The current landscape and emerging challenges of benchmarking single-cell methods

Abstract

With the rapid development of computational methods for single-cell sequencing data, benchmarking serves as a valuable resource. As the number of benchmarking studies surges, it is timely to assess the current state of the field. We conducted a systematic literature search and assessed 282 papers, including all 130 benchmark-only papers from the search and an additional 152 method development papers containing benchmarking. This collective effort provides the most comprehensive quantitative summary of the current landscape of single-cell benchmarking studies. We examine performances across nine broad categories, including often ignored aspects such as role of datasets, robustness of methods and downstream evaluation. Our analysis highlights challenges such as how to effectively combine knowledge across multiple benchmarking studies and in what ways can the community recognise the risk and prevent benchmarking fatigue. This paper highlights the importance of adopting a community-led research paradigm to tackle these challenges and establish best practice standards.