README.md

# Splatter

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![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 convient way to access this is online [here][vignette].

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 = {http://dx.doi.org/10.1186/s13059-017-1305-0},
    doi = {10.1186/s13059-017-1305-0},
  }
```

[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
[vignette]: https://bioconductor.org/packages/devel/bioc/vignettes/splatter/inst/doc/splatter.html
[paper]: http://dx.doi.org/10.1186/s13059-017-1305-0