agentmods.dev

multiomics

multiomics is an MCP server for Claude Code, Codex, Cursor, Gemini CLI, OpenCode from lynnlangit/precision-medicine-mcp. Its token cost is not measured, scanned A, a copy of fgbio, Apache-2.0.

A local add-on that connects a coding agent to multi-omics tools from the spatial-mcp Python package. Multi-omics means studying several kinds of biological measurements together, such as DNA, RNA, and proteins.

In plain words
What is it for?
Running multi-omics tasks with files in the configured data folder and cache, while keeping the add-on in dry-run mode for testing.
Why use it?
It gives the agent a defined local setup for multi-omics data without requiring a remote service. The available details do not specify which multi-omics operations it supports.

MCP server for Claude CodeCodexCursorGemini CLIOpenCode

Written for no agent in particular: it speaks MCP, so any client can run it. Also seen: listed in a Claude config.

Not installable: its command points at a path on the author’s own machine, so it runs nowhere else. The line is /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-multiomics.

One of 19 entries in claude_desktop_config.json upstream. Installing this one merges just its entry into your config; the other 18 are separate, each on its own page.

not rated 24repo 17d ago A scan tokens not measured copy · 86% Apache-2.0

Good fit Running multi-omics tasks with files in the configured data folder and cache, while keeping the add-on in dry-run mode for testing.

Compare 6 mcp servers from other repositories ↓
View source ↗ lynnlangit/precision-medicine-mcp
Install

Getting it into your agent

There is no command for this one: it runs only inside a plugin, and the catalogue could not identify which plugin ships it. The source is linked below.

Made for: Claude Code, Codex, Cursor, Gemini CLI, OpenCode.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for multiomics

README.md
[![agentmods](https://agentmods.dev/badge/mcp/lynnlangit/precision-medicine-mcp/desktop-configs-multiomics/github.svg)](https://agentmods.dev/mcp/lynnlangit/precision-medicine-mcp/desktop-configs-multiomics)
Your own site
<a href="https://agentmods.dev/mcp/lynnlangit/precision-medicine-mcp/desktop-configs-multiomics"><img src="https://agentmods.dev/badge/mcp/lynnlangit/precision-medicine-mcp/desktop-configs-multiomics/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for multiomics

Your own site · 80×15
<a href="https://agentmods.dev/mcp/lynnlangit/precision-medicine-mcp/desktop-configs-multiomics"><img src="https://agentmods.dev/badge/mcp/lynnlangit/precision-medicine-mcp/desktop-configs-multiomics.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session not measured What this adds to a session before it is invoked.
When invoked not measured Not applicable: nothing here is loaded into a session.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin 86% copy Near-identical to another mod in the catalogue.
Security

Grade A, and why

multiomics scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 12d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

Origin

This is a copy

86% identical to fgbio — 12 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.

docs/getting-started/desktop-configs/claude_desktop_config.json · 18 lines

What it actually says

{
  "multiomics": {
    "command": "uv",
    "args": [
      "run",
      "--directory",
      "/Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-multiomics",
      "python",
      "-m",
      "mcp_multiomics"
    ],
    "env": {
      "MULTIOMICS_DATA_DIR": "/Users/lynnlangit/Documents/GitHub/spatial-mcp/data/multiomics",
      "MULTIOMICS_CACHE_DIR": "/Users/lynnlangit/Documents/GitHub/spatial-mcp/data/cache/multiomics",
      "MULTIOMICS_DRY_RUN": "true"
    }
  }
}
Same file

What else claude_desktop_config.json configures

This page is one entry in a file that holds 19. Installing the file brings all of them; each is measured and scanned on its own page.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 12d ago First seen · 18 lines scan A f693493fd4d5

Subscribe to this mod's changes

multiomics is an MCP server published in the GitHub repository lynnlangit/precision-medicine-mcp (24 stars, last pushed 17d ago), licensed Apache-2.0. Its token cost is not measured: an MCP server costs its tool schemas, not its config file. A static security scan graded it A with 0 findings. It is 86% identical to fgbio, differing in 12 lines, and is treated as a copy.

Data and AIScientificagentic-aibioinformaticsmultiomicsprecision-medicinetranscriptomics
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