_pkgdown.yml

destination: docs
navbar:
  structure:
    left:  [home, reference, articles, news]
    right: [github]
reference:
  - title: "Plotting Functions"
    desc: >
      Functions used to plot the results of the data analysis
    contents:
      - plot_gates
      - plot_flowstyle
  - title: "Functions to handle tree models"
    desc: >
      Different functions that fit, visualize, output and print
      tree based models
    contents:
      - get_concensus_rules
      - print.concensus.rules
      - get_cluster_mapping
      - fit_ctree
      - as.garnett
      - cross_validate
  - title: "Marker Finding functions"
    desc: >
      Functions with output consistent with Seurat equivalents, but allow using
      other classifiers (such as RangerDE).
    contents:
      - FindAllMarkers
      - FindConservedMarkers
      - FindMarkers
  - title: "Handle Gene names"
    desc: >
      Utility functions to find gene names and their common aliases (ie. ITGAX <> CD11c)
    contents:
      - get_genesymbols
      - get_aliases
      - is_gene_membrane
  - title: "Antibodies"
    desc: >
      Query antibody vendors for products that match your gene of interest.
    contents:
      - antibodies
  - title: "Datasets"
    desc: >
      Small versions of sample datasets, they are commonly used to test the
      package functionality and have reproducible examples.
    contents:
      - small_5050_mix
      - small_9901_mix
  - title: "Utilities"
    desc: >
    contents:
      - as.data.frame.Seurat
      - as.frequency.matrix
      - autoplot.table
      - ranger_importances