Deem
Analyze time-course data with significance tests, clustering, modeling
...Generate network models, including linear or non-linear models. Variable selection and optimization routines included.
Written in Scala and R. The application is a cross-platform desktop app with a simple GUI and is fully functional currently.
The app was and is developed at the University of Rochester (http://cbim.urmc.rochester.edu) under the GPL 3.0 license. This is a fork of that project.