PBMCpedia MCP

Query PBMCpedia, a harmonized peripheral-blood-mononuclear-cell scRNA-seq atlas, for gene expression, differential expression and pathway results by cell type, sex, age group and disease.


Type	MCP server
Supplier	MCPmed (Chair for Clinical Bioinformatics, Saarland University)
Availability	Beta — last upstream commit 2026-02-25
Pricing	Free / OSS — BSD-3-Clause; the backing PBMCpedia web service is public and needs no API key
Capabilities	Read-only — six query tools against the public PBMCpedia API
Verified	works · 2026-08-17
Security	caution · 2026-08-17 — BSD-3-Clause and provenance confirmed; repo stale (last push 2026-02-25) and low-traffic

How to install

Requires Node.js with npm (the server is TypeScript, built on the TypeScript MCP SDK). There is no published npm package — install from a clone.

Clone and install dependencies:

git clone https://github.com/MCPmed/PBMCpediaMCP
cd PBMCpediaMCP
npm install

Pick one of the two transports below.

Option A — stdio (Claude launches the server)

Claude Code:
```
claude mcp add --transport stdio pbmcpedia -- npm start -- --transport stdio
```
Then open ~/.claude.json, find the pbmcpedia entry, and add a "cwd" key pointing at your clone — claude mcp add has no --cwd flag, and without it npm start runs in the wrong directory and the server will not launch:
```
"pbmcpedia": {
  "type": "stdio",
  "command": "npm",
  "args": ["start", "--", "--transport", "stdio"],
  "cwd": "/path/to/PBMCpediaMCP"
}
```
(replace /path/to/PBMCpediaMCP with the absolute path of your clone — e.g. /Users/you/repos/PBMCpediaMCP, or the output of pwd if you are still inside it from step 1).

Claude Desktop — add to claude_desktop_config.json:

{
  "mcpServers": {
    "pbmcpedia": {
      "command": "npm",
      "args": ["start", "--", "--transport", "stdio"],
      "cwd": "/path/to/PBMCpediaMCP"
    }
  }
}

Fully quit and relaunch Claude Desktop after editing.

With stdio, do not run the server yourself — Claude starts and stops the process.

Option B — HTTP (you run the server)

Start it and leave it running in its own terminal:

npm start

Then, in Claude Code:

claude mcp add --transport http pbmcpedia http://localhost:3002/mcp

3002 is the default port in server.ts; if you override it, use your port. Claude Desktop has no native HTTP transport — use Option A there, or proxy through mcp-remote.

What it does

Six tools, read from server.ts (the README does not enumerate them):

getMetaData — cohort metadata, optionally summarized, filtered by sex and/or disease
getExpressionPerGene — expression for named genes, at fine or broad cell-type granularity, paginated
getDEGs — differentially expressed genes filtered by age group, sex, disease and cell type, with ordering and pagination
getDEperCellType — differential expression for specific genes within a cell type
getPathways — pathway results with the same cohort and cell-type filters
getAntibodyChains — antibody chains for a given clone

Primary use cases: checking whether a gene is differentially expressed in a specific blood cell type in a given disease, sizing cohorts before an experiment, cross-referencing pathway signals across PBMC subsets.

Notes

PBMCpedia harmonizes published PBMC scRNA-seq studies under a unified reference mapping and cell-type annotation, and includes TCR/BCR and CITE-seq surface-protein layers alongside gene expression — which is why the server exposes an antibody-chain tool next to the expression tools.

The upstream README documents the install and transport wiring but not the tool surface; the tool list above was read directly from the repository’s server.ts on 2026-08-15 and may drift if upstream changes.

The repository is new and low-traffic (0 stars). It is one of a family of MCPmed servers over bioinformatics web resources — see also NCBI GEO, Allen Brain Atlas and UCSC Cell Browser MCP.

Sources

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