Package: MutationalPatterns 3.23.0

Introduction | Installation | Data | List reference genome | Load example data SNVs | Load example data indels, DBSs and MBSs | Mutation characteristics | SNVs | Base substitution types | Mutation spectrum | 96 mutational profile | Larger contexts | Indels | DBSs | MBSs | Pooling samples | Mutational signatures | De novo mutational signature extraction using NMF | NMF | Bayesian NMF | Changing the names of the extracted signatures | Visualizing NMF results | Signature refitting | Find mathematically optimal contribution of COSMIC signatures | Stricter refitting | Bootstrapped refitting. | Similarity between mutational profiles and signatures | Signature potential damage analysis | Using other signature matrixes | Strand bias analyses | Transcriptional strand bias analysis | Gene definitions | Strand bias profile | Strand bias test | Replicative strand bias analysis | Define replication direction | Replication bias analysis | Signatures with strand bias | Genomic distribution | Rainfall plot | Define genomic regions | Enrichment or depletion of mutations in genomic regions | Mutational patterns of genomic regions | Split mutations based on genomic regions | Mutation Spectrum | Mutational profiles | Mutation density | Unsupervised local mutational patterns | Lesion segregation | Visualizing lesion segregation | Calculating lesion segregation | A note on the graphics | Session Info | References