_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
  Vadim I. Nazarov:
    href: https://www.linkedin.com/in/vdnaz
  Vasily O. Tsvetkov:
    href: https://www.linkedin.com/in/vasily-tsvetkov-227218ab
  Siarhei Fiadziushchanka:
    href: https://www.linkedin.com/in/sergey-f-709b0415b/
  Eugene Rumynskiy:
    href: https://www.linkedin.com/in/erumynskiy/
  Aleksandr A. Popov:
    href: https://www.linkedin.com/in/aleksandr-popov-634878105/
  Ivan Balashov:
    href: https://www.linkedin.com/in/ivan-balashov/
  Maria Samokhina:
    href: https://www.linkedin.com/in/maria-volobueva-b0856a223/
articles:
- title: All tutorials
  desc: ~
  contents:
  - '`v1_introduction`'
  - '`v2_data`'
  - '`web_only/v21_singlecell`'
  - '`web_only/v3_basic_analysis`'
  - '`web_only/load_mixcr`'
  - '`web_only/load_10x`'
  - '`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`'
  - '`web_only/community`'
  - '`web_only/repFilter_v3`'
  - '`web_only/v10_prop`'
  - '`web_only/BCRpipeline`'
  - '`web_only/clustering`'
navbar:
  structure:
    left: [articles, reference, covid19]
    right: [im_link, twitter, github]
  components:
    home: ~
    news: ~
    covid19:
      text: "COVID-19"
      href: https://github.com/immunomind/covid19
    reference:
      text: Reference
      href: reference/index.html
    articles:
      text: Start Here
      menu:
      - text: Installation & troubleshooting
        href: articles/v1_introduction.html
      - text: '---'
      - text: First steps
      - text: Data loading
        href: articles/v2_data.html
      - text: 'How-to: Loading MiXCR Data'
        href: articles/web_only/load_mixcr.html
      - text: 'How-to: Loading 10x Genomics Data'
        href: articles/web_only/load_10x.html
      - text: 'How-to: Single-cell and paired chain data'
        href: articles/web_only/v21_singlecell.html
      - text: Basic statistics and clonality
        href: articles/web_only/v3_basic_analysis.html
      - text: 'Data filtering'
        href: articles/web_only/repFilter_v3.html
      - text: '---'
      - text: Repertoire-level exploration and comparison
      - text: Repertoire overlap and public clonotypes
        href: articles/web_only/v4_overlap.html
      - text: Gene usage
        href: articles/web_only/v5_gene_usage.html
      - text: Diversity estimation
        href: articles/web_only/v6_diversity.html
      - text: '---'
      - text: Clonotype-level exploration and comparison
      - text: Track clonotypes across samples and time
        href: articles/web_only/v8_tracking.html
      - text: Annotate clonotypes using immune receptor databases
        href: articles/web_only/v11_db.html
      - text: Kmer and sequence motif analysis and visualisation
        href: articles/web_only/v9_kmers.html
      - text: '---'
      - text: Preparing to publication
      - text: Make your plots publication-ready with fixVis
        href: articles/web_only/v7_fixvis.html
      - text: '---'
      - text: BCR analysis
      - text: BCR pipeline
        href: articles/web_only/BCRpipeline.html
      - text: Clustering
        href: articles/web_only/clustering.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: Filtering data
  contents:
  - has_concept("filters")
- subtitle: Single-cell
  desc: More coming soon!
  contents:
  - has_concept("single_cell")
- subtitle: Preprocessing
  contents:
  - has_concept("preprocessing")
- title: BCR data
- subtitle: Clustering
  contents:
  - has_concept("distance")
  - has_concept("seq_cluster")
- subtitle: BCR pipeline
  contents:
  - has_concept("germline")
  - has_concept("align_lineage")
  - has_concept("phylip")
  - has_concept("somatic_hypermutation")
- 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("k-mers")
- 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")