| Seurat: Tools for Single Cell Genomics | Seurat-package Seurat |
| Add Azimuth Results | AddAzimuthResults |
| Calculate module scores for feature expression programs in single cells | AddModuleScore |
| Aggregated feature expression by identity class | AggregateExpression |
| The AnchorSet Class | AnchorSet AnchorSet-class |
| Add info to anchor matrix | AnnotateAnchors AnnotateAnchors.default AnnotateAnchors.IntegrationAnchorSet AnnotateAnchors.TransferAnchorSet |
| Convert objects to CellDataSet objects | as.CellDataSet as.CellDataSet.Seurat |
| Convert objects to 'Seurat' objects | as.Seurat.CellDataSet as.Seurat.SingleCellExperiment |
| Convert objects to SingleCellExperiment objects | as.SingleCellExperiment as.SingleCellExperiment.Seurat |
| Cast to Sparse | as.data.frame.Matrix as.sparse.H5Group |
| The Assay Class | Assay-class |
| Augments ggplot2-based plot with a PNG image. | AugmentPlot |
| Automagically calculate a point size for ggplot2-based scatter plots | AutoPointSize |
| Averaged feature expression by identity class | AverageExpression |
| Plot the Barcode Distribution and Calculated Inflection Points | BarcodeInflectionsPlot |
| Determine text color based on background color | BGTextColor |
| Create a custom color palette | BlackAndWhite BlueAndRed CustomPalette PurpleAndYellow |
| Construct a dictionary representation for each unimodal dataset | BridgeCellsRepresentation |
| The BridgeReferenceSet Class The BridgeReferenceSet is an output from PrepareBridgeReference | BridgeReferenceSet BridgeReferenceSet-class |
| Phylogenetic Analysis of Identity Classes | BuildClusterTree |
| Construct an assay for spatial niche analysis | BuildNicheAssay |
| Calculate a perturbation Signature | CalcPerturbSig |
| Calculate the Barcode Distribution Inflection | CalculateBarcodeInflections |
| Match the case of character vectors | CaseMatch |
| Cell cycle genes | cc.genes |
| Cell cycle genes: 2019 update | cc.genes.updated.2019 |
| Seurat-CCA Integration | CCAIntegration |
| Score cell cycle phases | CellCycleScoring |
| Get Cell Names | Cells.SCTModel Cells.SlideSeq Cells.STARmap Cells.VisiumV1 |
| Cell-cell scatter plot | CellPlot CellScatter |
| Cell Selector | CellSelector FeatureLocator |
| Move outliers towards center on dimension reduction plot | CollapseEmbeddingOutliers |
| Slim down a multi-species expression matrix, when only one species is primarily of interenst. | CollapseSpeciesExpressionMatrix |
| Color dimensional reduction plot by tree split | ColorDimSplit |
| Combine ggplot2-based plots into a single plot | CombinePlots |
| Get the intensity and/or luminance of a color | contrast-theory Intensity Luminance |
| Create one hot matrix for a given label | CreateCategoryMatrix |
| Create a SCT Assay object | CreateSCTAssayObject |
| Run a custom distance function on an input data matrix | CustomDistance |
| DE and EnrichR pathway visualization barplot | DEenrichRPlot |
| Slim down a Seurat object | DietSeurat |
| Dimensional reduction heatmap | DimHeatmap PCHeatmap |
| Dimensional reduction plot | DimPlot ICAPlot PCAPlot TSNEPlot UMAPPlot |
| The DimReduc Class | DimReduc-class |
| Discrete colour palettes from pals | DiscretePalette |
| Feature expression heatmap | DoHeatmap |
| Dot plot visualization | DotPlot SplitDotPlotGG |
| Quickly Pick Relevant Dimensions | ElbowPlot |
| Calculate the mean of logged values | ExpMean |
| Calculate the standard deviation of logged values | ExpSD |
| Calculate the variance of logged values | ExpVar |
| Scale and/or center matrix rowwise | FastRowScale |
| Perform integration on the joint PCA cell embeddings. | FastRPCAIntegration |
| Visualize 'features' on a dimensional reduction plot | FeatureHeatmap FeaturePlot |
| Scatter plot of single cell data | FeatureScatter GenePlot |
| Calculate pearson residuals of features not in the scale.data | FetchResiduals |
| Filter stray beads from Slide-seq puck | FilterSlideSeq |
