How to conduct posthoc analysis for pairwise comparisons after Two-Way ANOVA?

MetaboAnalyst does not do posthoc testing after Two-Way ANOVA. However, I need to understand where the differences detected by the test are coming from. What is the best way to go about this? I am open to conducting the posthoc testing in R, but I would have to redo the whole ANOVA analysis from scratch. Any suggestions/help will be greatly appreciated. Thank you!