Man pages for gcday/seurat_fresh
Tools for Single Cell Genomics
| AddMetaData | Add in metadata associated with either cells or features. |
| AddModuleScore | Calculate module scores for feature expression programs in... |
| ALRAChooseKPlot | ALRA Approximate Rank Selection Plot |
| AnchorSet-class | The AnchorSet Class |
| as.CellDataSet | Convert objects to CellDataSet objects |
| as.Graph | 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 |
| Assay-class | The Assay Class |
| as.Seurat | Convert objects to Seurat objects |
| as.SingleCellExperiment | Convert objects to SingleCellExperiment objects |
| as.sparse | Convert between data frames and sparse matrices |
| AugmentPlot | Augments ggplot2-based plot with a PNG image. |
| AverageExpression | Averaged feature expression by identity class |
| BarcodeInflectionsPlot | Plot the Barcode Distribution and Calculated Inflection... |
| BuildClusterTree | Phylogenetic Analysis of Identity Classes |
| CalculateBarcodeInflections | Calculate the Barcode Distribution Inflection |
| CaseMatch | Match the case of character vectors |
| cc.genes | Cell cycle genes |
| CellCycleScoring | Score cell cycle phases |
| Cells | Get cells present in an object |
| CellScatter | Cell-cell scatter plot |
| CellSelector | Cell selector |
| CollapseSpeciesExpressionMatrix | Slim down a multi-species expression matrix, when only one... |
| CombinePlots | Combine ggplot2-based plots into a single plot |
| Command | 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 |
| DefaultAssay | Get and set the default assay |
| DietSeurat | Slim down a Seurat object |
| DimHeatmap | Dimensional reduction heatmap |
| DimPlot | Dimensional reduction plot |
| DimReduc-class | The Dimmensional Reduction Class |
| DoHeatmap | Feature expression heatmap |
| DotPlot | Dot plot visualization |
| ElbowPlot | Quickly Pick Relevant Dimensions |
| Embeddings | 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 |
| 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 |
| FindClusters | Cluster Determination |
| FindConservedMarkers | Finds markers that are conserved between the groups |
| FindIntegrationAnchors | Find integration anchors |
| FindMarkers | Gene expression markers of identity classes |
| FindNeighbors | SNN Graph Construction |
| FindTransferAnchors | Find transfer anchors |
| FindVariableFeatures | Find variable features |
| GetAssay | Get an Assay object from a given Seurat object. |
| GetAssayData | General accessor function for the Assay class |
| GetIntegrationData | Get integation data |
| GetResidual | Calculate pearson residuals of features not in the scale.data |
| Graph-class | The Graph Class |
| h5ad | Read from and write to h5ad files |
| HoverLocator | Hover Locator |
| HTODemux | Demultiplex samples based on data from cell 'hashing' |
| HTOHeatmap | Hashtag oligo heatmap |
| HVFInfo | Get highly variable feature information |
| Idents | Get, set, and manipulate an object's identity classes |
| IntegrateData | Integrate data |
| IntegrationData-class | The IntegrationData Class |
| JackStraw | Determine statistical significance of PCA scores. |
| JackStrawData-class | The JackStrawData Class |
| JackStrawPlot | JackStraw Plot |
| JS | Get JackStraw information |
| Key | Get a key |
| L2CCA | L2-Normalize CCA |
| L2Dim | L2-normalization |
| LabelClusters | Label clusters on a ggplot2-based scatter plot |
| LabelPoints | Add text labels to a ggplot2 plot |
| Loadings | 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 |
| merge.Seurat | Merge Seurat Objects |
| MetaFeature | Aggregate expression of multiple features into a single... |
| MinMax | Apply a ceiling and floor to all values in a matrix |
| Misc | Access miscellaneous data |
| MixingMetric | Calculates a mixing metric |
| MULTIseqDemux | Demultiplex samples based on classification method from... |
| NormalizeData | Normalize Data |
| oldseurat-class | The Seurat Class |
| OldWhichCells | Identify cells matching certain criteria |
| pbmc_small | A small example version of the PBMC dataset |
| PCASigGenes | Significant genes from a PCA |
| PercentageFeatureSet | Calculate the percentage of all counts that belong to a given... |
| PlotClusterTree | Plot clusters as a tree |
| PolyDimPlot | Polygon DimPlot |
| PolyFeaturePlot | Polygon FeaturePlot |
| print.DimReduc | Print the results of a dimensional reduction analysis |
| Project | Get and set project information |
| ProjectDim | Project Dimensional reduction onto full dataset |
| 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 |
| RelativeCounts | Normalize raw data to fractions |
| RenameCells | Rename cells |
| RidgePlot | Single cell ridge plot |
| RunALRA | Run Adaptively-thresholded Low Rank Approximation (ALRA) |
| RunCCA | Perform Canonical Correlation Analysis |
| RunICA | Run Independent Component Analysis on gene expression |
| RunLSI | Run Latent Semantic Indexing on binary count matrix |
| RunPCA | Run Principal Component Analysis |
| RunTSNE | Run t-distributed Stochastic Neighbor Embedding |
| RunUMAP | Run UMAP |
| SampleUMI | Sample UMI |
| ScaleData | Scale and center the data. |
| ScoreJackStraw | Compute Jackstraw scores significance. |
| SCTransform | Use regularized negative binomial regression to normalize UMI... |
| SelectIntegrationFeatures | Select integration features |
| SetAssayData | Setter for multimodal data |
| SetIntegrationData | Set integation data |
| Seurat-class | The Seurat Class |
| SeuratCommand-class | The SeuratCommand Class |
| Seurat-package | Tools for single-cell genomics |
| SeuratTheme | Seurat Themes |
| SplitObject | Splits object into a list of subsetted objects. |
| Stdev | Get the standard deviations for an object |
| StopCellbrowser | Stop Cellbrowser web server |
| SubsetByBarcodeInflections | Subset a Seurat Object based on the Barcode Distribution... |
| SubsetData | Return a subset of the Seurat object |
| subset.Seurat | Subset a Seurat object |
| TF.IDF | Term frequency-inverse document frequency |
| Tool | Get and set additional tool data |
| TopCells | Find cells with highest scores for a given dimensional... |
| TopFeatures | Find features with highest scores for a given dimensional... |
| TransferData | Transfer Labels |
| UpdateSeuratObject | Update old Seurat object to accomodate new features |
| VariableFeaturePlot | View variable features |
| VariableFeatures | Get and set variable feature information |
| VizDimLoadings | Visualize Dimensional Reduction genes |
| VlnPlot | Single cell violin plot |
| WhichCells | Identify cells matching certain criteria |
