Cosmic rays primarily consist of protons, which primarily decay into pions upon impact with the atmosphere of the Earth. The pions decay according to $$\pi^+ \to \mu^++\nu_\mu $$ and $$\pi^- \to \mu^- +\bar{\nu}_\mu$$ The muons subsequently decay according to $$\mu^+ \to e^+ + \nu_e + \bar{\nu}_\mu $$ and $$\mu^- \to e^- + \bar{\nu}_e + \nu_\mu $$ which implies that the ratio of muon neutrino flux to electron neutrino flux from the atmosphere is 2:1.
As is well known, the Super Kamiokande observatory observed a much lower value of this ratio, indicating and being consistent with neutrino oscillations $\nu_\mu \to \nu_\tau$.
However, in discussions of these results it never seems like oscillations of the electron neutrinos could be relevant. I understand they could not explain the result, since they would only make it worse, but is it not necessary to take them into account?
Electron neutrino oscillations have of course been confirmed in other experiments, so I reckon it is necessary to consider them in the interpretation of the Super Kamiokande results.