Hi,

Is it possible to run any of ToPASeq's: TopologyGSA, DEGraph, clipper, SPIA, TAPPA, PRS, PWEA with a custom list of fold-changes and associated p-values rather than having these functions run a DE analysis internally?

It doesn't seem so from the manual but that would be very helpful.

Your question is hard to understand. Can you elaborate or provide some simulated, or example data? What do you mean by 'custom' FCs and their associated p-value...do you mean simulated data?