Combine 2 cups of warm filtered water, yeast, and 1 tablespoon of agave or honey in a measuring cup. Let it rest for 5 minutes or until bubbles form on the surface.
Weigh on a scale 28.13 ounces flour. Add the flour, cranberries, salt, and the yeast mixture into the bowl of your stand mixer fitted with dough hook. Mix the dough at low speed for 6 minutes.
Turn dough out onto a floured surface. Knead 2 minutes or until smooth and elastic; add enough of remaining ¼ cup flour, 1 tablespoon at a time, to prevent dough from sticking to hands.
Place dough in a large bowl coated with cooking spray, turning to coat top. Cover and let rise in a warm place, free from drafts, 30 minutes (I put mine in a lightly preheated oven).
Turn dough out onto a lightly floured surface, and divide into 12 equal portions. Working with one portion at a time (cover remaining dough to prevent drying), shape each portion into a ball.
Make a hole in the center of each ball using your index finger. Using fingers of both hands, gently pull dough away from the center to make a 1 ½-inch hole. Place bagels on a baking sheet with parchment paper. Lightly coat bagels with cooking spray; cover with plastic wrap. Let rise 30 minutes (bagels will rise only slightly).
Place a heavy pan on the lower part of the oven and preheat to 400°.
Combine 12 cups water, 1 teaspoon baking soda, and ½ cup brown sugar in a big saucepan or Dutch oven, and bring to a boil. Gently lower 3 bagels into the saucepan. Cook for one side 1mn30 then flip the bagels and continue to cook 1mn30. Transfer the bagels to a wire rack lightly coated with cooking spray. Repeat the procedure with the remaining bagels, working in batches of 3.
Divide the bagels between two baking sheets lined with parchment paper. Pour some hot water in the heavy pan or throw a half dozen ice cubes. Put the bagels inside the oven and spray the door with some water and close the door quickly.
Bake at 450° for 7 minutes. Rotate pans, spray again the door close quickly and bake for 7 minutes or until golden. Cool on wire racks.