biomedical-knowledge-mining-book/_quarto.yml at master · YuLab-SMU/biomedical-knowledge-mining-book · GitHub

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project:
  type: book
  output-dir: docs

book:
  title: "Biomedical Knowledge Mining using GOSemSim and clusterProfiler"
  reader-mode: true
  author: "Guangchuang Yu"
  date: "11/18/2025"

  page-footer:
    left: |
      Biomedical Knowledge Mining using GOSemSim and clusterProfiler was written by Guangchuang Yu.
    right: |
      This book was built with <a href="https://quarto.org/">Quarto</a>.
  site-url: https://yulab-smu.top/biomedical-knowledge-mining-book/
  repo-url: https://github.com/YuLab-SMU/biomedical-knowledge-mining-book/
  repo-branch: main
  repo-actions: [edit, issue]
  chapters:
    - index.qmd

    - part: 01-semantic-similarity.qmd
      chapters:
        - 011-GOSemSim.qmd
        - 012-DOSE-semantic-similarity.qmd
        - 013-meshes-semantic-similarity.qmd

    - part: 02-Enrichment.qmd
      chapters:
        - 021-go.qmd
        - 022-kegg.qmd
        - 023-other-dbs.qmd
        - 024-reactome.qmd
        - 025-do-enrichment.qmd
        - 026-meshes-enrichment.qmd
        - 027-universal-enrichment.qmd
        - 028-chipseeker.qmd
        - 029-compareCluster.qmd
        - enrichplot.qmd
        - PPI.qmd
        - interpretation.qmd

    - part: misc.qmd
      chapters:
        - dplyr.qmd
        - utilities.qmd

    - part: appendix.qmd
      chapters:
        - FAQ.qmd

bibliography: references.bib

execute:
  cache: true

format:
  html:
    theme:
      - cosmo
    code-link: true

    author-meta: "Guangchuang Yu"
    callout-appearance: simple

editor: source