Recent observations of GeV gamma-rays from novae have led to a paradigm shift in the understanding of these objects. While it is now believed that shocks contribute significantly to the energy budget of novae, it is still unknown if the emission is hadronic or leptonic in origin. Neutrinos could hold the key to definitively differentiating between these two scenarios, though the energies of such particles would be much lower than are typically targeted with neutrino telescopes. Here, we present an analysis using IceCube DeepCore, a densely instrumented region of the IceCube detector, to lower the energy threshold and search for sub-TeV neutrino emission from novae. We also discuss implications for other potential GeV neutrino transients that can be targeted using this sample.