README.md

Mactop

Mactop is designed for identifying chromatin domains, domain communities, and chromunities in Hi-C data and higher-order interaction data.

Overview

Mactop, a Markov clustering-based tool to accurately identify TADs and provide biologically important classifications of TADs and their boundaries. Mactop distinguishes stable and dynamic boundaries based on biological significance. More importantly, leveraging spatial interactions among TADs, Mactop uncovers TAD communities characterized by chromatin accessibility and enriched histone modifications. Mactop unveils the ‘chromunity’ within TADs in high-order interaction data, showing that interactions within TADs are diverse rather than uniform. In short, Mactop is a versatile, accurate, robust tool for deciphering chromatin domain, domain community, and chromunity for 3D genome maps.

Getting start

Installation

It's recommended to create a conda environment:

conda create -n mactop python=3.6
conda activate mactop

Installation dependency

cooler >= 0.8.11
numpy  >= 1.17.3 
pandas >= 0.24.1 
scipy  >= 1.1.0 
iced   >= 0.5.10
networkx >= 2.5.1
markov_clustering >= 0.0.6
pickle >= 0.7.5

Installation Mactop

Install from PyPI:

pip install mactop3D

install from source

git clone https://github.com/ydduanran/Mactop.git
cd mactop
python setup.py build
python setup.py install

Documentation and Tutorials

You can download the mcool and mutiway data used in our tutorial at NCBI(GSE149117).

For Command Line Interface(CLI) user

The parameter file for mactop needs to be prepared according to the file in the example.

cd mactop
python mactop_CLI.py [path/to/you/paramaters.txt]

For Interactive user

See Mactop_Tutorials.ipynb.

Support

If you are having issues, please let us know. We have a mailing list located at:

• duanran@mail.ynu.edu.cn