Speeding up network creation in WGCNA I am following the tutorials on the WGCNA website for creating a coexpression network. It is taking way too long. Is there a way to speed up execution? All I need is to create the co-expression graph. I will then export to Python and do my analysis there. 
In particular, the step "calculating module eigengenes" is taking a lot of time. I do not really care about the modules. All I want is the graph with the genes and the weighted edges.
You can use the "manual network construction" approach. Calculate TOM, then use exportNetworkToCytoscape or exportNetworkToVisANT to export the network (or simply save the TOM matrix as a table and load it in Python).