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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
| AddImputedScore | Calculate imputed expression values |
| addImputedScore | Deprecated function(s) in the Seurat package |
| AddMetaData | Add Metadata |
| addMetaData | Deprecated function(s) in the Seurat package |
| AddModuleScore | Calculate module scores for gene expression programs in single cells |
| AddSamples | Add samples into existing Seurat object. |
| AddSmoothedScore | Calculate smoothed expression values |
| addSmoothedScore | Deprecated function(s) in the Seurat package |
| add_samples | Deprecated function(s) in the Seurat package |
| AlignSubspace | Align subspaces using dynamic time warping (DTW) |
| as.seurat | Convert Seurat objects to other classes and vice versa |
| as.seurat.SingleCellExperiment | Convert Seurat objects to other classes and vice versa |
| as.SingleCellExperiment | Convert Seurat objects to other classes and vice versa |
| as.SingleCellExperiment.seurat | Convert Seurat objects to other classes and vice versa |
| AssessNodes | Assess Internal Nodes |
| AssessSplit | Assess Cluster Split |
| AugmentPlot | Augments ggplot2 scatterplot with a PNG image. |
| average.expression | Deprecated function(s) in the Seurat package |
| average.pca | Deprecated function(s) in the Seurat package |
| AverageDetectionRate | Probability of detection by identity class |
| AverageExpression | Averaged gene expression by identity class |
| AveragePCA | Average PCA scores by identity class |
| batch.gene | Deprecated function(s) in the Seurat package |
| BatchGene | Identify potential genes associated with batch effects |
| BlackAndWhite | A black and white color palette |
| BuildClusterTree | Phylogenetic Analysis of Identity Classes |
| buildClusterTree | Deprecated function(s) in the Seurat package |
| BuildRFClassifier | Build Random Forest Classifier |
| BuildSNN | SNN Graph Construction |
| calc.insitu | Deprecated function(s) in the Seurat package |
| CalcAlignmentMetric | Calculate an alignment score |
| calcNoiseModels | Deprecated function(s) in the Seurat package |
| CalcVarExpRatio | Calculate the ratio of variance explained by ICA or PCA to CCA |
| calinskiPlot | Deprecated function(s) in the Seurat package |
| CaseMatch | Match the case of character vectors |
| cc.genes | Cell cycle genes |
| cell.cor.matrix | Deprecated function(s) in the Seurat package |
| CellCycleScoring | Score cell cycle phases |
| CellPlot | Cell-cell scatter plot |
| cellPlot | Deprecated function(s) in the Seurat package |
| ClassifyCells | Classify New Data |
| cluster.alpha | Deprecated function(s) in the Seurat package |
| CollapseSpeciesExpressionMatrix | Slim down a multi-species expression matrix, when only one species is primarily of interenst. |
| ColorTSNESplit | Color tSNE Plot Based on Split |
| CombineIdent | Sets identity class information to be a combination of two object attributes |
| Convert | Convert Seurat objects to other classes and vice versa |
| Convert.anndata.base.AnnData | Convert Seurat objects to other classes and vice versa |
| Convert.seurat | Convert Seurat objects to other classes and vice versa |
| Convert.SingleCellExperiment | Convert Seurat objects to other classes and vice versa |
| CreateSeuratObject | Initialize and setup the Seurat object |
| CustomDistance | Run a custom distance function on an input data matrix |
| CustomPalette | Create a custom color palette |
| DarkTheme | Dark Theme |
| DBClustDimension | Perform spectral density clustering on single cells |
| DBclust_dimension | Deprecated function(s) in the Seurat package |
| DESeq2DETest | Differential expression using DESeq2 |
| diffExp.test | Deprecated function(s) in the Seurat package |
| DiffExpTest | Likelihood ratio test for zero-inflated data |
| DiffTTest | Differential expression testing using Student's t-test |
| DimElbowPlot | Quickly Pick Relevant Dimensions |
| DimHeatmap | Dimensional reduction heatmap |
| DimPlot | Dimensional reduction plot |
| DimTopCells | Find cells with highest scores for a given dimensional reduction technique |
