gatom-metabolomic-predictions
CommunityIdentify active metabolic modules from data.
Authortony-zhelonkin
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Finds maximally-regulated metabolic subnetworks from differential expression data using atom-transition networks and BUM scoring, enabling interpretation of transcriptomic or metabolomic changes within metabolic pathways.
Core Features & Use Cases
- Atom-transition network approach to map metabolites and reactions with gene associations.
- BUM-scored SGMWCS optimization to identify active modules.
- Handles input DE data with raw p-values and linear baseMean; supports KEGG, combined, and Rhea network topologies.
- Output includes a ranked list of module components (genes/metabolites) with scores for interpretation.
Quick Start
Provide a differential expression table with raw p-values and baseMean to initialize the GATOM workflow and discover active metabolic modules.
Dependency Matrix
Required Modules
None requiredComponents
Standard package💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: gatom-metabolomic-predictions Download link: https://github.com/tony-zhelonkin/SciAgent-toolkit/archive/main.zip#gatom-metabolomic-predictions Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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