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