Multiplexed error-robust fluorescence in situ hybridization is a highly multiplexed version of smFISH. It uses combinatorial labeling, followed by imaging, and then error-resistant encoding to capture a high number of RNA molecules and spatial localization within the cell. The capture of a large number of RNA molecules enables elucidation of gene regulatory networks, prediction of function of unannotated genes, and identification of RNA molecule distribution patterns, which correlate with their associated proteins.