Cell-free DNA methylome and fragmentome analysis for relapse monitoring of Ewing Sarcoma - figure generation

This repository holds code behind the manuscript "Cell-free DNA methylome and fragmentome analysis for relapse monitoring of Ewing Sarcoma" by Richardson, Safrastyan, Karimpour et al. This contains the code and data required to regenerate all the figures in the paper. The code is structured as follows: input: Inputs required to generate the figures. Some will be generated by `final_markdowns` scripts. final_markdowns: Scripts to generate the figures in the paper, given all the inputs in `input`. These are separate RMarkdown files, and should be self-contained, and are able to be ran directly based on the files within `input`. They should be ideally run in order, or at the very least before the final Table generation/export. `Rlib_info` in `final_markdowns` contains commonly used R packages and their versions