Measure transcriptomic cell similarities between experimental groups in Single-cell RNAseq

Question

[sc-ruzafa]

Hello!

I am working on a project where we have scRNA-seq data from organoids from 3 different experimental conditions (Control, condition A and condition B). We want to measure the "similarity" at a transcriptomic level between control cells vs both conditions cells and study what condition is more similar to the control cells.

Thanks in advance

sc-ruzafa

Answer 1

[Trivas]

My guess is you would cluster your cells by cell type then make a correlation matrix of gene counts within each cell type comparing condition A to your control.