Using the output to differentiate between malignant and benign cells

[akiviaho]

Thank you for the great tool! I'm working with some data where clonal populations present are unknown. I'm hoping to use the copy number profiles to differentiate malignant epithelial (copy number altered) cells from benign epithelial cells. I have used all other cell types as reference.

I believe clustering based on the xclone output is the way to go? I'm not however sure which layer in thecombined_final.h5ad data object to use. Any help is much appreciated. Thanks!

[Rongtingting]

hi @akiviaho, thank you! You may find the content in this issue helpful. #16

Bests,
Rongting