Write, containerize and publish versioned Quarto books with Bioconductor

Author(s): Jacques Serizay

Affiliation(s): Institut Pasteur



Recently, several bioinformatics books have focused on describing state-of-the-art genomic analysis workflows, such as functional analysis of gene sets, single-cell transcriptomics, or spatial transcriptomics. R and the Bioconductor ecosystem have long been at the forefront of computational tools for genomics. With `Bookdown` and more recently with `Quarto`, the authoring of books on bioinformatics topics has been facilitated. However, the field of bioinformatics is constantly evolving, and ensuring reproducibility and consistency across software versions remains a challenge. BiocBook is a new package that facilitates the creation, editing, and publishing of versioned online books along with their corresponding Docker images. The end-user/author can initiate a book from a public template in minutes and start writing new chapters in Quarto-style markdown files. Synchronizing changes with a linked Github repository triggers (1) automated rendering of the book as an online website hosted in a separate branch and served by Github Pages, and (2) automated distribution of the Docker image used for rendering. Because the book repository follows the structure of R packages, it can be submitted to Bioconductor. Each new Bioconductor release will allow the creation of a separate version of the online book and Docker image. This way, major changes and new features are reflected in newer Bioconductor releases, while older versions are preserved.