How to distinguish malignant vs non-malignant cells based on gene expression data?

Question

[jabbari.parnian]

Hi all,

I have a data set of scRNA-seq of a tumor bulk which consists of malignant and non-malignant cells. I was wondering how I can distinguish these cells based on single cell expression profiles?

Thanks,

[piyushjo]

You can find the logic in various papers. For example, in neuronal cancers microglia and enothelial celsl would be non-malignant? Depends on the cancer type also. You also have to have knowledge about the wild type tissue composition.

[jabbari.parnian]

I am trying to retrieve data of endothelial cells in a malignant tumor, I was thinking of using SINCERA but I have problem installing its package in R

[piyushjo]

You can use general endothelial markers. Reading some related papers will give you an idea. Ask more specific question like how to do analysis rather than a conceptual question. Different people will address it differently, and ask about problems you are facing in that specific algorithm.Just my opinion.

Answer 1

[Kevin Blighe]

Hi jabbari,

Please go through the Seurat vignettes: SEURAT - R toolkit for single cell genomics.

Best of luck with it!

Kevin