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36 changes: 32 additions & 4 deletions documentation.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -62,10 +62,13 @@ All packages are required to have at least one Rmd, qmd, or Rnw vignette.
Vignettes go in the `vignettes/` directory of the package. Vignettes are often
used as standalone documents, so best practices are to include an informative
title, the primary author of the vignette, the last modification date of the
vignette, and a link to the package landing page. We encourage the use of
`r BiocStyle::Biocpkg("BiocStyle")` with `html_document` as the rendering
function. For example, in an R Markdown vignette one can use the following
specification in the yaml front matter:
vignette, and a link to the package landing page.

### RMarkdown vignettes

We encourage the use of `r BiocStyle::Biocpkg("BiocStyle")` with the
`html_document` rendering function. For example, in an R Markdown vignette one
can use the following specification in the yaml front matter:

```yaml
output:
Expand All @@ -91,6 +94,31 @@ vignette: >
%\VignetteEncoding{UTF-8}
```

### Quarto vignettes

More recently, `quarto` vignettes have been introduced as a new format for
vignettes. Quarto vignettes are similar to R Markdown but offer more advanced
features, flexibility, and multi-language support. The yaml front matter for a
Quarto vignette is similar to R Markdown, but it uses `quarto::html` as the
rendering function. For example, in a Quarto vignette one can use the following
specification in the yaml front matter:

```yaml
vignette: >
%\VignetteEngine{quarto::html}
%\VignetteIndexEntry{1. Quick Start: An Introduction}
%\VignetteEncoding{UTF-8}
```

In addition to the yaml front matter, vignette authors must ensure that the
`quarto` command line tool is listed as a `SystemRequirements` in the
`DESCRIPTION` file, as well as, indicate that the `VignetteBuilder` is set to
`quarto` in the `DESCRIPTION` file:

```r
VignetteBuilder: quarto
```

Some best practices and requirements for writing _Bioconductor_ vignettes are
detailed in the following sections.

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