deepMatchR/_pkgdown.yml at main · BorchLab/deepMatchR · GitHub

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url: https://www.borch.dev/uploads/deepMatchR

template:
  bootstrap: 5
  bootswatch: flatly
  bslib:
    primary: "#3288bd"
    border-radius: 0.5rem
    btn-border-radius: 0.25rem

home:
  title: deepMatchR - Deep Learning Models for HLA Matching
  description: >
    Tools for HLA testing, matching, and immunogenicity analysis using
    advanced statistical approaches and deep learning.
  sidebar:
    structure: [links, license, community, citation, authors, dev]

navbar:
  structure:
    left: [intro, reference, articles, tutorials, news]
    right: [search, github]
  components:
    intro:
      text: Get Started
      href: articles/deepMatchR.html
    articles:
      text: Articles
      menu:
      - text: Overview
        href: articles/index.html
      - text: "---"
      - text: "Core Workflows"
      - text: Sequence & Mismatch Analysis
        href: articles/sequence-analysis.html
      - text: Eplet Analysis
        href: articles/eplet-analysis.html
      - text: Peptide Binding Prediction
        href: articles/peptide-binding.html
      - text: "---"
      - text: "Visualization"
      - text: Antibody Visualization
        href: articles/antibody-visualization.html
    github:
      icon: fab fa-github
      href: https://github.com/BorchLab/deepMatchR
      aria-label: GitHub

reference:
- title: HLA Genotypes
  desc: Create and work with HLA genotype objects
  contents:
  - hlaGeno
  - validateHlaGeno
  - print.hla_genotype

- title: Sequence Analysis
  desc: Functions for retrieving and comparing HLA sequences
  contents:
  - getAlleleSequence
  - quantifyMismatch
  - calculateMismatchLoad
  - getSequenceStats
  - clearSequenceCache

- title: Eplet Analysis
  desc: Functions for eplet-based immunogenicity analysis
  contents:
  - quantifyEpletMismatch
  - calculateEpletLoad

- title: Peptide Binding Prediction
  desc: Deep learning models for peptide-MHC binding prediction
  contents:
  - predictMHCnuggets
  - calculatePeptideBindingLoad
  - visualizePeptideBinding

- title: Serology Conversion
  desc: Convert between molecular and serological HLA nomenclature
  contents:
  - toSerology
  - updateWmdaData
  - clearWmdaCache

- title: Antibody Visualization
  desc: Visualize SAB and PRA assay results
  contents:
  - plotAntibodies
  - plotEplets
  - epletAUC
  - calculateAUC

- title: Data
  desc: Built-in datasets
  contents:
  - deepMatchR_example
  - deepMatchR_cregs
  - deepMatchR_eplets
  - deepMatchR_wmda_pgroups
  - deepMatchR_wmda_serology
  - deepMatchR_wmda_splits
  - starts_with("wmda_")
  - starts_with("eplet_")

- title: Utilities
  desc: Helper functions and internal utilities
  contents:
  - deepmatchrEnv
  - batchGetSequences

articles:
- title: Getting Started
  navbar: ~
  contents:
  - deepMatchR

- title: Core Workflows
  desc: Detailed guides for specific analysis tasks
  contents:
  - sequence-analysis
  - eplet-analysis
  - peptide-binding

- title: Visualization
  desc: Creating publication-quality figures

  contents:
  - antibody-visualization

footer:
  structure:
    left: developed_by
    right: built_with

authors:
  Nick Borcherding:
    href: https://github.com/ncborcherding