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I would probably suggest getting a kit and going from there. Something like the HobbyPower F550 that comes with a PixHawk.
Another option would be to get a kit and use the BeagleBone Blue which is designed for robotics tinkering. As seen in the comments there are several open source codebases such as Ardupilot and PX4. MavLink is also open source so you can ...
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