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v0.1.0 — IGEM is in early access. See release notes.
IGEM Documentation
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IGEM Documentation

Getting Started

  • Getting Started
    • Installation
    • Quickstart
    • Concepts

User Guide — IGEM

  • User Guide — IGEM
    • Loading data
    • Describing data
    • Modifying data
    • Analyzing data
    • Plotting data
    • Reporting data
    • Report catalogue

User Guide — IGEM Server

  • User Guide — IGEM Server
    • The GE facade
    • Database
      • Alembic
      • Commands
      • Snapshots
      • Access
      • Models
      • Backup
    • ETL pipelines
    • NLP and entity resolution
    • Server-side reports

Operations

  • Operations
    • Server setup (PostgreSQL backend)
    • ETL pipeline
    • Snapshot generation
    • Container deployment (Docker / Apptainer)
    • Monitoring & maintenance

Cookbook

  • Cookbook
    • Phenotype analysis
    • Filtered EWAS on NHANES
    • GxE interaction with a pathway prior
    • Building a custom report end-to-end
    • Container and HPC workflows
    • HPC job array recipe

API Reference

  • API Reference
    • igem (client)
    • igem-server (backend)
    • Glossary

Development

  • Development
    • Contributing
    • Architecture deep-dive
    • Release process
    • Adding a new ETL data source

Release Notes

  • Release Notes
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Development¶

For contributors — repo layout, architecture deep-dive, release process, and how to add a new ETL data source.

  • Contributing
  • Architecture deep-dive
  • Release process
  • Adding a new ETL data source
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