efficient onversion back and forth to AnnData

[JM-Bader]

Proteomics data typically contains Protein intensity across samples (matrix X), with extra variable annotations (var, ie. protein annotation) and observation annotations (obs, ie sample annotations). a very efficient way of storing this in a single object is Anndata objects.

https://anndata.readthedocs.io/en/latest/

I use them alot and would like to efficiently input them into alphapeptstats and out of it (e.g. applying a transformation in alphapeptstats and then exporting it as modified Anndata object)

Note that metadata is already perfectly matched in the AnnData object, both for variables and observations.

Can you make input and output between alphapeptstats and AnnData objects efficient?

[josenimo]

I really like this idea, voting for visibility 👍