Preheat the oven to 375 °F. Line a standard-sized muffin tin with paper liners.
In a large bowl, combine the whole-wheat flour, flaxseed, oats, baking powder, and baking soda. Stir in nuts and raisins.
In a medium bowl, combine juice, eggs, oil, vanilla, and ginger. Whisk to blend. Add the juice mixture to the flour mixture and stir gently just until the batter is smooth and well blended; do not overmix.
Gently fold in carrots. Spoon batter evenly into the prepared muffin tin. Bake for about 20 minutes, until a toothpick inserted into the center, comes out clean.
Prepare the coffee to your liking.
Transfer muffins to a wire rack and let cool for 10 minutes. Remove muffins from tin; let cool completely.
Serve the muffins, spread with cream cheese if desired, and coffee.