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A B C D E F G H I J K L M N O P R S T U V W misc
| Seurat-package | Tools for single-cell genomics |
| AddMetaData | Add in metadata associated with either cells or features. |
| AddMetaData.Assay | Add in metadata associated with either cells or features. |
| AddMetaData.Seurat | Add in metadata associated with either cells or features. |
| AddModuleScore | Calculate module scores for feature expression programs in single cells |
| AddSamples | Merge Seurat Objects |
| ALRAChooseKPlot | ALRA Approximate Rank Selection Plot |
| AnchorSet | The AnchorSet Class |
| AnchorSet-class | The AnchorSet Class |
| as.CellDataSet | Convert objects to CellDataSet objects |
| as.CellDataSet.Seurat | Convert objects to CellDataSet objects |
| as.data.frame.Matrix | Convert between data frames and sparse matrices |
| as.Graph | Convert a matrix (or Matrix) to the Graph class. |
| as.Graph.Matrix | Convert a matrix (or Matrix) to the Graph class. |
| as.Graph.matrix | Convert a matrix (or Matrix) to the Graph class. |
| as.list.SeuratCommand | Coerce a SeuratCommand to a list |
| as.loom | Convert objects to loom objects |
| as.loom.Seurat | Convert objects to loom objects |
| as.Seurat | Convert objects to Seurat objects |
| as.Seurat.CellDataSet | Convert objects to Seurat objects |
| as.Seurat.loom | Convert objects to Seurat objects |
| as.Seurat.SingleCellExperiment | Convert objects to Seurat objects |
| as.SingleCellExperiment | Convert objects to SingleCellExperiment objects |
| as.SingleCellExperiment.Seurat | Convert objects to SingleCellExperiment objects |
| as.sparse | Convert between data frames and sparse matrices |
| as.sparse.data.frame | Convert between data frames and sparse matrices |
| as.sparse.H5Group | Convert between data frames and sparse matrices |
| as.sparse.Matrix | Convert between data frames and sparse matrices |
| as.sparse.matrix | Convert between data frames and sparse matrices |
| Assay | The Assay Class |
| Assay-class | The Assay Class |
| Assays | Pull Assays or assay names |
| AugmentPlot | Augments ggplot2-based plot with a PNG image. |
| AverageExpression | Averaged feature expression by identity class |
| BarcodeInflectionsPlot | Plot the Barcode Distribution and Calculated Inflection Points |
| BlackAndWhite | Create a custom color palette |
| BlueAndRed | Create a custom color palette |
| BoldTitle | Seurat Themes |
| BuildClusterTree | Phylogenetic Analysis of Identity Classes |
| CalculateBarcodeInflections | Calculate the Barcode Distribution Inflection |
| CaseMatch | Match the case of character vectors |
| cc.genes | Cell cycle genes |
| cc.genes.updated.2019 | Cell cycle genes: 2019 update |
| CellCycleScoring | Score cell cycle phases |
| CellPlot | Cell-cell scatter plot |
| Cells | Get cells present in an object |
| Cells.default | Get cells present in an object |
| Cells.DimReduc | Get cells present in an object |
| CellsByIdentities | Get cell names grouped by identity class |
| CellScatter | Cell-cell scatter plot |
| CellSelector | Cell selector |
| CollapseEmbeddingOutliers | Move outliers towards center on dimension reduction plot |
| CollapseSpeciesExpressionMatrix | Slim down a multi-species expression matrix, when only one species is primarily of interenst. |
| ColorDimSplit | Color dimensional reduction plot by tree split |
| CombinePlots | Combine ggplot2-based plots into a single plot |
| Command | Get SeuratCommands |
| Command.Seurat | Get SeuratCommands |
| CreateAssayObject | Create an Assay object |
| CreateDimReducObject | Create a DimReduc object |
| CreateGeneActivityMatrix | Convert a peak matrix to a gene activity matrix |
| CreateSeuratObject | Create a Seurat object |
