_pkgdown.yml

url: https://wanglabcsu.github.io/sigbridger/

favicons:
    - href: favicon.ico
    - href: favicon-16x16.png
      sizes: 16x16
      type: image/png
    - href: favicon-32x32.png
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      type: image/png
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template:
    bootstrap: 5
    light-switch: true
    bslib:
        bootswatch: sandstone
        code_font: { google: "JetBrains Mono" }
        pkgdown-nav-height: 100px
        bg: white
        fg: black
        primary: "#2c5f9b"

title: SigBridgeR
description: >-
    SigBridgeR: SigBridgeR integrates multiple algorithms, using single-cell RNA sequencing data, bulk expression data, and sample-related phenotypic data, to identify the cells most closely associated with the phenotypic data, performing as a bridge to existing tools.
logo:
    light: man/figures/logo_white.png
    dark: man/figures/logo_black.png

reference:
    - title: Data Preprocessing
      desc: >
          Functions for preprocessing inputs.
      contents:
          - BulkPreProcess
          - SCPreProcess
          - QCFilter
          - QCPatternDetect
          - Pattern2Colname
          - SymbolConvert
          - AggregateDups
          - AggregateDupRows
          - AggregateDupCols
          - SCIntegrate
          - CheckNA
          - PhenoPreProcess
          - PhenoMap

    - title: Result Integration & Visualization
      desc: >
          Merge and visualize screening results across methods or conditions.
      contents:
          - MergeResult
          - WeightedVote
          - ScreenFractionPlot
          - ScreenUpset

    - title: Screening Methods
      desc: >
          Built-in screening algorithms.
      contents:
          - Screen
          - DoLP_SGL
          - DoPIPET
          - DoScissor
          - DoscAB
          - DoscPAS
          - DoscPP
          - DoDEGAS
          - DoSIDISH
          - DoSCIPAC

    - title: Seurat Object Utilities
      contents:
          - AddMetaFeature
          - AddMisc
          - FindRobustElbow
          - ChooseNormalization

    - title: Annotate Cell Types in Single-cell Datasets
      desc: >
          Built-in annotationa algorithms.
      contents:
          - SCAnnotate
          - CellTypistAnnotate
          - SingleRAnnotate
          - mLLMCelltypeAnnotate

    - title: Reference Data & External Resources
      desc: >
          Load reference datasets.
      contents:
          - LoadRefData

    - title: Python Environment Management
      desc: >
          Manage Python environments for integrated R/Python workflows.
      contents:
          - SetupPyEnv
          - ListPyEnv

    - title: Extension Tools
      contents:
          - InterceptStrategy
          - Register
          - RegisterScreenMethod
          - RegisterAnnoMethod
          - RegisterSeuratMethod
          - ValidateScreenFunc
          - TemplateScreenFunc

    - title: Registry
      desc: >
          Extended registry for SigBridgeR
      contents:
          - SCPreProcessStrategy
          - SCAnnotateStrategy
          - ScreenStrategy

    - title: Package Configuration
      desc: >
          Get and set global options for SigBridgeR behavior.
      contents:
          - getFuncOption
          - setFuncOption
          - setThreads

# 导航栏配置
navbar:
    structure:
        left: [home, reference, articles, other_function, troubleshooting]
        right: [toggle_theme, github]
    components:
        toggle_theme: ~
        home:
            text: Home
            icon: fa-home
            href: index.html
        reference:
            text: Functions
            icon: fa-code
            href: reference/index.html
        articles:
            text: Articles
            icon: fa-book-open
            menu:
                - text: How to use SigBridgeR
                - text: Get Started
                  icon: fa-rocket
                  href: articles/Quick_Start.html
                - text: Full Tutorial
                  icon: fa-book
                  href: articles/Full_Tutorial.html
                - text: Sptial Workflow
                  icon: fa-map-location
                  href: articles/Spatial_Transcriptome.html
                - text: -------
                - text: Advanced Usage
                - text: Find the optimal parameters
                  icon: fa-cogs
                  href: articles/Optimal_Params.html
                - text: Extend SigBridgeR
                  icon: fa-code-branch
                  href: articles/Extending.html
            assets: vignettes/example_figures
        other_function:
            text: Auxiliary Utils
            icon: fa-bars
            href: articles/Other_Function_Details.html
        troubleshooting:
            text: Troubleshooting
            icon: fa-bug
            href: articles/Troubleshooting.html
        github:
            icon: fa-github
            href: https://github.com/wanglabcsu/sigbridger/

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