CEll LIne OmicS processor — extract omics data into integrated activity datasets for Boolean model calibration.
Used in the DrugLogics and TRAFIKK pipelines.
Install:
pip install -e .Run pipeline:
celios run --config config.yaml --verboseGet help:
celios --helpDetailed documentation is in the root-level markdown files:
| Document | Purpose |
|---|---|
| QUICKSTART.md | 5-minute quick reference with common commands |
| INSTALL.md | Installation guide, virtual environments, troubleshooting |
| PIPELINE.md | Detailed 3-step pipeline overview with configurations |
| USAGE.md | Full usage guide, advanced examples, and API reference |
| CONFIGURATION.md | Configuration reference with all options |
| OUTPUTS.md | Output file formats and interpretation |
| ARCHITECTURE.md | Code organization, module descriptions, architecture |
| notebooks/ | Interactive Jupyter notebooks with examples |
- 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)
- 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
See CONTRIBUTING.md (if available) or submit issues to GitHub.