Python package for analysing nuclear shape from 3D-genome models generated from Hi-C data.
Project description
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
pip install nuclear_shape
Basic Usage
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:
test/example_real_data_0.cmm
python test/test.py
License
MIT License
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