numpy>=1.24
scipy>=1.10
pandas>=2.0
scikit-learn>=1.3
matplotlib>=3.7
bed-reader>=1.0
PyYAML>=6.0
pydantic>=2.5
joblib>=1.3
pysam>=0.22

[dev]
pytest>=7.4
pytest-xdist>=3.5
ruff>=0.4
openpyxl>=3.1

[docs]
mkdocs>=1.5
mkdocs-material>=9.5

[gpu]
torch>=2.4
transformers==4.46.3

[mcp]
mcp>=1.0
