In the large bowl, mix together flour, flax meal, oat bran, brown sugar, baking soda, baking powder, salt, and spices.
In the small bowl, combine the milk, eggs, vanilla, and applesauce. Add to the dry ingredients and stir until just blended. Fold in the carrots, apples, and cranberries.
Fill prepared muffin tins ⅔ full with batter.
Bake for 15 to 20 minutes, or until a toothpick inserted into the center of a muffin comes out clean.