Many nodes under the Modify menu let you modify the shape of an object as a whole. Modifying only selected portions of an object is also supported using the EditGeo node.
You can modify 3D objects by selecting vertices or faces in the Viewer using the EditGeo node or by using lookup curves, power functions, images, a Perlin noise function, a distortion function, or trilinear interpolation.
Modifying Objects Using the EditGeo Node
Modifying Objects Using Lookup Curves
Modifying Objects Using a Power Function
Modifying Objects Using an Image - Method 1
Modifying Objects Using an Image - Method 2
Modifying Objects Using a Perlin Noise Function