| CustomDistance | Run a custom distance function on an input data matrix |
| CustomPalette | Create a custom color palette |
| DarkTheme | Seurat Themes |
| DefaultAssay | Get and set the default assay |
| DefaultAssay.Assay | Get and set the default assay |
| DefaultAssay.DimReduc | Get and set the default assay |
| DefaultAssay.Graph | Get and set the default assay |
| DefaultAssay.Seurat | Get and set the default assay |
| DefaultAssay.SeuratCommand | Get and set the default assay |
| DefaultAssay<- | Get and set the default assay |
| DefaultAssay<-.Seurat | Get and set the default assay |
| DietSeurat | Slim down a Seurat object |
| DimHeatmap | Dimensional reduction heatmap |
| DimPlot | Dimensional reduction plot |
| DimReduc | The Dimmensional Reduction Class |
| DimReduc-class | The Dimmensional Reduction Class |
| DiscretePalette | Discrete colour palettes from the pals package |
| DoHeatmap | Feature expression heatmap |
| DotPlot | Dot plot visualization |
| ElbowPlot | Quickly Pick Relevant Dimensions |
| Embeddings | Get cell embeddings |
| Embeddings.DimReduc | Get cell embeddings |
| Embeddings.Seurat | Get cell embeddings |
| ExpMean | Calculate the mean of logged values |
| ExportToCellbrowser | Export Seurat object for UCSC cell browser |
| ExpSD | Calculate the standard deviation of logged values |
| ExpVar | Calculate the variance of logged values |
| FeatureHeatmap | Visualize 'features' on a dimensional reduction plot |
| FeatureLocator | Cell selector |
| FeaturePlot | Visualize 'features' on a dimensional reduction plot |
| FeatureScatter | Scatter plot of single cell data |
| FetchData | Access cellular data |
| FindAllMarkers | Gene expression markers for all identity classes |
| FindAllMarkersNode | Gene expression markers for all identity classes |
| FindClusters | Cluster Determination |
| FindClusters.default | Cluster Determination |
| FindClusters.Seurat | Cluster Determination |
| FindConservedMarkers | Finds markers that are conserved between the groups |
| FindIntegrationAnchors | Find integration anchors |
| FindMarkers | Gene expression markers of identity classes |
| FindMarkers.default | Gene expression markers of identity classes |
| FindMarkers.Seurat | Gene expression markers of identity classes |
| FindMarkersNode | Gene expression markers of identity classes |
| FindNeighbors | SNN Graph Construction |
| FindNeighbors.Assay | SNN Graph Construction |
| FindNeighbors.default | SNN Graph Construction |
| FindNeighbors.dist | SNN Graph Construction |
| FindNeighbors.Seurat | SNN Graph Construction |
| FindTransferAnchors | Find transfer anchors |
| FindVariableFeatures | Find variable features |
| FindVariableFeatures.Assay | Find variable features |
| FindVariableFeatures.default | Find variable features |
| FindVariableFeatures.Seurat | Find variable features |
| FindVariableGenes | Find variable features |
| FontSize | Seurat Themes |
| GenePlot | Scatter plot of single cell data |
| GeneSymbolThesarus | Get updated synonyms for gene symbols |
| GetAssay | Get an Assay object from a given Seurat object. |
| GetAssay.Seurat | Get an Assay object from a given Seurat object. |
| GetAssayData | General accessor function for the Assay class |
| GetAssayData.Assay | General accessor function for the Assay class |
| GetAssayData.Seurat | General accessor function for the Assay class |
| GetIntegrationData | Get integation data |
| GetResidual | Calculate pearson residuals of features not in the scale.data |
| Graph | The Graph Class |
| Graph-class | The Graph Class |
| HoverLocator | Hover Locator |
| HTODemux | Demultiplex samples based on data from cell 'hashing' |
| HTOHeatmap | Hashtag oligo heatmap |
| HVFInfo | Get highly variable feature information |
