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