decoupler.op.dorothea

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decoupler.op.dorothea#

decoupler.op.dorothea(organism='human', levels=None, dict_weights=None, license='academic', verbose=False)#

DoRothEA gene regulatory network [GAHI+19].

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:

  • organism (str (default: 'human')) – The organism of interest. By default human.

  • levels (str | list | None (default: None)) – List of confidence levels to return. Goes from A to D, A being the most confident and D being the less.

  • dict_weights (dict | None (default: None)) – 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 (default: 'academic')) – Which license to use, available options are: academic, commercial, or nonprofit. By default, is set to academic to retrieve all possible interactions. Users are expected to comply with license regulations according to their affiliation.

  • verbose (bool (default: False)) – Whether to display progress messages and additional execution details.

Return type:

DataFrame

Returns:

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

Example

import decoupler as dc

do = dc.op.dorothea()
do
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