basic_workflow {scRNAstat}

Basic Workflow

Description

the workflow from Seurat, including: 'NormalizeData','FindVariableFeatures','ScaleData', 'RunPCA','RunTSNE','RunUMAP','FindNeighbors','FindClusters(sce, resolution = seq(0.1,1,by=0.1))' we use 'clustree' to check the different resolution for 'FindClusters'.

Usage

basic_workflow(sce, dir = ".")

Arguments

sce

An object of class Seurat

dir

the path for saving the figures by 'DotPlot' with known famous markers.

Value

list(p1,p2,p3,sce), the last one in the new sce with PCA,tSNE,UMAP information.

Examples

## Not run: 
basic_workflow(AJ064_small_sce,dir=tempdir())

## End(Not run)