Dependencies inside a single agile project and single agile development team are easy to manage informally without any tool, thus there is no explicit dependencies management in TargetProcess.
However, sometimes you have complex program with several projects and several development teams. Obviously, it is hard to avoid that all teams will work independently. In some cases a user story from project Alpha will depend on a user story from project Omega. How you may handle that in TargetProcess?
Luckily, there is a powerful Custom Fields concept to serve your needs. For example, you may create “Depends On” custom field for user story and select a user story from the project Omega to show the dependency explicitly.