_pkgdown.yml

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

template:
  bootstrap: 5
  bootswatch: flatly
  package: scRepertoire

home:
  sidebar:
    structure:
    - links
    - license
    - custom
    - authors
    - dev
    components:
      custom:
        title: Citation
        text: '[Citing scRepertoire](https://pubmed.ncbi.nlm.nih.gov/40577285/)'

navbar:
  left:
  - text: Home
    href: index.html
  - text: Vignettes
    menu:
    - text: "Getting Set Up"
    - text: Installation Instructions
      href: articles/Installation.html
    - text: Loading Data into scRepertoire
      href: articles/Loading.html
    - text: Combining Contigs into Clones
      href: articles/Combining_Contigs.html
    - text: Additional Processing Steps
      href: articles/Processing.html
    - text: '-------'
    - text: "Repertoire Analysis"
    - text: Basic Clonal Visualizations
      href: articles/Clonal_Visualizations.html
    - text: Visualizing Clonal Dynamics
      href: articles/Clonal_Dynamics.html
    - text: Summarizing Repertoires
      href: articles/Repertoire_Summary.html
    - text: Comparing Clonal Diversity and Overlap
      href: articles/Clonal_Diversity.html
    - text: Clustering by Edit Distance
      href: articles/Clonal_Cluster.html
    - text: '-------'
    - text: "Working with Single-Cell Objects"
    - text: Combining Clones and Single-Cell Objects
      href: articles/Attaching_SC.html
    - text: Visualizations for Single-Cell Objects
      href: articles/SC_Visualizations.html
    - text: Quantifying Clonal Bias
      href: articles/Clonal_Bias.html
  - text: Extensions
    menu:
    - text: "Related Packages"
    - text: Making Deep Learning Models with immApex
      href: articles/immApex.html
    - text: Combining Deep Learning and TCRs with Trex
      href: articles/Trex.html
    - text: Combining Deep Learning and BCRs with Ibex
      href: articles/Ibex.html
    - text: Bridging Python TCR Tools with immLynx
      href: articles/immLynx.html
    - text: TCR Specificity Grouping with immGLIPH
      href: articles/immGLIPH.html
    - text: Immune Reference Data with immReferent
      href: articles/immReferent.html
    - text: Single-cell Gene Set Enrichment with escape
      href: articles/Running_Escape.html
  - text: Compatible Packages
    menu:
    - text: "Third-Party Integrations"
    - text: Combining Immcantation and scRepertoire
      href: articles/immcantation.html
    - text: TCRpheno Applied to T Cell Fate
      href: articles/tcrpheno.html
    - text: Downstream Analysis with immunarch
      href: articles/immunarch.html
    - text: VDJ Trajectory Analysis with dandelionR
      href: articles/dandelionR.html
  - text: Reference
    href: reference/index.html
  - text: News
    href: news/index.html
  - text: FAQ
    href: articles/FAQ.html
  right:
  - icon: fa-github
    href: https://github.com/BorchLab/scRepertoire
    aria-label: GitHub

articles:
- title: Getting Set Up
  navbar: ~
  contents:
  - articles/Installation
  - articles/Loading
  - articles/Combining_Contigs
  - articles/Processing
- title: Repertoire Analysis
  navbar: ~
  contents:
  - articles/Clonal_Visualizations
  - articles/Clonal_Dynamics
  - articles/Repertoire_Summary
  - articles/Clonal_Diversity
  - articles/Clonal_Cluster
- title: Working with Single-Cell Objects
  navbar: ~
  contents:
  - articles/Attaching_SC
  - articles/SC_Visualizations
  - articles/Clonal_Bias
- title: Extensions (BorchLab Packages)
  navbar: ~
  contents:
  - articles/immApex
  - articles/Trex
  - articles/Ibex
  - articles/immLynx
  - articles/immGLIPH
  - articles/immReferent
  - articles/Running_Escape
- title: Compatible Packages
  navbar: ~
  contents:
  - articles/immcantation
  - articles/tcrpheno
  - articles/immunarch
  - articles/dandelionR
- title: Help
  navbar: ~
  contents:
  - articles/FAQ
- title: internal
  contents:
  - vignette

reference:
- title: Loading and Processing Contigs
  desc: Functions that load, combine, and process the single-cell contig information.
- contents:
  - loadContigs
  - combineTCR
  - combineBCR
  - clonalBin
  - addVariable
  - subsetClones
  - exportClones
  - createHTOContigList
  - getContigDoublets
  - annotateInvariant
- title: Visualizing Clones
  desc: Functions for visualizing clonal data across samples and groups.
- contents:
  - clonalAbundance
  - clonalCompare
  - clonalDiversity
  - clonalHomeostasis
  - clonalLength
  - clonalOverlap
  - clonalProportion
  - clonalQuant
  - clonalRarefaction
  - clonalScatter
  - clonalSizeDistribution
  - vizGenes
- title: Summarizing Repertoire
  desc: Functions to summarize clonal sequences across the repertoire.
- contents:
  - percentGeneUsage
  - percentGenes
  - percentVJ
  - percentAA
  - percentKmer
  - positionalEntropy
  - positionalProperty
- title: Clustering and Similarity
  desc: Functions for clustering clones by sequence similarity.
- contents:
  - clonalCluster
- title: Single-Cell Object Visualizations
  desc: Functions to add or visualize clonal information along a single-cell object.
- contents:
  - combineExpression
  - alluvialClones
  - clonalBias
  - clonalNetwork
  - clonalOccupy
  - clonalOverlay
  - getCirclize
  - vizCirclize
  - highlightClones
  - StartracDiversity
- title: Utilities
  desc: Helper functions for filtering gene signatures and converting data.
- contents:
  - quietVDJgenes
  - quietBCRgenes
  - quietTCRgenes
  - expression2List
- title: Data
  desc: Reference data for package functions.
- contents:
  - contig_list
  - scRep_example

deploy:
  install_metadata: yes