OUTRIDER is a tool to find aberrantly expressed genes in RNA-seq samples. Paper on AJHG
OUTRIDER is an R software package requiring a running R 3.4 version or higher.
We will use BiocManager to install the package and its dependencies. If you use an R version < 3.5.1 or Bioconductor version < 3.8, please install OUTRIDER with devtools from GitHub directly (see below).
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.
If you use a Bioconductor version prio 3.8 or 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 or MacOS X).
install.packages('devtools')
# latest development version
devtools::install_github('gagneurlab/OUTRIDER', dependencies=TRUE)
# installing specific version/tag of OUTRIDER
devtools::install_github("gagneurlab/OUTRIDER")
To check which versions/tags are available you can check the GitHub repo here.
To get started with OUTRIDER, please have a look at our vignette.
In order to get the pdf version, please type the following code in an R session:
library(OUTRIDER)
vignette('OUTRIDER')
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 libmysqld-dev
For centOS or RHEL based systems:
sudo yum install R-devel zlib-devel openssl-devel libcurl-devel libxml2-devel mariadb-devel