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# BiocBook <img src="inst/assets/cover.png" align="right" alt="" /> Checkout the [`{BiocBookDemo}` **package**]( and associated [**online book**]( for an example of a `BiocBook`. --- `BiocBook`s 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: ```r if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("BiocBook") ``` To install `BiocBook` development version from Bioconductor, you can use: ```r if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version = 'devel') BiocManager::install("BiocBook") ``` ## How to create a `BiocBook` ```r 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