Minimum number of cells for scVI?

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!

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?


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!