There's a beta version of an edgeR/deseq/voom wrapper and a companion htseq based count matrix maker in the test toolshed statistics section owned by me - fubar. Definitely not quite ready for production but installable and I'd appreciate feedback from anyone brave enough to try them out. Best installed on a test instance you plan on destroying because the R 3.0 dependency is about to swap over to Bjorns better one - should be done later this week when I get some time. 

Be warned it takes a long time to auto-install - 10-15 minutes or so on my laptop.