Is there a way to stop Snyk from creating GitHub pull requests with changes like dependency updates and patches?

Disable automated GitHub pull requests

Snyk notifies you about new vulnerabilities for your projects with an email, and by opening a pull request with fixes on GitHub. You can disable the automatic pull requests by going to 

  1. Settings
  2. Integrations
  3. 'Edit Settings' for GitHub
  4. Uncheck the setting 'Enable automatic pull requests for all projects in this organisation' and click the 'Update settings' button