In our modern. increasingly socialist. techno-State bureaucracy the administrative personality will be elitist and prescriptive. What you see in personalities such as Hillary Clinton, Macron, Merkel, and Butts in Canada fit very well the admin type. Trump wildly does not. He is an entrepreneur rather than a manager and planner. 
There will thus be a natural resistance to political leaders like Trump in any case. Add in that he has been elected specifically to dismantle or at least geld the vast administrative state and you should be able to understand the Deep State will be his opposition rather than a state apparatus at his disposal. Even without specific "examples", it is enough to know that for every Yates and Comey there are hundreds of Obama (and even Bush43) appointees still about who will use every measure available to resist Trump's policies. 
The US administrative state has been politicized and thinks it has a veto over the democratic choice of the voters. Dangerous.