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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: 24 days ago
JSON representation
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 (about 7 years ago)
- Default Branch: master
- Last Pushed: 2018-03-14T11:19:19.000Z (over 6 years ago)
- Last Synced: 2024-02-24T12:39:33.680Z (4 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
Lists
- awesome_single_cell - dropsim - [R] - Simulating droplet based scRNA-seq data. (Software packages / RNA-seq)
- awesome-single-cell - dropsim - [R] - Simulating droplet based scRNA-seq data. (Software packages / Simulation)
- awesome-single-cell - dropsim - [R] - Simulating droplet based scRNA-seq data. (Software packages / RNA-seq)
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")
```
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!