szabogtamas / epitope_spotter

Toying around with epitope selection from a given protein based on MHC binding, posttranslational modifications and sequence homology

epitope_spotter

Toying around with epitope selection from a given protein based on MHC binding, posttranslational modifications and sequence homology

Usage

Development is in progress!

Before building the docker image, please obtain a standalone version of NetMHC and NetChop from cbs.dtu.dk and copy the archive to the third_party folder.
Please note that you will also have to obtain additional score files and place them in the same folder.

To run rstudio inside the container, issue

docker run --rm -p 127.0.0.1:8787:8787 -v $PWD:/home/rstudio/local_files -e USERID=$UID -e PASSWORD=[SOME PASWORD] szabogtamas/epitope_spotter

Example notebooks can be found in the [notebooks folder] (notebooks). Any data not inside the folder local_files will be lost after quitting the container!