Aim of the package | Two sample tests for univariate distribution | General Setting | Kolmogorov-Smirnov test | Adding observation weights and threshold | Multivariate Distributions | The two-sample kernel test from [@Gretton2012] | Classifier Test | Considering more than 2 distributions | References

Installation | Load data | Fit negative binomial model | Within-lineage comparisons | Association of gene expression with pseudotime | Discovering progenitor marker genes | Comparing specific pseudotime values within a lineage | Between-lineage comparisons | Discovering differentiated cell type markers | Discovering genes with different expression patterns | Example on combining patternTest with diffEndTest results | Early drivers of differentiation | Differential expression in large datasets | Clustering of genes according to their expression pattern | Extracting fitted values to use with any clustering method | Clustering using RSEC, clusterExperiment | Contributing and requesting | Session | References

Initial pre-processing | Generating a synthetic dataset | Vizualisation | Differential Topology | Exploratory analysis | Trajectory Inference | Differential Progression | Visualization | Testing for differential progression | Differential fate selection | Testing for differential fate selection | Differential Expression | Conclusion | Session Info | References

Toy dataset | The topologyTest function | Changing the method or the threshold | Passing arguments to the test method | Using parallelisation | Differential progression and fate selection | Default | Changing the method and / or threshold | Passing more parameters to the test methods | Conclusion | Session Info | References

Introduction | Load data | Monocle3 | Constructing the trajectory | Extracting the pseudotimes and cell weights for tradeSeq | Session | References

Introduction | Installation | Load data | Choosing K: a deeper dive into the output from evaluateK | Fit additive models | Adding covariates to the model | Parallel computing | Fitting only a subset of genes | Zero inflation | Convergence issues on small or zero-inflated datasets | tradeSeq list output | Session | References

Installation | Initial visualization | Merging with Dune | Initial ARI | Actual merging | ARI improvement | Session