GLMsim: a GLM-based single cell RNA-seq simulator incorporating batch and biological effects

With development of the single cell RNA-seq technologies, large numbers of cells can now be routinely sequenced by different platforms. This requires us to choose an efficient integration tool to merge those cells, and computational sim- ulators to help benchmark and assess the performance of these tools. Although existing single cell RNA-seq simulators can simulate library size, biological and batch effects separately, they currently do not capture associations among these three factors. Here we present GLMsim, the first single cell RNA-seq simulator to simultaneously capture the library size, biology and unwanted variation and their associations via a generalized linear model, and to simulate data resembling the original experimental data in these respects. GLMsim is capable of quantita- tively benchmarking different single cell integration methods, and assessing their abilities to retain biology and remove library size and batch effects.