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saeyslab / nichenetr

NicheNet: predict active ligand-target links between interacting cells
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Inquiry about Signaling and Gene Regulatory Networks Data in Omnipath and NicheNet #249

Closed xuansuyang closed 2 months ago

xuansuyang commented 5 months ago

Firstly, thank you very much for developing this tool. I would like to inquire about the sources in the signaling-network and gr-network, specifically omnipath_ABC, omnipath_D, omnipath_directional, omnipath_undirectional, NicheNet_LT_frequent, and NicheNet_LT_infrequent. I searched in Omnipath and NicheNet but did not find them. Therefore, I would like to ask where these data come from in Omnipath and NicheNet.

csangara commented 2 months ago

You will be able to find the explanation of the model construction of NicheNet v2 in the MultiNicheNet preprint. The part on NicheNetLT(in)frequent is described in Supplementary Note 1. Moreover, the scripts on model construction is also deposited at https://zenodo.org/records/8016880, under NicheNet_V2.zip. For example, you can find how omnipath_ABC was generated under networks/scripts/gene_regulatory/Omnipath/process_omnipath_gr.R.