scPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies

Single cell RNA-seq has revolutionized transcriptomics by providing cell type resolution for differential gene expression and expression quantitative trait loci (eQTL) analyses. However, efficient power analysis methods for single cell data and inter-individual comparisons are lacking. Here, we present scPower; a statistical framework for the design and power analysis of multi-sample single cell transcriptomic experiments. We modelled the relationship between sample size, the number of cells per individual, sequencing depth, and the power of detecting differentially expressed genes within cell types. We systematically evaluated these optimal parameter combinations for several single cell profiling platforms, and generated broad recommendations.  In general, shallow sequencing of high numbers of cells leads to higher overall power than deep sequencing of fewer cells. The model, including priors, is implemented as an R package and is accessible as a web tool. scPower is a highly customizable tool that experimentalists can use to quickly compare a multitude of experimental designs and optimize for a limited budget. We performed 10X single cell RNA seq on PBMCs of pools of a total of 14 human study participants. The goal of the experiment was to benchmark different pooling and demultiplexing strategies for multisample single cell transcriptomics experiments. We performed 3 runs of sequencing on a pool of all 14 samples with targeted 8000 cells each. In addition we performed one run with overloading the 10X reaction with 25000 cells. Finally, for assesing the precision of the demultiplexing we split the pool into samples 1-7 and 8-14.