Magnetic skyrmions have attracted enormous research interest across a wide range of fields, from condensed matter physics to material science, since the first observation in 2009. Abundant theoretical, computational, and experimental studies have contributed to this emerging interdiscipline: skyrmionics. Especially, great expectations have been placed on exploiting the physics and dynamics of magnetic skyrmions as potential information carriers. In this topical review, we particularly focus on the computational studies of skyrmions during the last decade. After briefly introducing the mechanism of micromagnetic simulations, we review and discuss the manipulation of skyrmions, i. e., their creation, transformation, motion, and spin excitation, by both traditional and advanced methods, including electric currents, magnetic fields, spin waves, microwaves, etc. We take magnetic skyrmion as a typical example, while other skyrmion-related magnetic structures such as skyrmioniums and skyrmion tubes are also slightly involved. Through this review, we hope to give some insights into the further development of magnetic skyrmions in spintronics.