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Skill installation

Add the Element Biosciences multiomics skills to Claude Desktop, Claude Code, Cursor, or another AI app.

Install the multiomics skills one time with a prompt, the Element plugin, or the skills CLI. Your agent then loads the matching skill whenever your request calls for it.

The skills are published in the Elembio/agent-skills repository on GitHub as the multiomics plugin.

Tip:

If you use a sandbox, skip this installation. The Sandbox MCP provides the multiomics skills to your agent, and the multiomics Python package is pre-installed. A sandbox and a local installation are mutually exclusive, so do not also install multiomics locally.

Python package for local analysis​

Skills tell your agent how to analyze Cytos data. On your own compute, your agent also needs the multiomics Python package (elembio-spatialdata-analysis) in the Python environment where it runs code.

  1. Install the multiomics skills with one of the methods below.
  2. Install the multiomics Python package into that environment.
  3. Point the agent at a Spatial Data Object from Cells2Stats.

Install with a prompt​

Send your agent this prompt:

Install the Element Biosciences multiomics skills from
https://github.com/Elembio/agent-skills. Explain clearly any steps
that I need to take.

Your agent installs the skills and tells you any steps to finish in the app.

Install the plugin​

For Claude Desktop, Claude Code, and Cursor, install the multiomics plugin from the Element marketplace.

The plugin is published in the Elembio/agent-skills repository on GitHub. Your AI app adds that repository as the Element plugin marketplace, then installs multiomics from it.

  1. Open Customize > Plugins, select +, then select Add from a repository.
  2. Enter Elembio/agent-skills.
  3. Find multiomics and select Install.

Install with the skills CLI​

For Codex, Windsurf, Gemini CLI, and other AI apps that read Agent Skills, use the open-source skills CLI. The CLI requires Node.js.

  1. Run this command in a terminal:

    npx skills add Elembio/agent-skills --skill '*' -g

  2. Select your AI apps when the CLI asks.

  3. Start a new session in your AI app.

Try it​

After you install the skills — and, on your own compute, the Python package — try these prompts with your agent:

Which Element multiomics skills do you have?
Load the Spatial Data Object at <path to .zarr.zip> and give me
a run quality overview.
What conditions and replicates are in this run? Infer them from
the well labels, and show me the design to confirm.
Filter low-quality cells, normalize the 3′ transcriptome data,
and show a UMAP colored by well.
Cluster the cells and list the top marker genes for each cluster.
Run pseudobulk differential expression between <condition A> and
<condition B>, then make a volcano plot of the results.
Check whether cells separate by well or batch instead of
by condition.

See also​

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