Metadata-Version: 2.1
Name: ConsTADs
Version: 1.0.0
Summary: Defining the separation landscape of topological domains for decoding consensus domain organization of 3D genome
Project-URL: Homepage, https://github.com/zhanglabtools/ConsTADs
Author-email: Dachang Dang <dangdachang@163.com>
License: MIT License
        
        Copyright (c) [year] [fullname]
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
License-File: LICENSE
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.7
Requires-Dist: matplotlib>=3.5.0
Requires-Dist: numpy>=1.20.3
Requires-Dist: pandas>=1.3.5
Requires-Dist: scikit-learn>=1.0
Requires-Dist: scipy>=1.7.3
Requires-Dist: tqdm>=4.64.1
Description-Content-Type: text/markdown



# 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.

<p align="center">
<img src="./TAD%20separation%20landscape%20application.png" width="65%" height="65%" />

</p>

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 <u>Cons</u>ensus <u>T</u>opological <u>A</u>ssociating <u>D</u>omain<u>s</u> (ConsTADs).

<p align="center">
<img src="./TAD%20separation%20landscape%20construction.png"  width="65%" height="65%"/>


</p>

## Getting start

### Installation

It's recommended to create a conda environment:

```shell
conda create -n ConsTADs python=3.7
conda activate ConsTADs
```

Install required packages:

```shell
pip install -r requirements.txt
```

Install ConsTADs by PyPI:

```shell
pip install ConsTADs
```

Install from source code:

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

### Example usage

See [ConsTADs usage.ipynb](./ConsTADs%20usage.ipynb).

### Support

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

* dangdachang@163.com

### 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
