shennong-object/_pkgdown.yml at main · zerostwo/shennong-object · GitHub

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url: https://songqi.org/shennong-object

authors:
  Songqi Duan:
    href: https://songqi.org

destination: docs

template:
  bootstrap: 5
  includes:
    in_header:
      <script defer src="https://umami.catplot.org/script.js" data-website-id="f882249b-4b3c-49a9-baf1-c1d2060215bb"></script>

articles:
  - title: "Quick Start Guide"
    dropdown: true
    contents:
      - quick_start

reference:
  - title: "Core Object & Classes"
    desc: "Main S4 classes, constructor, package documentation, and example dataset."
    contents:
      - Shennong-class
      - sn_initialize_shennong_object
      - show,Shennong-method
      - so

  - title: "Data Accessors"
    desc: "Functions to retrieve data and metadata from Shennong objects."
    contents:
      - sn_active_assay
      - sn_active_ident
      - sn_active_layer
      - sn_active_reduction
      - sn_assays
      - sn_fetch_data
      - sn_layer_data
      - sn_layers
      - sn_metadata
      - sn_reductions
      - sn_features
      - sn_samples
      - sn_levels

  - title: "Data Manipulation"
    desc: "Functions to modify data within Shennong objects."
    contents:
      - sn_add_assay
      - sn_add_metadata

  - title: "Dimensionality Reduction"
    desc: "Class and functions related to dimensionality reduction results."
    contents:
      - has_concept("reduction")

  - title: "Plotting"
    desc: "Functions for visualizing Shennong objects."
  - contents:
    - has_concept("plot")

  - title: "Command Log"
    desc: "Class and functions for tracking computational history."
  - contents:
    - has_concept("command")

  - title: "Generic Methods & Utilities"
    desc: "Implementations of standard generics and other utility functions."
    contents:
      - filter.Shennong
      - dim,Shennong-method
      - dimnames,Shennong-method
      - head,Shennong-method
      - sn_misc
      - sn_project_name
      - sn_tools
      - sn_version
      - ShennongTool-class