mantispy.tl.gene_set_network#

mantispy.tl.gene_set_network(source='hallmark', organism='human')[source]#

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.