Conduct SCANVI after running SysVI on multi-platform data

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1

Hi,

I really appreciate the power of SysVI to correct large batch effects between different platforms. Once SysVI has been run between a reference on one platform and an unnanoted dataset on a second platform, how can we run SCANVI to conduct cell type labeling?

Thank you

Cristian

2

Hi, this is not supported and would require actually establishing the model, e.g. cycle-consistency loss should be guaranteed to provide same cell-type label. However, you can run a simple kNN classifier in latent space as done in our tutorials to perform cell-type transfer, see e.g. https://www.biorxiv.org/content/10.1101/2024.09.19.613883v3

3

Thank you very much, will try knn since sysVI did a much better job of integrating the datasets than anything else I tried.

Best regards

Cristian

4

For completeness, Querying the Human Lung Cell Atlas — scvi-tools provides a tutorial for a kNN classifier.