Assessment of scRNA-seq Differential Expression Analysis Methods

In recent years, various tools for analyzing single-cell RNA-sequencing data have been proposed, many of them with the purpose of performing differentially expression analysis.

Researchers from the Department of Information Engineering (Padova, Italy) compared four different tools for single-cell RNA-sequencing differential expression, together with two popular methods originally developed for the analysis of bulk RNA-sequencing data, but largely applied to single-cell data (List of tools in the table below).

In their work they discuss results obtained on two real and one synthetic dataset, along with considerations about the perspectives of single-cell differential expression analysis. In particular, they explore the methods performance in four different scenarios, mimicking different unimodal or bimodal distributions of the data, as characteristic of single-cell transcriptomics.

They observed marked differences between the selected methods, in terms of precision and recall, the number of detected differentially expressed genes and the overall performance.

Globally, the results obtained in this study suggest that it is difficult to identify a best performing tool and that efforts are needed to improve the methodologies for single-cell RNA-sequencing data analysis and gain better accuracy of results.