Overview

This repository contains all the scripts associated to the paper:

Convergence and divergence of DNA methylation and gene expression patterns in neopolyploid of Arabidopsis kamchatica, Milosavljevic et al. (2025)

Each folder includes different stages and output of the analyses:

• ARPEGGIO_analyses includes config.yaml and metadata.txt files to use to reproduce all the DNA methylation analyses done with ARPEGGIO together with reports about data quality analyses. These files are provided for all comparisons discussed. More details about how to use these files can be found in the README files in each folder. For additional questions, feel free to open an issue.

• METHImpute_analyses includes all scripts and files required to run and reproduce the results obtained with METHImpute. Since the procedure is more elaborate and the output was used for further downstream analyses, this part is in a separate folder. The results of these analyses were used for some downstream analyses and figures.

• RNAseq: includes all scripts and files related to the full RNAseq data analysis workflow.

• downstream_analyses includes all the scripts used for main and supplementary results (plots included).