_pkgdown.yml

title: phipmake
url: https://brandonsie.github.io/phipmake

template:
  params:
    bootswatch: sandstone
    ganalytics: UA-131446137-1
    docsearch:
      api_key: 398291142c6ea72cd7c19e0286eef8e1
      index_name: phipmake
reference:
  - title: Package Documentation
    desc: Helpfile for phipmake package.
    contents:
      - '`phipmake`'
  - title: User Functions
    desc: Functions intended to be called by user.
    contents:
      - '`define_plan`'
      - '`write_drake_params`'
  - title: Annotation Functions
    desc: For adding & interacting with metadata.
    contents:
      - '`annotate_data`'
      - '`read_annot`'
      - '`read_annot_list`'
      - '`read_pairs`'
      - '`read_pairs_list`'
      - '`u_pep_id_to_libnames`'
  - title: Prosum and Promax
    desc: For basic collapsing of peptide-level data to protein-level.
    contents:
      - '`compute_prosum`'
      - '`library_prosum`'
      - '`protein_prosum`'
      - '`compute_promax`'
      - '`library_promax`'
      - '`protein_promax`'
  - title: Hits and Polyclonal
    desc: Processing enrichment data based on a threshold.
    contents:
      - '`compute_hits`'
      - '`compute_polycl`'
      - '`library_polycl`'
      - '`protein_polycl`'
      - '`independence_filter`'
  - title: Helper Functions
    desc: Small functions for various tasks.
    contents:
      - '`check_order`'
      - '`getparam`'
      - '`pbar`'
      - '`split_data`'
      - '`subset_data`'
      - '`prepare_blast_pairs`'
      - '`trimDictionary`'
      - '`write_data`'
      - '`gather_samples`'
      - '`prepare_avarda_names`'
navbar:
  title: ~
  left:
    - icon: fas fa-home fa-lg
      href: index.html
    - text: "Reference"
      href: "reference/index.html"
    - text: "Articles"
      menu:
        - text: "Setup Guide for Larman Lab"
          href: articles/larmanguide.html
        - text: 'Dependency Graph'
          href: dependency_graph.html

  right:
    - text: Links
      menu:
      - text: Changelog
        href: https://brandonsie.github.io/phipmake/news/index.html
      - text: Github Repo
        href: https://github.com/brandonsie/phipmake/
      - text: brandonsie.github.io
        href: https://brandonsie.github.io/