Preheat oven to 350ºF. Line a 12-count muffin pan with cupcake liners.

In a mixing bowl, whisk together the flour, cocoa powder, baking powder, baking soda, and salt until combined; set aside.

In the bowl of a stand mixer fitted with a paddle attachment, beat the butter and both sugars together on medium speed until pale and fluffy. Beat in the eggs, one at a time, until combined, scraping down the sides and bottom of the bowl as needed. Beat in the Greek yogurt, vanilla, and vinegar on medium speed.

Pour the dry ingredients into the wet ingredients and mix until combined. Stir the food coloring into the buttermilk, then pour it into the batter. Mix until just combined, scraping down the sides and bottom of the bowl as needed.

Fill cupcake liners 3/4 of the way full. Bake for 19-21 minutes or until a toothpick inserted in the center comes out clean. Allow to cool in the pan for 5 minutes before transferring to a wire rack to cool completely.

Place the chocolate in a microwave-safe bowl and heat in the microwave until smooth and melted. Set aside to cool completely.

In the bowl of a stand mixer fitted with the paddle attachment, beat the butter, salt, and vanilla bean seeds on high until fluffy, about 4 minutes. Add the powdered sugar, a 1/2 cup at a time, until fully incorporated. Mix on high for 3 minutes.

Stop the mixer and use a rubber spatula to scrape down the sides and bottom of the mixing bowl. Add the melted chocolate and cream cheese. Beat frosting on high for 2-3 minutes until light and fluffy.

Pipe or spread frosting onto cupcakes, then garnish with sprinkles. Serve and enjoy!