_pkgdown.yml

url: https://cogdisreslab.github.io/KRSA/

template:
  bootstrap: 5
  light-switch: true
  includes:
    after_body: >
      <script data-goatcounter="https://cdrl.goatcounter.com/count"
        async src="//gc.zgo.at/count.js"></script>
  params:
    bslib:
      preset: bootswatch
      bootswatch: lumen

development:
  mode: release

navbar:
  structure:
    right: [search, github, lab, paper]
    left: [intro, reference, articles, tutorials, news, about]
  components:
      github:
        icon: "fab fa-github"
        href: https://github.com/CogDisResLab/KRSA
      lab:
        icon: "fas fa-flask"
        href: https://cdrl-ut.org/
      paper:
        icon: "fas fa-file-alt"
        href: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0260440
      about:
        text: About Us
        href: https://cdrl-ut.org/about/


reference:
  - title: Core Functions
    desc: Core functions for the KRSA package
    contents:
    - krsa
    - krsa_group_diff
    - krsa_quick_filter
    - krsa_read
    - krsa_scaleModel
  - title: Plotting Functions
    desc: Functions that generate plots for the KRSA package
    contents:
    - krsa_ball_model
    - krsa_sampling
    - krsa_coverage_plot
    - krsa_curve_plot
    - krsa_heatmap
    - krsa_heatmap_grouped
    - krsa_histogram_plot
    - krsa_reverse_krsa_plot
    - krsa_violin_plot
    - krsa_violin_plot_grouped
    - krsa_waterfall
    - krsa_zscores_plot
    - krsa_cv_plot
    - krsa_ce_output_kinases
    - krsa_ce_output_peptides
    - parse_BN_crosstabFile
    - krsa_enrichr_plot
  - title: Helper Functions
    desc: Helper functions for the KRSA package
    contents:
    - krsa_extractEndPoint
    - krsa_extractEndPointMaxExp
    - krsa_get_diff_byChip
    - krsa_get_diff
    - krsa_show_peptides
    - krsa_top_hits
    - krsa_enrichr
    - enrichr_lib_call
  - title: QC Functions
    desc: Quality control functions for the KRSA package
    contents:
    - krsa_filter_lowPeps
    - krsa_filter_nonLinear
    - krsa_filter_ref_pep
    - krsa_qc_steps
  - title: Data and curated files
    desc: Data and curated files for the KRSA package
    contents:
    - KRSA_Mapping_PTK_PamChip_86402_v1
    - KRSA_Mapping_STK_PamChip_87102_v1
    - KRSA_coverage_PTK_PamChip_86402_v1
    - KRSA_coverage_STK_PamChip_87102_v1
    - KRSA_coverage_STK_PamChip_87102_v2
    - ballModel_edges
    - ballModel_nodes
    - stk_pamchip_87102_mapping
    - ptk_pamchip_86402_mapping