Loss of relevant cell cluster with low-RNA content after cell bender #428
Description
Hi
I have a dataset with 3 patients that I have analyzed wihtout cellbender in the past. Is is mainly composed of tumor cells, a small CAF and a small immune_cell cluster. When I apply cell_bender, to eahc patient individually, I verify that besides excluding some tumor cells, it mainly excludes the immune cells. I am afraid this is due to the fact that they have lower RNA content.
Has anyone experienced this problem of exclusion of real but low-content cells, such as immune cells, fibroblasts, or other small populations, especially if their RNA content is low compared to tumor cells?
my dataset and paramenters used:
