Koskamo

Expression Atlas MCP

An MCP server that provides tools to search and retrieve metadata for approximately 4,500 curated gene and protein expression experiments from the EBI Expression Atlas. It allows agents to filter experiments by keyword, species, tissues, and conditions, and to fetch detailed metadata for specific experiments using their accession identifiers.

Visit Pipeworx

Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

Expression Atlas MCP logo, by PipeworxCommunity listingLocal stdioSource reviewed; not executedPublished by Pipeworx
Vendor documentation

What you can do with it

  • Search for gene expression experiments by keyword or species
  • Retrieve metadata for a specific experiment using its accession ID
  • Filter experiments by tissue type and experimental conditions
  • Access curated baseline and differential expression data

Source and maintenance

Community listingRegistry 0.2.1
mcp-registry: io.github.pipeworx-io/expression-atlas@0.2.1Source repositoryProject website
Maintenance checked

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

@pipeworx/mcp-expression-atlas 0.2.1

npm
@pipeworx/mcp-expression-atlas package definition
{
  "version": "0.2.1",
  "transport": "stdio",
  "identifier": "@pipeworx/mcp-expression-atlas",
  "registryType": "npm",
  "environmentVariables": [
    {
      "name": "PIPEWORX_API_KEY",
      "description": "Optional Pipeworx API key. Without it calls are anonymous and capped daily; a free key raises the cap."
    }
  ]
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

This server is operated by the named third party. Listing and endpoint checks are not an endorsement or a security audit. Review the operator's permissions, terms, and data handling before connecting. How listings are checked and corrected.

Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.
Cursor configuration
{
  "mcpServers": {
    "expression-atlas-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-expression-atlas@0.2.1"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.
Cline configuration
{
  "mcpServers": {
    "expression-atlas-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-expression-atlas@0.2.1"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.
VS Code configuration
{
  "servers": {
    "expression-atlas-mcp": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-expression-atlas@0.2.1"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.
Claude Desktop configuration
{
  "mcpServers": {
    "expression-atlas-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-expression-atlas@0.2.1"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

Let your agent find its tools

Find servers like Expression Atlas MCP from your agent. Add Koskamo once to search the index for endpoints, access requirements, and client setup. Public discovery needs no key.

Connect Koskamo Explore workflows
See all 1,963