To facilitate consideration of PAX7 target gene repression in the analysis of FSHD transcriptomic data, we provide a simple pipeline for extraction of PAX7 target gene repression, as well as three validated DUX4 target gene expression biomarkers, from normalized gene level expression data (Supplementary Material, File S1). The gene discussed is DUX4; the disease is facioscapulohumeral muscular dystrophy.