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A B C D F G H I J K L M N P R S T 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 |
| 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 |
| AssessNodes | Assess Internal Nodes |
| AssessSplit | Assess Cluster Split |
| average.expression | Deprecated function(s) in the Seurat package |
| average.pca | Deprecated function(s) in the Seurat package |
| 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 |
| 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 |
| calcNoiseModels | Deprecated function(s) in the Seurat package |
| calinskiPlot | Deprecated function(s) in the Seurat package |
| cell.cor.matrix | Deprecated function(s) in the Seurat package |
| 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 |
| ClusterAlpha | Probability of detection by identity class |
| ColorTSNESplit | Color tSNE Plot Based on Split |
| DBClustDimension | Perform spectral density clustering on single cells |
| DBclust_dimension | Deprecated function(s) in the Seurat package |
| diff.t.test | Deprecated function(s) in the Seurat package |
| 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 |
| dim.plot | Deprecated function(s) in the Seurat package |
| DimPlot | Dimensional reduction plot |
| 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 |
| 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 |
| FeaturePlot | Visualize 'features' on a dimensional reduction plot |
| fetch.data | Deprecated function(s) in the Seurat package |
| FetchData | Access cellular data |
| 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 |
| FindMarkers | Gene expression markers of identity classes |
| FindMarkersNode | Gene expression markers of identity classes defined by a phylogenetic clade |
| 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 |
| get.centroids | Deprecated function(s) in the Seurat package |
| GetCentroids | Get cell centroids |
| getNewScore | Deprecated function(s) in the Seurat package |
| getWeightMatrix | Deprecated function(s) in the Seurat package |
| HeatmapNode | Node Heatmap |
| ICA | Run Independent Component Analysis on gene expression |
| ica | Deprecated function(s) in the Seurat package |
| ica.plot | Deprecated function(s) in the Seurat package |
| ICAPlot | Plot ICA map |
| ICHeatmap | Independent component heatmap |
| icHeatmap | Deprecated function(s) in the Seurat package |
| 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 |
| 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 |
| KClustDimension | Perform spectral k-means clustering on single cells |
| Kclust_dimension | Deprecated function(s) in the Seurat package |
| kMeansHeatmap | Deprecated function(s) in the Seurat package |
| LogNormalize | Normalize raw data |
| 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 |
| mean.var.plot | Deprecated function(s) in the Seurat package |
| MeanVarPlot | Identify variable genes |
| MergeNode | Merge subchilden of a node |
| MergeSeurat | Merge Seurat Objects |
| NegBinomDETest | Negative binomial test for UMI-count based data |
| PCA | Run Principal Component Analysis on gene expression |
| 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 |
| PCAFast | Run Principal Component Analysis on gene expression using IRLBA |
| 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 | Visualize expression/dropout curve |
| 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 |
| print.pca | Deprecated function(s) in the Seurat package |
| PrintPCA | Print the results of a PCA analysis |
| project.pca | Deprecated function(s) in the Seurat package |
| project.samples | Deprecated function(s) in the Seurat package |
| ProjectPCA | Project Principal Components Analysis onto full dataset |
| Read10X | Load in data from 10X |
| refined.mapping | Deprecated function(s) in the Seurat package |
| RefinedMapping | Quantitative refinement of spatial inferences |
| RegressOut | Regress out technical effects and cell cycle |
| regulatorScore | Deprecated function(s) in the Seurat package |
| removePC | Deprecated function(s) in the Seurat package |
| rename.ident | Deprecated function(s) in the Seurat package |
| RenameIdent | Rename one identity class to another |
| reorder.ident | Deprecated function(s) in the Seurat package |
| ReorderIdent | Reorder identity classes |
| RunDiffusion | Run t-distributed Stochastic Neighbor Embedding |
| RunTSNE | Run t-distributed Stochastic Neighbor Embedding |
| run_diffusion | Deprecated function(s) in the Seurat package |
| run_tsne | Deprecated function(s) in the Seurat package |
| SampleUMI | Sample UMI |
| ScaleData | Scale and center 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 |
| SetIdent | Set identity class information |
| Setup | Setup Seurat object |
| setup | Deprecated function(s) in the Seurat package |
| seurat | The Seurat Class |
| seurat-class | The Seurat Class |
| Seurat-deprecated | Deprecated function(s) in the Seurat package |
| spatial.de | Deprecated function(s) in the Seurat package |
| StashIdent | Set identity class information |
| SubsetCells | Return a subset of the Seurat object |
| subsetCells | Deprecated function(s) in the Seurat package |
| SubsetData | Return a subset of the Seurat object |
| subsetData | Deprecated function(s) in the Seurat package |
| 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 |
| tsne.plot | Deprecated function(s) in the Seurat package |
| TSNEPlot | Plot tSNE map |
| ValidateClusters | Cluster Validation |
| ValidateSpecificClusters | Specific Cluster Validation |
| viz.ica | Deprecated function(s) in the Seurat package |
| viz.pca | Deprecated function(s) in the Seurat package |
| VizClassification | Highlight classification results |
| 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 |