I currently work on mouse model of bladder cancer xenium data. How can identify tumor vs normal cells in each sample. I already did some manual curation of marker genes for some cell types but I am looking for more specific approach.
A few thoughts and questions. What's your model? Has a mutation been introduced in a specific cell type or lineage? If so, you may be able to genotype it on a per-cell basis with vartrix. May not tell you if they're necessarily malignant or not, but it can be informative assuming the coverage is half-decent.
As others have mentioned, getting a pathologist to look at the slide is probably the simplest approach.
Depending on resolution, I imagine running inferCNV on each dot would get you pretty close given how mangled cancer cells often are if you have a section you know is "normal" to use as reference. Again, this may or may not work well for your model depending what it actually is.
Thank you for suggestion. I actually came across this tool Sctype https://www.nature.com/articles/s41467-022-28803-w which actually uses vartix and i think it can be trusted. inferCNV can be good option too validate the results.
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Are you looking to classify human vs mouse cells?
No these are only mouse samples. We are trying to develop a method for induction of bladder cancer in mouse and these samples are taken at different time points to investigate the tumor development.