Skip to content
Simple simulation of single-cell RNA sequencing data
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Type Name Latest commit message Commit time
Failed to load latest commit information.
inst Update NEWS for Bioc 3.8 Release Oct 29, 2018
man Add WithSpike when calling BASiCS_MCMC Oct 22, 2018
vignettes Fix bugs in vignette Nov 17, 2018
DESCRIPTION Merge branch 'RELEASE_3_8' Dec 5, 2018
appveyor.yml Turn off release builds Jan 30, 2018
codecov.yml remove useDevel mention Sep 7, 2018


Project Status Lifecycle Travis-CI Build Status Coverage Status AppVeyor Build Status Bioc Years Bioc Stats Bioc Build

Splatter logo

Splatter is an R package for the simple simulation of single-cell RNA sequencing data. Splatter provides a common interface to multiple simulations that have:

  • Functions for estimating simulation parameters
  • Objects for storing those parameters
  • Functions for simulating counts using those parameters

Splatter is built on top of scater and stores simulations in SingleCellExperiment objects. Splatter also has functions for comparing simulations and real datasets.


Splatter is available from Bioconductor for R >=3.4.

It can be installed from Bioconductor with:

if (!requireNamespace("BiocManager", quietly=TRUE))

If you wish to build a local version of the vignette use:

BiocManager::install("splatter", build_vignettes=TRUE)

This will also build the vignette and install all suggested dependencies (which aren't required for core functionality).

Getting started

Once installed the best place to get started is the vignette. For most users the most convient way to access this is online here.

Alternatively, if you chose to build the vignette, you can load Splatter, then browse the vignettes:


This is a detailed document that introduces the main features of Splatter.

Citing Splatter

If you use Splatter please cite our paper "Zappia L, Phipson B, Oshlack A. Splatter: Simulation Of Single-Cell RNA Sequencing Data. Genome Biology. 2017; doi:10.1186/s13059-017-1305-0".

    author = {Luke Zappia and Belinda Phipson and Alicia Oshlack},
    title = {Splatter: simulation of single-cell RNA sequencing data},
    journal = {Genome Biology},
    year = {2017},
    url = {},
    doi = {10.1186/s13059-017-1305-0},
You can’t perform that action at this time.