README.md

BiocBook

Checkout the {BiocBookDemo} package and associated online book for an example of a BiocBook.

---

BiocBooks are package-based, versioned online books with a supporting Docker image for each book version.

A BiocBook can be created by authors (e.g. R developers, but also scientists, teachers, communicators, ...) who wish to:

1. Write: compile a body of biological and/or bioinformatics knowledge;
2. Containerize: provide Docker images to reproduce the examples illustrated in the compendium;
3. Publish: deploy an online book to disseminate the compendium;
4. Version: automatically generate specific online book versions and Docker images for specific Bioconductor releases.

Installation

To install BiocBook from Bioconductor, proceed as follows:

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("BiocBook")

To install BiocBook development version from Bioconductor, you can use:

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install(version = 'devel')

BiocManager::install("BiocBook")

How to create a BiocBook

library(BiocBook)

## Make sure you have set up a Github token
gh::gh_whoami()
# check `usethis::gh_token_help()` for more information

## Create a new BiocBook
init("myNewPackage")

## Open the new BiocBook
bb <- BiocBook("./myNewPackage")

## Add pages
add_preamble(bb)
add_chapter(bb, title = "Chapter 1")
add_chapter(bb, title = "Chapter 2")

## Preview
preview(bb)

## Publish to Github
publish(bb)

Please read BiocBook vignette: vignette("BiocBook").

You can also check out the BiocBookDemo book to know more about BiocBook.

Acknowledgments

This works was inspired by and closely follows the strategy used in coordination by the Bioconductor core team and Aaron Lun to submit book-containing packages (from the OSCA series as well as SingleR and csaw books).

• @OSCA
• @SingleR
• @csaw

This package was also inspired by the *down package series, including:

• @knitr
• @pkgdown
• @bookdown