_pkgdown.yml

url: https://immunarch.com
template:
  bootstrap: 5
  bslib:
    bootswatch: cosmo
    pkgdown-nav-height: 100px
  params:
    ganalytics: UA-128418614-2
authors:
  ImmunoMind:
    href: https://immunomind.com
  Vadim I. Nazarov:
    href: https://www.linkedin.com/in/vdnaz
  Vasily O. Tsvetkov:
    href: https://www.linkedin.com/in/vasily-tsvetkov-227218ab
  Aleksandr A. Popov:
    href: https://www.linkedin.com/in/aleksandr-popov-634878105/
  Ivan Balashov:
    href: https://www.linkedin.com/in/ivan-balashov/
articles:
- title: "Immunarch v0.9"
  subtitle: "Deprecated"
  desc: ~
  contents:
  - '`immunarch_threads`'
  - '`web_only_v0/introduction`'
  - '`web_only_v0/data`'
  - '`web_only_v0/v21_singlecell`'
  - '`web_only_v0/v3_basic_analysis`'
  - '`web_only_v0/load_mixcr`'
  - '`web_only_v0/load_10x`'
  - '`web_only_v0/v4_overlap`'
  - '`web_only_v0/v5_gene_usage`'
  - '`web_only_v0/v6_diversity`'
  - '`web_only_v0/v7_fixvis`'
  - '`web_only_v0/v8_tracking`'
  - '`web_only_v0/v9_kmers`'
  - '`web_only_v0/v11_db`'
  - '`web_only_v0/repFilter_v3`'
  - '`web_only_v0/v10_prop`'
  - '`web_only_v0/BCRpipeline`'
  - '`web_only_v0/clustering`'
navbar:
  bg: dark
  type: dark
  structure:
    left: [tutorial, migration, articles, reference]
    right: [github]
  components:
    home: ~
    news: ~
    tutorial:
      text: "Immunarch v1.0"
      href: https://immunomind.github.io/docs/tutorials/single_cell/
    migration:
      text: "Migration Guide"
      href: https://immunomind.github.io/docs/tutorials/migration/
    reference:
      text: "Reference"
      href: reference/index.html
    articles:
      text: "Immunarch v0.9"
      menu:
      - text: "Installation & troubleshooting"
        href: articles/web_only_v0/introduction.html

      - text: '---'
      - text: First steps

      - text: Data loading
        href: articles/web_only_v0/data.html

      - text: 'How-to: Loading MiXCR Data'
        href: articles/web_only_v0/load_mixcr.html

      - text: 'How-to: Loading 10x Genomics Data'
        href: articles/web_only_v0/load_10x.html

      - text: 'How-to: Single-cell and paired chain data'
        href: articles/web_only_v0/v21_singlecell.html

      - text: Basic statistics and clonality
        href: articles/web_only_v0/v3_basic_analysis.html

      - text: 'Data filtering'
        href: articles/web_only_v0/repFilter_v3.html

      - text: '---'

      - text: Repertoire-level exploration and comparison

      - text: Repertoire overlap and public clonotypes
        href: articles/web_only_v0/v4_overlap.html

      - text: Gene usage
        href: articles/web_only_v0/v5_gene_usage.html

      - text: Diversity estimation
        href: articles/web_only_v0/v6_diversity.html

      - text: '---'

      - text: Clonotype-level exploration and comparison

      - text: Track clonotypes across samples and time
        href: articles/web_only_v0/v8_tracking.html

      - text: Annotate clonotypes using immune receptor databases
        href: articles/web_only_v0/v11_db.html

      - text: Kmer and sequence motif analysis and visualisation
        href: articles/web_only_v0/v9_kmers.html

      - text: '---'

      - text: Preparing to publication

      - text: Make your plots publication-ready with fixVis
        href: articles/web_only_v0/v7_fixvis.html

      - text: '---'

      - text: BCR analysis

      - text: BCR pipeline
        href: articles/web_only_v0/BCRpipeline.html

      - text: Clustering
        href: articles/web_only_v0/clustering.html
    github:
      icon: fa-github
      href: https://github.com/immunomind/immunarch
reference:
- title: Stable, v1.0
- subtitle: ... work in progress ...

- contents:
  - has_lifecycle("stable")

- title: Experimental, v1.0

- subtitle: Repertoire descriptive statistics
- contents:
  - starts_with("airr_stats")

- subtitle: Clonality
- contents:
  - starts_with("airr_clonality")
  - starts_with("annotate_clonality")

- subtitle: Diversity
- contents:
  - starts_with("airr_diversity")

- subtitle: Public indices
- contents:
  - starts_with("airr_public")

- subtitle: Technical
- contents:
  - has_lifecycle("experimental")
  - has_concept("data")
  - has_concept("migration_utility")
  - -starts_with("airr_stats")
  - -starts_with("airr_clonality")
  - -starts_with("airr_diversity")
  - -starts_with("airr_public")
  - -starts_with("annotate_clonality")

- title: Under Question, v0.9 -> v1.0

- contents:
  - has_concept("utility_private")
  - has_concept("utility_public")
  - has_concept("preprocessing")

- title: Deprecated, v0.9

- contents:
  - has_lifecycle("deprecated")