How can I use R/BioConductor from Taverna?

Bundled with Taverna you will find a RShell processor under Local services. The processor works in a similar way to the Beanshell processor, you specify input ports and output ports, which are available as variables inside the script, which you can either edit directly in the processor configuration or open from a file.

However, the actual execution is done by sending the script to an R execution server. To use RShell you need to install (preferably locally) R, the R execution server called RServe, and the R-libraries needed, such as BioConductor. We recommend that you configure your RServe to run on localhost only, preferably as a separate user, and with access allowed using some non-important username/password.

There's a short introduction available from University of Twente, although it's slightly outdated. An updated version of this tutorial will probably be a part of a future Taverna manual.