Geenee plugin

Drive Geenee from Claude, ChatGPT or Codex: one page beside the conversation holding the igv genome browser, the Juicebox Hi-C contact-map viewer and the Spacewalk 3D chromatin viewer. The plugin registers the Aiden Lab's hosted MCP server (https://geenee.3dg.io/mcp, Streamable HTTP, no auth, nothing installed locally) and a skill that teaches the assistant the workflow: open Geenee once, keep the Room id, then search, load, navigate, compare and share in any of the three viewers.

Server source: aidenlab/geenee.

Install

In Claude Code or Codex, paste this and the assistant installs everything:

Set up Geenee for me: fetch https://geenee-install.3dg.io and follow its instructions for the app you are running in.

In claude.ai, the Claude desktop app and Cowork no prompt can install it: a chat cannot change account settings. Those take four short steps, listed in the marketplace README. In ChatGPT, use Codex in the ChatGPT desktop app and paste the one-line prompt there. Geenee is installed only from the marketplace, never by adding the server address by hand. Quickest by hand: Claude Code /plugin install geenee --marketplace aidenlab/plugins then /reload-plugins; Codex codex plugin marketplace add aidenlab/plugins then codex plugin add geenee@aidenlab.

Try it

Open Geenee. In Juicebox, load the ENCODE GM12878 in situ Hi-C map at the HOXA cluster and add the gene track. In IGV, go to HOXA1 and add the GM12878 CTCF ChIP-seq track.

The assistant returns a Geenee link; open it in a tab, and you watch the Juicebox tab load the map at HOXA with a gene track, and the IGV tab show HOXA1 with a CTCF signal track. Then: "Show me an example 3D structure in Spacewalk."

Contents