decoupler.get_collectri

decoupler.get_collectri(organism: str | int = 'human', split_complexes=False, genesymbol_resource: Literal['uniprot', 'ensembl'] | dict[str, set[str]] | bool | None = None, **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.

genesymbol_resourcestr

Resource to query for Gene Symbols. Either “uniprot” or “ensembl”, or a dictionary with UniProt IDs as keys and sets of Gene Symbols as values. If None, the Gene Symbols provided by the web service will be left intact. If False, the Gene Symbols will be dropped and UniProt IDs will be used instead.

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.