integration Tutorial

This tutorial covers the integration skill in OmicsAgent.ai.

Run this skill

python3 omics_agent.py --skill integration

# Or via chat mode:
python3 omics_agent.py --chat
You: Run integration analysis on my PBMC data

What this skill does

See the Skills Library for full documentation of inputs, QC thresholds, pipeline steps, and outputs for this skill.

Reproducibility bundle

Every run produces:

• report.md — full analysis report
• figures/ — all publication-quality PNG figures
• tables/ — all result tables in CSV format
• commands.sh — exact commands to reproduce
• environment.yml — conda environment snapshot
• checksums.sha256 — SHA-256 verification