| DimTopGenes | Find genes with highest scores for a given dimensional reduction technique |
| DMEmbed | Diffusion Maps Cell Embeddings Accessor Function |
| DMPlot | Plot Diffusion map |
| DoHeatmap | Gene expression heatmap |
| doHeatMap | Deprecated function(s) in the Seurat package |
| DoKMeans | K-Means Clustering |
| doKMeans | Deprecated function(s) in the Seurat package |
| dot.plot | Deprecated function(s) in the Seurat package |
| DotPlot | Dot plot visualization |
| DotPlotOld | Old Dot plot visualization (pre-ggplot implementation) Intuitive way of visualizing how gene expression changes across different identity classes (clusters). The size of the dot encodes the percentage of cells within a class, while the color encodes the AverageExpression level of 'expressing' cells (green is high). |
| ExpMean | Calculate the mean of logged values |
| ExpSD | Calculate the standard deviation of logged values |
| ExpVar | Calculate the variance of logged values |
| ExtractField | Extract delimiter information from a string. |
| FastWhichCells | FastWhichCells Identify cells matching certain criteria (limited to character values) |
| feature.heatmap | Deprecated function(s) in the Seurat package |
| feature.plot | Deprecated function(s) in the Seurat package |
| feature.plot.keynote | Deprecated function(s) in the Seurat package |
| FeatureHeatmap | Vizualization of multiple features |
| FeatureLocator | Feature Locator |
| FeaturePlot | Visualize 'features' on a dimensional reduction plot |
| fetch.data | Deprecated function(s) in the Seurat package |
| FetchData | Access cellular data |
| FilterCells | Return a subset of the Seurat object |
| find.markers | Deprecated function(s) in the Seurat package |
| find.markers.node | Deprecated function(s) in the Seurat package |
| FindAllMarkers | Gene expression markers for all identity classes |
| FindAllMarkersNode | Find all markers for a node |
| FindClusters | Cluster Determination |
| FindConservedMarkers | Finds markers that are conserved between the two groups |
| FindGeneTerms | Find gene terms from Enrichr |
| FindMarkers | Gene expression markers of identity classes |
| FindMarkersNode | Gene expression markers of identity classes defined by a phylogenetic clade |
| FindVariableGenes | Identify variable genes |
| find_all_markers | Deprecated function(s) in the Seurat package |
| fit.gene.k | Deprecated function(s) in the Seurat package |
| fit.gene.mix | Deprecated function(s) in the Seurat package |
| FitGeneK | Build mixture models of gene expression |
| gene.cor.matrix | Deprecated function(s) in the Seurat package |
| GenePlot | Scatter plot of single cell data |
| genePlot | Deprecated function(s) in the Seurat package |
| genes.in.cluster | Deprecated function(s) in the Seurat package |
| geneScorePlot | Deprecated function(s) in the Seurat package |
| GenesInCluster | GenesInCluster |
| get.centroids | Deprecated function(s) in the Seurat package |
| GetAssayData | Accessor function for multimodal data |
| GetCellEmbeddings | Dimensional Reduction Cell Embeddings Accessor Function |
| GetCentroids | Get cell centroids |
| GetClusters | Get Cluster Assignments |
| GetDimReduction | Dimensional Reduction Accessor Function |
| GetGeneLoadings | Dimensional Reduction Gene Loadings Accessor Function |
| GetIdent | Get identity of cells |
| getNewScore | Deprecated function(s) in the Seurat package |
| HeatmapNode | Deprecated function(s) in the Seurat package |
| HoverLocator | Hover Locator |
| HTODemux | Demultiplex samples based on data from cell 'hashing' |
| HTOHeatmap | Hashtag oligo heatmap |
| ICA | Deprecated function(s) in the Seurat package |
| ica | Deprecated function(s) in the Seurat package |
| ica.plot | Deprecated function(s) in the Seurat package |
| ICAEmbed | ICA Cell Embeddings Accessor Function |
| ICALoad | ICA Gene Loadings Accessor Function |
| ICAPlot | Plot ICA map |
| ICHeatmap | Independent component heatmap |
| icHeatmap | Deprecated function(s) in the Seurat package |
| ICTopCells | Find cells with highest ICA scores |
| ICTopGenes | Find genes with highest ICA scores |
| icTopGenes | Deprecated function(s) in the Seurat package |
