search

Oshlack / splatter

Simple simulation of single-cell RNA sequencing data
http://oshlacklab.com/splatter/
GNU General Public License v3.0
218 stars 57 forks source link
bioconductor bioinformatics scrna-seq simulation

readme

Splatter

Project Status Lifecycle Codecov test coverage R-CMD-check-bioc Bioc release status Bioc devel status Bioc downloads rank Bioc support Bioc history Bioc last commit Bioc dependencies

Splatter logo

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:

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

Installation.

Splatter is available from Bioconductor for 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).

Getting started

Once installed the best place to get started is the vignette. For most users the most convenient way to access this is online here. To get started with population scale simulations, see the splatPop vignette here.

Alternatively, if you chose to build the vignette, you can load Splatter, then browse the vignettes:

library(splatter)
browseVignettes("splatter")

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

Citing Splatter

If you use Splatter please cite our paper "Zappia L, Phipson B, Oshlack A. Splatter: Simulation Of Single-Cell RNA Sequencing Data. Genome Biology. 2017; doi:10.1186/s13059-017-1305-0".

@Article{,
  author = {Luke Zappia and Belinda Phipson and Alicia Oshlack},
  title = {Splatter: simulation of single-cell RNA sequencing data},
  journal = {Genome Biology},
  year = {2017},
  url = {http://dx.doi.org/10.1186/s13059-017-1305-0},
  doi = {10.1186/s13059-017-1305-0},
}

If you use the splatPop functions, please also cite "Azodi CB, Zappia L, Oshlack A, McCarthy DJ. splatPop: simulating population scale single-cell RNA sequencing data. Genome Biology. 2021; doi:10.1186/s13059-021-02546-1".

@Article{,
  author = {Christina B Azodi and Luke Zappia and Alicia Oshlack and Davis J McCarthy},
  title = {splatPop: simulating population scale single-cell RNA sequencing data},
  journal = {Genome Biology},
  year = {2021},
  url = {http://dx.doi.org/10.1186/s13059-021-02546-1},
  doi = {10.1186/s13059-021-02546-1},
}