Metadata-Version: 2.4
Name: omniage
Version: 0.99.5
Summary: The package provides a comprehensive Python framework for aging research. It offers high-level interfaces for calculating a vast suite of aging-related clocks and biomarkers.
Author: Du Zhaozhen
Author-email: duzhaozhen2022@sinh.ac.cn
Requires-Python: >=3.10
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Requires-Dist: matplotlib (>=3.8.0,<4.0.0)
Requires-Dist: numpy (<2.0.0)
Requires-Dist: pandas (>=2.2.0,<3.0.0)
Requires-Dist: pyarrow (>=14.0.0)
Requires-Dist: pypmml (>=0.9.0,<2.0.0)
Requires-Dist: requests (>=2.25.0)
Requires-Dist: scanpy (>=1.10.0,<2.0.0)
Requires-Dist: scikit-learn (>=1.4.0,<2.0.0)
Requires-Dist: scipy (>=1.10.0,<2.0.0)
Requires-Dist: seaborn (>=0.13.0,<0.14.0)
Requires-Dist: statannotations (>=0.7.0,<0.8.0)
Requires-Dist: statsmodels (>=0.14.0,<0.15.0)
Description-Content-Type: text/markdown

# OmniAge

**A comprehensive Python framework for aging research and biological clock calculation**

**Authors:**
* **Zhaozhen Du** (Shanghai Institute of Nutrition and Health, CAS) - duzhaozhen2022@sinh.ac.cn
* **Andrew E. Teschendorff** (Shanghai Institute of Nutrition and Health, CAS) - andrew@sinh.ac.cn

---

## 📖 Overview

**OmniAge** offers high-level interfaces for calculating a vast suite of aging-related clocks and biomarkers. It is designed to integrate seamlessly with standard bioinformatics workflows (e.g., `scanpy`, `pandas`).

The package covers three main categories:
1.  **Epigenetic (DNAm) Clocks**: Including Chronological, Biological (e.g., GrimAge, DunedinPACE), Cellular (Mitotic), and Gestational age clocks.
2.  **Transcriptomic (RNA) Clocks**: Includes clocks based on bulk or single-cell RNA-seq data (e.g., scImmuAging, PASTA).
3.  **Proteomic Clocks** Comprises age predictors based on plasma protein expression levels(e.g., WyssCorayOrganAge, GladyshevOrganAge).
4.  **Other DNAm Human Aging-Related Surrogate Biomarkers** Provides specialized epigenetic markers for plasma proteins, inflammation, clonal hematopoiesis of indeterminate potential (CHIP), lifestyle traits, and specific disease risk indices (e.g., Episcores, CRP, DNMT3A, McCartney_Trait, and SmokeIndex).
3.  **Other Species**: Integrates universal cross-species clocks alongside models tailored specifically for non-human species(e.g., UniversalPanMammalianClocks, and MeerMouse).

> **✨ For a complete list of supported clocks and detailed usage examples, please refer to our [Tutorial Notebook](https://github.com/Duzhaozhen/OmniAgePy/blob/main/notebooks/tutorial.ipynb).**

## 🛠 Installation
Install via pip with the subdirectory flag:

```r
git clone https://github.com/Duzhaozhen/OmniAgePy.git
pip install .
```
> [!TIP]
> If you encounter errors building **pyarrow** or **h5py** (common on Linux servers), we recommend pre-installing these dependencies via Conda:
> 
> ```bash
> conda install -c conda-forge pyarrow h5py
> ```
---

