Minimum number of cells for scVI?

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1

Hi team.

Thank you very much for the great framework. Based on your experience, what would be the minimum number of cells you recommend applying scVI to?

Thank you!

2

We have used datasets in the low thousands of cells successfully.

It’s also important to note how many cells are observed per batch categorical. What are the statistics of your dataset?

3

Hi,

Thanks for your reply and time. I am actually working on a relatively small dataset with 10 batches and ~20 cells for each. So in total, I have ~200 cells.

The experiment throughput in terms of the number of cells is low while the sequencing depth (Uniq-mapped Reads) is ~10M reads.

Do you think scVI would overfit on my dataset?

Thank you!