Separate bioconductor dependencies from teal.slice

[donyunardi]

Summary

Prior discussion here

As part of preparing to release teal.slice to CRAN, we will create a new package that extends teal.slice to support MultiAssayExperiment and SummarizedExperiment dependencies.

The proposed package name is teal.slice.bio.

Tasks

For teal.slice.bio update

• Create a repo in insightengineering for teal.slice.bio (IDR support will be needed here)
• teal.slice.bio will be an extension of teal.slice with MultiAssayExperiment and SummarizedExperiment dependencies
  • teal.slice should be in Depends.
• Update changes in teal.gallery pipeline for RNA-seq example app (i.e. code update, renv.lock file, etc).
• Update this vignette in teal.
• Setup development chores:
  • pkgdown
  • create pre-commit config file
  • .lintr
  • stage_dependencies.yaml
• Setup verdepcheck
• Do we need vignette for this package?
• Add unit tests
• Pass R CMD Check

Notes from @danielinteractive:

• Please use this as resource: https://contributions.bioconductor.org/description.html#depends-imports-suggests-enhances
• Might be easier to release teal.slice.bio to CRAN than BioConductor due to:
  • extensive review process
  • forcing to move the repo to different organization

For teal.slice update

• Remove MultiAssayExperiment and SummarizedExperiment dependencies from teal.slice.
• Do we need to notify users when attempting to use MAE by prompting them to install and load teal.slice.bio?
• Check documentation to ensure to mention of MAE or SE (i.e. roxygen, vignettes, etc).
• Pass R CMD Check

For teal.modules.hermes update

• Update package dependencies for modules (i.e. tm.hermes) to use teal.slice.bio. It should be in Depends.
• Pass R CMD Check

For teal.modules.helios update

• Update package dependencies for modules (i.e. tm.hermes) to use teal.slice.bio. It should be in Depends.
• Pass R CMD Check

For teal.gallery update

• Update changes in teal.gallery pipeline for affected example app (i.e. code update, renv.lock file, etc).

[donyunardi]

cc'ing @danielinteractive @BFalquet for awareness

[lcd2yyz]

Agree with the proposed concept, but suggest to name new pkg to teal.slice.bioc