decoupler.get_progeny

decoupler.get_progeny(organism='human', top=inf, license='academic', **kwargs)

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. By default human.

topint

Number of genes per pathway to return. By default all of them.

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:

pDataFrame

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