SCOPIT: sample size calculations for single-cell sequencing experiments

Background: In single cell DNA and RNA sequencing experiments, the number of cells to sequence must be decided before running an experiment, and afterwards, it is necessary to decide whether sufficient cells were sampled. These questions can be addressed by calculating the probability of sampling at least a defined number of cells from each subpopulation (cell type or cancer clone).

Results: We developed an interactive web application called SCOPIT (Single-Cell One-sided Probability Interactive Tool), which calculates the required probabilities using a multinomial distribution (www.navinlab.com/SCOPIT). In addition, we created an R package called pmultinom for scripting these calculations.

Conclusions: Our tool for fast multinomial calculations provide a simple and intuitive procedure for prospectively planning single-cell experiments or retrospectively evaluating if sufficient numbers of cells have been sequenced. The web application can be accessed at navinlab.com/SCOPIT.