_pkgdown.yml

title: epitopefindr

url: https://brandonsie.github.io/epitopefindr

template:
  params:
    bootswatch: sandstone
    ganalytics: UA-131446137-1
    docsearch:
      api_key: c0f1e745bc83170b812c2f3ddbeb17c6
      index_name: epitopefindr

reference:
  - title: Package Info
    desc: epitopefindr package help file
    contents:
      - epitopefindr
  - title: Main Function
    desc: To execute a typical epitopefindr pipeline
    contents:
      - epfind
  - title: Sub Functions
    desc: Execute smaller steps of epfind
    contents:
      - pbCycleBLAST
      - cycleBLAST
      - epitopeBLAST
      - indexEpitopes
      - trimEpitopes
      - indexGroups
      - groupMSA
  - title: Helper Functions
    desc: Smaller functions to perform simple operations
    contents:
      - addPepSeq
      - chooseIndex
      - decipherGaps
      - epitopefindrEnv
      - epPB
      - filterBLAST
      - isOverlapping
      - makeIR
      - mergeFastaDuplicates
      - numAlignments
      - organizeBLAST
      - outputTable
      - prepareBLAST
      - qsSwap
      - queryBLASTaa
      - removeSmallAln
      - renameBLAST
      - renameFasta
      - selfBLASTaa
      - threshBLAST
      - tidyBLAST
      - tidyFasta
      - unmergeFastaDuplicates
      - writeFastaAA
  - title: Data
    desc: Example datasets
    contents:
      - pairwise_viral_hits
navbar:
  title: ~
  left:
    - icon: fas fa-home fa-lg
      href: index.html
    - text: "Reference"
      href: "reference/index.html"
    - text: "Articles"
      menu:
        - text: 'epitopefindr Application: Viral Peptides'
          href: articles/epitopefindr_avarda_vignette.html
  right:
    - text: Links
      menu:
      - text: Changelog
        href: https://brandonsie.github.io/epitopefindr/news/index.html
      - text: Github Repo
        href: https://github.com/brandonsie/epitopefindr/
      - text: brandonsie.github.io
        href: https://brandonsie.github.io/