Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq

Systematic measurement biases make normalization an essential step in single-cell RNA sequencing (scRNA-seq) analysis. There may be multiple competing considerations behind the assessment of normalization performance, of which some may be study specific. We have developed scone''-a flexible framework for assessing performance based on a comprehensive panel of data-driven metrics. Through graphical summaries and quantitative reports, scone summarizes trade-offs and ranks large numbers of normalization methods by panel performance. The method is implemented in the opensource Bioconductor R software package scone. Weshow that top-performing normalization methods lead to better agreement with independent validation data for a collection of scRNA-seq datasets. scone can be downloaded at http://bioconductor.org/packages/scone/.