PuSH - Publication Server of Helmholtz Zentrum München: splatPop: Simulating population scale single-cell RNA sequencing data.

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Azodi, C.B* ; Zappia, L. ; Oshlack, A.* ; McCarthy, D.J.*

splatPop: Simulating population scale single-cell RNA sequencing data.

Genome Biol. 22:341 (2021)

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Population-scale single-cell RNA sequencing (scRNA-seq) is now viable, enabling finer resolution functional genomics studies and leading to a rush to adapt bulk methods and develop new single-cell-specific methods to perform these studies. Simulations are useful for developing, testing, and benchmarking methods but current scRNA-seq simulation frameworks do not simulate population-scale data with genetic effects. Here, we present splatPop, a model for flexible, reproducible, and well-documented simulation of population-scale scRNA-seq data with known expression quantitative trait loci. splatPop can also simulate complex batch, cell group, and conditional effects between individuals from different cohorts as well as genetically-driven co-expression.

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