to run differential expression on SCT assay with multiple models",
      "concept": [
        "differential_expression",
        "future"
      ],
      "topics": [
        "PrepSCTFindMarkers"
      ]
    },
    {
      "page": "PrepSCTIntegration",
      "title": "Prepare an object list normalized with sctransform for integration.",
      "concept": [
        "integration"
      ],
      "topics": [
        "PrepSCTIntegration"
      ]
    },
    {
      "page": "ProjectData",
      "title": "Project full data to the sketch assay",
      "concept": [
        "sketching"
      ],
      "topics": [
        "ProjectData"
      ]
    },
    {
      "page": "ProjectDim",
      "title": "Project Dimensional reduction onto full dataset",
      "concept": [
        "dimensional_reduction"
      ],
      "topics": [
        "ProjectDim"
      ]
    },
    {
      "page": "ProjectDimReduc",
      "title": "Project query data to reference dimensional reduction",
      "concept": [
        "integration"
      ],
      "topics": [
        "ProjectDimReduc"
      ]
    },
    {
      "page": "ProjectIntegration",
      "title": "Integrate embeddings from the integrated sketched.assay",
      "concept": [
        "integration"
      ],
      "topics": [
        "ProjectIntegration"
      ]
    },
    {
      "page": "ProjectUMAP",
      "title": "Project query into UMAP coordinates of a reference",
      "concept": [
        "dimensional_reduction"
      ],
      "topics": [
        "ProjectUMAP",
        "ProjectUMAP.default",
        "ProjectUMAP.DimReduc",
        "ProjectUMAP.Seurat"
      ]
    },
    {
      "page": "PseudobulkExpression",
      "title": "Pseudobulk Expression",
      "concept": [
        "utilities"
      ],
      "topics": [
        "PseudobulkExpression",
        "PseudobulkExpression.Assay",
        "PseudobulkExpression.Seurat",
        "PseudobulkExpression.StdAssay"
      ]
    },
    {
      "page": "Radius",
      "title": "Get Spot Radius",
      "concept": [
        "objects",
        "spatial"
      ],
      "topics": [
        "Radius.SlideSeq",
        "Radius.STARmap",
        "Radius.VisiumV1",
        "Radius.VisiumV2"
      ]
    },
    {
      "page": "Read10X",
      "title": "Load in data from 10X",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "Read10X"
      ]
    },
    {
      "page": "Read10X_Coordinates",
      "title": "Load 10X Genomics Visium Tissue Positions",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "Read10X_Coordinates"
      ]
    },
    {
      "page": "Read10X_h5",
      "title": "Read 10X hdf5 file",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "Read10X_h5"
      ]
    },
    {
      "page": "Read10X_Image",
      "title": "Load a 10X Genomics Visium Image",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "Read10X_Image"
      ]
    },
    {
      "page": "Read10X_probe_metadata",
      "title": "Read10x Probe Metadata",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "Read10X_probe_metadata"
      ]
    },
    {
      "page": "Read10X_ScaleFactors",
      "title": "Load 10X Genomics Visium Scale Factors",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "Read10X_ScaleFactors"
      ]
    },
    {
      "page": "ReadAkoya",
      "title": "Read and Load Akoya CODEX data",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "LoadAkoya",
        "ReadAkoya"
      ]
    },
    {
      "page": "ReadMtx",
      "title": "Load in data from remote or local mtx files",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "ReadMtx"
      ]
    },
    {
      "page": "ReadNanostring",
      "title": "Read and Load Nanostring SMI data",
      "concept": [
        "future",
        "preprocessing"
      ],
      "topics": [
        "LoadNanostring",
        "ReadNanostring"
      ]
    },
    {
      "page": "ReadParseBio",
      "title": "Read output from Parse Biosciences",
