Split documentation to simplify onboarding process for new users

[lcolladotor]

We want to revise and update the current documentation. In particular, users frequently ask how to best transform the raw_counts. We plan to split the current documentation into multiple guides (vignettes) to differentiate the information that is useful for new users versus the information that advanced users might be interested in. Right now, all the information is contained as part of a very long vignette.