All shapes can be transformed, i.e. translated to another location, rotated by certain degrees, etc. In all cases, the transform function returns a new shape, not the original.

let circleA = circle({radius: 5})
let circleB = circleA.scale([5,10]) // a new cicle, scaled as requested

So, in order to modify the original, place that on the left-hand side of the expression.

let circleA = circle({radius: 5})
circleA = circleA.scale([5,10]) // a new circle, scaled as requested, reassigned to the original

In fact, the two lines above can be combined into a single line.

let circleA = circle({radius: 5}).scale([5,10]) // a new circle, and scaled as requested

Transforms can also be chained together.

// rotate the circle about the X axis by 45 degrees
// and translate the circle up the Z axis 10 units
// and assign the result to circleB
let circleB = circleA.rotateX(45).translate([0,0,10])

The original shape can be transformed any number of times. For example, the same cylinder can be rotated, making copies of the cylinders, and then unioned together. This is a common pattern when creating complex designs.

The standard for all 3D systems today, including graphics cards, design tools, etc. is orientating shapes using the right-hand rule. JSCAD follows the same rules internally, and produces shapes, applies transforms, etc. using the right-hand rule of orientation.

Learn about the right-hand rule at Wikipedia.org