KC-example - scCancer


G-Lab@THU , 2020-03-02 18:55:17

1 Cell statistics

1.1 Cell calling

plot of chunk nUMI

(Hi-res image: left, right)

1.2 The number of UMIs and detected genes in cells

After the cell calling by Cell Ranger V3, we further perform quality control to filter droplets with low quality cells according to nUMI (total number of UMIs) and nGene (total number of detected genes).

For nUMI :

For nGene :

Comment: The suggested thresholds (except the lower bound of nGene, which is set by convention) are determined based on the their distributions. Using them, the outliers identified will be filtered. The same below.

plot of chunk filter

(Hi-res image: left, right)

2 Gene statistics

The number of genes expressed in at least one cell : 21199.

2.1 Mitochondrial genes

Summary of mitochondrial genes percentage (mito.percent) in cells:

##       Min.    1st Qu.     Median       Mean    3rd Qu.       Max. 
## "0.000721" "0.049074" "0.084407" "0.095748" "0.120959" "0.970637"

plot of chunk mito

(Hi-res image: view)

2.2 Ribosome genes

Summary of ribosome genes percentage (ribo.percent) in cells:

##      Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
## "0.00506" "0.18533" "0.22266" "0.22026" "0.25968" "0.52744"

plot of chunk ribo

(Hi-res image: view)

2.3 Dissociation associated genes

Summary of dissociation associated genes percentage (diss.percent) in cells:

##     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
## "0.0000" "0.0244" "0.0294" "0.0318" "0.0367" "0.1760"