Introduction | The YAPSA package | Linear Combination Decomposition (LCD) | Signature-specific cutoffs | Confidence intervals for mutational signature exposures | Stratification of the Mutational Catalogue (SMC) | Indel signatures | Example: a cohort of B-cell lymphomas | Example data | Loading example data | Displaying example data | Loading the signature information | Loading the initial set of signatures | Loading the updated set of mutational signatures | Preparation for later analysis | Performing an LCD analysis | Building a mutational catalogue | LCD analysis without any cutoff | LCD analysis with a generalized cutoff | LCD analysis with signature-specific cutoffs | Cluster samples based on their signature exposures | References

Introduction | Overview of the data | Signatures | Optimal cutoffs | Application example | Comparison: analysis without any cutoffs | Making use of optimal signature-specific cutoffs | Reference

Introduction: Confidence Intervals | Recap: compute signature exposures | Compute the confidence intervals | References

Introduction | Recap: compute signature exposures (without stratification) | Stratified analysis of mutational signatures | Preparation | Performing a stratification based on mutation density | Testing for statistical significance of enrichment and depletion patterns

Introduction: PCAWG signatures | Classification of Indels | PCAWG Indel signatures | Example data: Genome of the Netherlands | Supervised Indel signature analysis | Loading example data | Data Preprocessing | LCD Analysis | Visualization | Confidence Intervals | References

Introduction | Loading the data | Correcting for the target capture | Performing the analysis of mutational signatures | References