Introduction | Installation | The example data | Subsetting for this vignette | Creating a scProkaR object | Other entry points | Quality control | Integration across treatment groups | MNN correction | Harmony correction | Registering your own embedding | UMAP and clustering on the integrated space | Visualisation | Benchmarking the integration | Pseudobulk differential expression | Defining replicates | Aggregating and normalising | Pairwise contrasts | Time-course testing with splines | Where to go next | Further reading | Session information

Introduction | The problem TATA addresses | Relationship to Bioconductor single-cell infrastructure | Installation | Setting up | A simulated multi-drug branching time course | The TATA pipeline, step by step | Build the cell--cell graph | Cluster cells into coarse states | Score cluster pairs on topology and on time | Build the abstract graph | Compute pseudotime | The run_tata() wrapper | Comparing time-informed and topology-only runs | Benchmarking helpers | Temporal consistency plots | Branch probabilities and plasticity | Selecting cells for a branch | Branch-specific gene trends | Compact result overview | Practical guidance | Further reading | Session information