_pkgdown.yml

url: ~
template:
  params:
    bootswatch: flatly

reference:
  - title: RFLOMICS User Interface
    contents:
      - runRFLOMICS
  - title: RFLOMICS Classes
    desc: Exported classes and their accessors
    contents:
      - RflomicsMAE-class
      - RflomicsSE-class
  - title: Constructor
    contents:
      - createRflomicsMAE
  - title: Statistical Setting
    contents:   
      - generateModelFormulae
      - generateExpressionContrast
  - title: Data Processing
    contents:   
      - runDataProcessing
      - runOmicsPCA
  - title: Differential expression analysis
    contents: 
      - runDiffAnalysis
  - title: Co-Expression Analysis
    contents: 
      - runCoExpression
  - title: Gene Enrichment Analysis
    contents: 
      - runAnnotationEnrichment      
  - title: Data Integration
    contents: 
      - filterFeatures
      - prepareForIntegration
      - runOmicsIntegration
  - title: Get Results
    contents: 
      - getAnalysis
  - title: Example Data
    contents: 
      - ecoseed
  - title: Export Results
    contents: 
      - generateReport

navbar:
  structure:
    left: [intro, reference, articles, tutorials, news]
    right: [gitlab]
  components:
    intro:
      text: Get started
      href: articles/RFLOMICS.html
    reference:
      text: Reference
      href: reference/index.html
    articles:
      text: Manuals
      menu:
      - text: RFLOMICS vignettes cmd line
        href: articles/RFLOMICS-cmd-line.html
      - text: RFLOMICS input data
        href: articles/RFLOMICS-input-data.html
    gitlab:
      icon: fa-gitlab
      href: https://forgemia.inra.fr/flomics/rflomics
      aria-label: Gitlab