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Preheat oven to 350F. Line a muffin tin with paper liners and lightly spray liners with oil for easy removal.
In a medium bowl, combine flours, sugar, baking soda, pumpkin spice, nutmeg, cinnamon, and salt with a wire whisk. Set aside.
In a large bowl mix pumpkin puree, oil, egg and vanilla; beat at medium speed until thick. Scrape down sides of the bowl.
Add flour mixture to the wet mixture, then blend at low speed until combined; do not over mix.
In a large bowl, beat the cream cheese until smooth. Slowly beat in the sugar, egg yolk and vanilla extract until combined.
Pour batter into prepared muffin tin. Drop about 1 tablespoon of the cream cheeseto the tops of each muffin. Using a toothpick gently swirl the frosting from the edge to the center into the batter.
Bake on the center rack for 24 to 26 minutes, or until a toothpick inserted in the center comes out clean.
Let them cool before serving.