| HVFInfo.Assay | Get highly variable feature information |
| HVFInfo.Seurat | Get highly variable feature information |
| ICAPlot | Dimensional reduction plot |
| Idents | Get, set, and manipulate an object's identity classes |
| Idents.Seurat | Get, set, and manipulate an object's identity classes |
| Idents<- | Get, set, and manipulate an object's identity classes |
| Idents<-.Seurat | Get, set, and manipulate an object's identity classes |
| IntegrateData | Integrate data |
| IntegrationData | The IntegrationData Class |
| IntegrationData-class | The IntegrationData Class |
| IsGlobal | Is an object global/persistent? |
| IsGlobal.default | Is an object global/persistent? |
| IsGlobal.DimReduc | Is an object global/persistent? |
| JackStraw | Determine statistical significance of PCA scores. |
| JackStrawData | The JackStrawData Class |
| JackStrawData-class | The JackStrawData Class |
| JackStrawPlot | JackStraw Plot |
| JS | Get JackStraw information |
| JS.DimReduc | Get JackStraw information |
| JS.JackStrawData | Get JackStraw information |
| JS<- | Get JackStraw information |
| JS<-.DimReduc | Get JackStraw information |
| JS<-.JackStrawData | Get JackStraw information |
| Key | Get a key |
| Key.Assay | Get a key |
| Key.DimReduc | Get a key |
| Key.Seurat | Get a key |
| Key<- | Get a key |
| Key<-.Assay | Get a key |
| Key<-.DimReduc | Get a key |
| L2CCA | L2-Normalize CCA |
| L2Dim | L2-normalization |
| LabelClusters | Label clusters on a ggplot2-based scatter plot |
| Labeler | Add text labels to a ggplot2 plot |
| LabelPoints | Add text labels to a ggplot2 plot |
| levels.Seurat | Get, set, and manipulate an object's identity classes |
| levels<-.Seurat | Get, set, and manipulate an object's identity classes |
| Loadings | Get feature loadings |
| Loadings.DimReduc | Get feature loadings |
| Loadings.Seurat | Get feature loadings |
| Loadings<- | Get feature loadings |
| Loadings<-.DimReduc | Get feature loadings |
| LocalStruct | Calculate the local structure preservation metric |
| LogNormalize | Normalize raw data |
| LogSeuratCommand | Log a command |
| LogVMR | Calculate the variance to mean ratio of logged values |
| MeanVarPlot | View variable features |
| merge | Merge Seurat Objects |
| merge.Assay | Merge Seurat Objects |
| merge.Seurat | Merge Seurat Objects |
| MergeSeurat | Merge Seurat Objects |
| MetaFeature | Aggregate expression of multiple features into a single feature |
| MinMax | Apply a ceiling and floor to all values in a matrix |
| Misc | Access miscellaneous data |
| Misc.Assay | Access miscellaneous data |
| Misc.Seurat | Access miscellaneous data |
| Misc<- | Access miscellaneous data |
| Misc<-.Assay | Access miscellaneous data |
| Misc<-.Seurat | Access miscellaneous data |
| MixingMetric | Calculates a mixing metric |
| MULTIseqDemux | Demultiplex samples based on classification method from MULTI-seq (McGinnis et al., bioRxiv 2018) |
| NoAxes | Seurat Themes |
| NoGrid | Seurat Themes |
| NoLegend | Seurat Themes |
| NormalizeData | Normalize Data |
| NormalizeData.Assay | Normalize Data |
| NormalizeData.default | Normalize Data |
| NormalizeData.Seurat | Normalize Data |
| OldWhichCells | Identify cells matching certain criteria |
| OldWhichCells.Assay | Identify cells matching certain criteria |
| OldWhichCells.Seurat | Identify cells matching certain criteria |
| pbmc_small | A small example version of the PBMC dataset |
| PCAPlot | Dimensional reduction plot |
| PCASigGenes | Significant genes from a PCA |
| PCHeatmap | Dimensional reduction heatmap |
| PercentageFeatureSet | Calculate the percentage of all counts that belong to a given set of features |
| PlotClusterTree | Plot clusters as a tree |
| PolyDimPlot | Polygon DimPlot |
