search

saezlab / ccc_protocols

LIANA x Tensor-cell2cell Protocols
https://ccc-protocols.readthedocs.io
MIT License
1 stars 3 forks source link

Possible to run liana_tensor_c2c function with external_resource/orthologs? #18

Open SteGruener opened 1 month ago

SteGruener commented 1 month ago

Dear developers,

Thank you for this great package and for your extensive effort to properly document it!

I have a question regarding the liana_tensor_c2c function/workflow: Is there somehow an implemented way to combine this with the use of an external resource (gene orthologs), e.g. for using it on mouse data?

All the best, Stephan

hmbaghdassarian commented 1 month ago

Hi Stephan,

For R, check out this tutorial on ortholog mapping. For python, liana has a human consensus 'consensus' and mouse consensus 'mouseconsensus' resource options you can specify in the resource_name argument. You can also map genes as shown here. This is all @dbdimitrov's work, so Daniel correct me if I'm wrong.

For use of custom resources see these sections of our tutorials in Python and R. Let me know if this answers your question.

dbdimitrov commented 1 month ago

Hi, yes you could. Both the R and Python liana packages support conversion /w external orthologues. For R it's the one that Hratch shared, for Python you could check this tutorial.