Reconstruct Gene Networks Using Shiny
Check out the application! http://trestletech.com:3838/grn/
We’ve been experimenting with RStudio’s new Shiny software as a way to quickly and easily create interactive, responsive web applications which are able to leverage complicated analytics back-ends built in the R programming language.
We created a simple interface which can infer the structure of an underlying Gene Regulatory information based on gene expression patterns; the application is available at http://trestletech.com:3838/grn/. (At the time of writing, Shiny’s file upload functionality is highly unstable and may not work from your machine — hopefully improvements to the project will resolve the issues shortly.)
I’m using Shiny/Glimmer to handle all web traffic, and ENA to wrap GeneNet to do the actual network inference (more methods could easily be added later). I used D3’s Force Layout to provide some interactive network visualization — I don’t know that it’s really the most practical way to view the data, but it’s some fun eye-candy.
I had stumbled through a few un-documented features of Shiny (app-specific
www directories, JS to handle custom Shiny outputs, fileInput() for uploading data, etc.) — if you find yourself in the same boat, all my source is available on Github here if anyone’s interested.