| PolyFeaturePlot | Polygon FeaturePlot |
| PrepSCTIntegration | Prepare an object list that has been run through SCTransform for integration |
| Print the results of a dimensional reduction analysis | |
| print.DimReduc | Print the results of a dimensional reduction analysis |
| Project | Get and set project information |
| Project.Seurat | Get and set project information |
| Project<- | Get and set project information |
| Project<-.Seurat | Get and set project information |
| ProjectDim | Project Dimensional reduction onto full dataset |
| PurpleAndYellow | Create a custom color palette |
| Read10X | Load in data from 10X |
| Read10X_h5 | Read 10X hdf5 file |
| ReadAlevin | Load in data from Alevin pipeline |
| ReadAlevinCsv | Load in data from Alevin pipeline |
| ReadH5AD | Read from and write to h5ad files |
| ReadH5AD.character | Read from and write to h5ad files |
| ReadH5AD.H5File | Read from and write to h5ad files |
| Reductions | Pull DimReducs or DimReduc names |
| RegroupIdents | Regroup idents based on meta.data info |
| RelativeCounts | Normalize raw data to fractions |
| RenameAssays | Rename assays in a 'Seurat' object |
| RenameCells | Rename cells |
| RenameCells.Assay | Rename cells |
| RenameCells.DimReduc | Rename cells |
| RenameCells.Seurat | Rename cells |
| RenameIdent | Get, set, and manipulate an object's identity classes |
| RenameIdents | Get, set, and manipulate an object's identity classes |
| RenameIdents.Seurat | Get, set, and manipulate an object's identity classes |
| ReorderIdent | Get, set, and manipulate an object's identity classes |
| ReorderIdent.Seurat | Get, set, and manipulate an object's identity classes |
| RestoreLegend | Seurat Themes |
| RidgePlot | Single cell ridge plot |
| RotatedAxis | Seurat Themes |
| RowMergeSparseMatrices | Merge two matrices by rowname |
| RunALRA | Run Adaptively-thresholded Low Rank Approximation (ALRA) |
| RunALRA.default | Run Adaptively-thresholded Low Rank Approximation (ALRA) |
| RunALRA.Seurat | Run Adaptively-thresholded Low Rank Approximation (ALRA) |
| RunCCA | Perform Canonical Correlation Analysis |
| RunCCA.default | Perform Canonical Correlation Analysis |
| RunCCA.Seurat | Perform Canonical Correlation Analysis |
| RunICA | Run Independent Component Analysis on gene expression |
| RunICA.Assay | Run Independent Component Analysis on gene expression |
| RunICA.default | Run Independent Component Analysis on gene expression |
| RunICA.Seurat | Run Independent Component Analysis on gene expression |
| RunLSI | Run Latent Semantic Indexing on binary count matrix |
| RunLSI.Assay | Run Latent Semantic Indexing on binary count matrix |
| RunLSI.default | Run Latent Semantic Indexing on binary count matrix |
| RunLSI.Seurat | Run Latent Semantic Indexing on binary count matrix |
| RunPCA | Run Principal Component Analysis |
| RunPCA.Assay | Run Principal Component Analysis |
| RunPCA.default | Run Principal Component Analysis |
| RunPCA.Seurat | Run Principal Component Analysis |
| RunTSNE | Run t-distributed Stochastic Neighbor Embedding |
| RunTSNE.DimReduc | Run t-distributed Stochastic Neighbor Embedding |
| RunTSNE.dist | Run t-distributed Stochastic Neighbor Embedding |
| RunTSNE.matrix | Run t-distributed Stochastic Neighbor Embedding |
| RunTSNE.Seurat | Run t-distributed Stochastic Neighbor Embedding |
| RunUMAP | Run UMAP |
| RunUMAP.default | Run UMAP |
| RunUMAP.Graph | Run UMAP |
| RunUMAP.Seurat | Run UMAP |
| SampleUMI | Sample UMI |
| ScaleData | Scale and center the data. |
| ScaleData.Assay | Scale and center the data. |
| ScaleData.default | Scale and center the data. |
| ScaleData.Seurat | Scale and center the data. |
| ScoreJackStraw | Compute Jackstraw scores significance. |
