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SplatPop: simulating population scale single-cell RNA sequencing data.

ABSTRACT: 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.

SUBMITTER: Azodi CB

PROVIDER: S-EPMC8672480 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature

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

Azodi Christina B CB Zappia Luke L Oshlack Alicia A McCarthy Davis J DJ

Genome biology 20211215 1

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 ...[more]

PMID: 34911537

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