Scripts for experiments in vmrseq paper

This repository contains the code to reproduce the analyses and figures in "vmrseq: Probabilistic Modeling of Single-cell Methylation Heterogeneity". These scripts rely on the package vmrseq from github (v0.99.0).

The directory contains three folders:

1. code - scripts for preprocessing steps, the analyses with vmrseq and other tools used in the comparisons.
2. plots - original plots generated from the scripts in code folder.
3. manuscript_related - publication-level figures and tables in the manuscript along with the scripts generated them.

To reproduce all results from the paper, run the code in the scripts in code/raw_data_process first to dowload and pre-process datasets used in the analyses, then scripts in code/sim_studies and code/case_studies can be run independently. Finally, run the scripts in manuscript_related to reproduce the results published in paper.