Aiden Lab plugins

Geenee lets you drive three genome viewers by chatting: the IGV genome browser, the Juicebox Hi-C viewer and the Spacewalk 3D chromatin viewer, side by side on one web page. Nothing runs on your computer.

Install

How you install depends on the app. Only Claude Code and Codex can install it for you; the others need a few clicks in settings, because a chat cannot change your account settings.

Claude Code or Codex (CLI or desktop app): paste one line

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

The assistant installs everything itself. Start a new session when it says so.

Claude (web, desktop app, Cowork): two parts, once

1. Open claude.ai/new#settings/customize-plugins.
2. Add → Add marketplace → Add from a repository, enter aidenlab/plugins.
3. Find Geenee, click Add.
4. Then click Connect. Open Geenee's Connectors tab: it says Not added until you click Connect. Claude never does this for you, and without it Geenee looks installed but does nothing.
5. Start a new chat.

You can also paste the one-line prompt above into a Claude chat: it walks you through these same clicks.

This covers every Claude app on your account, Claude Code included. Paid plans only.

Only if there is no Connect button: Settings → Connectors → Add custom connector, name Geenee, URL https://geenee.3dg.io/mcp, no authentication. This gets no plugin updates, so prefer the plugin.

ChatGPT: add the server by hand

chatgpt.com/plugins → + → Add custom MCP server, name Geenee, URL https://geenee.3dg.io/mcp, authentication None (if ChatGPT asks for Developer mode, turn it on in Settings). Then start a new chat and turn Geenee on in it from the + menu. ChatGPT does not use this marketplace.

Other MCP apps (Cursor and others)

Point them at https://geenee.3dg.io/mcp.

First thing to try

In a new chat:

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.

You get a link. Open it in a browser tab and keep it open: the assistant drives the viewers in that tab.

More

• Have the old juicebot plugin? Remove it, then install Geenee as above.
• Admins (Claude Team/Enterprise): add https://geenee.3dg.io/mcp as an organization connector and members need no setup.
• Maintainers: docs/maintaining.md. How plugins relate to a plain MCP URL: docs/from-mcp-url-to-plugin.md.

Server source: aidenlab/geenee. License: MIT.