2.2 years ago by
Cuffdiff inputs are compatible with cummeRbund as wrapped for Galaxy. I am not personally familiar enough with the tech requirements of Rstudio to comment on the compatibility with the stand-alone version with a definitive answer (but someone else reading may be).
We plan to test this specifically (Galaxy Cdiff output with stand-alone Rstudio, would be good to know), but don't wait for us. Going forward with your own testing is the quickest path to work out usage for 3rd party apps not integrated into Galaxy. Perhaps just try the SQlite to see if that works?
I can let you know that Galaxy-Rstudio integration has some development in progress, but it is not ready for use by most. Implementation is "non trivial" according to the developers working on this and would be best on a local if you want to give it a go.
"These instructions should cover setting up RStudio and IPython for 15.07 or later https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/interactive_environments.rst" via jmchilton
Hopefully this helps you to move forward! Jen, Galaxy team