insightsengineering / insightsengineering/teal.slice
Separate bioconductor dependencies from `teal.slice`
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- R
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Description
### Summary
Prior discussion [here](https://github.com/insightsengineering/teal.slice/issues/499#issuecomment-1859921788)
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](https://insightsengineering.github.io/teal/latest-tag/articles/including-mae-data-in-teal.html) 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).
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