GSEA taskforce: a standalone software for user-friendly Gene Set Enrichment Analysis

It is time to push boundaries to see what else can be accomplished by using R. I could never imagine putting together a standalone software to implement a complex and time-consuming algorithm simply by using R. If you think R is not a real-programming language, hopefully this example will make you to think again.

While I was working at Broad Institute, two of my colleagues asked me if Single Sample Gene Set Enrichment Analysis could be implemented as a user-friendly software. While there are R-scripts to run the algorithm, not everyone is familiar how to run a script on console and debug the errors. This sounded like a perfect challenge to learn if R-shiny package can be used to run this algorithm.

A typical analysis can take several hours depending on the gene set being used, and deploying a web-based Shiny server was not a practical solution. Instead, I took the painful approach to put together a software package using R-shiny and R-accessories. The resulting application is compressed into a .exe file, and it can be installed and run like any Windows software. The application can even e-mail back to user the results once the tasks are completed. Although there is a lot of room for improvement, it was a great learning experience and a lot of fun to develop this software!