We study Anderson localization in graphene with short-range disorder using the real-space Kubo-Greenwood method implemented on graphics processing units. Two models of short-range disorder, namely, the Anderson on-site disorder model and the vacancy defect model, are considered. For graphene with Anderson disorder, localization lengths of quasi-one-dimensional systems with various disorder strengths, edge symmetries, and boundary conditions are calculated using the real-space Kubo-Greenwood formalism, showing excellent agreement with independent transfer matrix calculations and superior computational efficiency. Using these data, we demonstrate the applicability of the one-parameter scaling theory of localization length and propose an analytical expression for the scaling function, which provides a reliable method of computing the two-dimensional localization length. This method is found to be consistent with another widely used method which relates the two-dimensional localization length to the elastic mean free path and the semiclassical conductivity. Abnormal behavior at the charge neutrality point is identified and interpreted to be caused by finite-size effects when the system width is comparable to or smaller than the elastic mean free path. We also demonstrate the finite-size effect when calculating the two-dimensional conductivity in the localized regime and show that a renormalization group β function consistent with the one-parameter scaling theory can be extracted numerically. For graphene with vacancy disorder, we show that the proposed scaling function of localization length also applies. Last, we discuss some ambiguities in calculating the semiclassical conductivity around the charge neutrality point due to the presence of resonant states.