In this study we apply the Remler formalism to charmonium production at SPS and GSI/FAIR energies in order to investigate the effects of baryon-rich matter on charmonium production and dissociation in heavy-ion collisions within the Parton-Hadron-String Dynamics (PHSD). As a first step the Remler formalism is tested in p+p collisions and then applied to p+A collisions in order to extract the nuclear absorption cross section of charmonium, which is then utilized in heavy-ion collisions. We find that the Remler formalism successfully describes charmonium production in heavy-ion collisions at SPS energies when an in-medium heavy quark potential is implemented, in which $J/\psi$ dissociates near $T_c$. Finally the same formalism is applied to the GSI/FAIR energies, where we estimate charmonium production.