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

Geenee installs only from the aidenlab marketplace, in every app. That is how it gets updates, which matter while Geenee is young.

Claude Code, Codex, or ChatGPT's Codex: 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 does the installing. Each time it asks for permission, click Approve (or Allow). When it finishes it gives you a message to paste into a new chat or session.

In the ChatGPT desktop app, open Codex first, then paste the line there. Plain ChatGPT chat cannot install Geenee.

Claude (desktop app, claude.ai, Cowork): click through once

Follow these steps to install Geenee.

1. Go to Customize → Plugins → +Add → Add marketplace → Add from a repository. Enter this URL: aidenlab/plugins
2. Click Sync
3. You will be on the Discover tab. Click Add (Not +Add).
4. Select the Connectors tab. Connect → Continue → Add

Things to know:

• You need a paid plan.
• If you see Sync automatically next to aidenlab, turn it on. That's how Geenee's updates reach you.
• If you still have the old juicebot plugin, or a connection to juicebot-mcp.3dg.io or geenee-dev.3dg.io, remove it. Otherwise you'll get duplicate tools.

To check it worked: start a new chat and ask me to open Geenee. I'll call open_geenee and give you a link to a page with IGV, Juicebox and Spacewalk tabs. Keep that browser tab open while you use it. If a step fails, report it at github.com/aidenlab/plugins/issues with a screenshot.

This covers every Claude app on your account, Claude Code included. You can also paste the one-line prompt above into a Claude chat: it walks you through these same steps.

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): an Owner may need to allow user-added marketplaces, and to add Geenee's connector for the organization, before members can complete the steps above.
• 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.