Preheat the oven to 350 degrees F and line a 12-cup muffin tin with cupcake liners.
Whisk the flour, baking powder and salt together in a medium bowl. Beat the eggs and sugar together in another medium bowl with an electric mixer on medium-high speed until light and foamy, about 2 minutes. While beating, gradually pour in the butter and then the vanilla.
Reduce the mixer speed to low and add half the flour mixture, followed by the milk and the remaining flour mixture, beating until each addition is just incorporated. Remove one-third of the batter (about 1 cup) and stir in the cocoa powder. Alternate dropping spoonfuls of the batters into the cupcake liners, using a larger spoon for the yellow batter and a smaller spoon for the chocolate batter. Swirl with an offset spatula or a skewer.
Bake until a toothpick inserted in the center of the cakes comes out clean, 18 to 20 minutes. Cool the cupcakes on a rack in the tin for 10 minutes, and then remove from the tin. Cool on the rack completely.
For the chocolate glaze:
Put the chocolate in a medium bowl. Heat the cream in a small saucepan over medium heat until it just simmers. Pour the cream over the chocolate and let sit for 1 minute. Then gently stir until smooth and glossy. Cool the glaze slightly until thickened but not hard. Spread 1 tablespoon of glaze on top of each cupcake or dip the top of the cupcake in the glaze.
When measuring flour, we spoon it into a dry measuring cup and level off the excess. (Scooping directly from the bag compacts the flour, resulting in dry baked goods.)
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