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:

1. Fork the project
2. Create a new branch
3. Commit changes to the new branch
4. Create a pull request (PR) back to the original repo
5. 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

Please note that the OMA project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.