ConsTADs 1.0.0

Defining the separation landscape of topological domains for decoding consensus domain organization of 3D genome

ConsTADs

Topologically associating domains (TADs) have emerged as basic structural and functional units of genome organization, and have been determined by many computational methods from Hi-C contact maps. However, the TADs obtained by different methods vary greatly, which makes the accurate determination of TADs a challenging issue and hinders subsequent biological analyses about their organization and functions. This project is about comparing different TAD-calling methods, building the TAD separation landscape and finding the consensus TADs from results of multiple methods.

Overview

This computational framework consists of three main steps, including:

1. Running different TAD-calling methods on the same Hi-C contact map;
2. Collecting the TAD boundaries identified by each method and performing boundary voting;
3. Refining the boundary score profile based on the contrast P-values of chromatin interactions using three operations, Add, Filter and Combine, to construct the TAD separation landscape.

The TAD separation landscape can be used in scenarios such as:

1. Comparing domain boundaries across multiple cell types for discovering conserved and divergent topological structures;
2. Deciphering three types of boundary regions with diverse biological features;
3. Identify Consensus Topological Associating Domains (ConsTADs).

Getting start

Installation

It's recommended to create a conda environment:

conda create -n ConsTADs python=3.7
conda activate ConsTADs

Install required packages:

pip install -r requirements.txt

Install ConsTADs by PyPI:

pip install ConsTADs

Install from source code:

git clone https://github.com/zhanglabtools/ConsTADs.git
cd ConsTADs
python setup.py build
python setup.py install

Example usage

See ConsTADs usage.ipynb.

Support

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

• [e-mail]

Citation

If ConsTADs is useful for your research, consider citing our preprint:

Defining the separation landscape of topological domains for decoding consensus domain organization of 3D genome. Dachang Dang, Shao-Wu Zhang, Ran Duan, Shihua Zhang. bioRxiv 2022.08.08.503155; doi: https://doi.org/10.1101/2022.08.08.503155