Supporting code for "DNA-methylation variability in normal mucosa: a field cancerization marker in patients with adenomatous polyps" [1]
To reproduce the analysis, one needs to have the right packages installed. An easy way to do so it through conda. With conda installed (see their website if not installed), just run
conda create --name crcpolypenv --file requirements.txt
to create the env crcpolypenv that will contain all necessary packages to reproduce this analysis.
Each folder contains the code necessary to reproduce the analysis. In particular, the folder notebooks contains a detailed explanation of how to reproduce the analysis, including links to download the data, how to process it, how to run the notebooks. For more details on folders, cf the respective READMEs.
This folder contains supporting for the analysis of adenoma-related differentially variable and differentially methylated CpG sites (aDVMCs).
This folder contains helper functions for downloading and preprocessing data.
This folder contains helper functions for plotting
This folder contains all notebooks necessary for reproducing the analysis as well as a detailed explanation of how to reproduce the figures and analysis presented in the manuscript.
Any questions on the analysis or the code can be addressed to josephine.yates@inf.ethz.ch
[1] Josephine Yates, Helen Schaufelberger, Roland Steinacher, Primo Schär, Kaspar Truninger, Valentina Boeva, DNA-methylation variability in normal mucosa: a field cancerization marker in patients with adenomatous polyps, JNCI: Journal of the National Cancer Institute, 2024;, djae016, https://doi.org/10.1093/jnci/djae016