/allele_specificity_paper

Analysis of allele-specific methylation (and changes in it)

Primary LanguageR

DAMEfinder: A method to detect allele-specific differential methylation

Code and data analysis

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.