These are chat archives for jdrudolph/goenrich
goenrichwas never published per se, but used in my publication http://dx.doi.org/10.1016/j.cels.2016.11.005 . I validated it's correctness against Webgestalt, a popular online tool which involves too much mouse clicking for my taste ;-).
goatoolsseems to provide a similar set of tools implemented by a set of custom classes etc... I enjoy using
goenrichfor it's simplicity. It uses data structures which are widely used in the community (
networkx.DiGraph) and provides only the functions you need for the analysis.