Preheat oven to 350 degrees F (175 degrees C). Grease and flour 12 muffin cups or line with paper muffin liners.
Combine oats and orange juice in a large bowl; soak for 15 minutes. Stir yogurt, sucralose sweetener, and molasses into oat mixture; add eggs and beat.
Mix whole wheat flour, rye flour, baking powder, salt, baking soda, and nutmeg into oat mixture; add vanilla and cranberries. Spoon batter into prepared muffin cups and sprinkle pecans over the top of each muffin.
Bake in the preheated oven until golden brown and cooked through, about 20 minutes.