splicekit/mkdocs.yml at main · bedapub/splicekit · GitHub

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site_name: splicekit
site_description: splicekit - splicing analysis from short-read RNA-seq
site_url: https://bedapub.github.io/splicekit/
repo_url: https://github.com/bedapub/splicekit
repo_name: bedapub/splicekit
docs_dir: docs/pages
site_dir: docs/site

theme:
  name: material
  logo: assets/splicekit_logo.png
  favicon: assets/splicekit_logo.png
  palette:
    # "custom" + extra_css below, rather than a built-in named color, so the
    # header/accent can be the exact brand blue (#3c78d7) instead of whichever
    # named material swatch happens to be closest.
    - scheme: default
      primary: custom
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - scheme: slate
      primary: custom
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  features:
    - navigation.tabs
    - navigation.top
    - content.code.copy
    - search.suggest

extra_css:
  - stylesheets/extra.css

markdown_extensions:
  - admonition
  - toc:
      permalink: true
  - pymdownx.highlight
  - pymdownx.superfences
  - pymdownx.inlinehilite

nav:
  - Home: index.md
  - Installation: installation.md
  - Quick Start: quickstart.md
  - Guides:
      - Configuration: configuration.md
      - Sample annotation: samples.md
      - Features & count tables: features.md
      - Differential splicing (edgeR): edgeR.md
      - Motif & RNA-binding analysis: motifs.md
      - juDGE plots: judge.md
      - Additional analyses: additional-analyses.md
      - Exploring results: jbrowse2.md
  - Reference:
      - Command-line reference: cli.md
      - File formats: fileformats.md
      - Genomic coordinates: coordinates.md
      - Dependencies: dependencies.md
  - About: about.md