OUTRIDER is a tool to find aberrantly expressed genes in RNA-seq samples. The method is published in the AJHG and available through Bioconductor. It is also part of the workflow DROP, which is described in Nature Protocols.
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
OUTRIDER is an R software package requiring a running R 3.6 version or higher.
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).
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 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 a specific version/tag of OUTRIDER
devtools::install_github('gagneurlab/OUTRIDER@1.20.1', dependencies=TRUE)
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 libmariadbd-dev
For centOS or RHEL based systems:
sudo yum install R-devel zlib-devel openssl-devel libcurl-devel libxml2-devel mariadb-devel