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# Splatter [![Project Status](]( [![Lifecycle](]( [![Travis-CI Build Status](]( [![Coverage Status](]( [![AppVeyor Build Status](]( ![R-CMD-check]( [![Bioc Years](]( [![Bioc Stats](]( [![Bioc Build](]( ![Splatter logo](vignettes/splatter-logo-small.png) 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 [`scater`][scater] 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]. ``` @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 = {}, 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]. ``` @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 = {}, doi = {10.1186/s13059-021-02546-1}, } ``` [scater]: [SCE]: [contrib]: [bioc]: [vignette]: [splatpopvignette]: [paper]: [splatpoppaper]: