Metadata-Version: 2.4
Name: genome-atlas
Version: 0.0.2
Summary: Unified knowledge graph and embedding space for programmable genome-writing enzymes
Author-email: Anees Ahmed <anees.ahmed2022@vitstudent.ac.in>
License: MIT
Project-URL: Homepage, https://github.com/ahmedanees-m/genome-atlas
Project-URL: Documentation, https://genome-atlas.readthedocs.io
Project-URL: Repository, https://github.com/ahmedanees-m/genome-atlas
Project-URL: Changelog, https://github.com/ahmedanees-m/genome-atlas/blob/main/CHANGELOG.md
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pen-core>=0.0.1
Requires-Dist: duckdb>=0.10.0
Requires-Dist: networkx>=3.2
Requires-Dist: rdflib>=7.0
Requires-Dist: torch>=2.2
Requires-Dist: torch-geometric>=2.5
Requires-Dist: pandas>=2.2
Requires-Dist: pyarrow>=15.0
Requires-Dist: click>=8.1
Provides-Extra: dev
Requires-Dist: pytest>=8.1; extra == "dev"
Requires-Dist: pytest-cov>=5.0; extra == "dev"
Requires-Dist: ruff>=0.3; extra == "dev"
Requires-Dist: mypy>=1.9; extra == "dev"
Requires-Dist: pre-commit>=3.7; extra == "dev"
Provides-Extra: docs
Requires-Dist: sphinx>=7.3; extra == "docs"
Requires-Dist: sphinx-autodoc-typehints; extra == "docs"
Requires-Dist: furo; extra == "docs"
Requires-Dist: myst-nb; extra == "docs"
Dynamic: license-file

# genome-atlas

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[![Docs](https://img.shields.io/badge/docs-readthedocs-blue)](https://genome-atlas.readthedocs.io)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)

A unified knowledge graph and embedding space for programmable genome-writing enzymes — CRISPR, CAST, bridge recombinases, Fanzor, and more — with cross-system selection decision support.

Part of the [PEN-STACK](https://github.com/ahmedanees-m/pen-stack) infrastructure for non-destructive genome engineering.

## Install

```bash
pip install genome-atlas
```

## Quickstart

```python
from genome_atlas import Atlas

atlas = Atlas.load()
recs = atlas.select_editor(
    cell_type="HEK293T",
    edit_type="insertion",
    cargo_size_bp=1500,
    delivery="AAV",
    top_k=5,
)
for r in recs:
    print(r.system, r.pen_score, r.aav_fit)
```

## Citation

See [CITATION.cff](CITATION.cff) or cite the preprint:
> Ahmed, A. (2026). *GENOME-ATLAS: A unified knowledge graph for programmable genome-writing enzymes.* bioRxiv.

## License

MIT — see [LICENSE](LICENSE).
