Jia, P.; Yang, X.; Yang, X.; Wang, T.; Xu, Y.; Ye, K.

Background: Microsatellite instability (MSI) is an indispensable biomarker in cancer immunotherapy. Currently, MSI scoring methods by high-throughput omics methods have gained popularity and demonstrated better performance than the gold standard method for MSI detection. However, MSI detection method on expression data, especially single-cell expression data is still lacking, limiting the scope of clinical application and prohibiting investigation of MSI at single cell level. Results: Herein, we developed MSIsensor-RNA, an accuracy, robust, adaptable, and standalone software, to detect MSI status by its associated genes\' expression values. We demonstrated the favorable performance and promise of MSIsensor-RNA in both bulk and single-cell gene expression data in multiplatform technologies including RNA-seq, Microarray, and single-cell RNA-seq. Conclusions: MSIsensor-RNA is a versatile, efficient, and robust method for MSI status detection from both bulk and single-cell gene expression data in clinical researches and applications. MSIsensor-RNA is available at https://github.com/xjtu-omics/msisensor-rna.