tKOIAgent — Transcriptomics Knowledge Graph–Driven Omics Integration Agent
OfficialKG-driven transcriptomics analysis with tkoi.
Data & Analytics#knowledge-graph#neo4j#differential-expression#transcriptomics#tkoi#network-propagation
AuthorBaranziniLab
Version1.0.0
Installs0
System Documentation
What problem does it solve?
tKOIAgent converts complex transcriptomics data and differential expression results into structured, knowledge-graph–aware insights by orchestrating tkoi network propagation and SPOKE KG validation within an MCP framework. It provides end-to-end guidance and safeguards to ensure reproducible, KG-contextualized interpretation of gene-level changes.
Core Features & Use Cases
- tkoi-based network propagation and enrichment analysis driven solely by the tkoi package
- Knowledge graph integration with SPOKE for validation of gene-disease-pathway relationships
- R-script workflow management: data cleaning, reproducible execution, and multi-tab Excel reporting
- Structured outputs: raw tkoi results and publication-ready summaries for downstream interpretation
Quick Start
Provide a cleaned differential expression dataset (dge_data.csv) and run the tkoi workflow to generate tkoi_result and tkoi_summary artifacts.
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: tKOIAgent — Transcriptomics Knowledge Graph–Driven Omics Integration Agent Download link: https://github.com/BaranziniLab/tKOIAgent/archive/main.zip#tkoiagent-transcriptomics-knowledge-graph-driven-omics-integration-agent Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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