You are correct that SerDes bus analysis is quite different from DDR. HyperLynx SI has very good functions for PCIe analysis, too. First, you can export S parameters of a diff pair channel and run some specification checks in the Touchstone Viewer. Check out this short video on Support Center.
Beyond that, you can run fast eye diagram simulations either with or without an IBIS-AMI model.
If you have an IBIS-AMI model, look at this webinar.
If you do not have IBIS-AMI models, but some other buffer model for simulation then look at this short video about the FastEye Wizard.