intro-spatial-transcriptomics-training/_quarto.yml at main · sib-swiss/intro-spatial-transcriptomics-training · GitHub

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project:
  type: website
  execute-dir: project
  render:
    - "**/*.qmd"
    - "!CONTRIBUTIONG.md"
    - "!LICENSE.md"
    - "!scripts/prepare_2026_course_data.qmd"

website:
  title: "Spatial Transcriptomics"
  favicon: assets/SIB_logo.svg
  search: true
  page-navigation: true
  # google-analytics: G-1H5B39PY7V
  # cookie-consent: true
  navbar:
    background: "#003eaa"
    left:
      - href: index.qmd
        text: Home
      - href: qmd/precourse_preparations.qmd
      - href: qmd/course_schedule.qmd
      - text: "day 1"
        menu:
          - href: "day1/day1-0_setup.qmd"
          - href: "day1/day1-1a_SpatialExperiment.qmd"
          - href: "day1/day1-1b_SpatialFeatureExperiment.qmd"
          - href: "day1/day1-2_spotsweeper_qc.qmd"
          - href: "day1/day1-1_SpatialExperiment_P1.qmd"
          - href: "day1/day1-2_spotsweeper_qc_P1.qmd"
          - href: "day1/day1-3_img_qc.qmd"
      - text: "day 2"
        menu:
          - href: "day2/day2-1a_normalization_visium.qmd"
          - href: "day2/day2-1b_normalization_xenium.qmd"
          - href: "day2/day2-2_feature_dimred.qmd"
          - href: "day2/day2-3_clustering_find_markers.qmd"
          - href: "day2/day2-4_annotation.qmd"
      - text: "day 3"
        menu:
          - href: "day3/day3-1_spatial_stats.qmd"
          - href: "day3/day3-2_svg_feature_set_signatures.qmd"
          - href: "day3/day3-3_differential_spatial_pattern.qmd"
    right:
      - icon: github
        href: https://github.com/sib-swiss/intro-spatial-transcriptomics-training
        aria-label: GitHub
  sidebar:
    logo: assets/SIB_LogoQ_GBv.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">
      <!-- Cookie Consent & Matomo Tracking -->
      <script src="assets/cookie-consent.js"></script>
      <!-- End Matomo Code -->


execute:
  freeze: auto
  cache: true
  tidy: true