Federico Marini

Hi @lazappi , thanks for your comprehensive review, we'll get right onto it to improve it following your suggestions! @ldammer and I will get back to you once we have...

As for your point of accommodating the `edgeR` framework, which can take a while to implement properly, we are nonetheless trying to think ahead, and have some of the deseq-centric...

> You could also use S3 dispatch with methods for different classes if you prefer, which can be more work to set up but can also help with organising/modularising code....

Thanks for the swift reply! For some of the points you mentioned, we were already in touch before initiating the submission process with @lshep about the runtime, so she might...

Thanks Luke for the reply! I have used a couple of other times the equivalent of ``` file.edit(system.file("scripts", "create_mosdef_data.R", package = "mosdef")) ``` to access such scripts directly in the...

For more context - we tried to follow the way described here -> https://contributions.bioconductor.org/docs.html#doc-inst-script (specifically, §12.4 and §12.3.3)

Hy @davemcg, I tried to run the vignette also with the interactive chunks of code to launch the app. At this point https://github.com/davemcg/geyser/blob/c2747ad0ea1aef68948b36c3fa43671c046057de/vignettes/Gene_Expression_Plotting_GUI.Rmd#L157 I am encountering an error crashing the...

Yep, still sounds like a good idea to me even if it aged "lonely" 😄 The hexagons would actually simplify the things, we would simply have to "accept" a slightly...

Hi @tamuanand - see the conversation above. Since GeneTonic can accept the objects at runtime as well, it is a simple thing to do to create a "separate" app.R file...

I just checked and it also curiously doesn't work in the local versions either. Maybe something changed in the way how a modalDialog is handled? OR did we change something...