MCP Genelab
未认领A Model Context Protocol (MCP) server for querying Neo4j Graph Databases with customized tools to query the NASA GeneLab Knowledge Graph
01 / 选择客户端
03 / 添加配置
claude mcp add --transport stdio 'mcp-genelab' -- 'uvx' 'mcp-genelab'04 / 在客户端中确认
打开客户端的 MCP 设置，确认服务器已连接并列出工具。复制配置不代表连接成功。
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已认领和已认证的服务器每周接受一次静态扫描，显示代码能触及的范围（外部服务、环境变量、shell 命令、代理配置目录）以及带有已知公告的依赖。认领此列表即可获得。 安全概况的工作原理
22 个工具中显示 22 个
文档中列出的工具 (22)
内容来自项目文档。服务器握手不会验证每个工具的说明或行为。
clean_mermaid_diagram
Clean and validate a Mermaid class diagram of the KG schema
create_chat_transcript
Export the current chat as a formatted transcript
create_venn_diagram
Create a Venn diagram comparing DEGs / DMRs / DA organisms across 2 or 3 assays (also supports the expressionmethylation 2×2 grid variant); PNG returned inline and registered for resource fetch
create_volcano_plot
Generate a volcano plot of differential expression / methylation / abundance results; PNG returned inline and registered for resource fetch
fetch_plot
Re-fetch the canonical PNG bytes of a previously generated plot from the in-memory registry (last 8 plots, FIFO eviction). Returns the bytes as an EmbeddedResource so clients can render them inline. Safe to call repeatedly — no Cypher, no matplotlib, no re-render
find_common_de_genes_overlapping_dm_regions
Identify DE genes whose promoter (or other region) is also differentially methylated — supports method-aware significance filtering and pooled-DM evidence across multiple methylation assays
find_common_differentially_abundant_organisms
Intersect differentially abundant organisms across multiple assays
find_common_differentially_expressed_genes
Intersect DEGs across multiple assays (up and down directions kept separate)
find_common_differentially_methylated_regions
Intersect DMRs across multiple assays, with optional MethylationRegion filters
find_differentially_abundant_organisms
Find organisms with differential abundance for a given assay (DESeq2 and/or ANCOM-BC)
find_differentially_expressed_genes
Find up/downregulated genes for a given assay (DESeq2)
find_differentially_methylated_regions
Find hyper/hypomethylated regions for a given assay, with optional inpromoter / inexon / inintron / distance filters
get_neo4j_schema
List all node types, their attributes, and relationships in the knowledge graph
get_node_metadata
Get descriptions of all node types from MetaNode entries
get_output_directory
Return the currently configured output directory
get_relationship_metadata
Get descriptions of all relationship types and their properties
get_save_script
Return a markdown block with multiple save options for a previously generated plot: right-click save, ask-LLM-client-to-save, or fetch via the plot:// resource URI
get_study_info
Get detailed information about a specific study and its assays (metadata + assay inventory)
query
Execute a read-only Cypher query on the Neo4j database. Fallback for questions the specialists don't cover — the DEFAULTINSTRUCTIONS policy directs the LLM to use specialist tools first
select_assays
Browse and filter assays by study, organism, technology, or measurement; resolve a factor pair to one or more assay IDs
set_output_directory
Set the user-facing directory where plots and CSV files should be saved
visualize_schema
Generate a visual schema diagram of the knowledge graph