You should place <script src="js/scene.js"></script>
into the <head>
tag. Inside your JavaScript, do something like this:
// get a reference to your canvas container
const container = document.getElementById( 'CanvasFrame' );
// create your renderer
const renderer = new THREE.WebGLRenderer( { antialias: true } );
renderer.setPixelRatio( window.devicePixelRatio );
renderer.setSize( window.innerWidth, window.innerHeight );
// apply the internal canvas of the renderer to the DOM
container.appendChild( renderer.domElement );