Splatter: simulation of single-cell RNA sequencing data

Abstract

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, we 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, our own simulation, based on a gamma-Poisson distribution. Splat can simulate single populations of cells, populations with multiple cell types, or differentiation paths.

Citation

BibTeX citation:

@article{zappia2017,
  author = {Zappia, Luke and Phipson, Belinda and Oshlack, Alicia},
  title = {Splatter: Simulation of Single-Cell {RNA} Sequencing Data},
  journal = {Genome Biology},
  volume = {18},
  number = {1},
  pages = {174},
  date = {2017-09-01},
  url = {https://lazappi.id.au/publications/2017-zappia-splatter},
  doi = {10.1186/s13059-017-1305-0},
  issn = {1465-6906, 1474-760X},
  langid = {en},
  abstract = {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, we 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, our own simulation, based on a
    gamma-Poisson distribution. Splat can simulate single populations of
    cells, populations with multiple cell types, or differentiation
    paths.}
}

For attribution, please cite this work as:

Zappia, Luke, Belinda Phipson, and Alicia Oshlack. 2017. “Splatter: Simulation of Single-Cell RNA Sequencing Data.” Genome Biology 18 (September): 174. https://doi.org/10.1186/s13059-017-1305-0.