_pkgdown.yml

url: https://buenrostrolab.github.io/FigR/

template:
  bootstrap: 5
  bootswatch: sandstone
  theme: github-light
  bslib:
    pkgdown-nav-height: 150px

reference:
 - title: Peak-gene correlations
   contents:
    - runGenePeakcorr
    - dorcJPlot
    - getDORCScores

 - title: TF-DORC associations
   contents:
    - runFigRGRN
    - motifPeakZtest

 - title: scATAC-scRNA scOptMatch cell pairing
   contents:
    - pairCells
    - plotPairs

 - title: Visualizing FigRGRN results
   contents:
    - plotDrivers
    - rankDrivers
    - plotfigRHeatmap
    - plotfigRNetwork

 - title: Miscellaneous helper functions
   contents:
    - centerCounts
    - smoothScoresNN
    - plotMarker2D
    - splitAndFetch

navbar:
 bg: primary
 structure:
   left: [tutorials, reference, news]
   right: [search, github, contact]
 components:
   tutorials:
     text: "Tutorials"
     menu:
     - text: "Pairing scATAC and scRNA-seq"
       href: articles/FigR_stim.html
     - text: "FigR on multi-modal data"
       href: articles/FigR_shareseq.html

   reference:
      icon: fa-gears
      text: "Functions"
      href: reference/index.html

   news:
      icon: fa-newspaper-o
      text: "News"

resource_files:
  - media/FigR.PNG
  - media/skinv2.png
  - media/PBMCs.png
  - vignettes/web_only/FigR_shareseq_tutorial.html
  - vignettes/web_only/FigR_stim_tutorial.html