_book.yml

language: 
  search-box-placeholder: Search
book:
  title: "Orchestrating Microbiome Analysis"
  search: 
    location: sidebar
    type: textbox
  navbar:
    logo: "assets/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
    - part: "Introduction"
      chapters:
        - pages/intro.qmd
        - pages/miaverse.qmd
    - part: "Data containers & importing"
      chapters:
        - pages/containers.qmd
        - pages/import.qmd
        - pages/convert.qmd
    - part: "Data wrangling"
      chapters:
        - pages/taxonomy.qmd
        - pages/wrangling.qmd
        - pages/subsetting.qmd
        - pages/agglomeration.qmd
        - pages/transformation.qmd
    - part: "Exploration & QC"
      chapters:
        - pages/quality_control.qmd
        - pages/composition.qmd
    - part: "Diversity & similarity"
      chapters:
        - pages/alpha_diversity.qmd
        - pages/beta_diversity.qmd
        - pages/clustering.qmd
    - part: "Association"
      chapters:
        - pages/differential_abundance.qmd
        - pages/correlation.qmd
    - part: "Networks"
      chapters:
        - pages/network_learning.qmd
        - pages/network_comparison.qmd
    - part: "Multiomics"
      chapters:
        - pages/cross_correlation.qmd
        - pages/multiassay_ordination.qmd
        - pages/integrated_learner.qmd
    - part: "Machine learning & statistical modeling"
      chapters:
        - pages/machine_learning.qmd
        - pages/statistical_modeling.qmd
    - part: "Workflows"
      chapters:
        - pages/introductory_workflow.qmd
        - pages/introductory_workflow_french_version.qmd
        - pages/introductory_workflow_dutch_version.qmd
    - part: "Training"
      chapters:
        - pages/training.qmd
        - pages/exercises.qmd
    - part: "Support & resources"
      chapters:
        - pages/support.qmd
        - pages/resources.qmd
        - pages/acknowledgments.qmd
  appendices:
    - pages/msea.qmd
    - pages/mmuphin_meta_analysis.qmd
    - pages/extra_material.qmd
    - pages/visualization.qmd
    - pages/session_info.qmd
  favicon: assets/favicon.png
  sidebar: 
    style: "docked"
    background: "light"
    collapse-level: 1