All the rnaseq data simulation stuff I've found seems to be based on simulating reads, and applying a full analysis stack to those simulated reads.

I'd prefer to simulate the counts matrix directly.

Is there a package to generate synthetic counts data for testing/comparing rnaseq analysis software?

The following link gives complete code for the simulations presented in the voom paper:

  http://bioinf.wehi.edu.au/voom/