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SMNN: Batch Effect Correction for Single-cell RNA-seq data via Supervised Mutual Nearest Neighbor Detection

By Yuchen Yang, Gang Li, Huijun Qian, Kirk C. Wilhelmsen, Yin Shen, Yun Li

Posted 17 Jun 2019
bioRxiv DOI: 10.1101/672261 (published DOI: 10.1093/bib/bbaa097)

Batch effect correction has been recognized to be indispensable when integrating single-cell RNA sequencing (scRNA-seq) data from multiple batches. State-of-the-art methods ignore single-cell cluster label information, but such information can improve effectiveness of batch effect correction, particularly under realistic scenarios where biological differences are not orthogonal to batch effects. To address this issue, we propose SMNN for batch effect correction of scRNA-seq data via supervised mutual nearest neighbor detection. Our extensive evaluations in simulated and real datasets show that SMNN provides improved merging within the corresponding cell types across batches, leading to reduced differentiation across batches over MNN, Seurat v3, and LIGER. Furthermore, SMNN retains more cell type-specific features, partially manifested by differentially expressed genes identified between cell types after SMNN correction being biologically more relevant, with precision improving by up to 841%. ### Competing Interest Statement The authors have declared no competing interest.

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