FastQDesign/_pkgdown.yml at main · yuw444/FastQDesign · GitHub

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url: https://yuw444.github.io/FastQDesign/
title: FastQDesign

template:
  bootstrap: 5
  bslib:
    primary_color: "#1f77b4"

navbar:
  title: "FastQDesign"
  type: inverse
  left:
    - icon: fa-home
      href: index.html
    - text: "Getting Started"
      href: articles/experiment-design.html
    - text: "Articles"
      menu:
        - text: "Getting Started"
          href: articles/experiment-design.html
        - text: "---"
        - text: "fastF Tool"
          href: articles/fastF-tool.html
        - text: "Sample Analysis"
          href: articles/sample-prep.html
        - text: "Data Sources"
          href: articles/data-sources.html
        - text: "Power Metadata Generation"
          href: articles/generate-power-metadata.html
    - text: "Reference"
      href: reference/index.html
  right:
    - icon: fa-github
      href: https://github.com/yuw444/FastQDesign

home:
  title: FastQDesign
  description: >
    Guide investigators in designing scRNA-seq experiments by shifting focus
    from UMI matrix back to raw FastQ reads.
  links:
    - text: GitHub
      href: https://github.com/yuw444/FastQDesign
    - text: Paper
      href: https://www.nature.com/articles/s42003-025-07938-8

reference:
  - title: Main Functions
    contents:
      - FastQDesign
      - SamplePrep
      - SampleMatch
      - DownSample
      - FindPseudotime
  - title: Analysis Utilities
    contents:
      - ConditionalShannonEntropy
      - Entropy
      - ExtractMTX
      - FindAllMarkersByCondition
      - FixedNumClusters
      - JaccardIndex
      - MarkerGeneFilter
      - OptimalNumClusters
      - PPV
      - RootNodeSelect
  - title: fastF Subcommands
    contents:
      - fastF_freq
      - fastF_filter
      - fastF_crb
      - fastF_bam2db
      - fastF_extract

articles:
  - title: Getting Started
    contents:
      - experiment-design
  - title: fastF Tool
    contents:
      - fastF-tool
  - title: Sample Analysis
    contents:
      - sample-prep
  - title: Data
    contents:
      - data-sources
  - title: Power Metadata Generation
    contents:
      - generate-power-metadata

development:
  mode: auto