Refined Chern-Simons invariants of torus knots can be defined by using modular matrices associated to Macdonald polynomials or DAHA, generalizing colored quantum invariants. The theory was originally defined in string theory, and conifold transition in string theory leads to a positivity conjecture of refined Chern-Simons invariants of torus knots. This conjecture connects refined Chern-Simons theory to enumerative geometry.