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:

* 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
`SCESet` objects.

## Installation.

### Development version

Splatter has been accepted into the development version of [Bioconductor][bioc]
and hence requires the development version of R (>=3.4) and the development
version of Bioconductor (3.5).

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

```{r}
source("https://bioconductor.org/biocLite.R")
biocLite("splatter")
```

If you wish to build a local version of the vignette use:

```{r}
biocLite("splatter", build_vignettes=TRUE)
```

This will also build the vignette and install all suggested dependencies (which
aren't required for core functionality). Building the vignette may sometimes 
fail when run from the command line, if this happens try running the install
command in RStudio.

### Release version

The last version of Splatter that is compatible with the current version of
R (3.3) is v0.99.0 which can be downloaded [here][rel33]. There are no
significant changes to functionality and this version should be fine for most
users until the next R/Bioconductor release (in approximately April 2017).

## 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.

[scater]: https://github.com/davismcc/scater
[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
[rel33]: https://github.com/Oshlack/splatter/releases/tag/v0.99.0