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Find a way to allow users to determine which type of coefficient to use, either the Jaccard, Overlap, or combined, while still using the default.

The easiest way to do this is to probably make it a property of one of the classes, that gets automatically set based on whether using GO or KEGG, but user can modify it.

Given that we are pretty much doing the same thing as EM, why would we bother actually comparing.

The advantage of doing it in R is keeping everything in R, and not having to go between systems. Maybe hype this up in the article.

try out the pie graph visualization, using desaturation to indicate non-significance.

Note that we PROBABLY don't want to just include the sig colors, because that will likely overwhelm the user in the visualization.

do rat vs mouse, and check difference in annotation to see if should do orthologues or not

do UC vs Crohn's

Find a cell type that responds to cancer drug, and does not respond, and do metab to transcript