_pkgdown.yml

reference:
    - title: "Loading, transforming and summarizing"
      desc: "Functions to load data, add covariates or annotations, or provide high-level summaries."
      contents: 
        - starts_with("From")
        - ends_with("Assay")
        - freq
        - getConcordance
        - melt.SingleCellAssay
        - read.fluidigm
        - subset
        - primerAverage
        - filter
    - title: "Thresholding"
      desc: "Adaptive thresholding of background noise."
      contents:
        - thresholdSCRNACountMatrix
        - print.summaryThresholdSCRNA
        - summary.thresholdSCRNACountMatrix
        - plot.thresholdSCRNACountMatrix
    - title: "Differential Expression Testing with Hurdle Model"
      desc: "Fit a Hurdle linear model to test for zero-inflated differential expression."
      contents:
        - zlm
        - summary
        - LMERlike-class
        - BayesGLMlike-class
        - print.summaryZlmFit
        - ebayes
        - defaultPrior
    - title: "Specifying hypothesis and contrasts to test"
      desc: "Testing linear functions of coefficients."
      contents:
        - Hypothesis
        - CoefficientHypothesis
        - lrTest
        - waldTest
        - lrTest,ZlmFit,character-method
    - title: "Low-level manipulation of fitted hurdle models"
      desc: "Return coefficients, standard errors, etc.  Calculate and return residuals from models."
      contents: 
        - coef
        - vcov
        - se.coef
        - ZlmFit-class
        - predict.ZlmFit
        - getLogFC
        - collectResiduals
        - impute
    - title: "Gene set enrichment testing"
      desc: "Tests on the average differential expression effect in a gene set, accounting for gene-gene correlations.  Uses bootstraps to assess the gene-gene correlations."
      contents:
        - gseaAfterBoot
        - bootVcov1
        - pbootVcov1
        - summary,GSEATests-method
    - title: "Plotting methods"
      desc: "Miscellaneous plotting methods. Concordance, PCA biplots, and effects plots for fitted hurdle models."
      contents:
        - myBiplot
        - plotSCAConcordance
        - stat_ell
    - title: "Legacy methods"
      desc: "Older and perhaps obsoleted methods."
      contents:
        - LRT
        - computeEtFromCt
        - mast_filter
        - expavg
        - filterLowExpressedGenes