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https://github.com/gagneurlab/outrider

OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data
https://github.com/gagneurlab/outrider

count-data diagnostics expression-analysis mendelian-genetics outlier-detection r rna-seq

Last synced: 7 days ago
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OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data

Host: GitHub
URL: https://github.com/gagneurlab/outrider
Owner: gagneurlab
License: mit
Created: 2018-03-23T17:42:32.000Z (over 6 years ago)
Default Branch: master
Last Pushed: 2024-04-09T13:47:22.000Z (7 months ago)
Last Synced: 2024-04-09T17:45:27.415Z (7 months ago)
Topics: count-data, diagnostics, expression-analysis, mendelian-genetics, outlier-detection, r, rna-seq
Language: R
Homepage:
Size: 10.9 MB
Stars: 45
Watchers: 12
Forks: 8
Open Issues: 14
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

README

        # 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/[email protected]', 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

```