Noncoding RNAs (ncRNAs) play key roles in cancer initiation, promotion, and progression via regulating the expression of critical genes. Existing methods performed simple bivariate analysis on each pair of ncRNA and gene separately without considering the complex interactions among ncRNAs and genes. We developed a statistically rigorous and computationally efficient software tool to identify essential ncRNA-gene regulatory pairs from transcriptome-wide ncRNA and gene expression data. Here we provide a practical guidance with real data examples on the use of the tool implemented in the R package “NGP.”