Understanding how to use the database files and extract a simple ligand/receptor table

Teichlab / cellphonedb

MIT License

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Understanding how to use the database files and extract a simple ligand/receptor table #342

Closed nathanin closed 2 years ago

nathanin commented 2 years ago

Hello, I'm looking for a simple table with curated ligand/receptor pairs (+ligands/receptor complexes composed of several gene products). Is it possible to create such a table from the files saved at ~/.cpdb/releases/v2.0.0 by the command cellphonedb database download --version latest? Thanks for all the great work creating this amazing resource!

Zaein commented 2 years ago

Did you ever figure this out @nathanin?

nathanin commented 2 years ago

@Zaein I haven't spent much time with this yet but there is this "omnipath" database that includes cellphonedb, and others and sounds straightforward to work with.

https://github.com/saezlab/omnipath