Splatter

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 SCESet objects. Splatter also has functions for comparing simulations and real datasets.

Installation.

Development version

Splatter has been accepted into the latest version of Bioconductor and hence requires the latest version of R (>=3.4).

If you have these installed Splatter can be installed from Bioconductor using biocLite:

source("https://bioconductor.org/biocLite.R")
biocLite("splatter")

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

biocLite("splatter", build_vignettes=TRUE)

This will also build the vignette and install all suggested dependencies (which aren't required for core functionality). Building the vignette may sometimes fail when run from the command line, if this happens try running the install command in RStudio.

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:

library(splatter)
browseVignettes("splatter")

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. bioRxiv. 2017; doi:10.1101/133173".

@Article{,
    author = {Luke Zappia and Belinda Phipson and Alicia Oshlack},
    title = {Splatter: Simulation Of Single-Cell RNA Sequencing Data},
    journal = {bioRxiv},
    year = {2017},
    url = {http://dx.doi.org/10.1101/133173},
    doi = {10.1101/133173},
  }