_pkgdown.yml

reference:
  - title: "Model fit and check"
    desc: >
      Contain the fitGam function used to fit the model, as well as functions to
      check the fit, extract components and decide on the appropriate number of knots.
    contents:
      - '`fitGAM`'
      - '`evaluateK`'
      - '`nknots`'
      - '`getSmootherPvalues`'
      - '`getSmootherTestStats`'
  - title: "Tests"
    desc: >
      All tests currently implemented in tradeSeq. All tests are of the form
      xxxTest. Tests can either be run in an omnibus fashion (all lineages) or on
      an individual basis (lineages for within-lineage tests, and pairwise form
      between-lineages tests).
    contents:
      - '`associationTest`'
      - '`diffEndTest`'
      - '`earlyDETest`'
      - '`patternTest`'
      - '`startVsEndTest`'
  - title: Visualization
    desc: "Functions to plot the results"
    contents:
      - '`plotGeneCount`'
      - '`plotSmoothers`'
  - title: Data
    desc: "The dataset used in example"
    contents:
      - '`gamList`'
      - '`celltype`'
      - '`countMatrix`'
      - '`crv`'
      - '`sds`'
  - title: Clustering
    desc: "Clustering of gene expression patterns"
    contents:
      - '`clusterExpressionPatterns`'
      - '`predictCells`'
      - '`predictSmooth`'

navbar:
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      href: reference/index.html
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      href: articles/tradeSeq.html