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scVI vs Harmony, which is better for cell type based clustering in brain tissue?

Hello, I have a post-mortem dataset with 50+ donors. I do not have a brain region specific reference so I cannot use scANVI. I was wondering whether scVI or Harmony would be better in my case? I know both are good and available in python.

Thanks

harmony scvi single cell
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updated by ATpoint ATpoint • written by biotrekker • biotrekker

1 answer

There is no "better" is my experience. It always depends on the dataset. Try both and integrate your biological knowledge to decide which makes more sense. I always go with harmony first (and fastMNN from batchelor second) as it is fast and usually sufficient.

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written by ATpoint ATpoint

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