manipulate

Manipulation comes from manipulate which means to control or influence something for your own benefit. Manipulation often implies something negative.

For example:

Manipulation of people who love you is never a good idea. When they realize what you are doing, they may never trust you again.

In a research context, manipulation of variables has a neutral, not a negative meaning.

For example:

Manipulation of variables in a research study enables researchers to examine what affects the variables in their study.