bw2 / FRASER

FRASER - Find RAre Splicing Events in RNA-seq

FRASER is a tool to detect aberrant splicing events in RNA-seq data. The method is currently available as a preprint on bioRxiv.

The FRASER framework and workflow aims to assist the diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects. For a short tutorial on how to use FRASER on a dataset please use our Colab tutorial at: http://tinyurl.com/RNA-ASHG-colab. This is based on a workshop we presented at ASHG 2019.

Installation

FRASER is an R/Bioconductor software package requiring a running R 3.6 version or higher.

The recommanded way of installing FRASER is to use Bioconductor:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages('BiocManager')
BiocManager::install('FRASER')

If you use an R version below 4.0.0 you have to install it from source. To this end, we will use devtools to install it. For this, you need a working development environment to compile the C++ code (see for details: Windows or MacOS X).

if (!requireNamespace("devtools", quietly=TRUE))
    install.packages('devtools')

# latest development version
devtools::install_github('gagneurlab/FRASER', dependencies=TRUE)

# or a specific version of FRASER (search for tags on github)
devtools::install_github('gagneurlab/FRASER', ref='1.0.0', dependencies=TRUE)

If you have dependency issues while installing any package, please have a look at the Troubleshooting section or submit an issue on GitHub.

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 libmysqld-dev

For centOS or RHEL based systems:

sudo yum install R-devel zlib-devel openssl-devel libcurl-devel libxml2-devel mariadb-devel