Splatter

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

• 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.

Installation.

Development version

Splatter is currently under consideration for acceptance into Bioconductor (you can follow the progress here) and hence requires the development version of R (>=3.4) and the development version of Bioconductor (3.5).

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

source("https://bioconductor.org/biocLite.R")
biocLite("Oshlack/splatter", dependencies=TRUE, build_vignettes=TRUE)

This will also build the vignette and install 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. If you still have problems or want a quicker install (without the vignette) use:

biocLite("Oshlack/splatter")

Release version

The last version of Splatter that is compatible with the current version of R (3.3) is v0.99.0 which can be downloaded here. There are no significant changes to functionality and this version should be fine for most users until the next R/Bioconducor release.

Getting started

Once installed the best place to get started is the vignette. Load Splatter, then browse the vignettes:

library(splatter)
browseVignettes("splatter")

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