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Deep learning enables accurate clustering and batch effect removal in single-cell RNA-seq analysis

By Xiangjie Li, Yafei Lyu, Jihwan Park, Jingxiao Zhang, Dwight Stambolian, Katalin Susztak, Gang Hu, Mingyao Li

Posted 25 Jan 2019
bioRxiv DOI: 10.1101/530378

Single-cell RNA sequencing (scRNA-seq) can characterize cell types and states through unsupervised clustering, but the ever increasing number of cells imposes computational challenges. We present an unsupervised deep embedding algorithm for single-cell clustering (DESC) that iteratively learns cluster-specific gene expression signatures and cluster assignment. DESC significantly improves clustering accuracy across various datasets and is capable of removing complex batch effects while maintaining true biological variations.

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