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saezlab / CARNIVAL

CAusal Reasoning for Network Identification with integer VALue programming in R
https://saezlab.github.io/CARNIVAL/
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Feature Request: Omnipath network from original paper #100

Closed josiahbjorgaard closed 2 months ago

josiahbjorgaard commented 4 months ago

Can the omnipath network used in the original paper be provided as part of the repo?

Is it already publically available?

gabora commented 4 months ago

@anikaliu @enio23 @ptrairatphisan

enio23 commented 4 months ago

Hi @josiahbjorgaard ,

On the original paper (https://www.nature.com/articles/s41540-019-0118-z) the Omnipath prior knowledge contained 9306 signed and directed edges connecting 3610 nodes pooled and curated from multiple resources including Signor, Reactome, and Wikipathways.

You can find the omnipath interactions that have been used on the paper release version of CARNIVALhere: https://github.com/saezlab/CARNIVAL/blob/package_paper_version/inst/Ex2_network_SBV_Omnipath.sif.

You can check also on some tutorials on this paper release version of the CARNIVAL package: https://github.com/saezlab/CARNIVAL/tree/package_paper_version.

Cheers, Enio