1. Preheat oven to 350 degrees Fahrenheit. Grease 6 muffin cups with nonstick spray or line with paper cupcake liners.
2. Put all dry ingredients in a mixing bowl, and whisk to combine. If your beets are already pureed, add all wet ingredients to the dry and whisk to combine. If your beets are whole, first puree them in a food processor before measuring out 1/2 cup of beet puree and adding it to the dry mix with all reaming cupcake ingredients.
3. Use a 1/4 cup dry measuring cup to portion the batter into the muffin cups. You should get between 6 and 8 cupcakes. Bake for 14-16 minutes, or until cooked through. Let cupcakes cool completely before frosting.
4. While cupcakes bake, make frosting. Put shredded beets in a small bowl, and add heavy cream. Let the beets steep in the cream for a few minutes while you prepare the rest of the frosting.
5. Put cream cheese in a stand mixer with the vanilla and whisk until smooth. Strain the cream through a fine mesh strainer (it should be pink by now) and pour the cream into the cream cheese. Whisk on high for 2-3 minutes, until fluffy. Add powdered sugar and salt, and whisk again to combine. Taste and add more powdered sugar, if desired. Transfer frosting to the fridge to chill while the cupcakes cool. The frosting will be soft, but shouldn't be liquid-y, and will firm up more as it chills.
6. When cupcakes are cool, add a heaping spoonful of frosting to each, and gently flatten. Top with berries, if desired. Eat immediately.