scDesign

scDesign is an R package simulator that helps researchers optimize the design of single-cell RNA sequencing (scRNA-seq) experiments. It is the first statistical framework that allows quantitative assessment of scRNA-seq experimental design in the context of differential gene expression analysis. scDesign assists in balancing the exploration of the depth and breadth of transcriptome information by guiding choices of sequencing platforms, sequencing depths, and cell numbers.

In addition to experimental design, scDesign generates high-quality synthetic scRNA-seq datasets under customized experimental settings, aiding in the development of computational methods. The tool outperformed four state-of-the-art scRNA-seq simulation methods and demonstrated reproducibility across biological replicates and independent studies.