mantispy.tl.gene_sets

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mantispy.tl.gene_sets#

mantispy.tl.gene_sets(source='hallmark', organism='human')#

Fetch a gene-set network, or read one from a GMT file.

Parameters:

  • source (str (default: 'hallmark')) – One of SOURCES, or a path ending in .gmt. "hallmark" (50 broad programs) is a good default for a morphological screen.

  • organism (str (default: 'human')) – Passed to the OmniPath resource.

Return type:

DataFrame

Returns:

A frame with source, target and weight. Unweighted resources get weight = 1.0.

Raises:

ValueError – source is neither one of SOURCES nor a path to a .gmt file.

Notes

Named resources are downloaded on first use and cached by decoupler.

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