---
license: mit
tags:
- Hi-C
- deep-learning
- chromatin-loop-detection
- biology
- 3D-genomics
---

<img src="./doc/logo.png" alt="Polaris" title="Polaris" width="400">

# A Versatile Framework for Chromatin Loop Annotation in Bulk and Single-cell Hi-C Data

<a href="https://github.com/ai4nucleome/Polaris/releases/latest">
   <img src="https://img.shields.io/badge/Polaris-v1.0.0-green">
   <img src="https://img.shields.io/badge/platform-Linux%20%7C%20Mac%20-green">
   <img src="https://img.shields.io/badge/Language-python3-green">
   <!-- <img src="https://img.shields.io/badge/dependencies-tested-green"> -->
</a>  

### See https://github.com/ai4nucleome/Polaris for more details.

🌟 **Polaris** is a versatile and efficient command line tool tailored for rapid and accurate chromatin loop detectionfrom from contact maps generated by various assays, including bulk Hi-C, scHi-C, Micro-C, and DNA SPRITE. Polaris is particularly well-suited for analyzing **sparse scHi-C data and low-coverage datasets**.

## [📝Documentation](https://nucleome-polaris.readthedocs.io/en/latest/)
 **Detailed documentation** can be found at: [Polaris Doc](https://nucleome-polaris.readthedocs.io/en/latest/).

## Citation:
Yusen Hou, Audrey Baguette, Mathieu Blanchette*, & Yanlin Zhang*. __A versatile tool for chromatin loop annotation in bulk and single-cell Hi-C data__. _bioRxiv_, 2024. [Paper](https://doi.org/10.1101/2024.12.24.630215)
<br>
```
@article {Hou2024Polaris,
	title = {A versatile tool for chromatin loop annotation in bulk and single-cell Hi-C data},
	author = {Yusen Hou, Audrey Baguette, Mathieu Blanchette, and Yanlin Zhang},
	journal = {bioRxiv}
	year = {2024},
}
```

## 📩 Contact
A [GitHub issue](https://github.com/ai4nucleome/Polaris/issues) is preferable for all problems related to using Polaris. 

For other concerns, please email Yusen Hou or Yanlin Zhang (yhou925@connect.hkust-gz.edu.cn,  yanlinzhang@hkust-gz.edu.cn).