| Gene expression markers for all identity classes | FindAllMarkers FindAllMarkersNode |
| Find integration bridge anchors between query and extended bridge-reference | FindBridgeIntegrationAnchors |
| Find bridge anchors between query and extended bridge-reference | FindBridgeTransferAnchors |
| Cluster Determination | FindClusters FindClusters.default FindClusters.Seurat |
| Finds markers that are conserved between the groups | FindConservedMarkers |
| Find integration anchors | FindIntegrationAnchors |
| Gene expression markers of identity classes | FindMarkers FindMarkers.Assay FindMarkers.default FindMarkers.DimReduc FindMarkers.SCTAssay FindMarkers.Seurat FindMarkersNode |
| Construct weighted nearest neighbor graph | FindMultiModalNeighbors |
| (Shared) Nearest-neighbor graph construction | FindNeighbors FindNeighbors.Assay FindNeighbors.default FindNeighbors.dist FindNeighbors.Seurat |
| Find spatially variable features | FindSpatiallyVariableFeatures FindSpatiallyVariableFeatures.Assay FindSpatiallyVariableFeatures.default FindSpatiallyVariableFeatures.Seurat FindSpatiallyVariableFeatures.StdAssay |
| Find subclusters under one cluster | FindSubCluster |
| Find transfer anchors | FindTransferAnchors |
| Find variable features | FindVariableFeatures FindVariableFeatures.Assay FindVariableFeatures.SCTAssay FindVariableFeatures.Seurat FindVariableFeatures.V3Matrix FindVariableGenes |
| Fold Change | FoldChange FoldChange.Assay FoldChange.default FoldChange.DimReduc FoldChange.SCTAssay FoldChange.Seurat |
| Get an Assay object from a given Seurat object. | GetAssay GetAssay.Seurat |
| Get Image Data | GetImage.SlideSeq GetImage.STARmap GetImage.VisiumV1 GetImage.VisiumV2 |
| Get integration data | GetIntegrationData |
| Calculate pearson residuals of features not in the scale.data | GetResidual |
| Get Tissue Coordinates | GetTissueCoordinates.SlideSeq GetTissueCoordinates.STARmap GetTissueCoordinates.VisiumV1 GetTissueCoordinates.VisiumV2 |
| Get the predicted identity | GetTransferPredictions |
| The Graph Class | Graph-class |
| Compute the correlation of features broken down by groups with another covariate | GroupCorrelation |
| Boxplot of correlation of a variable (e.g. number of UMIs) with expression data | GroupCorrelationPlot |
| Harmony Integration | HarmonyIntegration |
| Hover Locator | HoverLocator |
| Demultiplex samples based on data from cell 'hashing' | HTODemux |
| Hashtag oligo heatmap | HTOHeatmap |
| Get Variable Feature Information | HVFInfo.SCTAssay |
| Visualize features in dimensional reduction space interactively | IFeaturePlot |
| Spatial Cluster Plots | ImageDimPlot |
| Spatial Feature Plots | ImageFeaturePlot |
| Integrate data | IntegrateData |
| Integrate low dimensional embeddings | IntegrateEmbeddings IntegrateEmbeddings.IntegrationAnchorSet IntegrateEmbeddings.TransferAnchorSet |
| Integrate Layers | IntegrateLayers |
| The IntegrationAnchorSet Class | IntegrationAnchorSet IntegrationAnchorSet-class |
| The IntegrationData Class | IntegrationData IntegrationData-class |
| Visualize clusters spatially and interactively | ISpatialDimPlot |
| Visualize features spatially and interactively | ISpatialFeaturePlot |
| Determine statistical significance of PCA scores. | JackStraw |
| The JackStrawData Class | JackStrawData-class |
| JackStraw Plot | JackStrawPlot |
| Seurat-Joint PCA Integration | JointPCAIntegration |
| L2-Normalize CCA | L2CCA |
| L2-normalization | L2Dim |
| Label clusters on a ggplot2-based scatter plot | LabelClusters |
| Add text labels to a ggplot2 plot | Labeler LabelPoints |
| Leverage Score Calculation | LeverageScore LeverageScore.Assay LeverageScore.default LeverageScore.Seurat LeverageScore.StdAssay |
| Visualize spatial and clustering (dimensional reduction) data in a linked, interactive framework | LinkedDimPlot LinkedFeaturePlot LinkedPlot LinkedPlots |
| Load a 10x Genomics Visium Spatial Experiment into a 'Seurat' object | Load10X_Spatial |
