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gagneurlab / OUTRIDER

OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data
MIT License
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count-data diagnostics expression-analysis mendelian-genetics outlier-detection r rna-seq

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OUTRIDER

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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

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).

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@1.20.1', 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