_book.yml

language: 
  search-box-placeholder: Search
book:
  title: "Orchestrating Microbiome Analysis"
  search: 
    location: sidebar
    type: textbox
  navbar:
    logo: "pages/images/mia_logo.png"
    background: transparent
    align: center
    left:
      - icon: github
        menu:
          - text: Source Code
            url:  https://github.com/microbiome/OMA/
          - text: Browse version `devel`
            url:  https://microbiome.github.io/OMA/docs/devel/
      - icon: twitter
        href: https://twitter.com
    title: "Orchestrating Microbiome Analysis"
  chapters:
    - index.qmd
    - pages/01_intro.qmd
    - part: "OMA ecosystem"
      chapters:
        - pages/06_packages.qmd
        - pages/04_containers.qmd
    - part: "Focus topics"
      chapters:
        - pages/10_manipulation.qmd
        - pages/12_quality_control.qmd
        - pages/11_taxonomic_information.qmd
        - pages/14_alpha_diversity.qmd
        - pages/20_beta_diversity.qmd
        - pages/21_microbiome_community.qmd
        - pages/24_clustering.qmd
        - pages/30_differential_abundance.qmd
        - pages/40_machine_learning.qmd
        - pages/23_multi-assay_analyses.qmd
    - part: "Advanced topics"
      chapters:
        - pages/60_network_learning.qmd
        - pages/61_network_comparison.qmd
        - pages/IntegratedLearner.qmd
        - pages/MMUPHin_meta_analysis.qmd
        - pages/MSEA.qmd
        - pages/19_visualization_techniques.qmd
    - part: "Training"
      chapters:
        - pages/80_training.qmd
        - pages/95_resources.qmd
        - pages/98_exercises.qmd
  appendices:
    - pages/97_extra_materials.qmd
    - pages/90_acknowledgments.qmd
    - pages/Session_info.qmd
  favicon: assets/favicon.png
  sidebar: 
    style: "docked"
    background: "light"
    collapse-level: 1