| Load the Annoy index file | LoadAnnoyIndex |
| Load Curio Seeker data | LoadCurioSeeker |
| Load STARmap data | LoadSTARmap |
| Read and Load 10x Genomics Xenium in-situ data | LoadXenium ReadXenium |
| Calculate the local structure preservation metric | LocalStruct |
| Normalize Raw Data | LogNormalize LogNormalize.data.frame LogNormalize.default LogNormalize.V3Matrix |
| Calculate the variance to mean ratio of logged values | LogVMR |
| Metric for evaluating mapping success | MappingScore MappingScore.AnchorSet MappingScore.default |
| Map query cells to a reference | MapQuery |
| Merge SCTAssay objects | merge.SCTAssay |
| Aggregate expression of multiple features into a single feature | MetaFeature |
| Apply a ceiling and floor to all values in a matrix | MinMax |
| Calculates a mixing metric | MixingMetric |
| Differential expression heatmap for mixscape | MixscapeHeatmap |
| Linear discriminant analysis on pooled CRISPR screen data. | MixscapeLDA |
| The ModalityWeights Class | ModalityWeights ModalityWeights-class |
| Demultiplex samples based on classification method from MULTI-seq (McGinnis et al., bioRxiv 2018) | MULTIseqDemux |
| The Neighbor Class | Neighbor-class |
| Highlight Neighbors in DimPlot | NNPlot |
| Convert Neighbor class to an asymmetrical Graph class | NNtoGraph |
| Normalize Data | NormalizeData NormalizeData.Assay NormalizeData.Seurat NormalizeData.V3Matrix |
| Significant genes from a PCA | PCASigGenes |
| Calculate the percentage of a vector above some threshold | PercentAbove |
| Calculate the percentage of all counts that belong to a given set of features | PercentageFeatureSet |
| Plot clusters as a tree | PlotClusterTree |
| Function to plot perturbation score distributions. | PlotPerturbScore |
| Polygon DimPlot | PolyDimPlot |
| Polygon FeaturePlot | PolyFeaturePlot |
| Predict value from nearest neighbors | PredictAssay |
| Prepare the bridge and reference datasets | PrepareBridgeReference |
| Function to prepare data for Linear Discriminant Analysis. | PrepLDA |
| Prepare object to run differential expression on SCT assay with multiple models | PrepSCTFindMarkers |
| Prepare an object list normalized with sctransform for integration. | PrepSCTIntegration |
| Project full data to the sketch assay | ProjectData |
| Project Dimensional reduction onto full dataset | ProjectDim |
| Project query data to reference dimensional reduction | ProjectDimReduc |
| Integrate embeddings from the integrated sketched.assay | ProjectIntegration |
| Project query into UMAP coordinates of a reference | ProjectUMAP ProjectUMAP.default ProjectUMAP.DimReduc ProjectUMAP.Seurat |
| Pseudobulk Expression | PseudobulkExpression PseudobulkExpression.Assay PseudobulkExpression.Seurat PseudobulkExpression.StdAssay |
| Get Spot Radius | Radius.SlideSeq Radius.STARmap Radius.VisiumV1 Radius.VisiumV2 |
| Load in data from 10X | Read10X |
| Load 10X Genomics Visium Tissue Positions | Read10X_Coordinates |
| Read 10X hdf5 file | Read10X_h5 |
| Load a 10X Genomics Visium Image | Read10X_Image |
| Read10x Probe Metadata | Read10X_probe_metadata |
| Load 10X Genomics Visium Scale Factors | Read10X_ScaleFactors |
| Read and Load Akoya CODEX data | LoadAkoya ReadAkoya |
| Load in data from remote or local mtx files | ReadMtx |
| Read and Load Nanostring SMI data | LoadNanostring ReadNanostring |
| Read output from Parse Biosciences | ReadParseBio |
| Load Slide-seq spatial data | ReadSlideSeq |
| Read output from STARsolo | ReadSTARsolo |
| Read Data From Vitessce | LoadHuBMAPCODEX ReadVitessce |
| Read and Load MERFISH Input from Vizgen | LoadVizgen ReadVizgen |
| Regroup idents based on meta.data info | RegroupIdents |
| Normalize raw data to fractions | RelativeCounts |
| Rename Cells in an Object | RenameCells.SCTAssay RenameCells.SlideSeq RenameCells.STARmap RenameCells.VisiumV1 |
| Single cell ridge plot | RidgePlot |
| Seurat-RPCA Integration | RPCAIntegration |
