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Position a rack in the center of the oven and preheat oven to 350 degrees.
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Place paper baking cups in twelve 2 inch muffin pan cups.
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To make the filling: Using an electric mixer on medium speed, beat cream cheese, sugar, and egg until smooth.
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Fold in the chocolate chips.
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To make the cupcakes: combine the flour, cocoa powder, baking soda and salt.
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In a large bowl, using an electric mixer on medium speed, beat the sugar, oil, water and vinegar until combined Gradually stir in the dry ingredients.
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Fill the prepared muffin cups one third full.
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Spoon heaping teaspoonsfuls of the cream cheese mixture onto the chocolate batter in each cup.
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Bake for 20 to 25 minutes, or until the tops spring back when touched.
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Remove from the pan to a wire rack to cool.