Metadata-Version: 2.4
Name: coolbox
Version: 0.4.0
Summary: Jupyter notebook based genomic data visulization toolkit.
Author-email: Weize Xu <vet.xwz@gmail.com>
License: GPLv3
Project-URL: Homepage, https://github.com/GangCaoLab/CoolBox
Project-URL: Documentation, https://gangcaolab.github.io/CoolBox/index.html
Project-URL: Repository, https://github.com/GangCaoLab/CoolBox
Project-URL: Bug Tracker, https://github.com/GangCaoLab/CoolBox/issues
Keywords: genomics,bioinformatics,visualization,Jupyter
Classifier: Development Status :: 3 - Alpha
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Requires-Python: <4,>=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: scipy>=1.0.0
Requires-Dist: numpy
Requires-Dist: pandas>=1.0.0
Requires-Dist: statsmodels
Requires-Dist: matplotlib>=3.8.4
Requires-Dist: jupyter>=1.0.0
Requires-Dist: ipywidgets>=7.5.1
Requires-Dist: nbformat
Requires-Dist: voila
Requires-Dist: svgutils
Requires-Dist: intervaltree
Requires-Dist: dna_features_viewer
Requires-Dist: h5py
Requires-Dist: cooler
Requires-Dist: numpydoc
Requires-Dist: fire
Requires-Dist: oxbow>=0.4.2
Provides-Extra: doc
Requires-Dist: sphinx_rtd_theme; extra == "doc"
Requires-Dist: autodocsumm; extra == "doc"
Requires-Dist: recommonmark; extra == "doc"
Requires-Dist: nbsphinx; extra == "doc"
Requires-Dist: sphinx_gallery; extra == "doc"
Requires-Dist: sphinx-autobuild; extra == "doc"
Provides-Extra: strawc
Requires-Dist: strawC; extra == "strawc"
Provides-Extra: dev
Requires-Dist: pytest; extra == "dev"
Requires-Dist: pytest-cov; extra == "dev"
Requires-Dist: build; extra == "dev"
Dynamic: license-file

<p align="center">
  <img src="docs/images/banner.png">
</p>

<hr>

<p align="center">

  <a href="https://mybinder.org/v2/gh/GangCaoLab/CoolBox/master?filepath=tests%2FTestRegion.ipynb">
    <img src="https://mybinder.org/badge_logo.svg" alt="Binder" />
  </a>
  
  <a href="https://anaconda.org/bioconda/coolbox">
    <img src="https://img.shields.io/conda/v/bioconda/coolbox" alt="Install with conda" />
  </a>
  
  
  <a href="https://pypi.python.org/pypi/coolbox/">
    <img src="https://img.shields.io/pypi/v/coolbox.svg" alt="Install with PyPi" />
  </a>
  
  <a href="https://hub.docker.com/r/nanguage/coolbox">
  	<img src="https://img.shields.io/docker/v/nanguage/coolbox?label=docker&logo=docker&sort=semver" alt="Docker version">
  </a>
  
  <a href="https://github.com/GangCaoLab/CoolBox/releases">
  	<img src="https://img.shields.io/github/v/release/gangcaolab/coolbox?include_prereleases&label=github" alt="Github release">
  </a>
 
  <a href="https://gangcaolab.github.io/CoolBox/index.html">
  	<img src="https://readthedocs.org/projects/ansicolortags/badge/?version=latest" alt="Documentation">
  </a>
  
  <a href="https://pypi.python.org/pypi/coolbox">
    <img src="https://img.shields.io/pypi/pyversions/coolbox.svg" alt="Version">
  </a>
  
  <a href="https://pepy.tech/project/coolbox">
    <img src="https://pepy.tech/badge/coolbox" alt="Downloads">
  </a>

  <a href="https://pepy.tech/project/coolbox">
    <img src="https://pepy.tech/badge/coolbox/week" alt="Downloads per week">
  </a>
  
  <a href="https://github.com/GangCaoLab/coolbox/actions/workflows/python-package-conda.yml">
    <img src="https://github.com/GangCaoLab/coolbox/actions/workflows/python-package-conda.yml/badge.svg" alt="Build Status">
  </a>

  <a href="https://www.biorxiv.org/content/10.1101/2021.04.15.439923v1">
    <img src="https://img.shields.io/badge/preprint-biorxiv-red" alt="biorxiv">
  </a>

  <a href="https://github.com/GangCaoLab/CoolBox/blob/master/LICENSE">
    <img src="https://img.shields.io/github/license/GangCaoLab/coolbox" alt="license">
  </a>

</p>


Flexible, user-friendly genomic data visualization toolkit. 

![](docs/images/api_and_cli.png)

## Highlights:

* Multi-omics data interactively visualization.
* User-friendly [API (ggplot2-like Python EDSL)](https://gangcaolab.github.io/CoolBox/quick_start_API.html) and [CLI](https://gangcaolab.github.io/CoolBox/quick_start_CLI.html).
* Show within Jupyter notebook.
* Ease to fetch data and in cooperation with other Python package.
* Ease to implement/add custom track and integrate into CoolBox.

More details please read the [documentation](https://gangcaolab.github.io/CoolBox/index.html).
Interactively online demo: [binder](https://mybinder.org/v2/gh/GangCaoLab/CoolBox/master?filepath=tests%2FTestRegion.ipynb)

## Develop

See [CONTRIBUTING.md](https://github.com/GangCaoLab/CoolBox/blob/master/CONTRIBUTING.md) 

## Citation

```
@article{xu2021coolbox,
  title={CoolBox: A flexible toolkit for visual analysis of genomics data},
  author={Xu, Weize and Zhong, Quan and Lin, Da and Zuo, Ya and Dai, Jinxia and Li, Guoliang and Cao, Gang},
  journal={BMC bioinformatics},
  volume={22},
  number={1},
  pages={1--9},
  year={2021},
  publisher={Springer}
}
```

## Thanks

+ [pyGenomeTracks](https://github.com/deeptools/pyGenomeTracks),
CoolBox's plot system is fork from it.

### Contributors 
This project exists thanks to all the people who contribute. 

<a href="https://github.com/GangCaoLab/CoolBox/graphs/contributors">
  <img src="https://contrib.rocks/image?repo=GangCaoLab/CoolBox" />
</a>

