Metadata-Version: 2.4
Name: lipid-pathway-integrator
Version: 1.0.2
Summary: Unifies lipid ontology-aware representation and pathway-based multi-omics integration in a single framework
Author-email: Dylan Ross <dylan.ross@pnnl.gov>
Project-URL: Repository, https://github.com/pnnl-compbio/lipid_pathway_integrator
Project-URL: Documentation, https://lipi.readthedocs.io
Project-URL: Issues, https://github.com/pnnl-compbio/lipid_pathway_integrator/issues
Requires-Python: >=3.14
Description-Content-Type: text/markdown
Requires-Dist: PyYAML>=6.0.3
Requires-Dist: networkx>=3.6
Requires-Dist: requests>=2.32.5
Requires-Dist: matplotlib>=3.10.7
Requires-Dist: polars>=1.38.1
Requires-Dist: jupyter>=1.1.1
Requires-Dist: scipy>=1.18.0
Requires-Dist: lipidimea>=2.0.1
Provides-Extra: docs
Requires-Dist: sphinx>=7.0; extra == "docs"
Requires-Dist: sphinx-rtd-theme>=2.0; extra == "docs"
Requires-Dist: numpydoc>=1.5; extra == "docs"
Requires-Dist: sphinx-autodoc-typehints>=1.24; extra == "docs"
Requires-Dist: sphinx-autobuild>=2024.0; extra == "docs"

# LiPI
<b>Li</b>pidomics   <b>P</b>athway   <b>I</b>ntegrator

- Unifies lipid ontology-aware representation and pathway-based multi-omics integration in a single framework
- Ingests existing reference pathways from KEGG and supports defining custom pathways via YAML
- Pathways are represented as editable graph-structured data specifically designed to accommodate individual molecular lipid species
- Feature-level statistics from any -omics data type can be mapped to pathway nodes and visualized to support interpretation


## Installation
```sh
    pip install lipid-pathway-integrator
```

## Documentation
- [https://lipi.readthedocs.io/](https://lipi.readthedocs.io/)

## Demos
- [GBM (CPTAC3)](demos/cptac_3_gbm/demo.ipynb)
- [AML (CPTAC4)](demos/cptac_4_aml/demo.ipynb)

## License & Disclaimer
- [license (BSD)](license.txt)
- [disclaimer](disclaimer.txt)

## Contributors:
- Dylan Ross (dylan.ross@pnnl.gov)

