One of the primary ways scientists in this field would like to use to analyze the data coming out of Skyline is with R scripts. We need to work on really tight integration for R scripts as external tools. At the moment, anyone with an R script is forced to write a batch file that runs it.

We should look at both running them directly as command-line tools, as well as integrating the R D-COM component for direct integration with R without requiring a command prompt.

Nick got this working for Meena by calling R.exe directly, which is desirable, when it is so easy to have multiple versions of R installed, and tools dependent on different versions.