Scyan statistical analysis?

[KunHHE]

Hi @quentinblampey, thanks for this message. I know the scyan package is mostly developed for cell type annotation and potential new cell population discovery.

1. May I ask if there is any way for downstream statistical analysis i.e. population proportion comparison between or among different groups?
2. For normal cytometry at least for spectral flow cytometry, the traditional flow cytometry analysis first gate out single cells by getting rid of doublets and gate live cells by live/dead dye. Does the package of scyan can do those as well? Then we go to the cell population gatings based on difference markers.

Thank you!

Kun

[quentinblampey]

Hi @KunHHE,

For any downstream analysis, you can use Scanpy, which should contain all you need.

For the preprocessing, you can use Pytometry. You can also use Scyan, although it's not it's main usage. To do that, you can create a very small table that mimics the preprocessing you want to do. For instance, you can annotate "Immune cells", "Epithelial cell", "Dead cells", ... and then keep only the cell types you're interested in before actually running a precise cell-type annotation.

Hope this helps!