SpaTalk/_pkgdown.yml at main · WaveoffBioMed/SpaTalk · GitHub

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url: https://zaoqu-liu.github.io/SpaTalk/
destination: docs

template:
  bootstrap: 5
  bootswatch: cosmo
  bslib:
    primary: "#0d6efd"
    border-radius: 0.5rem
    btn-border-radius: 0.25rem

home:
  title: SpaTalk - Spatial Cell-Cell Communication
  description: >
    Knowledge-graph-based cell-cell communication inference for
    spatially resolved transcriptomic data.

authors:
  Zaoqu Liu:
    href: https://github.com/Zaoqu-Liu
  Xin Shao:
    href: https://github.com/ZJUFanLab

navbar:
  structure:
    left:  [intro, reference, articles, news]
    right: [search, github]
  components:
    intro:
      text: Get Started
      href: articles/SpaTalk.html
    articles:
      text: Tutorials
      menu:
        - text: "Getting Started"
        - text: Quick Start Guide
          href: articles/SpaTalk.html
        - text: "---"
        - text: "Methodology"
        - text: Algorithm & Methods
          href: articles/algorithm.html
        - text: "---"
        - text: "Usage Guides"
        - text: Visualization Guide
          href: articles/visualization.html
        - text: Platform-Specific Workflows
          href: articles/platforms.html
        - text: Advanced Usage
          href: articles/advanced.html
    github:
      icon: fab fa-github
      href: https://github.com/Zaoqu-Liu/SpaTalk
      aria-label: GitHub

reference:
  - title: "Object Creation"
    desc: "Create and manage SpaTalk objects"
    contents:
      - createSpaTalk
      - SpaTalk-class
      - show,SpaTalk-method

  - title: "Cell-Type Deconvolution"
    desc: "Deconvolve spot-based ST data"
    contents:
      - dec_celltype
      - generate_spot
      - set_expected_cell

  - title: "Cell-Cell Communication"
    desc: "Infer spatially resolved CCIs"
    contents:
      - find_lr_path
      - dec_cci
      - dec_cci_all
      - get_lr_path

  - title: "Visualization"
    desc: "Plot spatial and CCI results"
    contents:
      - starts_with("plot_")

  - title: "Utilities"
    desc: "Helper functions"
    contents:
      - rev_gene

  - title: "Data"
    desc: "Built-in databases and demo data"
    contents:
      - lrpairs
      - pathways
      - geneinfo
      - starts_with("demo_")

  - title: "C++ Functions"
    desc: "Optimized computational routines"
    contents:
      - starts_with("cpp_")

  - title: "Internal"
    desc: "Internal helper functions"
    contents:
      - starts_with(".")

articles:
  - title: "Getting Started"
    navbar: ~
    contents:
      - SpaTalk

  - title: "Methodology"
    navbar: ~
    contents:
      - algorithm

  - title: "Usage Guides"
    navbar: ~
    contents:
      - visualization
      - platforms
      - advanced

footer:
  structure:
    left: developed_by
    right: built_with
  components:
    developed_by: >
      Developed by [Zaoqu Liu](https://github.com/Zaoqu-Liu).
      Originally created by [Xin Shao](https://github.com/ZJUFanLab).