KC-example - scCancer


G-Lab@THU , 2020-03-02 19:23:10

1 Read data

Read the expression data and filter cells and genes according to quality control steps.

Index Low.threshold High.threshold
nUMI 0 12496.000
nGene 200 3268.000
mito.percent -Inf 0.229
ribo.percent -Inf 0.371
diss.percent -Inf 0.055

2 Data preprocessing

After the quality control, we perform following preprocessing steps based on some functions of the R package Seurat V3.

plot of chunk hvgPlot

(Hi-res image: view)

3 Cells annotation

3.1 Markers expression profile

Here are the scatter plots colored by the normalized expression of some cell type markers.

Cell Type Markers
T cells (CD4+) PTPRC, CD3D, CD4
T cells (CD8+) PTPRC, CD3D, CD8A, CD8B
B cells PTPRC, CD79A
NK cell PTPRC, NKG7
Myeloid cells PTPRC, LYZ
Endothelial PLVAP
Fibroblast ACTA2
Epithelial EPCAM, KRT8