decoupler.op.collectri

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decoupler.op.collectri#

decoupler.op.collectri(organism='human', remove_complexes=False, license='academic', verbose=False)#

CollecTRI gene regulatory network [MullerDTV+23].

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

Parameters:

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

  • remove_complexes (bool (default: False)) – Whether to remove complexes.

  • 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 if available, the PMIDs supporting each interaction.

Example

import decoupler as dc

ct = dc.op.collectri()
ct
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