Splatter – simulation of single-cell RNA sequencing data

As single-cell RNA sequencing (scRNA-seq) technologies have rapidly developed, so have analysis methods. Many methods have been tested, developed, and validated using simulated datasets. Unfortunately, current simulations are often poorly documented, their similarity to real data is not demonstrated, or reproducible code is not available. Here,  researchers from the University of Melbourne present the Splatter Bioconductor package for simple, reproducible, and well-documented simulation of scRNA-seq data. Splatter provides an interface to multiple simulation methods including Splat, their own simulation, based on a gamma-Poisson distribution. Splat can simulate single populations of cells, populations with multiple cell types, or differentiation paths.

The Splat simulation model


Input parameters are indicated with double borders and those that can be estimated from real data are shaded blue. Red shading indicates the final output. The simulation begins by generating means from a gamma distribution. Outlier expression genes are added by multiplying by a log-normal factor and the means are proportionally adjusted for each cell’s library size. Adjusting the means using a simulated Biological Coefficient of Variation (BCV) enforces a mean-variance trend. These final means are used to generate counts from a Poisson distribution. In the final step dropout is (optionally) simulated by randomly setting some counts to zero, based on each gene’s mean expression. DoF degrees of freedom

Availability – The code and dataset files are available at https://github.com/Oshlack/splatter-paper under an MIT license.

Zappia L, Phipson B, Oshlack A. (2017) Splatter: simulation of single-cell RNA sequencing data. Genome Biol 18(1):174. [article]

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