Man pages for huayc09/SeuratExtend
SeuratExtend
| activate_python | Activate Python Environment for SeuratExtend |
| adata.Load | Seurat to AnnData Conversion and Management Tools |
| BarOfCluster | Cluster proportion bar plot |
| BuildAUCRank | Build AUCell Rank |
| CalcScoreGeneral | CalcScoreGeneral, ScoreAndOrder |
| CalcStats | Calculate Matrix Statistics Grouped by Clusters |
| Cellrank-Methods | Compute and Visualize Cell Trajectories Using CellRank |
| ClusterDistrBar | Cluster proportion bar plot |
| color_iwh | Default discrete color presets by 'I want hue' |
| color_pro | Professional discrete color presets by 'I want hue' |
| create_condaenv_seuratextend | Create the 'seuratextend' Conda Environment |
| DimPlot2 | Create an Enhanced Dimensional Reduction Plot |
| DotPlot2 | Enhanced Dot Plot for Single-Cell Data Visualization |
| feature_percent | Proportion of features |
| FeaturePlot3 | Simultaneous Visualization of Three Features in a Single Plot |
| FeaturePlot3-grid | Simultaneous Visualization of Three Features on a Grid of... |
| FilterGOTerms | Filter GO/Reactome Gene Sets |
| gene-naming-conversions | Gene Naming Conversion Functions |
| GeneSetAnalysis | Gene Set Enrichment Analysis |
| GeneTrendCurve-Methods | Visualize Gene Expression Dynamics Along Differentiation... |
| GeneTrendHeatmap-Methods | Visualize Gene Expression Dynamics Along Trajectories with... |
| GSEAplot | GSEA plot |
| Heatmap | Heatmap |
| ImportPyscenicLoom | Import SCENIC Loom Files into Seurat |
| Palantir-Magic | Run MAGIC for Gene Expression Smoothing |
| Palantir-Methods | Run Palantir Diffusion Map and Calculate Pseudotime |
| RenameGO | Convert GO/Reactome Pathway IDs to Full Names |
| RunBasicSeurat | Run Standard Seurat Pipeline |
| RunPalantirDiffusionMap | (Deprecated) Run Palantir Diffusion Map |
| RunSlingshot | Calculate Pseudotime and Map Trajectories Using Slingshot |
| ryb2rgb | Mix RYB color |
| save_colors | Save Custom Color Settings to a Seurat Object |
| scVelo.SeuratToAnndata | Convert Seurat Object to AnnData and Generate scVelo Plots... |
| scVelo-SeuratToLoom-and-RunBasic | (Deprecated) Export Seurat Object and Velocyto Data to Loom... |
| SearchDatabase | Search Pathways in GO/Reactome Database |
| SearchPathways | Search Pathways in a Given Geneset List |
| show_col2 | Display Multiple Color Palettes in a Grid Layout |
| StackedViolin | StackedViolin |
| theme_umap_arrows | Add Simplified Axis Indicators to ggplot |
| UniprotToGenesymbol | Convert UniProt IDs to Gene Symbols |
| VlnPlot2 | Enhanced Violin Plot |
| VolcanoPlot | Create a Volcano Plot Comparing Two Groups |
| WaterfallPlot | Waterfall Plot |
| WaterfallPlot_v3 | WaterfallPlot_v3 |
