Deepmap FAQs

Question 1

What is Deepmap and what problem does it solve?

Accepted Answer

Deepmap is an AI agent tool that provides Large Language Models (LLMs) with direct, structured access to Broad Institute's DepMap CRISPR datasets. It enables high-performance functional genomics analysis, specifically for 'Therapeutic Target Evidence Collection' across over 1,000 cancer cell lines.

Question 2

What types of functional genomics analyses can I perform with Deepmap?

Accepted Answer

With Deepmap, you can search for valid HGNC gene symbols, retrieve global statistical metrics for specific genes (e.g., average gene effect), and identify the top cancer cell lines most sensitive to the loss of a target gene, which is critical for therapeutic target discovery.

Question 3

How does Deepmap provide data access to AI agents?

Accepted Answer

Deepmap functions as a high-performance Model Context Protocol (MCP) server. This allows AI agents to directly query and retrieve specific gene dependency metrics, global statistical summaries, and identify top cell line sensitivities from locally cached DepMap CRISPR datasets.

Question 4

Is Deepmap compatible with AI agent platforms or LLMs?

Accepted Answer

Yes, Deepmap is designed for seamless integration with MCP-compatible AI clients like Claude Desktop or other agent orchestrators. It supports both stdio and HTTP SSE transport protocols for flexible deployment.

Question 5

How do I get started with Deepmap?

Accepted Answer

Getting started is straightforward: install Deepmap using `pip`, then run the `deepmap-mcp-download-data` command to initialize your local CRISPR dataset cache. Finally, run the server using `deepmap-mcp --transport stdio` or as an HTTP server.

Deepmap

Deepmap

Key Features

Use Cases

Key Features

Use Cases