A new tool is up from the Broad Institute. It is named as GeNets Just had a look to it today. Seems very comprehensive and wide range of things catering to both network and pathway analysis. Also the tutorials and website have a very aesthetic feel. I would like the community to take a look and use it. I tried for my own use but sadly not enough publicly available data sets for kidney but still looks very impressive. There is a tool called QUACK which is based on a ML model for de noising and also seems like one can upload their private data as well.
Simple sign up and dashboard.
The paper can be found here.
Tutorials are available here.
The ML based algorithm QUACK to predict related pathway based on functional networks can be seen in this github link
Hope the community can use it and also enjoy and share.
Update 1: [Date: 06/18/2018] A blog post with a talk.
P.S: Not endorsing and I am not remotely involved with the work. Just found it today in my twitter feed and wanted to share it to the community. I am always a big fan of Broad Institute works but this one seems pretty comprehensive and powerful.