| initial.mapping | Deprecated function(s) in the Seurat package |
| InitialMapping | Infer spatial origins for single cells |
| jackRandom | Deprecated function(s) in the Seurat package |
| JackStraw | Determine statistical significance of PCA scores. |
| jackStraw | Deprecated function(s) in the Seurat package |
| jackStraw.permutation.test | Deprecated function(s) in the Seurat package |
| jackStrawFull | Deprecated function(s) in the Seurat package |
| jackStrawMC | Deprecated function(s) in the Seurat package |
| JackStrawPlot | JackStraw Plot |
| jackStrawPlot | Deprecated function(s) in the Seurat package |
| JoyPlot | Deprecated function(s) in the Seurat package |
| KClustDimension | Perform spectral k-means clustering on single cells |
| Kclust_dimension | Deprecated function(s) in the Seurat package |
| KMeansHeatmap | Plot k-means clusters |
| kMeansHeatmap | Deprecated function(s) in the Seurat package |
| LogNormalize | Normalize raw data |
| LogVMR | Calculate the variance to mean ratio of logged values |
| MakeSparse | Make object sparse |
| map.cell | Deprecated function(s) in the Seurat package |
| marker.test | Deprecated function(s) in the Seurat package |
| MarkerTest | ROC-based marker discovery |
| MASTDETest | Differential expression using MAST |
| MatrixRowShuffle | Independently shuffle values within each row of a matrix |
| MeanVarPlot | Deprecated function(s) in the Seurat package |
| MergeNode | Merge childen of a node |
| MergeSeurat | Merge Seurat Objects |
| MetageneBicorPlot | Plot CC bicor saturation plot |
| MinMax | Apply a ceiling and floor to all values in a matrix |
| minusc | Deprecated function(s) in the Seurat package |
| minusr | Deprecated function(s) in the Seurat package |
| MultiModal_CCA | Run Canonical Correlation Analysis (CCA) on multimodal data |
| MultiModal_CIA | Run coinertia analysis on multimodal data |
| NegBinomDETest | Negative binomial test for UMI-count based data |
| NegBinomRegDETest | Negative binomial test for UMI-count based data (regularized version) |
| NormalizeData | Normalize Assay Data |
| NumberClusters | Convert the cluster labels to a numeric representation |
| OldDoHeatmap | Gene expression heatmap |
| pbmc_small | A small example version of the PBMC dataset |
| PCA | Deprecated function(s) in the Seurat package |
| pca | Deprecated function(s) in the Seurat package |
| pca.plot | Deprecated function(s) in the Seurat package |
| pca.sig.genes | Deprecated function(s) in the Seurat package |
| PCAEmbed | PCA Cell Embeddings Accessor Function |
| PCALoad | PCA Gene Loadings Accessor Function |
| PCAPlot | Plot PCA map |
| PCASigGenes | Significant genes from a PCA |
| PCElbowPlot | Quickly Pick Relevant PCs |
| PCHeatmap | Principal component heatmap |
| pcHeatmap | Deprecated function(s) in the Seurat package |
| PCTopCells | Find cells with highest PCA scores |
| pcTopCells | Deprecated function(s) in the Seurat package |
| PCTopGenes | Find genes with highest PCA scores |
| pcTopGenes | Deprecated function(s) in the Seurat package |
| PlotClusterTree | Plot phylogenetic tree |
| plotClusterTree | Deprecated function(s) in the Seurat package |
| plotNoiseModel | Deprecated function(s) in the Seurat package |
| PoissonDETest | Poisson test for UMI-count based data |
| posterior.plot | Deprecated function(s) in the Seurat package |
| PrintAlignSubspaceParams | Print AlignSubspace Calculation Parameters |
| PrintCalcParams | Print the calculation |
| PrintCalcVarExpRatioParams | Print Parameters Associated with CalcVarExpRatio |
| PrintCCAParams | Print CCA Calculation Parameters |
| PrintDim | Print the results of a dimensional reduction analysis |
| PrintDMParams | Print Diffusion Map Calculation Parameters |
| PrintFindClustersParams | Print FindClusters Calculation Parameters |
| PrintICA | Print the results of a ICA analysis |
| PrintICAParams | Print ICA Calculation Parameters |
| PrintPCA | Print the results of a PCA analysis |
| PrintPCAParams | Print PCA Calculation Parameters |
| PrintSNNParams | Print SNN Construction Calculation Parameters |
| PrintTSNEParams | Print TSNE Calculation Parameters |
