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BiocBook

This is the development version of BiocBook; for the stable release version, see BiocBook.

Write, containerize, publish and version Quarto books with Bioconductor


Bioconductor version: Development (3.19)

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), and 4) version (automatically generate specific online book versions and Docker images for specific Bioconductor releases).

Author: Jacques Serizay [aut, cre]

Maintainer: Jacques Serizay <jacquesserizay at gmail.com>

Citation (from within R, enter citation("BiocBook")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("BiocBook")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BiocBook")
BiocBook HTML R Script
Reference Manual PDF
LICENSE Text

Details

biocViews Infrastructure, ReportWriting, Software
Version 1.1.3
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.3)
Imports BiocGenerics, available, cli, glue, gert, gh, gitcreds, httr, usethis, dplyr, purrr, tibble, methods, rprojroot, stringr, yaml, tools, utils, rlang, quarto, renv
System Requirements
URL https://bioconductor.org/packages/BiocBook
Bug Reports https://github.com/js2264/BiocBook/issues
See More
Suggests BiocStyle, knitr, testthat (>= 3.0.0), rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package BiocBook_1.1.3.tar.gz
Windows Binary
macOS Binary (x86_64) BiocBook_1.1.3.tgz
macOS Binary (arm64) BiocBook_1.1.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/BiocBook
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BiocBook
Bioc Package Browser https://code.bioconductor.org/browse/BiocBook/
Package Short Url https://bioconductor.org/packages/BiocBook/
Package Downloads Report Download Stats