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abelson-lab / scATOMIC

Pan-Cancer Single Cell Classifier
MIT License
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Mouse tumors? #20

Closed EzequielD-86 closed 7 months ago

EzequielD-86 commented 1 year ago

Hey Team! very nice work, a lot of people talking about it. I have to annotate a lung tumor from mice. Is there any way to do it? I was thinking maybe converting the genes in my Seurat obj to human orthologs? Thank you!

inofechm commented 1 year ago

Hi Ezequeil,

Thank you for your interest in our work and the kind comment! scATOMIC currently is not designed for mouse genomes. However, it is possible to do exactly what you suggested and convert your mouse genes to human orthologs. I am not an expert on the differences between human and mouse when it comes to the genes associations with cell types, so I cannot really comment on the limitations and accuracy. I would also recommend you use the parameter known_cancer_type = "Lung Cancer Cell" in create_summary_matrix() as the models for the cancer types are also exclusively trained on human samples. I believe this workflow can assist with converting to human orthologs: https://www.r-bloggers.com/2016/10/converting-mouse-to-human-gene-names-with-biomart-package/

Let me know if this works, Ido