jDMRgrid

Description

jDMRgrid is a tool for conducting efficient and heuristic DMR (Differentially Methylated Region) calling in population-level or control/treatment WGBS data. Its functionality relies on a grid-based methodology that involves dividing the genome into sliding windows or bins of customizable sizes. For each sample and sliding window methylation state calls are obtained via a Hidden Markov Model (HMM). These calls are then consolidated into a DMR matrix format.

Installing from the Github

To install from GitHub (development version), follow the steps given below.

Step 1 — Install a last version of R (>=3.6)

Step 2 — In R, please install all dependencies and execute the following commands:

install.packages("devtools")
library(devtools)
devtools::install_github("jlab-code/jDMRgrid")

How to use?

Please open the vignette file.

Contributors

Robert Piecyk - robert.piecyk@tum.de

Rashmi Hazarika - rashmi.hazarika@tum.de

Yadi Shahryary - y.shahryary@tum.de

Frank Johannes - frank@johanneslab.org

Ming Zhou - ming.zhou@tum.de