decoupler.get_progeny

decoupler.get_progeny(organism: str | int = 'human', top: int = 100, **kwargs) → DataFrame

Pathway RespOnsive GENes for activity inference (PROGENy).

Wrapper to access PROGENy model gene weights. Each pathway is defined with a collection of target genes, each interaction has an associated p-value and weight. The top significant interactions per pathway are returned.

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.

topint

Number of genes per pathway to return.

kwargs

Passed to omnipath.requests.Annotations.get.

Returns:

pDataFrame

Dataframe in long format containing target genes for each pathway with their associated weights and p-values.