Metadata-Version: 2.4
Name: nuclear_shape
Version: 0.1.1
Summary: Python package for analysing nuclear shape from 3D-genome models generated from Hi-C data.
Author: Rudi
License: MIT
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: scipy
Requires-Dist: scikit-learn
Requires-Dist: tqdm
Requires-Dist: pandas
Requires-Dist: seaborn
Requires-Dist: matplotlib
Requires-Dist: Jinja2
Requires-Dist: trimesh
Requires-Dist: cvxpy
Provides-Extra: dev
Requires-Dist: pytest; extra == "dev"
Requires-Dist: pytest-cov; extra == "dev"
Requires-Dist: black; extra == "dev"
Requires-Dist: flake8; extra == "dev"
Dynamic: license-file

# nuclear_shape

A small Python library for analysing nuclear shape from 3D‑genome models (Chrom3D `.cmm` files).  
Includes ellipsoid fitting, PCA, basic shape metrics, and simple plotting/rendering.

## Installation

```bash
pip install nuclear_shape
```


## Basic Usage

```python
from nuclear_shape import NuclearShape

shape = NuclearShape("path/to/file.cmm")

shape.ellipsoid_fit()
shape.ellipsoid_inner()
shape.ellipsoid_outer()
shape.compute_pca()

shape.print_metrics()
shape.plot("sphericity", show=True)
shape.render("ellipsoid", show=True)
```

## Example Data
An example .cmm file and a test script are included:

```code
test/example_real_data_0.cmm
python test/test.py
```

## License
MIT License

