_pkgdown.yml

authors:
  Federico Marini:
    href: https://federicomarini.github.io

template:
  params:
    bootswatch: cosmo
    
navbar:
  structure:
    left:
    - home
    - intro
    - reference
    - articles
    - tutorials
    - news
    right: github
  components:
    home:
      icon: fa-home fa-lg
      href: index.html
    reference:
      text: Reference
      href: reference/index.html
    intro:
      text: User guide
      href: articles/pcaExplorer.html
    github:
      icon: fa-github fa-lg
      href: https://github.com/federicomarini/pcaExplorer

reference:
- title: The pcaExplorer package
  desc: Main functions and info on the `pcaExplorer` package
  contents:
  - '`pcaExplorer-pkg`'
  - '`pcaExplorer`'
- title: Working with Principal Components
  desc: Functions for working efficiently with Principal Components
  contents:
  - '`pcaplot`'
  - '`pcaplot3d`'
  - '`pcascree`'
  - '`correlatePCs`'
  - '`genespca`'
  - '`hi_loadings`'
  - '`plotPCcorrs`'
- title: Annotation and Functional interpretation
  desc: Functions for annotating and performing functional interpretation
  contents:
  - '`get_annotation`'
  - '`get_annotation_orgdb`'
  - '`topGOtable`'
  - '`pca2go`'
  - '`limmaquickpca2go`'
- title: Expression data exploration
  desc: ~
  contents:
  - '`pair_corr`'
  - '`distro_expr`'
  - '`geneprofiler`'
  - '`makeExampleDESeqDataSet_multifac`'
- title: Deprecated functions in pcaExplorer
  desc: ~
  contents:
  - '`deprecated`'