Orchestrating Microbiome Analysis Book

Overview

This is a reference cookbook for performing Microbiome Analysis with Bioconductor in R. This is a book based on R Markdown and bookdown (https://github.com/rstudio/bookdown).

Deployment

For now the book is deployed to GitHub Pages from GitHub Actions. The book can also be built locally:

bookdown::render_book("index.Rmd", "bookdown::gitbook")

You can view the book also with:

bookdown::serve_book()

To install the necessary dependencies to build to book, run

BiocManager::install(remotes::local_package_deps(dependencies=TRUE))

Development and Contribtions

To contribute reports, follow the Git flow procedure:

Fork the project
Create a new branch
Commit changes to the new branch
Create a pull request (PR) back to the original repo
Fix and discuss issues in the review process

Please note that chapters should be independent of each other.

Adding new sections

Create the relevant Rmd file; follow the numbering logic
Add it also to the list in file _bookdown.yml.

Code of conduct