The detection of astrophysical neutrinos from transient sources can help to understand the origin of the neutrino diffuse flux and to constrain the underlying production mechanisms. In particular, proton-neutron collisions may produce GeV neutrinos. However, at these energies, neutrino data from large water Cherenkov telescopes, like KM3NeT and IceCube, are dominated by the well-known atmospheric neutrino flux. It is then necessary to identify a sub-dominant component due to an astrophysical emission based on time correlation across messengers. The contribution covers several methods to search for such a signal in short time windows centered on observed transient sources, including a novel approach based on the distribution of time differences. Their performance is compared in the context of subpopulations of astrophysical sources that may show prompt or delayed neutrino emissions. The outlook for the usage of such techniques in actual analyses is also presented.