In a bowl, combine yogurt and cereal; let stand for 5 minutes. In a large bowl, combine flours, baking powder, baking soda and salt. Stir the orange juice, honey, butter, egg and orange zest into yogurt mixture. Stir into dry ingredients just until moistened. Fold in cranberries.
Coat muffin cups with cooking spray; fill three-fourths full. Bake at 375° for 18-22 minutes or until a toothpick comes out clean. Cool for 5 minutes before removing from the pans to wire racks.