mapa-tutorial/_quarto.yml at main · jaspershen-lab/mapa-tutorial · GitHub

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project:
  type: book
  output-dir: docs

book:
  title: "MAPA Tutorial"
  author: "[Yifei Ge](https://www.shen-lab.org/author/yifei-ge/), [Xiaotao Shen](https://www.jaspershenlab.com/), [Yuchen Shen](https://github.com/EthanShenx)"
  date: "6/8/2025"
  favicon: "/images/mapa_logo.png"
  description: Functional Module Identification and Annotation for Pathway Analysis Results Using LLM
  url: http://www.shen-lab.org/mapa-tutorial/
  sidebar:
    logo: "images/mapa_logo.png"
    search: true
  repo-url: https://github.com/jaspershen-lab/mapa-tutorial
  repo-actions: [edit, issue, source]
  image: "images/mapa_logo.png"

  chapters:
    - index.qmd

    - part: "MAPA R Package"
      chapters:
        - 01_package_installation.qmd
        - 02_input.qmd
        - 03_enrichment_analysis.qmd
        - 04_pathway_similarity.qmd
        - 05_determine_optimal_clustering_params.qmd
        - 06_get_functional_modules.qmd
        - 07_llm_interpretation.qmd
        - 08_data_vis.qmd
        - 09_res_report.qmd

    - part: "MAPA Shiny App/Web"
      chapters:
        - 10_shinyapp_installation.qmd
        - 11_input_shiny.qmd
        - 12_enrichment_analysis_shiny.qmd
        - 13_pathway_similarity_shiny.qmd
        - 14_get_functional_modules_shiny.qmd
        - 15_llm_interpretation_shiny.qmd
        - 16_data_vis_shiny.qmd
        - 17_res_report_shiny.qmd

    - references.qmd

bibliography: references.bib

format:
  html:
    theme:
      light: cosmo
      dark: superhero
    css: custom.css

editor: visual