The 10x Genomics integration transforms single cell and spatial analysis into a simple, conversational workflow. Biologists can easily analyze their own sequencing data, while core labs can quickly perform batch processing. This article explains how to set up and use the 10x Genomics integration with Claude to advance your analysis workflows.
The 10x Genomics integration is available as a desktop extension in the Claude Desktop App (download here), and it relies upon Claude's ability to use local connectors via a desktop extension.
What this integration provides
The 10x Genomics integration enables researchers to create and manage single cell genomics analysis workflows in conversation with Claude. Users can upload data, configure and launch Cell Ranger pipelines, monitor analysis status, and download results using natural language prompts instead of command-line tools or web interfaces. The integration translates conversational requests into actions on the 10x Cloud Analysis platform, streamlining workflows for gene expression, cell multiplexing, and CRISPR screening analyses.
Who should use the 10x Genomics integration
Computational Biologists: Researchers who analyze single cell genomics data and want to streamline cloud-based analysis workflows
Bioinformaticians: Scientists who process multiple samples and need efficient batch processing capabilities
Research Scientists: Lab researchers who generate single cell data and want an intuitive interface for running standard pipelines
Core Facility Managers: Staff who process samples for multiple research groups and need to manage numerous analyses
Who can access the 10x Genomics integration
Any user with a 10x Cloud Analysis account (create a free account here)
More details on accessing the integration can be found in the 10x Genomics MCP Server Documentation.
Setting up the 10x Genomics integration
The 10x Genomics integration is available as a desktop extension in the Claude Desktop App (download here). For Organization Owners (Team and Enterprise), setting up the integration involves making the extension available to your organization. For individual users, setting up the integration involves installing the extension from inside the Claude Desktop App.
For Organization Owners (Team and Enterprise)
Navigate to Admin settings > Extensions
In the search field, type “10x Genomics”
Click “Enable”
Instruct your team to download the Claude Desktop App to access the integration
For Individual Claude Users
Download the Claude Desktop App
Navigate to Settings > Extensions
Click “Browse extensions”
Click “10x Genomics”
Click “Install”
Follow the instructions to authenticate with your 10x Cloud Analysis account
Learn about installing desktop extensions from the directory.
Technical details of the 10x Genomics integration can be found in the 10x Genomics MCP Server Documentation.
For Claude Code Users
Command:
/plugin marketplace add anthropics/life-sciencesCommand:
/plugin install 10x-genomics@life-sciencesRestart Claude Code
Command:
/pluginNavigate to “Manage and uninstall plugins" and configure the 10x Genomics MCP with your access token
Restart Claude Code one more time
Verify that the server is connected with
/mcp
Common use cases
Set up a Cell Ranger count analysis
Set up a Cell Ranger multi analysis with multiplexing
Batch process multiple samples
Monitor and download analysis results
Interpret QC metrics and results
Sample prompts and prompting best practices can be found in the 10x Genomics MCP Server Documentation.