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saeyslab / nichenetr

NicheNet: predict active ligand-target links between interacting cells
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Data question #224

Closed almaan closed 9 months ago

almaan commented 10 months ago

Hi,

thank you for a great package and resource. I was wondering whether there's a way to extract the information you show in this figure:

image

More specifically: for each L/R-pair, a list of the downstream target(s) that it has an effect on.

I'm pretty confident this should be possible given the different operations/functions that your package provides. I've looked through some of the rds/rda objects in your data folder but am just not sure exactly which objects that should be used and/or combined. Any pointers would be much appreciated.

Thank you again, Alma

csangara commented 9 months ago

Hi Alma,

Unfortunately, there is not an automated way to always get the ligand-receptor-target links. We do have a vignette constructing the signaling pathway from ligand to target (ligand_to_target_signaling_path.md), but as mentioned in #44, receptors may not always be present in these pathways.

Also related issue: #58

almaan commented 9 months ago

Hi @csangara ,

thank you for taking some time to reply, I appreciate it. I'll look into the resources you linked and see whether I can extract the information I'm looking for.

Closing this issue.