A comparison of marker gene selection methods for single-cell RNA sequencing data

The development of single-cell RNA sequencing (scRNA-seq) has enabled scientists to catalogue and probe the transcriptional heterogeneity of individual cells in unprecedented detail. A common step in the analysis of scRNA-seq data is the selection of so-called marker genes, most commonly to enable annotation of the biological cell types present in the sample. In this paper we benchmarked 56 computational methods for selecting marker genes in scRNA-seq data. The performance of the methods was compared using 10 real scRNA-seq datasets and over 170 additional simulated datasets. Methods were compared on their ability to recover simulated and expert-annotated marker genes, the predictive performance and characteristics of the gene sets they select, their memory usage and speed and their implementation quality. In addition, various case studies were used to scrutinise the most commonly used methods, highlighting issues and inconsistencies. Overall, we present a comprehensive evaluation of methods for selecting marker genes in scRNA-seq data. Our results highlight the efficacy of simple methods, especially the Wilcoxon rank-sum test, Students t-test and logistic regression. All code used in the evaluation, including an extensible Snakemake pipeline, is available at: https://gitlab.svi.edu.au/biocellgen-public/mage_2020_marker-gene-benchmarking.