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A best practice is to write, document, and test the code doing the 'work' of the shiny app as functions in an R package. Implement the user interface and server components of the shiny app in a minimal layer under inst/yourapp/. A silly and incomplete example is in mtmorgan/Elbo (developed for a workshop) where the UI consist exclusively of interface components, and the server component loads the Elbo library but otherwise consists exclusively of server reactive components and calls to the (public interface of the) package.
It would be interesting to hear (on the bioc-devel mailing list) from other developers and their 'best practices' related to shiny app development.