Metadata-Version: 2.4
Name: heredicalc
Version: 4.1.0
Summary: Full Likelihood Bayes factor computation for hereditary cosegregation analysis
Project-URL: Homepage, https://github.com/heredicalc/heredicalc
Project-URL: Documentation, https://heredicalc.github.io/heredicalc
Project-URL: Repository, https://github.com/heredicalc/heredicalc
Project-URL: Changelog, https://github.com/heredicalc/heredicalc/blob/main/CHANGELOG.md
Author: HerediCalc Contributors
License: MIT
Keywords: Bayesian,FLB,cosegregation,genetics,pathogenicity,pedigree
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Requires-Python: >=3.12
Requires-Dist: numpy>=1.26
Requires-Dist: packaging>=24.0
Requires-Dist: pandas>=2.0
Requires-Dist: platformdirs>=4.2
Requires-Dist: pydantic>=2.5
Requires-Dist: pyyaml>=6.0
Requires-Dist: rich>=13.7
Requires-Dist: typer>=0.12
Provides-Extra: dev
Requires-Dist: black>=24.4; extra == 'dev'
Requires-Dist: mkdocs-jupyter>=0.24; extra == 'dev'
Requires-Dist: mkdocs-material>=9.5; extra == 'dev'
Requires-Dist: mkdocstrings[python]>=0.25; extra == 'dev'
Requires-Dist: nbformat>=5.9; extra == 'dev'
Requires-Dist: pytest-cov>=5.0; extra == 'dev'
Requires-Dist: pytest>=8.2; extra == 'dev'
Requires-Dist: ruff>=0.5; extra == 'dev'
Provides-Extra: docs
Requires-Dist: mkdocs-jupyter>=0.24; extra == 'docs'
Requires-Dist: mkdocs-material>=9.5; extra == 'docs'
Requires-Dist: mkdocstrings[python]>=0.25; extra == 'docs'
Requires-Dist: nbformat>=5.9; extra == 'docs'
Provides-Extra: gui
Requires-Dist: pyqt6>=6.7; extra == 'gui'
Requires-Dist: sqlalchemy>=2.0; extra == 'gui'
Provides-Extra: web
Requires-Dist: fastapi>=0.111; extra == 'web'
Requires-Dist: psycopg2-binary>=2.9; extra == 'web'
Requires-Dist: sqlalchemy>=2.0; extra == 'web'
Requires-Dist: streamlit>=1.36; extra == 'web'
Requires-Dist: uvicorn>=0.30; extra == 'web'
Description-Content-Type: text/markdown

# HerediCalc v4

**Full Likelihood Bayes (FLB) factor computation for Bayesian cosegregation analysis.**

HerediCalc quantifies whether a genetic entity co-segregates with a heritable
phenotype in a pedigree beyond what is expected by chance. The resulting FLB
factor supports pathogenicity classification of genetic variants (FLB > 10:
strong evidence of pathogenicity).

## Requirements

- Python ≥ 3.12
- R ≥ 4.2 with packages: `segregatr`, `kinship2`

## Quick Install

```bash
pip install heredicalc
```

For R dependency setup, see the [documentation](https://heredicalc.github.io/heredicalc).

## Quick Start

```bash
# Generate a config file interactively
heredicalc add config

# Run FLB computation
heredicalc run Belman.ped --config heredicalc.yml

# Batch computation over a directory of pedigrees
heredicalc batch pedigrees/ --config heredicalc.yml
```

Example `heredicalc.yml`:

```yaml
computation:
  genetic_entity: BRCA1
  allele_freq: 0.0001

plugins:
  incidence_source: ci5_ix
  phenotype_model: hbopc
  trait_mapper: ci5_ix_hbopc
  penetrance_model: victor
  flb_calculator: segregatr
  params:
    population: Latvia
    age_bands: [30, 40, 50, 60, 65, 70, 80]
```

## Documentation

Full documentation: [https://heredicalc.github.io/heredicalc](https://heredicalc.github.io/heredicalc)

## Contributing

See [CONTRIBUTING.md](CONTRIBUTING.md).

## License

MIT
