Preheat the oven to 350° and fill 12 muffin cups with paper liners. In a medium heatproof bowl, combine the oats with the cranberries, millet and flax seeds. Cover with hot water and let stand until plumped, about 20 minutes. Rinse the mixture and drain well.
In a large bowl, whisk the flour with the baking powder, baking soda, salt and cinnamon.
In a medium bowl, whisk the yogurt with the brown sugar, eggs, oil, molasses and vanilla. Add the wet ingredients and oat mixture to the dry ingredients and stir until combined.
Spoon the batter into the muffin cups and bake for 25 to 30 minutes, until a toothpick inserted into the center comes out clean. Let cool for 5 minutes. Transfer the muffins to a rack, brush with honey and let cool completely.
The muffins can be stored in an airtight container for up to 2 days.
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