1) is it recommended to run copyKat for a merged count matrix from multiple samples? If so, how do you deal with batch effects?
2) Can I run copykat without annotating cell types? What is the best strategy to identify normal and tumor cells using this tool?
Hi, I have two questions regarding copykat:
1) is it recommended to run copyKat for a merged count matrix from multiple samples? If so, how do you deal with batch effects? 2) Can I run copykat without annotating cell types? What is the best strategy to identify normal and tumor cells using this tool?