decoupler.get_collectri

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).

Parameters:

organismstr

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.

split_complexesbool

Whether to split complexes into subunits. By default complexes are kept as they are.

kwargs

Passed to omnipath.interactions.CollecTRI.get.

Returns:

ctDataFrame

Dataframe in long format containing target genes for each TF with their associated weights, and if available, the PMIDs supporting each interaction.