      "concept": [
        "convenience"
      ],
      "topics": [
        "ReadParseBio"
      ]
    },
    {
      "page": "ReadSlideSeq",
      "title": "Load Slide-seq spatial data",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "ReadSlideSeq"
      ]
    },
    {
      "page": "ReadSTARsolo",
      "title": "Read output from STARsolo",
      "concept": [
        "convenience"
      ],
      "topics": [
        "ReadSTARsolo"
      ]
    },
    {
      "page": "ReadVitessce",
      "title": "Read Data From Vitessce",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "LoadHuBMAPCODEX",
        "ReadVitessce"
      ]
    },
    {
      "page": "ReadVizgen",
      "title": "Read and Load MERFISH Input from Vizgen",
      "concept": [
        "future",
        "preprocessing"
      ],
      "topics": [
        "LoadVizgen",
        "ReadVizgen"
      ]
    },
    {
      "page": "RegroupIdents",
      "title": "Regroup idents based on meta.data info",
      "concept": [
        "utilities"
      ],
      "topics": [
        "RegroupIdents"
      ]
    },
    {
      "page": "RelativeCounts",
      "title": "Normalize raw data to fractions",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "RelativeCounts"
      ]
    },
    {
      "page": "RenameCells",
      "title": "Rename Cells in an Object",
      "concept": [
        "objects"
      ],
      "topics": [
        "RenameCells.SCTAssay",
        "RenameCells.SlideSeq",
        "RenameCells.STARmap",
        "RenameCells.VisiumV1"
      ]
    },
    {
      "page": "RidgePlot",
      "title": "Single cell ridge plot",
      "concept": [
        "visualization"
      ],
      "topics": [
        "RidgePlot"
      ]
    },
    {
      "page": "RPCAIntegration",
      "title": "Seurat-RPCA Integration",
      "concept": [
        "utilities"
      ],
      "topics": [
        "RPCAIntegration"
      ]
    },
    {
      "page": "RunCCA",
      "title": "Perform Canonical Correlation Analysis",
      "concept": [
        "dimensional_reduction"
      ],
      "topics": [
        "RunCCA",
        "RunCCA.default",
        "RunCCA.Seurat"
      ]
    },
    {
      "page": "RunGraphLaplacian",
      "title": "Run Graph Laplacian Eigendecomposition",
      "concept": [
        "dimensional_reduction"
      ],
      "topics": [
        "RunGraphLaplacian",
        "RunGraphLaplacian.default",
        "RunGraphLaplacian.Seurat"
      ]
    },
    {
      "page": "RunICA",
      "title": "Run Independent Component Analysis on gene expression",
      "concept": [
        "dimensional_reduction"
      ],
      "topics": [
        "RunICA",
        "RunICA.Assay",
        "RunICA.default",
        "RunICA.Seurat"
      ]
    },
    {
      "page": "RunLDA",
      "title": "Run Linear Discriminant Analysis",
      "concept": [
        "mixscape"
      ],
      "topics": [
        "RunLDA",
        "RunLDA.Assay",
        "RunLDA.default",
        "RunLDA.Seurat"
      ]
    },
    {
      "page": "RunLeiden",
      "title": "Run Leiden clustering algorithm",
      "concept": [
        "clustering"
      ],
      "topics": [
        "RunLeiden"
      ]
    },
    {
      "page": "RunMarkVario",
      "title": "Run the mark variogram computation on a given position matrix and expression matrix.",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "RunMarkVario"
      ]
    },
    {
      "page": "RunMixscape",
      "title": "Run Mixscape",
      "concept": [
        "mixscape"
      ],
      "topics": [
        "RunMixscape"
      ]
    },
    {
      "page": "RunMoransI",
      "title": "Compute Moran's I value.",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "RunMoransI"
      ]
    },
    {
      "page": "RunPCA",
      "title": "Run Principal Component Analysis",
      "concept": [
        "dimensional_reduction"
      ],
      "topics": [
        "RunPCA",
        "RunPCA.Assay",
        "RunPCA.default",
