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README.md
# OUTRIDER # [![Build](https://github.com/gagneurlab/OUTRIDER/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/gagneurlab/OUTRIDER/actions/workflows/check-bioc.yml) [![Version](https://img.shields.io/github/v/release/gagneurlab/OUTRIDER)](https://github.com/gagneurlab/OUTRIDER/releases) [![Coverage status](https://codecov.io/gh/gagneurlab/OUTRIDER/branch/master/graph/badge.svg)](https://codecov.io/github/gagneurlab/OUTRIDER?branch=master) [![License](https://img.shields.io/github/license/mashape/apistatus.svg?maxAge=2592000)](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@1.22.0', 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 ```