decoupler.get_dorothea

decoupler.get_dorothea(organism='human', levels=['A', 'B', 'C'], weight_dict=None, license='academic', **kwargs) → DataFrame

DoRothEA gene regulatory network.

Wrapper to access DoRothEA gene regulatory network. DoRothEA is a comprehensive resource containing a curated collection of transcription factors (TFs) and their target genes. Each interaction is weighted by its mode of regulation (either positive or negative) and by its confidence level.

Parameters:

organismint | str

The organism of interest. By default human.

levelslist

List of confidence levels to return. Goes from A to D, A being the most confident and D being the less.

weight_dictdict

Dictionary of values to divide the mode of regulation (-1 or 1), one for each confidence level. Bigger values will generate weights close to zero.

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:

doDataFrame

Dataframe in long format containing target genes for each TF with their associated weights and confidence level.