1. A method to enable assessment of a significance of a network perturbation amplitude (NPA) score with respect to a treated and control contrast, the method comprising: resampling experimental replicates for each of the treated and control conditions one or more times; for each resampling, computing an NPA score using a machine having a hardware element; plotting, as a distribution, the NPA scores computed from the resampled experimental replicates; and identifying a confidence interval for each contrast from the distribution.