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Are you talking about iOS apps sitting in iTunes or OSX apps?

All the apps I have in my iTunes is also synced to my iPad. I checked the size of the folder that contains all the apps in my iTunes. It's 12gb big, but my iPad is showing 25gb worth of apps
 
Without more information, I would assume that the size that you are looking at on your iPad includes the app data (emails, document, etc.)
 
Without more information, I would assume that the size that you are looking at on your iPad includes the app data (emails, document, etc.)

Is there any way I can view the individual apps and their app data size?
 
Settings -> General -> Usage

You can tap on an individual app in the list to see how much storage it is using for documents and data.

^it is this. The only way to clear the cache is to delete and reinstall the app. If you're jailbroken, you can use icleaner to clear the cache
 
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