khdc-me / marge

MMARGE: Motif Mutation Analysis for Regulatory Genomic Elements

This repository stores the source code, as well as the Dockerfile and the installation package for MMARGE (Motif Mutation Analysis of Regulatory Genomic Elements). MMARGE is the first publicly available suite of software tools that integrates genome-wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. MMARGE is optimized to work with chromatin accessibility assays (such as ATAC-seq or DNase I hypersensitivity), as well as transcription factor binding data collected by ChIP-seq. The manuscript describing the algorithm in detail is currently under review. A reference will be posted as soon as the manuscript is publicly available.

Motivation

MMARGE was originally developed to analyze transcription factor binding data in different strains of inbred mice. In the last years we extended this to all homozygous and heterozygous individuals where genetic variation data is available. However, the software was only tested on mouse and human data so far. We are currently maintaining MMARGE actively.

Installation

A detailed description on how to install MMARGE, as well as how to run it, can be found in MMARGE_documentation.pdf. In short, download MMARGE_v1.0.tar.gz, unzip it and run the installation script (install.pl).

Bug Report

Please send all bug reports to [email protected]. We will try to address everything as soon as possible.