| ScoreJackStraw.DimReduc | Compute Jackstraw scores significance. |
| ScoreJackStraw.JackStrawData | Compute Jackstraw scores significance. |
| ScoreJackStraw.Seurat | Compute Jackstraw scores significance. |
| SCTransform | Use regularized negative binomial regression to normalize UMI count data |
| SelectIntegrationFeatures | Select integration features |
| SetAssayData | Setter for multimodal data |
| SetAssayData.Assay | Setter for multimodal data |
| SetAssayData.Seurat | Setter for multimodal data |
| SetDimReduction | Create a DimReduc object |
| SetIdent | Get, set, and manipulate an object's identity classes |
| SetIdent.Seurat | Get, set, and manipulate an object's identity classes |
| SetIntegrationData | Set integation data |
| Seurat | The Seurat Class |
| seurat | The Seurat Class |
| Seurat-class | The Seurat Class |
| seurat-class | The Seurat Class |
| SeuratAccess | Add in metadata associated with either cells or features. |
| SeuratAxes | Seurat Themes |
| SeuratCommand | The SeuratCommand Class |
| SeuratCommand-class | The SeuratCommand Class |
| SeuratTheme | Seurat Themes |
| SpatialTheme | Seurat Themes |
| SplitDotPlotGG | Dot plot visualization |
| SplitObject | Splits object into a list of subsetted objects. |
| StashIdent | Get, set, and manipulate an object's identity classes |
| StashIdent.Seurat | Get, set, and manipulate an object's identity classes |
| Stdev | Get the standard deviations for an object |
| Stdev.DimReduc | Get the standard deviations for an object |
| Stdev.Seurat | Get the standard deviations for an object |
| StopCellbrowser | Stop Cellbrowser web server |
| subset | Subset a Seurat object |
| subset.Seurat | Subset a Seurat object |
| SubsetByBarcodeInflections | Subset a Seurat Object based on the Barcode Distribution Inflection Points |
| SubsetData | Return a subset of the Seurat object |
| SubsetData.Assay | Return a subset of the Seurat object |
| SubsetData.Seurat | Return a subset of the Seurat object |
| TF.IDF | Term frequency-inverse document frequency |
| Tool | Get and set additional tool data |
| Tool.Seurat | Get and set additional tool data |
| Tool<- | Get and set additional tool data |
| Tool<-.Seurat | Get and set additional tool data |
| Tools | Get and set additional tool data |
| TopCells | Find cells with highest scores for a given dimensional reduction technique |
| TopFeatures | Find features with highest scores for a given dimensional reduction technique |
| TransferData | Transfer Labels |
| TSNEPlot | Dimensional reduction plot |
| UMAPPlot | Dimensional reduction plot |
| UpdateSeuratObject | Update old Seurat object to accomodate new features |
| UpdateSymbolList | Get updated synonyms for gene symbols |
| VariableFeaturePlot | View variable features |
| VariableFeatures | Get and set variable feature information |
| VariableFeatures.Assay | Get and set variable feature information |
| VariableFeatures.Seurat | Get and set variable feature information |
| VariableFeatures<- | Get and set variable feature information |
| VariableFeatures<-.Assay | Get and set variable feature information |
| VariableFeatures<-.Seurat | Get and set variable feature information |
| VariableGenePlot | View variable features |
| VizDimLoadings | Visualize Dimensional Reduction genes |
| VlnPlot | Single cell violin plot |
| WhichCells | Identify cells matching certain criteria |
| WhichCells.Assay | Identify cells matching certain criteria |
| WhichCells.Seurat | Identify cells matching certain criteria |
| WhiteBackground | Seurat Themes |
| WriteH5AD | Read from and write to h5ad files |
| WriteH5AD.Seurat | Read from and write to h5ad files |
| [.Seurat | Subset a Seurat object |
| [[<--method | Add in metadata associated with either cells or features. |