Function reference • SeuratExtend

All functions
`BarOfCluster()`	Cluster proportion bar plot
`BuildAUCRank()`	Build AUCell Rank
`CalcScoreGeneral()` `CalcScoreGeneral_v3()` `ScoreAndOrder()`	CalcScoreGeneral, ScoreAndOrder
`CalcStats()`	Calculate Matrix Statistics Grouped by Clusters
`Cellrank.Compute()` `Cellrank.Plot()`	Compute and Visualize Cell Trajectories Using CellRank
`ClusterDistrBar()`	Cluster proportion bar plot
`DimPlot2()`	Create an Enhanced Dimensional Reduction Plot
`DotPlot2()`	Enhanced Dot Plot for Single-Cell Data Visualization
`FeaturePlot3.grid()`	Simultaneous Visualization of Three Features on a Grid of Plots
`FeaturePlot3()`	Simultaneous Visualization of Three Features in a Single Plot
`FilterGOTerms()` `FilterReactomeTerms()`	Filter GO/Reactome Gene Sets
`GSEAplot()`	GSEA plot
`GeneSetAnalysis()` `GeneSetAnalysisGO()` `GeneSetAnalysisReactome()`	Gene Set Enrichment Analysis
`GeneTrendCurve.Palantir()` `GeneTrendCurve.Slingshot()`	Visualize Gene Expression Dynamics Along Differentiation Trajectories
`GeneTrendHeatmap.Palantir()` `GeneTrendHeatmap.Slingshot()`	Visualize Gene Expression Dynamics Along Trajectories with Heatmaps
`Heatmap()`	Heatmap
`ImportPyscenicLoom()`	Import SCENIC Loom Files into Seurat
`Palantir.Magic()`	Run MAGIC for Gene Expression Smoothing
`Palantir.RunDM()` `Palantir.Pseudotime()`	Run Palantir Diffusion Map and Calculate Pseudotime
`RenameGO()` `RenameReactome()`	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
`SearchDatabase()`	Search Pathways in GO/Reactome Database
`SearchPathways()`	Search Pathways in a Given Geneset List
`StackedViolin()` `StackedViolin_v3()`	StackedViolin
`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
`adata.Load()` `adata.Save()` `adata.AddDR()` `adata.AddMetadata()` `adata.LoadLoom()` `Seu2Adata()` `Seu2Loom()`	Seurat to AnnData Conversion and Management Tools
`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
`feature_percent()`	Proportion of features
`HumanToMouseGenesymbol()` `MouseToHumanGenesymbol()` `EnsemblToGenesymbol()` `GenesymbolToEnsembl()`	Gene Naming Conversion Functions
`ryb2rgb()`	Mix RYB color
`save_colors()`	Save Custom Color Settings to a Seurat Object
`scVelo.SeuratToLoom()` `scVelo.RunBasic()`	(Deprecated) Export Seurat Object and Velocyto Data to Loom for scVelo Analysis
`scVelo.SeuratToAnndata()` `scVelo.Plot()`	Convert Seurat Object to AnnData and Generate scVelo Plots for Single-Cell RNA Velocity Analysis
`show_col2()`	Display Multiple Color Palettes in a Grid Layout
`theme_umap_arrows()`	Add Simplified Axis Indicators to ggplot

Reference

All functions