Fail to restore applications with Time Machine

After changing my hard drive in the Apple store due to a clicking sound, I tried to restore all my previously saved files on Time Machine. All settings and documents were restored but ALL applications were not. I attempted a new restoration with migration assistant only for the applications folder but again all my applications are missing and dock shows questionmarks. Some of my applications include valuable data and a new complete re-installation of all of them is I think dangerous for missing all my data