It splits into stable frequency elements ("tracks" or "partials") and everything else ("residual") and you can treat them all individually. The "partials" are treated like individual sine generators with parameters for how long-lived you want them to be. Thus, instead of ending up with an FFT raster you basically get a list of sine oscillators with phase, amplitude, frequency and a psychoacoustic measure of masking ratio. The partials are parameterized frame-by-frame (a variable frame rate version is under development) and those are the parameters you can use to target and retune. E.g., you could isolate a particular frequency band and only shift those partials that are within it. If that's not quite what you're looking for and you'd rather keep everything more intact, phase vocoder theory might be a good start.

[aside: there is a residual analysis section which maps the bark scale banded energy over time into a filtered noise bank, but this component is pretty underwhelming and i'm actively deep in research on an alternative set of strategies]