Preheat oven to 375°F Butter a 12-cup nonstick muffin pan or line with paper liners.
In a bowl, combine cranberries, milk, and yogurt. In a large bowl, combine all-purpose flour, whole wheat flour, flax seeds, baking powder, cinnamon, baking soda, and salt. Whisk sugar, egg and butter into milk mixture; pour over dry ingredients and stir just until moistened.
Spoon into prepared muffin pan. Press a few extra cranberries gently into tops if desired. Bake go 20-25 minutes or until tops are firm to the touch. Let cool in pan for 10 minutes. Transfer to rack to cool completely.