backward_sel_WIC        Backward selection function for MARGE - uses
                        the Wald information criterion (WIC).
biasCorrectGEE          Bias-correct the GEE sandwich
                        variance-covariance matrix.
bootstrapRandomEffects
                        Generate bootstrapped confidence intervals for
                        random effects.
chooseCandidateGenes    Choose candidate genes for trajectory DE
                        analysis.
clusterGenes            Cluster the fitted values from a set of
                        'scLANE' models.
createCellOffset        Create an offset vector before modeling.
createSlopeTestData     A helper function to create a dataframe of
                        breakpoints and associated _p_-values from a
                        'marge' model.
embedGenes              Generate PCA & UMAP embeddings of fitted gene
                        dynamics.
enrichDynamicGenes      Perform GSEA on dynamic genes identified by
                        'scLANE'.
extractBreakpoints      Identify breakpoints in a 'marge' model.
fitGLMM                 Build an NB GLMM using truncated power basis
                        functions.
geneProgramDrivers      Identify driver genes for a given gene program.
geneProgramScoring      Add per-cell module scores for gene programs.
geneProgramSignificance
                        Test significance of gene program enrichment
                        across a trajectory.
getFittedValues         Generate a table of fitted values and celltype
                        metadata for genes of interest.
getKnotDist             Pull the set of knots for dynamic genes across
                        each lineage.
getResultsDE            Tidy the results of 'testDynamic'.
marge2                  Fit 'MARGE' models of single cell counts.
max_span                Truncates the predictor variable value to
                        exclude extreme values in knots selection.
min_span                A truncation function applied on the predictor
                        variable for knot selection.
modelLRT                Perform a likelihood ratio test for one model
                        against another.
nbGAM                   Fit a negative-binomial GAM.
npConvolve              Convolution that matches 'np.convolve'.
plotClusteredGenes      Generate tidy results from 'clusterGenes' to
                        use in plotting.
plotModelCoefs          Plot gene dynamics with estimated coefficients.
plotModels              Plot results of 'marge' and other models using
                        'ggplot2'.
print.summary.scLANE    Print method for summary.scLANE objects.
pullMARGESummary        Generate a summary of the MARGE model.
pullNullSummary         Generate a summary of the null model.
scLANE_models           An object of class 'scLANE'.
score_fun_gee           Given estimates from the null model fit and the
                        design matrix for alternative model, find the
                        score statistic (this is used for GEEs only).
score_fun_glm           Given estimates from the null model fit and the
                        design matrix for alternative model, find the
                        score statistic (this is used for GLMs only).
scoreTestGEE            Use a Lagrange multiplier (score) test to
                        compare nested GEE models.
sim_counts              A 'SingleCellExperiment' object containing
                        simulated counts.
sim_pseudotime          A data.frame containing ground-truth
                        pseudotime.
smoothedCountsMatrix    Generate a smoothed matrix of gene expression
                        using 'scLANE' models.
sortGenesHeatmap        Sort genes by where their peak expression
                        occurs across pseudotime.
sortObservations        Sort observations by sample ID and pseudotime.
stat_out                Fits a linear regression model and calculates
                        RSS/GCV measures (used for MARS linear models).
stat_out_score_gee_null
                        Calculate part of the score statistic for a
                        GEE.
stat_out_score_glm_null
                        Calculate part of the score statistic for a
                        GLM.
stripGLM                Make GLM objects much smaller.
summarizeModel          Represent a 'marge' model as a series of
                        piecewise equations.
summary.scLANE          Summary method for scLANE objects.
testDynamic             Test whether a gene is dynamic over pseudotime.
testSlope               Test whether a gene is dynamic over a
                        pseudotime interval.
theme_scLANE            A 'ggplot2' theme for 'scLANE'.
tp1                     Truncated p-th power function (positive part).
tp2                     Truncated p-th power function (negative part).
waldTestGEE             Use a Wald test to compare nested GEE models.
