- decoupler.get_collectri(organism: str | int = 'human', split_complexes=False, **kwargs) DataFrame
CollecTRI gene regulatory network.
Wrapper to access CollecTRI gene regulatory network. CollecTRI is a comprehensive resource containing a curated collection of transcription factors (TFs) and their target genes. It is an expansion of DoRothEA. Each interaction is weighted by its mode of regulation (either positive or negative).
The organism of interest: either NCBI Taxonomy ID, common name, latin name or Ensembl name. Organisms other than human will be translated from human data by orthology.
Whether to split complexes into subunits. By default complexes are kept as they are.
Passed to omnipath.interactions.CollecTRI.get.
Dataframe in long format containing target genes for each TF with their associated weights, and if available, the PMIDs supporting each interaction.