README.md

Splatter

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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 scater 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.

If you have this installed Splatter can be installed from Bioconductor using biocLite:

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 convient way to access this is online 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},
  }


Oshlack/splatter documentation built on Sept. 3, 2018, 5:38 a.m.