Man pages for mayer-lab/SeuratForMayer2018
Seurat : R Toolkit for Single Cell Genomics
| AddImputedScore | Calculate imputed expression values |
| AddMetaData | Add Metadata |
| AddModuleScore | Calculate module scores for gene expression programs in... |
| AddSamples | Add samples into existing Seurat object. |
| AddSmoothedScore | Calculate smoothed expression values |
| AlignSubspace | Align subspaces using dynamic time warping (DTW) |
| AssessNodes | Assess Internal Nodes |
| AssessSplit | Assess Cluster Split |
| AverageDetectionRate | Probability of detection by identity class |
| AverageExpression | Averaged gene expression by identity class |
| AveragePCA | Average PCA scores by identity class |
| BlackAndWhite | A black and white color palette |
| BuildClusterTree | Phylogenetic Analysis of Identity Classes |
| BuildRFClassifier | Build Random Forest Classifier |
| BuildSNN | SNN Graph Construction |
| CalcVarExpRatio | Calculate the ratio of variance explained by ICA or PCA to... |
| CaseMatch | Match the case of character vectors |
| CellCycleScoring | Score cell cycle phases |
| CellPlot | Cell-cell scatter plot |
| ClassifyCells | Classify New Data |
| ColorTSNESplit | Color tSNE Plot Based on Split |
| 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 |
| 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... |
| DimTopGenes | Find genes with highest scores for a given dimensional... |
| DMEmbed | Diffusion Maps Cell Embeddings Accessor Function |
| DMLoad | Diffusion Maps Gene Loading Accessor Function |
| DMPlot | Plot Diffusion map |
| DoHeatmap | Gene expression heatmap |
| DoKMeans | K-Means Clustering |
| DotPlot | Dot plot visualization |
| DotPlotOld | Old Dot plot visualization (pre-ggplot implementation)... |
| 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... |
| FeatureHeatmap | Vizualization of multiple features |
| FeatureLocator | Feature Locator |
| FeaturePlot | Visualize 'features' on a dimensional reduction plot |
| FetchData | Access cellular data |
| FilterCells | Return a subset of the Seurat object |
| 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 |
| FindMarkers | Gene expression markers of identity classes |
| FindMarkersNode | Gene expression markers of identity classes defined by a... |
| FindVariableGenes | Identify variable genes |
| FitGeneK | Build mixture models of gene expression |
| GenePlot | Scatter plot of single cell data |
| GenesInCluster | GenesInCluster |
| 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 |
| HoverLocator | Hover Locator |
| ICAEmbed | ICA Cell Embeddings Accessor Function |
| ICALoad | ICA Gene Loadings Accessor Function |
| ICAPlot | Plot ICA map |
| ICHeatmap | Independent component heatmap |
| ICTopCells | Find cells with highest ICA scores |
| ICTopGenes | Find genes with highest ICA scores |
| InitialMapping | Infer spatial origins for single cells |
| JackStraw | Determine statistical significance of PCA scores. |
| JackStrawPlot | JackStraw Plot |
| JoyPlot | Single cell joy plot |
| KClustDimension | Perform spectral k-means clustering on single cells |
| KMeansHeatmap | Plot k-means clusters |
| LogNormalize | Normalize raw data |
| LogVMR | Calculate the variance to mean ratio of logged values |
| MakeSparse | Make object sparse |
| MarkerTest | ROC-based marker discovery |
| MatrixRowShuffle | Independently shuffle values within each row of a matrix |
| MergeNode | Merge childen of a node |
| MergeSeurat | Merge Seurat Objects |
| MinMax | Apply a ceiling and floor to all values in a matrix |
| MultiModal_CCA | Run Canonical Correlation Analysis (CCA) on multimodal data |
| NegBinomDETest | Negative binomial test for UMI-count based data |
| NegBinomRegDETest | Negative binomial test for UMI-count based data (regularized... |
| NodeHeatmap | Node Heatmap |
| NormalizeData | Normalize Assay Data |
| NumberClusters | Convert the cluster labels to a numeric representation |
| OldDoHeatmap | Gene expression heatmap |
| 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 |
| PCTopCells | Find cells with highest PCA scores |
| PCTopGenes | Find genes with highest PCA scores |
| PlotClusterTree | Plot phylogenetic tree |
| PoissonDETest | Poisson test for UMI-count based data |
| PosteriorPlot | Posterior Plot |
| 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 PCA 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 |
| 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 |
| RefinedMapping | Quantitative refinement of spatial inferences |
| RegressOutResid | Regress out technical effects and cell cycle |
| RemoveFromTable | Remove data from a table |
| RenameIdent | Rename one identity class to another |
| ReorderIdent | Reorder identity classes |
| RunCCA | Perform Canonical Correlation Analysis |
| RunDiffusion | Run diffusion map |
| RunICA | Run Independent Component Analysis on gene expression |
| RunPCA | Run Principal Component Analysis on gene expression using... |
| RunTSNE | Run t-distributed Stochastic Neighbor Embedding |
| 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... |
| 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-deprecated | Deprecated function(s) in the Seurat package |
| show-methods | show method for seurat |
| Shuffle | Shuffle a vector |
| SplitDotPlotGG | Split Dot plot visualization |
| StashIdent | Set identity class information |
| SubsetColumn | Return a subset of columns for a matrix or data frame |
| SubsetData | Return a subset of the Seurat object |
| SubsetRow | Return a subset of rows for a matrix or data frame |
| TobitTest | Differential expression testing using Tobit models |
| TSNEPlot | Plot tSNE map |
| UpdateSeuratObject | Update old Seurat object to accomodate new features |
| ValidateClusters | Cluster Validation |
| ValidateSpecificClusters | Specific Cluster Validation |
| VariableGenePlot | View variable genes |
| VizClassification | Highlight classification results |
| VizDimReduction | Visualize Dimensional Reduction genes |
| VizICA | Visualize ICA genes |
| VizPCA | Visualize PCA genes |
| VlnPlot | Single cell violin plot |
| WhichCells | Identify cells matching certain criteria |
| zfRenderSeurat | Zebrafish analysis functions |
