Man pages for Morriseylab/scExtras
Single cell data analysis helper functions
| BiGenePlot | bi_getValues utility function. |
| celltypeVlnPlot | Function to plot multiple genes in a single Violin plot |
| ClusterDR | Run all Dimension Reduction methods and find marker genes... |
| CurvePlot | CurvePlot Deprecated, Please use lineageDimPlot |
| DimPCAPlot | Plot Pairwise PCA plots. |
| DotPlotTopGenes | Plot dotplot of top n genes |
| getClusterMarkers | Get marker genes for the given cluster |
| getMaxDim | Get maximum number of PC dimensions |
| getSDS | getSDS Plot Slingshot Curves |
| HeatMapTopGenes | Plot heatmap of top n genes |
| lineageDimPlot | lineageDimPlot Plot Slingshot Curves |
| LineageFeaturePlot | LineageFeaturePlot Plot Slingshot Curves |
| make3dPlot | Create a 3D plot |
| PCAPwPlot | Plot Pairwise PCA plots. |
| PCATools | Run PCA and Jackstaw and plots. |
| plotLineageHeatMap | Plot heatmap of the pseudotime data |
| plotLineangeGene | Plot heatmap of the pseudotime data |
| plotLRHeatmap | Create ligand receptor heatmap plot |
| plotLRnetwork | Create ligand receptor network plot |
| processExper | Preprocess single cell RNA-seq data with seurat and return... |
| projectname-Project-name | Create Seurat object from 10x output |
| RunDiffusion | Run Diffusion map |
| RunDoubletfinder | Function to run doublet finder |
| RunLigRec | Get ligand receptor pairs between all clusters |
| runPseudoTimeDGE | run Psuedotime Diff Expression |
| RunQC | Perform QC on single cell RNA-seq data with seurat, store all... |
| runSlingshot | run Slingshot |
| runtopgene | Run topGene API and convert it to enrichResult |
| sampleBarGraph | Plot a stacked bar graph of |
| setSDS | setSDS Plot Slingshot Curves |
| SplitMetaPlot | Function to plot |
