To do an initial conversion of vignettes of a package from Rnw to Rmd:

1. Click "Use this template" - "Create a new repository" above
2. Give the new repository the name of the Bioconductor package whose Rnw vignettes you would like to convert to Rmd
3. In the new repository, under settings go to "Actions - General" then the section "Workflow permissions" to select:
   • "Read and write permissions"
   • "Allow GitHub Actions to create and approve pull requests"
4. Click on "Actions", click on the "Initial commit" job, and click "Re-run all jobs". This seems to be necessary to have the new permissions take effect.
5. Once the GitHub Action has finished (~10 minutes), click on the "Pull requests" tab to merge the pull request it created.
6. Check and edit the Rmd vignettes of the new repository until they work
7. Optional: activate GitHub Pages on the new repository; it will already have pkgdown running in its GitHub Action. (TODO: add pkgdown Action and instructions)