Daniel Dimitrov

Should we exclude CellTalkDB from curated resources list?

4

@deeenes I keep finding strange interactions that occur as PPIs but not actual CCC and are reported as such in CellTalkDB - e.g. SORBS1-INSR or interactions with SMAD3. Might be...

Currently scanpy is being used as a core dependency of LIANA. However, in reality it's used only in a couple of places, the most problematic being the calculation of DEGs...

Querying Pypath & BioCypher knowledge graph

1

LIANA's resources should be directly accessed via Pypath. Extensive PK graphs with BioCypher would also allow further refining of results and inference. This is to be added in future updates.

Proper Caching for MetalinksDB & HCOP

2

Currently, downloading and storing resources is quite bare bones: https://github.com/saezlab/liana-py/blob/main/liana/resource/_orthology.py https://github.com/saezlab/liana-py/blob/main/liana/resource/get_metalinks.py I should implement proper caching.