GitHub Apps have been the preferred way to integrate with GitHub for nearly a year. The advantages over regular OAuth apps include granular permissions, as well as tighter control over where the Apps are installed. However, GitHub Apps could only integrate with GitHub using REST API calls.
The GraphQL API now supports requests made by GitHub Apps. This means that any query or mutation available in our public schema can be made by users authorized through a GitHub App. GraphQL is a great way to fetch data about a variety of resources in a payload that matches your request precisely. For more information on the advantages of GraphQL over REST, see "Migrating from REST."