_pkgdown.yml

url: https://immunarch.com

template:
  params:
    bootswatch: cosmo
    ganalytics: UA-128418614-2
    docsearch:
      api_key: '94207562f34b455c0796790d104e3549'
      index_name: 'immunarch'

authors:
  ImmunoMind:
    href: https://immunomind.io

articles:
- title: All tutorials
  desc: ~
  contents:
  - '`v1_introduction`'
  - '`v2_data`'
  - '`web_only/v21_singlecell`'
  - '`web_only/v3_basic_analysis`'
  - '`web_only/v4_overlap`'
  - '`web_only/v5_gene_usage`'
  - '`web_only/v6_diversity`'
  - '`web_only/v7_fixvis`'
  - '`web_only/v8_tracking`'
  - '`web_only/v9_kmers`'
  - '`web_only/v11_db`'

navbar:
  structure:
    left: [covid19, intro, articles, reference]
    right: [im_link, twitter, github]
  components:
    home: ~
    news: ~
    covid19:
      text: "COVID-19"
      href: https://github.com/immunomind/covid19
    intro:
      text: "Get started"
      href: articles/v1_introduction.html
    reference:
      text: Reference
      href: reference/index.html
    articles:
      text: Tutorials
      menu:
      - text: First steps
      - text: Introduction to immunarch
        href: articles/v1_introduction.html
      - text: Working with data in immunarch
        href: articles/v2_data.html
      - text: Basic analysis and clonality
        href: articles/web_only/v3_basic_analysis.html
      - text: Single-cell and paired chain data
        href: articles/web_only/v21_singlecell.html

      - text: '---'

      - text: Explore and compare repertoires
      - text: Repertoire overlap and public clonotypes
        href: articles/web_only/v4_overlap.html
      - text: Gene usage analysis
        href: articles/web_only/v5_gene_usage.html
      - text: Diversity estimation
        href: articles/web_only/v6_diversity.html
      - text: Annotate clonotypes using immune receptor databases
        href: articles/web_only/v11_db.html

      - text: '---'

      - text: Preparing to publication
      - text: Make your plots publication-ready with fixVis
        href: articles/web_only/v7_fixvis.html

      - text: '---'

      - text: Advanced methods
      - text: Tracking clonotypes across time points
        href: articles/web_only/v8_tracking.html
      - text: Kmer and sequence motif analysis and visualisation
        href: articles/web_only/v9_kmers.html
    twitter:
      icon: fa-lg fa-twitter
      href: http://twitter.com/immunomind
    im_link:
      text: ImmunoMind
      href: https://immunomind.io
    github:
      icon: fa-github
      href: https://github.com/immunomind/immunarch

reference:
- title: Bulk and single-cell data
- subtitle: Loading and saving any data
  contents:
  - has_concept("io")
- subtitle: Single-cell
  desc: More coming soon!
  contents:
  - has_concept("single_cell")
- subtitle: Preprocessing
  contents:
  - has_concept("preprocessing")

- title: Basic immune repertoire statistics
- subtitle: Exploratory data analysis
  contents:
  - has_concept("explore")
- subtitle: Clonality analysis
  contents:
  - has_concept("clonality")


- title: Clonotype annotation and dynamics
- subtitle: Clonotype annotation
  desc: Annotate clonotypes in immune repertoires using external immune receptor databases (VDJDB, McPAS and PIRD).
  contents:
  - has_concept("annotation")
- subtitle: Immune repertoire dynamics
  desc: Track the differences in clonotype abundances over time.
  contents:
  - has_concept("dynamics")

- title: Compare repertoires
- subtitle: Repertoire diversity analysis
  contents:
  - has_concept("diversity")
- subtitle: Gene usage
  desc: V-gene and J-gene usage statistics, analysis and visualisations
  contents:
  - has_concept("gene_usage")
- subtitle: Overlap
  contents:
  - starts_with("repOverlap")
  - has_concept("overlap")
- subtitle: Public repertoire
  contents:
  - has_concept("pubrep")

- title: Advanced immune repertoire analysis
- subtitle: Kmers analysis
  contents:
  - has_concept("kmers")
- subtitle: Post-analysis
  desc: Advanced methods for post-analysis of gene usage, overlap and other statistics.
  contents:
  - has_concept("post_analysis")

- title: Visualisations
- subtitle: General visualisation functions
  desc: Functions for visualisations of different data types. For analysis-specific visualisation see related sections.
  contents:
  - starts_with("vis")
  - has_concept("vis")
- subtitle: Publication-ready plots
  contents:
  - has_concept("fixvis")

- title: Utilities
- subtitle: Data
  contents:
  - has_concept("data")
- subtitle: Public utility utilities
  contents:
  - has_concept("utility_public")
- subtitle: Internal utility functions
  contents:
  - has_concept("utility_private")