Metadata-Version: 2.4
Name: celios
Version: 0.1.0
Summary: CELIOS: extract omics data into integrated activity datasets for Boolean model calibration. Part of the DrugLogics and the TRAFIKK pipelines.
Author: Viviam Solangeli Bermúdez Paiva
Author-email: viviambermudez@gmail.com
License: MIT
Project-URL: Homepage, https://github.com/druglogics/celios
Project-URL: Source, https://github.com/druglogics/celios
Project-URL: Issues, https://github.com/druglogics/celios/issues
Keywords: omics cell-lines boolean-models druglogics pipeline
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pandas>=1.0.0
Requires-Dist: pyyaml>=5.0.0
Provides-Extra: dev
Requires-Dist: pytest>=6.0.0; extra == "dev"
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: keywords
Dynamic: license
Dynamic: license-file
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# CELIOS

**CEll LIne OmicS processor** — extract omics data into integrated activity datasets for Boolean model calibration.

[![Python 3.8+](https://img.shields.io/badge/Python-3.8%2B-blue)](https://www.python.org)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)

Used in the [DrugLogics](https://github.com/druglogics) and [TRAFIKK](https://github.com/druglogics/trafikk) pipelines.

---

## 📊 What You Get

✅ **Node Dictionary** (`node_HGNC_dict.csv`)
- Network nodes mapped to HGNC gene symbols
- Enables consistent gene annotation

✅ **Activity Master Matrix** (`activity_master_matrix.csv`)
- All omics data sources combined (mutations, CNV, TF, expression) for each node in the network across cell lines
- Format: nodes × cell_lines__data_source

✅ **Priority-Filtered Activity** (`activity_from_master.csv`)
- One activity value per node-cell line (highest priority source)
- Ready for downstream analysis

✅ **Per-Cell-Line Training Files** (optional)
- DrugLogics or Trafikk compatible format
- Saved to `cellfiles_dir/` if specified

---

## Quick Start

**Install:**
```bash
pip install -e .
```

**Run pipeline:**
```bash
celios run --config config.yaml --verbose
```

**Get help:**
```bash
celios --help
```

---

## 📚 Documentation

Detailed documentation is in the documentation markdown files:

| Document | Purpose |
|----------|---------|
| **[QUICKSTART.md](documentation/QUICKSTART.md)** | 5-minute quick reference with common commands |
| **[INSTALL.md](documentation/INSTALL.md)** | Installation guide, virtual environments, troubleshooting |
| **[USAGE.md](documentation/USAGE.md)** | Full usage guide, advanced examples, and API reference |
| **[CONFIGURATION.md](documentation/CONFIGURATION.md)** | Configuration reference with all options |
| **[OUTPUTS.md](documentation/OUTPUTS.md)** | Output file formats and interpretation |
| **[notebooks/](notebooks/)** | Interactive Jupyter notebooks with examples |

---

## Features

- **Step 1:** Node dictionary generation from biological networks (SIF format)
- **Step 2:** Cell-line identifier resolution and tissue-aware organization
- **Step 3:** Multi-source omics integration (mutations, CNV, TF activity, expression)
- **Step 4:** DrugLogics and Trafikk pipeline training file generation (specific calibration file used in the Gitsbe module)
- **Format support:** Legacy CCLE (genes × SIDM) and 26Q1 (ModelID × genes) formats
- **Configuration-driven:** JSON or YAML configs for easy reproducibility
- **Tissue organization:** Optional per-tissue output structure for DrugLogics compatibility

---

## License

[MIT License](LICENSE)

