Metadata-Version: 2.4
Name: hicue
Version: 0.3.5
Summary: A visualisation tool for Hi-C dataset.
Project-URL: Homepage, https://github.com/Mae-4815162342/HiCue
Project-URL: Issues, https://github.com/Mae-4815162342/HiCue/issues
Author-email: Maelys Delouis <maelys.delouis@pasteur.fr>
License: CC BY-NC 4.0
License-File: LICENSE
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
Requires-Dist: bcbio-gff
Requires-Dist: chromosight
Requires-Dist: click
Requires-Dist: cooler>=0.10
Requires-Dist: matplotlib
Requires-Dist: numpy
Requires-Dist: pandas>=1.5.0
Requires-Dist: pybigwig
Provides-Extra: dev
Requires-Dist: black; extra == 'dev'
Requires-Dist: codecov; extra == 'dev'
Requires-Dist: hatch; extra == 'dev'
Requires-Dist: hatchling; extra == 'dev'
Requires-Dist: ipython; extra == 'dev'
Requires-Dist: mypy; extra == 'dev'
Requires-Dist: pylint; extra == 'dev'
Requires-Dist: pytest; extra == 'dev'
Requires-Dist: pytest-cov; extra == 'dev'
Requires-Dist: pytest-order; extra == 'dev'
Requires-Dist: pytest-pylint; extra == 'dev'
Requires-Dist: ruff; extra == 'dev'
Requires-Dist: twine; extra == 'dev'
Provides-Extra: test
Requires-Dist: codecov; extra == 'test'
Requires-Dist: pylint; extra == 'test'
Requires-Dist: pytest; extra == 'test'
Requires-Dist: pytest-cov; extra == 'test'
Requires-Dist: pytest-order; extra == 'test'
Requires-Dist: pytest-pylint; extra == 'test'
Requires-Dist: ruff; extra == 'test'
Description-Content-Type: text/markdown

# HiCue

A visualization tool for Hi-C datasets that enables extraction, analysis, and visualization of chromatin interaction data.

## Features

- Extract submatrices from Hi-C data around (pairs of) genomic positions
- Generate pileup visualizations of chromatin interactions
- Support for multiple file formats (BED, GFF, BigWig)
- Compare Hi-C datasets

## Installation

```bash
pip install hicue
```

For development:

```bash
git clone https://github.com/Mae-4815162342/HiCue.git
cd HiCue
pip install -e .
```

## Usage

### Extract submatrices around genomic positions

```bash
hicue extract output_dir positions.bed data.cool
```

### Generate pileup visualizations

```bash
hicue extract output_dir positions.bed data.cool --pileup
```

...

## Command Line Interface

HiCue provides several commands:

- `extract`: Extract submatrices around genomic positions
- `extract2d`: Extract submatrices for 2D genomic intervals
- `tracks`: Overlay genomic tracks on Hi-C visualizations
- `compare`: Compare two Hi-C datasets
- `annotate`: Annotate genomic positions with GFF features

Use `hicue <command> --help` for detailed options.

## License

This project is licensed under CC BY-NC 4.0. See the [LICENSE](LICENSE) file for details.

## Citation

If you use HiCue in your research, please cite:

```
...
```

