Preheat oven to 350° F. Line muffin pan with cupcake wrappers (or spray with cooking spray).
In a large bowl, whisk together oats (the oats may be added to a blender to break them down a bit, but not into a flour-like consistency), flour, flaxseed, baking soda, baking powder, cinnamon, and nutmeg.
In a separate bowl, whisk together eggs and oil until smooth, then stir in applesauce and sugar.
Add wet ingredients to dry ingredients and stir just until combined; fold in pecans.
Spoon batter into muffin cups and bake for 18-20 minutes. Check at 18 minutes by inserting a toothpick. If it comes out fairly clean, they are done; if not, bake for another few minutes.
Cool on a wire rack before serving.