TGx-DDI Biomarker for DNA Damage Classification

The TGx-DDI biomarker was developed as a toxicogenomics signature to identify chemicals that can cause DNA damage in human cells in culture. Development of this biomarker was as a collaborative effort between the Genomics Committee of the Health and Environmental Sciences Institute (HESI), Health Canada, the University of Ottawa, and Georgetown University. The NIEHS Division of Translational Toxicology (DTT) collaborated on the development of the classification tool.

Overview

This repo is a containerized version of the TGx-DDI Biomarker for DNA Damage Classification tool (https://cebs.niehs.nih.gov/tgxddi/) with some modifications to better allow running multiple chemicals through the classifier.

Installation as a Package (Non-Docker use case):

Because this package has dependencies on Bioconductor packages, you'll need to install it using Biocmanager. Here is an example syntax that will use bioconductor to pull this package from GitHub and install the necessary CRAN and Bioconductor packages:

BiocManager::install("bselman1/tgx_ddi", subdir = "src")

Note that we also have a dependency on the Cairo package which may require some system level dependencies be present. On linux, these can be installed via:

sudo apt-get install libcairo2-dev libxt-dev

Interactive Use

This use case fits best if you want to make changes to the data and or code in real time and have those changes be reflected in the docker container. This setup will mount a working directory on the host computer into the container so any changes on either side (host or in RStudio) will change the file on the host computer.

Building the image

docker build --tag tgx_ddi .

Running an interactive RStudio container

docker run -it --rm -e PASSWORD=test123 -p 8788:8787 --mount type=bind,source="$(pwd)/src",destination=/home/rstudio/project tgx_ddi