It seems that Popalign doesn't permission filtering at cell level. In addition, how to integrate analysis with Anndata? Thanks!

[zhuy16]

No description provided.

[sisichen-dev]

Hi @zhuy16! Cell-level filtering is not something that is currently implemented in the software. We also do not have integration with anndata, but I can send you a snippet of code I use to translate an anndata object into a pop object.

Just so you know, PopAlign is not currently a production-ready piece of software -- It was designed to implement the concepts highlighted in the PopAlign PNAS paper. In order to develop the software into a fully supported system, we would need more funding and a bigger team (i.e. more than just me) to make sure all modules can flexibly handle data across many use cases. That being said, I am happy to give you snippets of code that you can rework for your purposes.

[zhuy16]

Hi @sisichen-dev yes, some code translating an anndata object into a pop object would be great. I don't know how do you plan to share, my email is [email protected].
I likes the idea implemented in the Popalign, it is simple and straightforward. In a way that people came from a biological background like me can understand it well :) Hope you will get an chance continue to work on this cool package. Best wishes!