We study the production of heavy quarkonium states in high energy proton-nucleus collisions. Following earlier work of Blaizot, Fujii, Gelis, and Venugopalan, we systematically include both small $x$ evolution and multiple scattering effects on heavy quark pair production within the Color Glass Condensate (CGC) framework. We obtain for the first time expressions in the Non-Relativistic QCD (NRQCD) factorization formalism for heavy quarkonium differential cross sections as a function of transverse momentum and rapidity. We observe that the production of color singlet heavy quark pairs is sensitive to both "quadrupole" and "dipole" Wilson line correlators, whose energy evolution is described by the Balitsky-JIMWLK equations. In contrast, the color octet channel is sensitive to dipole correlators alone. In a quasi-classical approximation, our results for the color singlet channel reduce to those of Dominguez et. al. [1]. We compare our results to those obtained combining the CGC with the color evaporation model and point to qualitative differences in the two approaches.
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