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  "Package": "Seurat",
  "Version": "4.4.0",
  "Date": "2023-09-26",
  "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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    },
    {
      "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": "CellsByImage",
      "title": "Get a vector of cell names associated with an image (or set of images)",
      "topics": [
        "CellsByImage"
      ]
    },
    {
      "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": "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": "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": "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": "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"
      ]
    },
    {
      "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.default",
        "FindVariableFeatures.SCTAssay",
        "FindVariableFeatures.Seurat",
        "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"
      ]
    },
    {
      "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"
      ]
    },
    {
      "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": "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",
      "topics": [
        "HVFInfo.SCTAssay"
      ]
    },
    {
      "page": "IFeaturePlot",
      "title": "Visualize features in dimensional reduction space interactively",
      "concept": [
        "visualization"
      ],
      "topics": [
        "IFeaturePlot"
      ]
    },
    {
      "page": "ImageDimPlot",
      "title": "Spatial Cluster Plots",
      "topics": [
        "ImageDimPlot"
      ]
    },
    {
      "page": "ImageFeaturePlot",
      "title": "Spatial Feature Plots",
      "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": "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": "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": "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"
      ]
    },
    {
      "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": "NormalizeData",
      "title": "Normalize Data",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "NormalizeData",
        "NormalizeData.Assay",
        "NormalizeData.default",
        "NormalizeData.Seurat"
      ]
    },
    {
      "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": "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": "ProjectDim",
      "title": "Project Dimensional reduction onto full dataset",
      "concept": [
        "dimensional_reduction"
      ],
      "topics": [
        "ProjectDim"
      ]
    },
    {
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