| project.pca | Deprecated function(s) in the Seurat package |
| project.samples | Deprecated function(s) in the Seurat package |
| ProjectDim | Project Dimensional reduction onto full dataset |
| ProjectPCA | Project Principal Components Analysis onto full dataset |
| PurpleAndYellow | A purple and yellow color palette |
| Read10X | Load in data from 10X |
| Read10X_h5 | Read 10X hdf5 file |
| refined.mapping | Deprecated function(s) in the Seurat package |
| RefinedMapping | Quantitative refinement of spatial inferences |
| RegressOut | Deprecated function(s) in the Seurat package |
| regulatorScore | Deprecated function(s) in the Seurat package |
| RemoveFromTable | Remove data from a table |
| removePC | Deprecated function(s) in the Seurat package |
| rename.ident | Deprecated function(s) in the Seurat package |
| RenameCells | Rename cells |
| RenameIdent | Rename one identity class to another |
| ReorderIdent | Reorder identity classes |
| RidgePlot | Single cell ridge plot |
| RunCCA | Perform Canonical Correlation Analysis |
| RunDiffusion | Run diffusion map |
| RunICA | Run Independent Component Analysis on gene expression |
| RunMultiCCA | Perform Canonical Correlation Analysis with more than two groups |
| RunPCA | Run Principal Component Analysis on gene expression using IRLBA |
| RunPHATE | Run PHATE |
| RunTSNE | Run t-distributed Stochastic Neighbor Embedding |
| RunUMAP | Run UMAP |
| run_diffusion | Deprecated function(s) in the Seurat package |
| run_tsne | Deprecated function(s) in the Seurat package |
| SampleUMI | Sample UMI |
| SaveClusters | Save cluster assignments to a TSV file |
| ScaleData | Scale and center the data. |
| ScaleDataR | Old R based implementation of ScaleData. Scales and centers the data |
| set.all.ident | Deprecated function(s) in the Seurat package |
| set.ident | Deprecated function(s) in the Seurat package |
| SetAllIdent | Switch identity class definition to another variable |
| SetAssayData | Assay Data Mutator Function |
| SetClusters | Set Cluster Assignments |
| SetDimReduction | Dimensional Reduction Mutator Function |
| SetIdent | Set identity class information |
| seurat | The Seurat Class |
| seurat-class | The Seurat Class |
| Seurat-deprecated | Deprecated function(s) in the Seurat package |
| Shuffle | Shuffle a vector |
| spatial.de | Deprecated function(s) in the Seurat package |
| SplitDotPlotGG | Split Dot plot visualization |
| SplitObject | Splits object into a list of subsetted objects. |
| StashIdent | Set identity class information |
| SubsetByPredicate | Return a subset of the Seurat object. |
| subsetCells | Deprecated function(s) in the Seurat package |
| SubsetColumn | Return a subset of columns for a matrix or data frame |
| SubsetData | Return a subset of the Seurat object |
| subsetData | Deprecated function(s) in the Seurat package |
| SubsetRow | Return a subset of rows for a matrix or data frame |
| tnse.plot | Deprecated function(s) in the Seurat package |
| tobit.test | Deprecated function(s) in the Seurat package |
| TobitTest | Differential expression testing using Tobit models |
| TransferIdent | Transfer identity class information (or meta data) from one object to another |
| tsne.plot | Deprecated function(s) in the Seurat package |
| TSNEPlot | Plot tSNE map |
| UpdateSeuratObject | Update old Seurat object to accomodate new features |
| ValidateClusters | Cluster Validation |
| ValidateSpecificClusters | Specific Cluster Validation |
| VariableGenePlot | View variable genes |
| viz.ica | Deprecated function(s) in the Seurat package |
| viz.pca | Deprecated function(s) in the Seurat package |
| VizClassification | Deprecated function(s) in the Seurat package |
| VizDimReduction | Visualize Dimensional Reduction genes |
| VizICA | Visualize ICA genes |
| VizPCA | Visualize PCA genes |
| VlnPlot | Single cell violin plot |
| vlnPlot | Deprecated function(s) in the Seurat package |
| which.cells | Deprecated function(s) in the Seurat package |
| WhichCells | Identify cells matching certain criteria |
| WilcoxDETest | Differential expression using Wilcoxon Rank Sum |
| writ.table | Deprecated function(s) in the Seurat package |