perishky / epidelta

EpiDelta: Epigenome-wide change and variation in DNA methylation in childhood

An interactive web application for exploring DNA methylation change in childhood using data generated for participants in ALSPAC and Generation R.

Mulder RH, Neumann A, Cecil CAM, Walton E, Houtepen LC, Simpkin AJ, Rijlaarsdam J, Heijmans BT, Gaunt TR, Felix JF, Jaddoe VWV, Bakermans-Kranenburg MJ, Tiemeier H, Relton CL, van IJzendoorn MH, Suderman M. Epigenome-wide change and variation in DNA methylation in childhood: trajectories from birth to late adolescence. Hum Mol Genet. 2021 Mar 25;30(1):119-134. doi: 10.1093/hmg/ddaa280. PMID: 33450751; PMCID: PMC8033147.

The app is implemented in R using Shiny.

Installing the app

The app is designed to run as a docker container. Docker will need to be installed.

Build the docker container. This may take a few minutes, mainly to install R packages.

docker-compose build

Start the app:

docker-compose up -d 

Omit '-d' unless the app is ready for production.

View the app in a web browser at http://localhost:3405/.

Image plots and data

The app displays images found in app/plots and data in app/data. These are not provided on github because of space requirements; there are over 900K plots and the data uses 180Mb.

Debugging the container and the app

To get a bash session in the running docker container:

docker exec -it epidelta_prod bash

Once in, it is possible to run basic linux commands and run R.

To debug a Dockerfile, comment out the offending line and every line after it. Then, rebuild and restart the container, initiate a bash session in the container and then investigate the problematic command.

Stopping the app

To stop the app:

docker-compose stop

Docker container output (for debugging purposes) is saved in the log/ directory.