Bioconductor Code: splatter (original) (raw)

# Splatter [\](http://www.repostatus.org/#active) [\](https://lifecycle.r-lib.org/articles/stages.html#stable) [\](https://app.codecov.io/gh/Oshlack/splatter) [\](https://github.com/Oshlack/splatter/actions/workflows/check.yml) [\](https://bioconductor.org/checkResults/release/bioc-LATEST/splatter) [\](https://bioconductor.org/checkResults/devel/bioc-LATEST/splatter) [\](http://bioconductor.org/packages/stats/bioc/splatter/) [\](https://support.bioconductor.org/tag/splatter) [\](https://bioconductor.org/packages/release/bioc/html/splatter.html#since) [\](http://bioconductor.org/checkResults/devel/bioc-LATEST/splatter/) [\](https://bioconductor.org/packages/release/bioc/html/splatter.html#since)  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: * Functions for estimating simulation parameters * Objects for storing those parameters * Functions for simulating counts using those parameters Splatter is built on top of several [Bioconductor](bioc-home) packages and stores simulations in [`SingleCellExperiment`][SCE] objects. Splatter also has functions for comparing simulations and real datasets. ## Installation. Splatter is available from [Bioconductor][bioc] for R >=3.4. It can be installed from Bioconductor with: ```r if (!requireNamespace("BiocManager", quietly=TRUE)) { install.packages("BiocManager") } BiocManager::install("splatter") ``` If you wish to build a local version of the vignette use: ```r 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][vignette]. To get started with population scale simulations, see the splatPop vignette [here][splatpopvignette]. Alternatively, if you chose to build the vignette, you can load Splatter, then browse the vignettes: ```r 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"][paper]. ```bibtex @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"][splatpoppaper]. ```bibtex @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}, } ``` [scater]: https://github.com/davismcc/scater [SCE]: https://github.com/drisso/SingleCellExperiment [contrib]: https://github.com/Bioconductor/Contributions/issues/209 [bioc]: https://bioconductor.org/packages/devel/bioc/html/splatter.html [bioc-home]: https://www.bioconductor.org/ [vignette]: https://bioconductor.org/packages/devel/bioc/vignettes/splatter/inst/doc/splatter.html [splatpopvignette]: http://www.bioconductor.org/packages/devel/bioc/vignettes/splatter/inst/doc/splatPop.html [paper]: http://dx.doi.org/10.1186/s13059-017-1305-0 [splatpoppaper]: http://dx.doi.org/10.1186/s13059-021-02546-1