_pkgdown.yml

authors:
  Michael Stadler:
    href: https://github.com/mbstadler
  Dania Machlab:
    href: https://github.com/machlabd
  Lukas Burger:
    href: https://github.com/LukasBurger
  Charlotte Soneson:
    href: https://github.com/csoneson

url: https://fmicompbio.github.io/monaLisa

template:
  bootstrap: 5
  params:
    bootswatch: cerulean

navbar:
  structure:
    left:
    - home
    - intro
    - reference
    - articles
    - tutorials
    - news
    right: github
  components:
    articles:
      text: Articles
      menu:
      - text: "Binned motif enrichment analysis"
        href: articles/monaLisa.html
      - text: "Identifying motifs by stability selection"
        href: articles/selecting_motifs_with_randLassoStabSel.html
    github:
      icon: fab fa-github fa-lg
      href: https://github.com/fmicompbio/monaLisa

reference:
- title: monaLisa package overview
  contents:
    - '`monaLisa-package`'
- title: Binned motif-enrichment analysis
  desc: "Bin regions of interest and analyse motifs enrichments in bins."
  contents:
    - '`bin`'
    - '`getZeroBin`'
    - '`calcBinnedMotifEnrR`'
    - '`calcBinnedMotifEnrHomer`'
    - '`plotBinDiagnostics`'
    - '`plotBinDensity`'
    - '`plotBinHist`'
    - '`plotBinScatter`'
    - '`plotMotifHeatmaps`'
- title: K-mer analysis
  desc: "Functions for analysing word (k-mer) occurrences in sequences."
  contents:
    - '`getKmerFreq`'
    - '`calcBinnedKmerEnr`'
- title: Identify predictive motifs using stability selection
  desc: "Functions for selecting motifs that explain observed changes using Stability Selection."
  contents:
    - '`randLassoStabSel`'
    - '`plotSelectionProb`'
    - '`plotStabilityPaths`'
- title: Miscellaneous
  desc: "Various utilites and helper functions, typically used in the functions above."
  contents:
    - '`findMotifHits`'
    - '`annoSeqlogo`'
    - '`dumpJaspar`'
    - '`homerToPFMatrixList`'
    - '`findHomer`'
    - '`prepareHomer`'
    - '`parseHomerOutput`'
    - '`motifSimilarity`'
    - '`motifKmerSimilarity`'
    - '`seqLogoGrob`'
    - '`getColsByBin`'
    - '`sampleRandomRegions`'