Welcome to the GenePattern help forum. This is a place to get help from GenePattern team members and fellow GenePattern users and also a place to post anything you've found useful in using GenePattern.

Shut Down

On June 15, 2026, the main, freely available GenePattern server, cloud.genepattern.org, will be retired from service and all user data deleted. If you have any data you would like to retain, please download it before that date. This notice also applies to the GenePattern Notebook and g2nb applications.

If you would like to use any of the GenePattern analyses or run GenePattern locally, you can do any of the following:

Run a local GenePattern server. Instructions can be found on the releases page at https://github.com/genepattern/genepattern-server/releases

Run GenePattern modules via an LLM. Use the local GenePattern runner utility https://github.com/genepattern/local_genepattern_runner_mcp to run analyses on your own computer without a GenePattern server. This supports running modules from a terminal window or installing a MCP server to allow your LLM (e.g. Claude Desktop) to run modules for you.

Download the GenePattern modules and run them as command-line tools. The collection of publicly released GenePattern modules is available at https://github.com/genepattern/GenePatternModuleCatalog/.

The GenePattern website, www.genepattern.org, will continue to be available.

It has been the pleasure of the GenePattern team to serve the analysis needs of the worldwide genomics community since 2004.

Announcement: AffySTExpressionFileCreator has been updated to R 4.0.3 and now accepts Clariom arrays

GenePattern Help Forum