An approach to efficient quantum computation with probabilistic gates is proposed and analyzed in both a local and nonlocal setting. It combines heralded gates previously studied for atom or atomlike qubits with logical encoding from linear optical quantum computation in order to perform high-fidelity quantum gates across a quantum network. The error-detecting properties of the heralded operations ensure high fidelity while the encoding makes it possible to correct for failed attempts such that deterministic and high-quality gates can be achieved. Importantly, this is robust to photon loss, which is typically the main obstacle to photonic-based quantum information processing. Overall this approach opens a path toward quantum networks with atomic nodes and photonic links.