The effect of pairing on small and large amplitude dynamics is discussed. Pairing correlation is treated in a fully microscopic transport theory using a simplified BCS version of the Time-Dependent Hartree-Fock Bogolyubov (TDHFB) theory. The approach is applied to study the Giant Dipole and Giant Quadrupole Resonance in spherical and/or deformed magnesium isotopes showing very good agreement with QRPA theory. The present framework also provides a consistent approach to describe nuclear reactions around the Coulomb barrier. As an illustration, the influence of pairing correlations on multi-nucleon transfer is studied for reactions at sub-barrier energy.