Assess if normalized or not

Help scvi-tools
1

Hi,
we are currently writing some (in-house) code for scRNA and we want to check if the counts are normalized or not. I remember that you raised a flag there if it is normalized.
How do you do that?
Which function would it be to check and get some inspiration?

Thanks

2

You can see what we do here.

It’s not cheap to check every entry, especially if it’s a dense matrix. There’s also fancy things you can do with vectorized numba functions, like use them in a numpy style like array.is_not_count(axis=1), but we didn’t go all out with this.

1 Like