Metadata-Version: 2.4
Name: pyEpiAneufinder
Version: 0.3.6
Summary: Identify copy number variations from single-cell ATAC-seq data
Author-email: Katharina Schmid <katharina.schmid@bmc.med.lmu.de>, Aikaterini Symeonidi <asymeonidi@bmc.med.lmu.de>, Angelos Nikolaou <anguelos.nicolaou@gmail.com>, Ida Büschel <Ida.Bueschel@helmholtz-munich.de>, Maria Colomé-Tatché <maria.colome@bmc.med.lmu.de>
License-Expression: GPL-3.0-only
Project-URL: Homepage, https://github.com/colomemaria/pyEpiAneufinder
Project-URL: Repository, https://github.com/colomemaria/pyEpiAneufinder
Project-URL: Documentation, https://pyepianeufinder.readthedocs.io/
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy>=1.26.4
Requires-Dist: pandas>=2.2.0
Requires-Dist: matplotlib>=3.7.1
Requires-Dist: seaborn>=0.12.2
Requires-Dist: scipy>=1.8.0
Requires-Dist: anndata>=0.8.0
Requires-Dist: natsort>=8.0.2
Requires-Dist: biopython>=1.79
Requires-Dist: scikit-misc>=0.5.2
Requires-Dist: tqdm>=4.67.1
Provides-Extra: test
Requires-Dist: pytest>=8.0; extra == "test"
Provides-Extra: docs
Requires-Dist: sphinx>=8.1.3; extra == "docs"
Requires-Dist: furo>=2025.12.19; extra == "docs"
Requires-Dist: myst-parser>=4.0.1; extra == "docs"
Dynamic: license-file

# pyEpiAneufinder: Identifying copy number alterations from single-cell ATAC-seq data

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This package is the Python re-implementation of our R package
`epiAneufinder`, developed for identifying copy number variations (CNVs) from
single-cell ATAC-seq data.

**Important remark:** The Python package is still in beta testing. Please
report issues and improvement suggestions through GitHub Issues.

Single-cell open chromatin profiling through scATAC-seq provides fragment count
information that can be used to infer copy number variation. `pyEpiAneufinder`
uses this information to extract genome-wide CNV profiles for individual cells,
adding a layer of genomic variation analysis without requiring additional
experiments.

The original `epiAneufinder` publication is:

Ramakrishnan, A., Symeonidi, A., Hanel, P. et al. epiAneufinder identifies copy
number alterations from single-cell ATAC-seq data. *Nature Communications* 14,
5846 (2023). https://doi.org/10.1038/s41467-023-41076-1

The R version, including additional background information, is available at:
https://github.com/colomemaria/epiAneufinder

### Installation

```bash
pip install pyEpiAneufinder
```

For development, including tests and docs:

```bash
pip install -e ".[test,docs]"
```

The full workflow guide, figures, API usage, and example analyses are available
in the Read the Docs documentation:
https://pyepianeufinder.readthedocs.io/

### Cite

If you use `pyEpiAneufinder`, please cite both the package and the original
`epiAneufinder` publication.

Package / repository:

Schmid, K., Symeonidi, A., Nikolaou, A., Bueschel, I., and Colome-Tatche, M.
`pyEpiAneufinder`. GitHub repository:
https://github.com/macelik/pyEpiAneufinder

Original method paper:

Ramakrishnan, A., Symeonidi, A., Hanel, P. et al. epiAneufinder identifies copy
number alterations from single-cell ATAC-seq data. *Nature Communications* 14,
5846 (2023). https://doi.org/10.1038/s41467-023-41076-1

### Authors of the Python Re-implementation

Katharina Schmid (katharina.schmid@bmc.med.lmu.de)

Aikaterini Symeonidi (asymeonidi@bmc.med.lmu.de and ksymeonidh@gmail.com)

Angelos Nikolaou (anguelos.nicolaou@gmail.com)

Ida Bueschel (Ida.Bueschel@helmholtz-munich.de)

Maria Colome-Tatche (maria.colome@bmc.med.lmu.de)

### Version history

* 0.3.6
    * Test release for GitHub Release and PyPI publishing workflows
* 0.1
    * Initial Release (based on epiAneufinder v1.1.3)
