iSMNN: batch effect correction for single-cell RNA-seq data via iterative supervised mutual nearest neighbor refinement

In the current study, we present iSMNN, a supervised batch effect correction method for scRNA-seq data via multiple iterations of mutual nearest neighbor refinement. To validate the performance of iSMNN, we performed single-cell RNA-seq for adult murine heart using 10X Chromium platform. Single-cell RNA-seq profile of cardiac cells isolated at two 10-12 week old mouse was generated by deep sequencing using 10x Genomics Chromium System.