# OUTRIDER #
[](https://github.com/gagneurlab/OUTRIDER/actions/workflows/check-bioc.yml)
[](https://github.com/gagneurlab/OUTRIDER/releases)
[](https://codecov.io/github/gagneurlab/OUTRIDER?branch=master)
[](https://github.com/gagneurlab/OUTRIDER/blob/master/LICENSE)
OUTRIDER is a tool to find aberrantly expressed genes in RNA-seq samples.
The method is published in the [AJHG](https://doi.org/10.1016/j.ajhg.2018.10.025)
and available through [Bioconductor](http://bioconductor.org/packages/release/bioc/html/OUTRIDER.html).
It is also part of the workflow [DROP](https://github.com/gagneurlab/drop), which is described in [Nature Protocols](https://www.nature.com/articles/s41596-020-00462-5).
Please cite our method paper if you use it in a publication:
> Brechtmann F, Mertes C, Matusevičiūtė A, *et al.* OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data. *Am J Hum Genet. 2018;103(6):907-917*. https://doi.org/10.1016/j.ajhg.2018.10.025
## Installation
`OUTRIDER` is an R software package requiring a running [R 3.6 version or higher](https://cran.r-project.org/).
We will use `BiocManager` to install the package and its dependencies. If you
want to install the devel version of `OUTRIDER`, please install it
with devtools from GitHub directly [(see below)](#OUTRIDER-development-installation).
```
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install('OUTRIDER')
```
If you have dependency issues while installing any package, please have a look
at the Troubleshooting section or submit an issue on [GitHub](https://github.com/gagneurlab/OUTRIDER/issues).
### OUTRIDER development installation
If you want to get the latest
development version of `OUTRIDER`, you can install it from GitHub with
`devtools`. For this, you need a working development environment to compile the
C++ code (see for details: [Windows](https://cran.r-project.org/bin/windows/Rtools/)
or [MacOS X](https://cran.r-project.org/bin/macosx/tools/)).
```
install.packages('devtools')
# latest development version
devtools::install_github('gagneurlab/OUTRIDER', dependencies=TRUE)
# installing a specific version/tag of OUTRIDER
devtools::install_github('gagneurlab/OUTRIDER@1.16.1', dependencies=TRUE)
```
To check which versions/tags are available you can check the GitHub repo
[here](https://github.com/gagneurlab/OUTRIDER/releases).
### Quick tour through OUTRIDER
To get started with `OUTRIDER`, please have a look at our
[vignette](http://bioconductor.org/packages/release/bioc/vignettes/OUTRIDER/inst/doc/OUTRIDER.pdf).
In order to get the pdf version, please type the following code in an R session:
```
library(OUTRIDER)
vignette('OUTRIDER')
```
### Toubleshooting
#### Missing libraries while compiling R packages
On some Linux distributions we need the developer libraries for compiling the R packages.
To install those packages, please run as administrator:
For Ubuntu or debian based systems:
```
sudo apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev zlib1g-dev libmariadbd-dev
```
For centOS or RHEL based systems:
```
sudo yum install R-devel zlib-devel openssl-devel libcurl-devel libxml2-devel mariadb-devel
```
