MCP server

Expression Atlas

io.github.pipeworx-io/expression-atlas

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

EBI Expression Atlas MCP.

Working at last checkOfficial: pipeworx.io's GitHub account (pipeworx-io)About 26,768 tokens per request once connected44 tools

Website Source

https://gateway.pipeworx.io/expression-atlas/mcp

At a glance

Type: MCP server
Publisher: pipeworx.io (verified by the MCP Registry)
Status: Working at last check
Tools: 44
Token cost: About 26,768 tokens per request
Sets up in: Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok
Last checked: 26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to Cursor Add to VS Code VS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http expression-atlas https://gateway.pipeworx.io/expression-atlas/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.expression-atlas]
url = "https://gateway.pipeworx.io/expression-atlas/mcp"

Gemini CLI

{"mcpServers":{"expression-atlas":{"httpUrl":"https://gateway.pipeworx.io/expression-atlas/mcp"}}}

Cursor

{"mcpServers":{"expression-atlas":{"url":"https://gateway.pipeworx.io/expression-atlas/mcp"}}}

VS Code

{"servers":{"expression-atlas":{"type":"http","url":"https://gateway.pipeworx.io/expression-atlas/mcp"}}}

Antigravity

agy mcp add expression-atlas https://gateway.pipeworx.io/expression-atlas/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"expression-atlas","server_url":"https://gateway.pipeworx.io/expression-atlas/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"expression-atlas","server_url":"https://gateway.pipeworx.io/expression-atlas/mcp"}

Tools

get_experiment ~136 tokens
Get metadata for a single EBI Expression Atlas experiment by accession (e.g. "E-MTAB-4045"). Returns accession, description, species, type, assay count, and experimental factors.
search_experiments ~329 tokens
Search EBI Expression Atlas — ~4,500 curated gene/protein expression experiments (baseline & differential) across species, tissues, and conditions. Filter by keyword (matches description/experimental factors), species (e.g. "Homo sapiens", "Mus musculus"), and/or type ("Baseline" or "Differential").

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