Pre-heat the oven to 350ºF and arrange a rack in the middle. Line 2 twelve well muffin pans with paper liners or alternatively coat the wells with vegetable oil; set aside.
Place the flour, baking powder, cinnamon, cloves, allspice, nutmeg, baking soda, and salt in a large bowl and whisk to break up any lumps; set aside.
Place the sugar and measured oil and Rouge’s Pumpkin Patch Ale in a medium bowl. Use a mixer and beat on medium speed until the sugar is incorporated, about 1 minute. Stop the mixer and scrape down the sides of the bowl with a rubber spatula.
Return the mixer to medium speed and add the eggs 1 at a time, beating well after each addition, about 1 1/2 minutes total mixing time.
Reduce the speed to medium low, add the pumpkin, and beat until just combined, about 30 seconds. Stop the mixer and scrape down the sides of the bowl with a rubber spatula.
Turn the mixer to low speed, slowly add the flour mixture, and Beat until almost completely incorporated, about 1 minute. Remove the bowl from the mixer and fold in any unincorporated flour at the edges with a rubber spatula, making sure to scrape to the bottom of the bowl.
Fill the muffin wells three-quarters of the way (about a heaping 1/4 cup per well). Place the muffin pans side by side in the oven and bake for 12 minutes. Rotate the pans front to back and side to side and bake until a toothpick inserted into the center of the cupcakes comes out clean, about 10 minutes more.
Place the pans on wire racks and let them cool for 5 minutes. Remove the cupcakes from the pans and cool completely on the racks. Frost with Pumpkin–Cream Cheese Frosting.
Cream Cheese Frosting
Place the sugar, cinnamon, and nutmeg in a medium bowl and whisk to combine; set aside.
Place the cream cheese and butter in the bowl of a stand mixer fitted with a paddle attachment and beat on medium speed until fully combined and smooth, about 1 minute.
Reduce the speed to low, slowly add the powdered sugar mixture, and beat until fully incorporated and smooth, about 3 minutes. Stop the mixer and scrape down the paddle and sides of the bowl with a rubber spatula.
Turn the mixer to medium speed, add the pumpkin, and mix until fully incorporated and smooth, about 1 minute.
Scrape down sides of bowl with a rubber spatula and chill in fridge for 10 mins before using on cupcakes.