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Abstract The impact of measurements of heavy-flavour production in deep inelastic ep scattering and in pp collisions on parton distribution functions is studied in a QCD analysis at next-to-leading order. Recent combined results of inclusive and heavy-flavour produc- tion cross sections in deep inelastic scattering at HERA are investigated together with heavy-flavour production measurements at the LHC. Differential cross sections of charm- and beauty-hadron production measured by the LHCb collaboration at the centre-of-mass energies of 5, 7 and 13 TeV as well as the recent measurements of the ALICE experiment at the centre-of-mass energies of 5 and 7 TeV are explored. These data impose additional constraints on the gluon and the sea-quark distributions at low partonic fractions x of the proton momentum, down to x ≈ 10 −6. The impact of the resulting parton distribution function in the predictions for the prompt atmospheric-neutrino fluxes is studied.