https://github.com/marchinilab/dropsim

R Package for Single Cell RNAseq Synthetic Data Simulation
https://github.com/marchinilab/dropsim

r-package scrnaseq simulation single-cell

Last synced: about 2 months ago
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R Package for Single Cell RNAseq Synthetic Data Simulation

• Host: GitHub
• URL: https://github.com/marchinilab/dropsim
• Owner: marchinilab
• License: mit
• Created: 2017-04-16T19:55:28.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2018-03-14T11:19:19.000Z (almost 7 years ago)
• Last Synced: 2024-08-02T16:44:31.270Z (5 months ago)
• Topics: r-package, scrnaseq, simulation, single-cell
• Language: R
• Homepage:
• Size: 1.26 MB
• Stars: 5
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# 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](https://github.com/Oshlack/splatter) may be better suited. Sinsynthr shares a similar core model to Splatter but is overall much simpler.

## Installation

```R

# install.packages("devtools")

devtools::install_github("marchinilab/dropsim")

```

## Quick Start

```R

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](example.png)

For more detailed examples of how to use this package please see the [vignette](vignettes/vignette.md).

## Directory Organisation

The [R/](R/) directory contains source code of the functions to simulate the data.

The [man/](man/) directory contains the manual pages for the functions, compiled by roxygen.

The [vignettes/](vignettes/) directory contains uncompiled Rmarkdown with examples of use.

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

Contributions of any size or form are welcome!