Man pages for alexthiery/scHelper
R package containing helper functions for single cell analysis
| ArchRAddUniqueIdsToSe | ArchR function: Add unique id to se object |
| ArchRCellCounting | ArchR function: Plot table of cell counts from different... |
| ArchRCellCountsHeatmap | ArchR function: Plot heatmap of cell counts |
| ArchR_ClustRes | ArchR function: Plot multiple cluster resolutions |
| ArchR_ExtractIds | ArchR function: Extract IDs for plotting |
| ArchR_ExtractMeansFromSe | ArchR function: Extract mean matrix from se object |
| ArchR_FeaturePlotGrid | ArchR function: Plots grid of featureplots |
| ArchR_IdentifyOutliers | ArchR function: Identify oulier clusters |
| ArchR_PlotMarkerHeatmap | ArchR function: Plots marker heatmap |
| ArchR_PseudoreplicateCounts | ArchR function: Plot table of cell counts in pseudoreplicates |
| ArchR_SplitbyStage | ArchR function: Split by stage |
| ArchR_Subset | ArchR function: Subset ArchR |
| AverageGeneModules | AverageGeneModules |
| BoxPlot | Box Plot |
| CellLabelPieCharts | Cell Labels Pie Charts |
| CheckIntegration | Check Integration |
| ClusterClassification | ClusterClassification |
| ClusterDimplot | Cluster Dimplot |
| ClustRes | Plot multiple cluster resolutions |
| ClustStagePlot | DimPlots of cell stage and cluster identities |
| CreateCellTypeAnnotation | Function to create cell type annotation for Complex peak... |
| CreateStageAnnotation | Function to create stage annotation for Complex peak module... |
| DEGeneModules | Filter gene modules based on differential expression... |
| ElbowCutoff | Elbow Cutoff |
| ExportAntlerModules | Exports antler peak modules |
| ExtractModuleContents | Extract module contents |
| GeneModuleClassify | #' GeneModuleClassify |
| GeneModuleOrder | #' GMOrder |
| GeneModulePheatmap | Function for plotting gene module pheatmap from Seurat object |
| ggPlotColours | Function to access default ggpplot colours used by Seurat... |
| IdentifyOutliers | Identify oulier clusters |
| MultiFeaturePlot | Plot FeaturePlots for a list of genes |
| OrderCellClusters | Automatic ordering of cell clusters based on cluster... |
| PCALevelComparison | PCA level comparison |
| PlotCelltype | PlotCelltype |
| PlotGeneVariance | PlotGeneVariance |
| PlotOutliers | PlotOutliers |
| PrepPeakModuleHeatmap | Function for prep data to plot peak module heatmap using... |
| QCPlot | Generate a QC plot from Seurat metadata |
| SEACells_MetacellFrequencies | SEACells function: Frequency of metacells in each category |
| SEACells_PiechartProportionThreshold | SEACells function: Purity of metacells plotted on piechart |
| SEACells_SummariseGeneScoreMatrix | SEACells function: Summarises gene score counts across... |
| SEACells_SummariseSeuratData | SEACells function: Summarises data from seurat object across... |
| SubsetGeneModules | Subset Antler gene modules based on selected gene list... |
| TenxPheatmap | Function for plotting heatmap from seurat 10x object |
| UMAPGeneList | Generate individual FeaturePlots for given list of genes |
