Course-on-scRNA-seq-data-analysis/_quarto.yml at master · bioinfocz/Course-on-scRNA-seq-data-analysis · GitHub

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project:
  type: website
  output-dir: docs
  execute-dir: project
  render:
    - "*.qmd"
    - "!CONTRIBUTING.md"
    - "!LICENSE.md"
    - "!assets/"
    - "!advanced_exercise/"

profiles:
  - v2025.3
  - latest

website:
  title: "Single cell transcriptomics"
  favicon: assets/imglogo-basic-color-nobg-cmyk.svg
  search: true
  page-navigation: true
  # google-analytics: G-1H5B39PY7V
  # cookie-consent: true
  navbar:
    background: "#003eaa"
    left:
      - href: index.qmd
        text: Home
      - href: precourse_preparations.qmd
      - href: course_schedule.qmd
      - text: "day 1"
        menu:
          - href: "day1/day1-1_setup.qmd"
          - href: "day1/day1-1a_cellranger.qmd"
          - href: "day1/day1-2_analysis_tools_qc.qmd"
      - text: "day 2"
        menu:
          - href: "day2/day2-1_normalization_scaling.qmd"
          - href: "day2/day2-2_dimensionality_reduction.qmd"
          - href: "day2/day2-3_integration.qmd"
          - href: "day2/day2-4_clustering.qmd"
      - text: "day 3"
        menu:
          - href: "day3/day3-1_cell_annotation.qmd"
          - href: "day3/day3-2_differential_gene_expression.qmd"
          - href: "day3/day3-3_enrichment_analysis.qmd"
      - text: "projects"
        menu:
          - href: "projects/introduction.qmd"
          - href: "projects/project1.qmd"
          - href: "projects/project2.qmd"
          - href: "projects/project3.qmd"
          - href: "projects/project4.qmd"

      # - text: "Versions"
      #   menu:
      #     - href: /v2025.3/
      #       text: "v2025.3"
      #     - href: /latest/
      #       text: "Latest"

    right:
      - icon: github
        href: https://github.com/bioinfocz/Course-on-scRNA-seq-data-analysis
        aria-label: GitHub
  sidebar:
    logo: assets/logo_stranky.svg

format:
  html:
    code-link: true
    theme:
      - default
      - custom.scss
    toc: true
    header-includes: |
      <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Source+Sans+Pro">
      <!-- Matomo -->
      <script>
        var _paq = window._paq = window._paq || [];
        /* tracker methods like "setCustomDimension" should be called before "trackPageView" */
        _paq.push(['trackPageView']);
        _paq.push(['enableLinkTracking']);
        (function() {
          var u="https://matomo.sib.swiss/";
          _paq.push(['setTrackerUrl', u+'matomo.php']);
          _paq.push(['setSiteId', '220']);
          var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
          g.async=true; g.src=u+'matomo.js'; s.parentNode.insertBefore(g,s);
        })();
      </script>
      <!-- End Matomo Code -->

execute:
  freeze: auto
  cache: true
  tidy: true