# Model Gene Expression Dynamics with Spline-Based NB GLMs, GEEs, & GLMMs

## Documentation for package ‘scLANE’ version 1.0.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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'.
scoreTestGEE | Use a Lagrange multiplier (score) test to compare nested GEE models.
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).
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.