        "RunPCA.Seurat"
      ]
    },
    {
      "page": "RunSLSI",
      "title": "Run Supervised Latent Semantic Indexing",
      "concept": [
        "dimensional_reduction"
      ],
      "topics": [
        "RunSLSI",
        "RunSLSI.Assay",
        "RunSLSI.default",
        "RunSLSI.Seurat",
        "RunSLSI.StdAssay"
      ]
    },
    {
      "page": "RunSPCA",
      "title": "Run Supervised Principal Component Analysis",
      "concept": [
        "dimensional_reduction"
      ],
      "topics": [
        "RunSPCA",
        "RunSPCA.Assay",
        "RunSPCA.Assay5",
        "RunSPCA.default",
        "RunSPCA.Seurat"
      ]
    },
    {
      "page": "RunTSNE",
      "title": "Run t-distributed Stochastic Neighbor Embedding",
      "concept": [
        "dimensional_reduction"
      ],
      "topics": [
        "RunTSNE",
        "RunTSNE.DimReduc",
        "RunTSNE.dist",
        "RunTSNE.matrix",
        "RunTSNE.Seurat"
      ]
    },
    {
      "page": "RunUMAP",
      "title": "Run UMAP",
      "concept": [
        "dimensional_reduction"
      ],
      "topics": [
        "RunUMAP",
        "RunUMAP.default",
        "RunUMAP.Graph",
        "RunUMAP.Neighbor",
        "RunUMAP.Seurat"
      ]
    },
    {
      "page": "SampleUMI",
      "title": "Sample UMI",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "SampleUMI"
      ]
    },
    {
      "page": "SaveAnnoyIndex",
      "title": "Save the Annoy index",
      "concept": [
        "utilities"
      ],
      "topics": [
        "SaveAnnoyIndex"
      ]
    },
    {
      "page": "ScaleData",
      "title": "Scale and center the data.",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "ScaleData",
        "ScaleData.Assay",
        "ScaleData.default",
        "ScaleData.IterableMatrix",
        "ScaleData.Seurat"
      ]
    },
    {
      "page": "ScaleFactors",
      "title": "Get image scale factors",
      "concept": [
        "objects",
        "spatial"
      ],
      "topics": [
        "ScaleFactors",
        "scalefactors",
        "ScaleFactors.VisiumV1",
        "ScaleFactors.VisiumV2"
      ]
    },
    {
      "page": "ScoreJackStraw",
      "title": "Compute Jackstraw scores significance.",
      "concept": [
        "dimensional_reduction"
      ],
      "topics": [
        "ScoreJackStraw",
        "ScoreJackStraw.DimReduc",
        "ScoreJackStraw.JackStrawData",
        "ScoreJackStraw.Seurat"
      ]
    },
    {
      "page": "SCTAssay-class",
      "title": "The SCTModel Class",
      "concept": [
        "objects"
      ],
      "topics": [
        "levels.SCTAssay",
        "levels<-.SCTAssay",
        "SCTAssay",
        "SCTAssay-class",
        "SCTModel"
      ]
    },
    {
      "page": "SCTransform",
      "title": "Perform sctransform-based normalization",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "SCTransform",
        "SCTransform.Assay",
        "SCTransform.default",
        "SCTransform.IterableMatrix",
        "SCTransform.Seurat"
      ]
    },
    {
      "page": "SCTResults",
      "title": "Get SCT results from an Assay",
      "concept": [
        "objects"
      ],
      "topics": [
        "SCTResults",
        "SCTResults.SCTAssay",
        "SCTResults.SCTModel",
        "SCTResults.Seurat",
        "SCTResults<-",
        "SCTResults<-.SCTAssay",
        "SCTResults<-.SCTModel"
      ]
    },
    {
      "page": "SelectIntegrationFeatures",
      "title": "Select integration features",
      "concept": [
        "integration"
      ],
      "topics": [
        "SelectIntegrationFeatures"
      ]
    },
    {
      "page": "SelectIntegrationFeatures5",
      "title": "Select integration features",
      "concept": [
        "integration"
      ],
      "topics": [
        "SelectIntegrationFeatures5"
      ]
    },
    {
      "page": "SelectSCTIntegrationFeatures",
      "title": "Select SCT integration features",
