decoupler.op.hallmark

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decoupler.op.hallmark#

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

Hallmark gene sets [LSP+11].

Hallmark gene sets summarize and represent specific well-defined biological states or processes and display coherent expression.

Parameters:

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

  • 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 the hallmark gene sets.

Example

import decoupler as dc

hm = dc.op.hallmark()
hm
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