Matrix elements of six-quark operators are needed to extract new physics constraints from experimental searches for neutron-antineutron oscillations. This work presents in detail the first lattice quantum chromodynamics calculations of the necessary neutron-antineutron transition matrix elements including calculation methods and discussions of systematic uncertainties. Implications of isospin and chiral symmetry on the matrix elements, power counting in the isospin limit, and renormalization of a chiral basis of six-quark operators are discussed. Calculations are performed with a chiral-symmetric discretization of the quark action and physical light quark masses in order to avoid the need for chiral extrapolation. Non-perturbative renormalization is performed, including a study of lattice cutoff effects. Excited-state effects are studied using two nucleon operators and multiple values of source-sink separation. Results for the dominant matrix elements are found to be significantly larger compared to previous results from the MIT bag model. Future calculations are needed to fully account for systematic uncertainties associated with discretization and finite-volume effects but are not expected to significantly affect this conclusion.
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