There's no possibility of using directories in shinyapp.io. An easy fix is to place an upload button inside the app, perform all the manipulations you need and finally download the result with a download button again. Getting the data from a remote server is also a good option.
As shown in this Article
"Local vs remote storage
Before diving into the different storage methods, one important distinction to understand is local storage vs remote storage.
Local storage means saving a file on the same machine that is running the Shiny application. Functions like write.csv(), write.table(), and saveRDS() implement local storage because they will save a file on the machine running the app. Local storage is generally faster than remote storage, but it should only be used if you always have access to the machine that saves the files.
Remote storage means saving data on another server, usually a reliable hosted server such as Dropbox, Amazon, or a hosted database. One big advantage of using hosted remote storage solutions is that they are much more reliable and can generally be more trusted to keep your data alive and not corrupted.
When going through the different storage type options below, keep in mind that if your Shiny app is hosted on shinyapps.io, you will have to use a remote storage method for the time being. In the meantime, using local storage is only an option if you’re hosting your own Shiny Server. If you want to host your own server, here is a guide that describes in detail how to set up your own Shiny Server."
