SplineOmics/_pkgdown.yml at main · csbg/SplineOmics · GitHub

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template:
  bootstrap: 5

url: https://csbg.github.io/SplineOmics/

pkgdown:
  title: SplineOmics

navbar:
  structure:
    left:
      - home
      - get-started
      - reference
      - articles
      - faq
      - changelog

  components:
    get-started:
      text: "Get started"
      href: articles/get_started.html

    articles:
      text: "Articles"
      menu:
        # --- Section 1: Further use cases
        - text: "Further use cases"
          html: true
        - text: "RNA-seq analysis"
          href: articles/RNA-seq-analysis.html
        - text: "Glycan analysis"
          href: articles/glycan-analysis.html
        - text: "Peak-Valley-Cliff (PVC) analysis"
          href: articles/PVC_analysis.html
        - text: "Gene-centric multiomics clustering"
          href: articles/Gene_centric_multiomics_clustering.html

        - text: "---"   # divider between sections

        # --- Section 2: Guides
        - text: "Guides"
          html: true
        - text: "limma result categories"
          href: articles/limma_result_categories.html
        - text: "Designing a limma design formula"
          href: articles/design_limma_design_formula.html
        - text: "Docker container instructions"
          href: articles/Docker-instructions.html
        - text: "Docker permission denied"
          href: articles/Docker_permission_denied.html

    changelog:
      text: "Changelog"
      href: articles/CHANGELOG.html

    faq:
      text: "FAQ"
      href: articles/faq.html

reference:
  - title: User Available Functions
    desc: This section contains the documentation for all functions available
          to the user in the SplineOmics package.
    contents:
      - compare_results
      - cluster_genes_multiomics
      - cluster_hits
      - create_clustering_report
      - create_limma_report
      - create_ora_report
      - create_pvc_report
      - create_splineomics
      - extract_gene_sets
      - download_enrichr_databases
      - explore_data
      - extract_data
      - find_pvc
      - plot_umap_clusters
      - preprocess_rna_seq_data
      - print.SplineOmics
      - run_ora
      - run_limma_splines
      - update_splineomics

extra_files:
  - googleabfeff244193b2bc.html

# Keep the articles index so pkgdown is happy (not linked in navbar).
articles:
  - title: "Further use cases"
    contents:
      - get_started
      - RNA-seq-analysis
      - glycan-analysis
      - PVC_analysis
      - Gene_centric_multiomics_clustering
  - title: "Guides"
    contents:
      - design_limma_design_formula
      - limma_result_categories
      - Docker-instructions
      - Docker_permission_denied
  - title: "Special pages"
    contents:
      - faq
      - CHANGELOG