Identify common R and Python software to include

[tschaffter]

The current environment includes the following software:

• Synapse Python Client: Interact with Synapse API.
• Challengeutils: Utility program to create and manage challenges.
• Sagethemes: R library to apply Sage theme (color and font) to plots.

@kelshmo @Aryllen Are there other R and Python packages that could be useful to a large portion of users?

[Aryllen]

There's a few things that come to mind immediately:

• Bioconductor. There's a lot of bioinformatics packages available through this resource.
• reticulate to bring the Synapse Python Client into R.
• Tidyverse packages. Many users are versed in Tidyverse and will be uncomfortable without it. It takes a while to install, as well, so less good to have to do on run-time.

[tschaffter]

@Aryllen

• I have in mind that Bioconductor is a massive library but maybe I'm wrong. We could do a quick test to see how much space it would take in the image.
• reticulate is already included. The notebook r-and-python.Rmd and synapse.Rmd makes use of it.
• I would love to see this project promoting the use of Tidyverse packages! I'm myself not well "versed" with it but would like to explorer it at some point. In addition to include Tidyverse packages, another way to promote its could be to design all example notebooks to rely on it.

[Aryllen]

I have in mind that Bioconductor is a massive library but maybe I'm wrong. We could do a quick test to see how much space it would take in the image.

That's a good point. In my mind, I think of Bioconductor as being similar to CRAN, which it is since they both host R packages, but tend to forget that it's actually BiocManager that's the package management tool. I wouldn't install all of the Bioconductor packages, but we could give people the option to install them by adding in the BiocManager package from CRAN.

reticulate is already included. The notebook r-and-python.Rmd and synapse.Rmd makes use of it.

Oh good. I thought I remembered seeing it when I was skimming through, but didn't double check.

I would love to see this project promoting the use of Tidyverse packages! I'm myself not well "versed" with it but would like to explorer it at some point. In addition to include Tidyverse packages, another way to promote its could be to design all example notebooks to rely on it.

I am not well-versed in the Tidyverse, either -- I tend to work in base R and just bring in Tidyverse-related functions when they could be helpful. There are a lot of people who do rely on Tidyverse, though. I wouldn't make all example notebooks rely on it, but rather just some.