decoupler.get_dorothea

decoupler.get_dorothea(organism='human', levels=['A', 'B', 'C'], weight_dict={'A': 1, 'B': 2, 'C': 3, 'D': 4})

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
organismstr

Which organism to use. Only human and mouse are available.

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.

Returns
doDataFrame

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