Package index
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AbundancePlot() - Plot cell abundances across groups in a Seurat object
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AssignQuantiles() - Assign cells to feature-specific quantiles.
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BackgatePlot() - Plot a metadata selection in a biaxial FeatureScatter plot
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BuildAnnoyUMAP() - Run UMAP on a Seurat object
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BuildSNNfromKNN() - Derive an SNN from a kNN Graph object in Seurat
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ClipDSB() - Clip DSB assay with quantiles per feature
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DimPlotEdges() - Seurat DimPlot enhancement
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DimPlotHighlight() - Seurat DimPlot enhancement III
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DimPlotPlus() - Seurat DimPlot enhancement II
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DoClusteredDotPlot() - Seurat DotPlot enhancement with hierarchical clustering
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DoClusteredHeatmap() - Heatmap of average expression values per group
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DoStarHeatmap() - Heatmap of average expression values per group with stars
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ExtractClusterProportions() - Extract cell proportions and counts across groups in a Seurat object
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FeaturePlotPlus() - Seurat FeaturePlot enhancement
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FindClustersLeiden() - Calculate Leiden clustering for a Graph object in Seurat
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FindJaccard() - Determine overlap measure between a list of genes
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FlowPlot() - Plot a metadata selection in a biaxial FeatureScatter plot
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MetaDataPlot() - Plot Seurat metadata distribution as a bar graph for indicated groups.
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ModulePlot() - Plot avereage feature expression per sample across groups in a Seurat object
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ReadGMT() - Read in a GMT file
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RunAUCell() - Run AUCell on a Seurat object
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RunHarmonyForSymphony() - Run Harmony with necessary internal object tinkering for Symphony
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RunSCA() - Perform Shannon Component Analysis on a Seurat object
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ScaleADT() - Scale ADT assay from 0 to 1 per feature
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ScaleDSB() - Scale DSB assay to [0-1] per feature
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SeuratToAnnData() - Save a Seurat object as an anndata h5ad file
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TrueAverageExpression() - Average feature expression across clustered samples in a Seurat object using fast sparse matrix methods
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dissociation.genes - Dissociation-associated gene signature