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# OUTRIDER # [![Build](]( [![Version](]( [![Coverage status](]( [![License](]( 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*. ## Installation `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)](#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]( ### 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]( 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@1.22.0', dependencies=TRUE) ``` To check which versions/tags are available you can check the GitHub repo [here]( ### Quick tour through OUTRIDER 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') ``` ### 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 ```