Intro-to-scRNAseq/_quarto.yml at master · hbctraining/Intro-to-scRNAseq · GitHub

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project:
  type: website
  output-dir: docs
  resources:
    - img/
    - css/
    - slides/
    - schedule/


website:
  title: "Introduction to single-cell RNA-seq"
  google-analytics: G-68JBPLLNLG
  page-footer: >
      This lesson has been developed by members of the teaching team at the [Harvard Chan Bioinformatics Core (HBC)](http://bioinformatics.sph.harvard.edu/). <br>
      These are open access materials distributed under the terms of the [Creative Commons Attribution license](https://creativecommons.org/licenses/by/4.0/) (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. <br>
      A portion of these materials and hands-on activities were adapted from the [Satija Lab's](https://satijalab.org/) [Seurat - Guided Clustering Tutorial](https://satijalab.org/seurat/pbmc3k_tutorial.html)


  navbar:
    left:
      - text: "Schedule"
        href: schedule/schedule.qmd
    right:
      - text: "HBC"
        href: https://bioinformatics.sph.harvard.edu/
      - text: "GitHub"
        href: https://github.com/hbctraining/Intro-to-scRNAseq
      - text: "Contact us"
        href: mailto:hbctraining@hsph.harvard.edu


  sidebar:
    title: "Lessons"      # Optional title above the sidebar
    style: "docked"       # Sidebar is docked to the left
    collapse-level: 1     # At what header level to start collapsing
    # contents: auto      # Creates automatic TOC from page headers (no sections)
    contents:
      - section: "Pre-reading:"
        contents:
        - lessons/01_intro_to_scRNA-seq.qmd
        - lessons/02_generation_of_count_matrix.qmd

      - section: "Day 1:"
        contents:
          - lessons/03_quality_control-setup.qmd
      - section: "Day 1 Self-learning:"
        contents:
          - lessons/04_cellranger_QC.qmd
          - lessons/06_theory_of_PCA.qmd

      - section: "Day 2:"
        contents:
          - lessons/05_quality_control.qmd
          - lessons/07_SCT_normalization.qmd
          - lessons/08_integration_cca_theory.qmd
      - section: "Day 2 Self-learning"
        contents:
          - lessons/09_integration_code_harmony.qmd

      - section: "Day 3:"
        contents:
          - lessons/10_clustering_cells_SCT.qmd
          - lessons/11_clustering_quality_control.qmd
      - section: "Day 3 Self-learning"
        contents:
          - lessons/12_seurat_cheatsheet.qmd

      - section: "Day 4:"
        contents:
          - lessons/13_marker_identification.qmd
          - lessons/14_scRNAseq_workflow.qmd


format:
  html:
    theme: simplex
    css: css/styles.css
    fig-align: "center"
    toc: true
    number-sections: false
    code-block-bg: true
    code-copy: true      # enables copy button (default in most themes)
    code-tools: true     # enables the copy button!
    code-line-wrap: wrap
    google-analytics: G-68JBPLLNLG
    prompt: true
    self-contained: true

# Global Execution Defaults
execute:
  echo: true               # show code
  eval: true               # run code
  warning: false           # show warnings
  error: false             # show errors
  message: false           # show messages
  prompt: true