      "concept": [
        "integration"
      ],
      "topics": [
        "SelectSCTIntegrationFeatures"
      ]
    },
    {
      "page": "SetIntegrationData",
      "title": "Set integration data",
      "concept": [
        "objects"
      ],
      "topics": [
        "SetIntegrationData"
      ]
    },
    {
      "page": "SetQuantile",
      "title": "Find the Quantile of Data",
      "concept": [
        "utilities"
      ],
      "topics": [
        "SetQuantile"
      ]
    },
    {
      "page": "Seurat-class",
      "title": "The Seurat Class",
      "topics": [
        "Seurat-class"
      ]
    },
    {
      "page": "SeuratCommand-class",
      "title": "The SeuratCommand Class",
      "topics": [
        "SeuratCommand-class"
      ]
    },
    {
      "page": "SeuratTheme",
      "title": "Seurat Themes",
      "concept": [
        "visualization"
      ],
      "topics": [
        "BoldTitle",
        "CenterTitle",
        "DarkTheme",
        "FontSize",
        "NoAxes",
        "NoGrid",
        "NoLegend",
        "RestoreLegend",
        "RotatedAxis",
        "SeuratAxes",
        "SeuratTheme",
        "SpatialTheme",
        "WhiteBackground"
      ]
    },
    {
      "page": "SketchData",
      "title": "Sketch Data",
      "concept": [
        "sketching"
      ],
      "topics": [
        "SketchData"
      ]
    },
    {
      "page": "SlideSeq-class",
      "title": "The SlideSeq class",
      "concept": [
        "spatial"
      ],
      "topics": [
        "SlideSeq",
        "SlideSeq-class"
      ]
    },
    {
      "page": "SpatialImage-class",
      "title": "The SpatialImage Class",
      "topics": [
        "SpatialImage-class"
      ]
    },
    {
      "page": "SpatialPlot",
      "title": "Visualize spatial clustering and expression data.",
      "concept": [
        "convenience",
        "spatial",
        "visualization"
      ],
      "topics": [
        "SpatialDimPlot",
        "SpatialFeaturePlot",
        "SpatialPlot"
      ]
    },
    {
      "page": "SplitObject",
      "title": "Splits object into a list of subsetted objects.",
      "concept": [
        "objects"
      ],
      "topics": [
        "SplitObject"
      ]
    },
    {
      "page": "STARmap-class",
      "title": "The STARmap class",
      "concept": [
        "objects",
        "spatial"
      ],
      "topics": [
        "STARmap",
        "STARmap-class"
      ]
    },
    {
      "page": "subset.AnchorSet",
      "title": "Subset an AnchorSet object",
      "concept": [
        "objects"
      ],
      "topics": [
        "subset.AnchorSet"
      ]
    },
    {
      "page": "SubsetByBarcodeInflections",
      "title": "Subset a Seurat Object based on the Barcode Distribution Inflection Points",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "SubsetByBarcodeInflections"
      ]
    },
    {
      "page": "TopCells",
      "title": "Find cells with highest scores for a given dimensional reduction technique",
      "concept": [
        "objects"
      ],
      "topics": [
        "TopCells"
      ]
    },
    {
      "page": "TopFeatures",
      "title": "Find features with highest scores for a given dimensional reduction technique",
      "concept": [
        "objects"
      ],
      "topics": [
        "TopFeatures"
      ]
    },
    {
      "page": "TopNeighbors",
      "title": "Get nearest neighbors for given cell",
      "concept": [
        "objects"
      ],
      "topics": [
        "TopNeighbors"
      ]
    },
    {
      "page": "TransferAnchorSet-class",
      "title": "The TransferAnchorSet Class",
      "concept": [
        "objects"
      ],
      "topics": [
        "TransferAnchorSet",
        "TransferAnchorSet-class"
      ]
    },
    {
      "page": "TransferData",
      "title": "Transfer data",
      "concept": [
        "integration"
      ],
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