basic_workflow

<p>the path for saving the figures by `DotPlot` with known famous markers.</p>

<p>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`.</p>

A pipeline that can process single or multiple Single Cell RNAseq
samples primarily specializes in Clustering and Dimensionality Reduction.
Meanwhile we use common cell type marker genes for T cells, B cells, Myeloid cells,
Epithelial cells, and stromal cells (Fiboblast, Endothelial cells, Pericyte,
Smooth muscle cells) to visualize the Seurat clusters, to facilitate labeling
them by biological names. Once users named each cluster, they can evaluate the
quality of them again and find the de novo marker genes also.

Yonghe Xia

scRNAstat

basic_workflow: Basic Workflow

Description

Usage

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Examples