| Perform Canonical Correlation Analysis | RunCCA RunCCA.default RunCCA.Seurat |
| Run Graph Laplacian Eigendecomposition | RunGraphLaplacian RunGraphLaplacian.default RunGraphLaplacian.Seurat |
| Run Independent Component Analysis on gene expression | RunICA RunICA.Assay RunICA.default RunICA.Seurat |
| Run Linear Discriminant Analysis | RunLDA RunLDA.Assay RunLDA.default RunLDA.Seurat |
| Run Leiden clustering algorithm | RunLeiden |
| Run the mark variogram computation on a given position matrix and expression matrix. | RunMarkVario |
| Run Mixscape | RunMixscape |
| Compute Moran's I value. | RunMoransI |
| Run Principal Component Analysis | RunPCA RunPCA.Assay RunPCA.default RunPCA.Seurat |
| Run Supervised Latent Semantic Indexing | RunSLSI RunSLSI.Assay RunSLSI.default RunSLSI.Seurat RunSLSI.StdAssay |
| Run Supervised Principal Component Analysis | RunSPCA RunSPCA.Assay RunSPCA.Assay5 RunSPCA.default RunSPCA.Seurat |
| Run t-distributed Stochastic Neighbor Embedding | RunTSNE RunTSNE.DimReduc RunTSNE.dist RunTSNE.matrix RunTSNE.Seurat |
| Run UMAP | RunUMAP RunUMAP.default RunUMAP.Graph RunUMAP.Neighbor RunUMAP.Seurat |
| Sample UMI | SampleUMI |
| Save the Annoy index | SaveAnnoyIndex |
| Scale and center the data. | ScaleData ScaleData.Assay ScaleData.default ScaleData.IterableMatrix ScaleData.Seurat |
| Get image scale factors | ScaleFactors scalefactors ScaleFactors.VisiumV1 ScaleFactors.VisiumV2 |
| Compute Jackstraw scores significance. | ScoreJackStraw ScoreJackStraw.DimReduc ScoreJackStraw.JackStrawData ScoreJackStraw.Seurat |
| The SCTModel Class | levels.SCTAssay levels<-.SCTAssay SCTAssay SCTAssay-class SCTModel |
| Perform sctransform-based normalization | SCTransform SCTransform.Assay SCTransform.default SCTransform.IterableMatrix SCTransform.Seurat |
| Get SCT results from an Assay | SCTResults SCTResults.SCTAssay SCTResults.SCTModel SCTResults.Seurat SCTResults<- SCTResults<-.SCTAssay SCTResults<-.SCTModel |
| Select integration features | SelectIntegrationFeatures |
| Select integration features | SelectIntegrationFeatures5 |
| Select SCT integration features | SelectSCTIntegrationFeatures |
| Set integration data | SetIntegrationData |
| Find the Quantile of Data | SetQuantile |
| The Seurat Class | Seurat-class |
| The SeuratCommand Class | SeuratCommand-class |
| Seurat Themes | BoldTitle CenterTitle DarkTheme FontSize NoAxes NoGrid NoLegend RestoreLegend RotatedAxis SeuratAxes SeuratTheme SpatialTheme WhiteBackground |
| Sketch Data | SketchData |
| The SlideSeq class | SlideSeq SlideSeq-class |
| The SpatialImage Class | SpatialImage-class |
| Visualize spatial clustering and expression data. | SpatialDimPlot SpatialFeaturePlot SpatialPlot |
| Splits object into a list of subsetted objects. | SplitObject |
| The STARmap class | STARmap STARmap-class |
| Subset an AnchorSet object | subset.AnchorSet |
| Subset a Seurat Object based on the Barcode Distribution Inflection Points | SubsetByBarcodeInflections |
| Find cells with highest scores for a given dimensional reduction technique | TopCells |
| Find features with highest scores for a given dimensional reduction technique | TopFeatures |
| Get nearest neighbors for given cell | TopNeighbors |
| The TransferAnchorSet Class | TransferAnchorSet TransferAnchorSet-class |
| Transfer data | TransferData |
| Transfer data from sketch data to full data | TransferSketchLabels |
| Transfer embeddings from sketched cells to the full data | UnSketchEmbeddings |
| Update pre-V4 Assays generated with SCTransform in the Seurat to the new SCTAssay class | UpdateSCTAssays |
| Get updated synonyms for gene symbols | GeneSymbolThesarus UpdateSymbolList |
| View variable features | MeanVarPlot VariableFeaturePlot VariableGenePlot |
| The VisiumV1 class | VisiumV1 VisiumV1-class |
| The VisiumV2 class | VisiumV2 VisiumV2-class |
| Visualize Dimensional Reduction genes | VizDimLoadings |
| Single cell violin plot | VlnPlot |
