# BiocBook <img src="inst/assets/cover.png" align="right" alt="" />
Checkout the [`{BiocBookDemo}` **package**](https://github.com/js2264/BiocBookDemo)
and associated [**online book**](https://js2264.github.io/BiocBookDemo/devel/)
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](https://contributions.bioconductor.org/use-devel.html).
## 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](https://js2264.github.io/BiocBookDemo/devel/) 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
