ENCODE Toolkit MCP Server
by ammawlaio.github.ammawla/encode-toolkitv0.3.0-beta.5
Search, download, track and analyze functional genomics experiments from the ENCODE Project.
context tax
queued
security
queued
cold start
queued
freshness
Active18d ago
Install ENCODE Toolkit MCP server
Install in Claude Code
claude mcp add encode-toolkit -- npx -y encode-toolkitInstall in Cursor
{
"mcpServers": {
"encode-toolkit": {
"command": "npx",
"args": [
"-y",
"encode-toolkit"
]
}
}
}Add to ~/.cursor/mcp.json (global) or .cursor/mcp.json (project).
Install in Claude Desktop
{
"mcpServers": {
"encode-toolkit": {
"command": "npx",
"args": [
"-y",
"encode-toolkit"
]
}
}
}Settings → Developer → Edit Config (claude_desktop_config.json), then restart.
Install in VS Code
{
"servers": {
"encode-toolkit": {
"type": "stdio",
"command": "npx",
"args": [
"-y",
"encode-toolkit"
]
}
}
}Add to .vscode/mcp.json in your workspace.
Install in Windsurf
{
"mcpServers": {
"encode-toolkit": {
"command": "npx",
"args": [
"-y",
"encode-toolkit"
]
}
}
}Add to ~/.codeium/windsurf/mcp_config.json.
Freshness
Active — last maintenance signal 18d ago. The newest of the signals below sets the band.
Last commit (default branch)
2026-09-21 · 18d ago · GitHub
Latest release
2026-09-21 · 18d ago · GitHub · v0.3.4
Package published
no data · npm/PyPI
Registry entry updated
2026-03-09 · 7mo ago · official registry · v0.3.0-beta.5
FAQ
›How do I install the ENCODE Toolkit MCP server in Claude Code?
Run: claude mcp add encode-toolkit -- npx -y encode-toolkit. For Cursor, VS Code, Claude Desktop and Windsurf, use the install tabs above.
›Does ENCODE Toolkit require an API key?
No required environment variables are declared in its published metadata.
›Can I use ENCODE Toolkit as a remote (hosted) MCP server?
No hosted endpoint is published; it runs locally over stdio.
›Is ENCODE Toolkit in the official MCP registry?
Yes, as io.github.ammawla/encode-toolkit.
Alternatives to ENCODE Toolkit
Other science & research MCP servers.
WigoloActiveLocal web search, fetching, crawling, extraction and research, with multi-engine search, local ML reranking, a SQLite cache and JavaScript rendering.
ZoteroActiveSearch, read, annotate, and add to your Zotero research library, local or web.
ExaActiveConnect AI agents to Exa for web search, content fetching, and multi-step research.
PostgresMaintainedPostgres development and operations: performance analysis, tuning and health checks.
ArxivActiveSearch arXiv papers, read original LaTeX sections, get BibTeX from arXiv metadata and set topic watches, with papers stored locally.
Perplexity API PlatformActiveReal-time web search, reasoning, and research through Perplexity's API