You can now enable or disable the dependency graph, Dependabot alerts, Dependabot security updates, and secret scanning for all repositories in an organization with one click. You can also set whether each feature will be enabled or disabled for newly-created repositories. Look for the "Security & analysis" tab in your organization settings page and on your user settings page.
In addition, we've consolidated the repository-level settings for dependency graph, Dependabot alerts, Dependabot security updates, and secret scanning to a "Security & analysis" tab in the repository settings page.