cfde-multiomics/_quarto.yml at main · KumarLabJax/cfde-multiomics · GitHub

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project:
  type: website
  output-dir: docs
  render:
    - "vignettes/*.qmd"
    - "!vignettes/guides/lif-cachexia-validation-framework.qmd"
    - "vignettes/under-construction.qmd"
    - "vignettes/introduction/*.qmd"
    - "vignettes/setup/*.qmd"
    - "vignettes/gtex/*.qmd"
    - "vignettes/kpc-cross-study/sra-fetch-prjna773714.qmd"
    - "vignettes/kpc-cross-study/prjna773714-rna-qc.qmd"
    - "vignettes/kpc-cross-study/st003927-metabolomics-qc.qmd"
    - "vignettes/kpc-cross-study/prjna773714-rna-gsea.qmd"
    - "vignettes/kpc-cross-study/st003927-metabolomics-msea.qmd"
    - "vignettes/kpc-cross-study/gse133523-cachexia-gsea.qmd"
    - "vignettes/kpc-cross-study/kpc-rna-metabolomics-cachexia.qmd"
    - "vignettes/integration/*.qmd"
    - "vignettes/guides/*.qmd"
    - "vignettes/reference/**/*.qmd"

execute:
  engine: knitr
  cache: false
  freeze: auto

website:
  page-navigation: true
  back-to-top-navigation: true
  page-footer: ""
  title: "Multi-Omics Analysis: From Public Data to Biological Insight"
  navbar:
    left:
      - text: "Home"
        href: vignettes/index.qmd
      - text: "Workshop Flow"
        menu:
          - text: "Prerequisites"
          - text: "Background & Biology"
            href: vignettes/introduction/lif-cachexia-biology-background.qmd
          - text: "Environment Setup"
            href: vignettes/setup/env-setup.qmd
          - text: "---"
          - text: "Cross-Study Integration Demo"
          - text: "SRA Data Fetch (PRJNA773714)"
            href: vignettes/kpc-cross-study/sra-fetch-prjna773714.qmd
          - text: "RNA-seq QC"
            href: vignettes/kpc-cross-study/prjna773714-rna-qc.qmd
          - text: "Metabolomics QC"
            href: vignettes/kpc-cross-study/st003927-metabolomics-qc.qmd
          - text: "RNA-seq GSEA"
            href: vignettes/kpc-cross-study/prjna773714-rna-gsea.qmd
          - text: "Metabolomics MSEA"
            href: vignettes/kpc-cross-study/st003927-metabolomics-msea.qmd
          - text: "8. Human Cachexia GSEA (GSE133523)"
            href: vignettes/kpc-cross-study/gse133523-cachexia-gsea.qmd
          - text: "9. KPC RNA–Metabolomics Concordance"
            href: vignettes/kpc-cross-study/kpc-rna-metabolomics-cachexia.qmd
          - text: "10. GTEx–Cachexia NES Concordance"
            href: vignettes/integration/gtex-cachexia-nes-concordance.qmd
          - text: "11. Conclusion: LIF Biology and Cachexia"
            href: vignettes/integration/kpc-lif-cachexia-concordance.qmd
          - text: "---"
          - text: "GTEx Workshop"
          - text: "1. GTEx Sample Metadata Access"
            href: vignettes/gtex/gtex-meta-data-access.qmd
          - text: "2. GTEx Expression Data Download (Portal .gct)"
            href: vignettes/gtex/gtex-expression-access.qmd
          - text: "3. Sample Quality Assessment"
            href: vignettes/gtex/gtex-sample-qa.qmd
          - text: "4. Expression Data Structure"
            href: vignettes/gtex/gtex-expression-cache-structure.qmd
          - text: "5. Expression Prep & QC"
            href: vignettes/gtex/gtex-expression-prep-qc.qmd
          - text: "6. Expression Analysis"
            href: vignettes/gtex/gtex-expression-lif-analysis.qmd
          - text: "---"
          - text: "Interpretation & Translation"
          - text: "Spearman Correlation Deep Dive"
            href: vignettes/guides/lif-spearman-correlation-guide.qmd
          - text: "GSEA & GO Enrichment"
            href: vignettes/guides/go-enrichment-gsea-guide.qmd
          - text: "Cachexia Validation Framework"
            href: vignettes/under-construction.qmd
      - text: "References"
        menu:
          - text: "Acronym & Term Index"
            href: vignettes/guides/acronym-index.qmd
          - text: "---"
          - text: "R: Workshop Function References"
            href: vignettes/reference/helpers/workshopr.qmd
          - text: "Global References"
            href: vignettes/reference/references.qmd


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