Overview | Load the GLUCOLD data | Check and align the samples | Define the visit order | Create the LongOmicsTraj object | Empirical trajectory estimation | maSigPro trajectory estimation | OTS distribution | Query treatment-specific trajectories | Query result summary | Representative genes | Prepare expression profiles | Add OTS labels | Plot representative trajectories | Using your own data | Summary | Quick reference | Session information

Overview | Required packages | Load and prepare the GLUCOLD example | Construct feature-level trajectories | Map feature trajectories to OTS labels | Cluster genes across all treatment groups | Map cluster centres to topology labels | Inspect topology composition within clusters | Trajectory-arm plot | Quantify topology purity | Calculate topology coverage and duplication | Plot cluster-centre trajectories | Alternative clustering with PAM | Topology-aware FlexMix clustering within one treatment arm | Plot the cluster-selection path | Plot representative cluster trajectories and OTS composition | Plot topology deviations | Plot representative genes | Interpretation | Session information

Introduction | Quick Start Example | Session information