mscherer/medecom repository overview

The repository comprises the necessary tools to perform reference-free deconvolution of complex DNA methylation data: DecompPipeline (https://github.com/CompEpigen/DecompPipeline⁠), MeDeCom (https://github.com/lutsik/MeDeCom⁠), FactorViz (https://github.com/CompEpigen/FactorViz⁠), and RnBeads (https://rnbeads.org/⁠). For a step-by-step protocol for performing reference-free deconvolution, we refer to our publication "Reference-free deconvolution, visualization and interpretation of complex DNA methylation data using DecompPipeline, MeDeCom and FactorViz" (https://www.nature.com/articles/s41596-020-0369-6⁠) and the RMD tutorial at (https://github.com/CompEpigen/DecompPipeline/blob/master/vignettes/DeconvolutionProtocol.Rmd⁠).

To start the Docker container and in order to have a functional version of FactorViz available, you'll have to execute the following lines in your terminal/PowerShell:

# Windows
docker run -e DISPLAY=<YOUR_IP>:0.0 -it mscherer/medecom

# Linux
xhost +"local:docker@"
docker run --env DISPLAY=$DISPLAY --privileged --volume $XAUTH:/root/.Xauthority --network=host --volume /tmp/.X11-unix:/tmp/.X11-unix --rm --rm -it mscherer/medecom