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＜正＞Exploiting crop germplasm with multi-omics data can greatly enhance the power of gene discovery and interpret the genetic relations of genes. Here, we present MODAS （Multi-Omics Data Association Studies） software, freely available at https://modasbio.github.io/, to cope with high dimensional, noisy, and heterogeneous features typical of multi-omics data with advanced machine learning and statistical methods. MODAS features four analytical modules with extraordinary computing efficiency （Fig. S1 online）.