decoupler.get_collectri
- decoupler.get_collectri(organism='human', split_complexes=False, license='academic', **kwargs)
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).
- Parameters:
- organismint | str
The organism of interest. By default human.
- split_complexesbool
Whether to split complexes into subunits. By default complexes are kept as they are.
- license: str
Which license to use, available options are: academic, commercial, or nonprofit. By default, is set to academic to retrieve all possible interactions.
- kwargs
Passed to decoupler.translate_net.
- Returns:
- ctDataFrame
Dataframe in long format containing target genes for each TF with their associated weights, and if available, the PMIDs supporting each interaction.