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dropsim: Single Cell RNAseq Simulator

This is an R package for quickly simulating single cell RNAseq read count data. The model is based on data from droplet based methods, for other methods Splatter may be better suited. Sinsynthr shares a similar core model to Splatter but is overall much simpler.

Installation

# install.packages("devtools")
devtools::install_github("marchinilab/dropsim")

Quick Start

library(dropsim)

# Use default parameters
new_parameters <- dropsim_parameters()

# Simulate counts
simulation <- simulateDGE(new_parameters)

# Normalise Counts matrix
normalised_dge <- normaliseDGE(simulation$counts)

# Do a PCA to check
dge_pca <- prcomp(normalised_dge)
qplot(dge_pca$x[,1], dge_pca$x[,2], colour=rownames(dge_pca$x)) + labs(colour="Group", y="PC2", x="PC1")

PCA on simulated data

For more detailed examples of how to use this package please see the vignette.

Directory Organisation

The R/ directory contains source code of the functions to simulate the data.

The man/ directory contains the manual pages for the functions, compiled by roxygen.

The vignettes/ directory contains uncompiled Rmarkdown with examples of use.

The tests/ directory contains the unit tests which are carried out by the testthat R package.

Contributions of any size or form are welcome!