_pkgdown.yml

url: https://www.borch.dev/uploads/scRepertoire/
Template:
  params:
    bootswatch: flatly
home:
  sidebar:
    structure:
    - links
    - license
    - custom
    - authors
    - dev
    components:
      custom:
        title: Citation
        text: '[Citing scRepertoire](https://f1000research.com/articles/9-47)'
navbar:
  left:
  - text: Getting Started
    href: index.html
  - text: Install
    href: articles/Installation.html
  - text: Vignettes
    menu:
    - text: Loading Data
      href: articles/Loading.html
    - text: Combining Contigs into Clones
      href: articles/Combining_Contigs.html
    - text: Additional Processing
      href: articles/Processing.html
    - text: '-------'
    - text: Basic Clonal Analysis
      href: articles/Clonal_Visualizations.html
    - text: Visualizing Clonal Dynamics
      href: articles/Clonal_Dynamics.html
    - text: Summarizing Repertoires
      href: articles/Repertoire_Summary.html
    - text: Clonal Diversity, Rarefaction, and Overlap
      href: articles/Clonal_Diversity.html
    - text: Clustering Sequences by Edit Distance
      href: articles/Clonal_Cluster.html
    - text: '-------'
    - 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: '-------'
    - 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: Single-cell Gene Set Enrichment Analysis
      href: articles/Running_Escape.html
  - text: News/Changelog
    href: news/index.html
  - text: Reference
    href: reference/index.html
  - text: FAQ
    href: articles/FAQ.html
reference:
- title: Loading and Processing Contigs
  desc: Functions that load, combine, and process the single-cell contig information.
- contents:
  - addVariable
  - combineBCR
  - combineTCR
  - createHTOContigList
  - getContigDoublets
  - exportClones
  - loadContigs
  - subsetClones
- title: Visualizing Clones
  desc: Functions plotting clonal data.
- contents:
  - clonalAbundance
  - clonalCluster
  - clonalCompare
  - clonalDiversity
  - clonalHomeostasis
  - clonalLength
  - clonalOverlap
  - clonalProportion
  - clonalQuant
  - clonalRarefaction
  - clonalScatter
  - clonalSizeDistribution
  - vizGenes
- title: Summarizing Repertoire
  desc: Functions to summarize clonal sequences across the repertoire.
- contents:
  - percentAA
  - positionalEntropy
  - positionalProperty
  - percentGenes
  - percentKmer
  - percentVJ
- title: Single-Cell Object Processing and Visualizations
  desc: Functions to add or visualize clonal information along a single-cell object.
- contents:
  - alluvialClones
  - clonalBias
  - clonalNetwork
  - clonalOccupy
  - clonalOverlay
  - combineExpression
  - getCirclize
  - highlightClones
  - StartracDiversity
- title: Data
  desc: Reference data for package functions.
- contents:
  - contig_list
  - mini_contig_list
  - scRep_example
deploy:
  install_metadata: yes