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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
  • Functions for comparing simulations and real datasets

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

!Please note! This site provides documentation for the development version of Splatter. For details on the current release please refer to https://bioconductor.org/packages/splatter.

Installation.

Release version

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

It can be installed from Bioconductor with:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("splatter")

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). Building the vignette may sometimes fail when run from the command line, if this happens try running the install command in RStudio.

Development version

If you want to try the development version this can also be installed from Bioconductor:

library(BiocManager)
valid()              # checks for out of date packages
BiocManager::install()               # (optional) updates out of date packages
BiocManager::install("splatter")

Depending on the current release cycle you may also need to install the development version of R. See here for more details.

Alternatively the development version can be installed directly from Github:

devtools::install("Oshlack/splatter")