Suggestion: The analyses modules should know which files to download/analyze

[armish]

Users currently need to download files manually one by one and then switch to one of the analysis tabs to run a particular analysis of interest. Assuming that the GUI is intended for relatively non-tech scientists, I imagine users having difficulty in picking the right files and loading them for their analysis of interest. It would be great to make the file loading smarter by filtering for particular file types by default or suggest which files to download when/if the user picks one of the studies as the context (this would especially facilitate the integrative analyses)

[tiagochst]

To select a file from the server, we are using shinyFiles package. This package can filter by the file extension, which we are doing, but not for a pattern in the beginning or in the middle of the name.

For example, the first DNA methylation analysis steps will produce a file that starts with "DMR" prefix, this will be the input for the next steps. But we can't do this filter because the shinyFiles does not do that. We might need to change the code of shinyFiles and then wait the author merge and push it to CRAN. Then I can add this feature.

Other suggestion that we had was to create a history with latest files created (either from a download or from an analysis), as it is expected that those files will be used in the next steps. This feature might take more time than the first one, but the problem is the integratation with shinyFiles package.