This repository contains the code for the following paper:
- S Orjuela, D Machlab, M Menigatti, G Marra, MD Robinson: DAMEfinder: A method to detect allele-specific differential methylation. preprint
The structure of this repository is as follows:
data/Metadata from samples analyzed and R objects (.RData files).real_data_analysis/Contains R scripts ans bash scripts with to analyze raw BS-seq FASTQ files from two datasets: Monocyte datasets and CRC dataset.score_evaluation/R scripts to evaluate the ASMtuple score.FDR_control/R scripts to generate simulations and evaluate the FDR control in the DAME detection.