LipiNet Documentation

Main:

• Introduction
  • Core features
• Installation
• Quick Start
• LipiNet API
  • lipinet package

Notebooks:

• Parse SwissLipids
  • Parsing the manual way
  • Using the LipiNet parse_swisslipids function
• Explore SwissLipids
  • Loading dependencies and data
  • Building the network with OnionNet
  • Filtering the network
  • Exploring bipartite networks
• Parse Rhea
  • Parsing the manual way
  • Using the LipiNet parse_rhea function
• Explore Rhea
  • Loading the node and edge info
  • Building the network with OnionNet
  • Filtering the network
  • Analyse the Rhea network
• Build LipiNet
  • 1) Cache status
  • 2) Build the combined LipiNet (public API)
  • 3) Behind the scenes: parse each source
  • 4) Cross-source linking: ChEBI (SwissLipids ↔ Rhea)
  • 5) Merging node frames (origin tagging & prefixing unique columns)
  • 6) Merging edge frames (source edges + interlayer links)
  • 7) Quick QC: orphans & coverage by layer
  • 8) Optional: Write outputs to .data/processed/
• Explore LipiNet
  • Setup
  • Explore LipiNet
  • Conclusion

> [!WARNING] Under Development  
> This package is still in development and is subject to change. Some functions may be deprecated or modified in the near future. We welcome feature requests or feedback.