Comprehensive genome-wide analysis of mutational processes

binomial_test | Binomial test for enrichment or depletion testing |

cluster_signatures | Signature clustering function |

cos_sim | Cosine similarity function |

cos_sim_matrix | Compute all pairwise cosine similarities between mutational... |

enrichment_depletion_test | Test for enrichment or depletion of mutations in genomic... |

explained_by_signatures | This function has been renamed to 'cos_sim_matrix'. |

extract_signatures | Extract mutational signatures from 96 mutation matrix using... |

fit_to_signatures | Find optimal nonnegative linear combination of mutation... |

genomic_distribution | Find overlaps between mutations and a genomic region. |

MutationalPatterns-package | MutationalPatterns: an integrative R package for studying... |

mutation_context | This function has been removed. Use 'mut_context' instead. |

mutations_from_vcf | Retrieve base substitutions from vcf |

mutation_types | This function has been renamed. Use 'mut_type' instead. |

mut_context | Retrieve context of base substitutions |

mut_matrix | Make mutation count matrix of 96 trinucleotides |

mut_matrix_stranded | Make mutation count matrix of 96 trinucleotides with strand... |

mut_strand | Find strand of mutations |

mut_type | Retrieve base substitution types from a VCF object |

mut_type_occurrences | Count the occurrences of each base substitution type |

plot_192_profile | Plot 192 trinucleotide profile |

plot_96_profile | Plot 96 trinucleotide profile |

plot_compare_profiles | Compare two 96 mutation profiles |

plot_contribution | Plot signature contribution barplot |

plot_contribution_heatmap | Plot signature contribution heatmap |

plot_cosine_heatmap | Plot cosine similarity heatmap |

plot_enrichment_depletion | Plot enrichment/depletion of mutations in genomic regions |

plot_rainfall | Plot genomic rainfall |

plot_signature_strand_bias | Plot signature strand bias |

plot_spectrum | Plot point mutation spectrum |

plot_strand | Plot strand per base substitution type |

plot_strand_bias | Plot strand bias per base substitution type per group |

read_vcfs_as_granges | Read VCF files into a GRangesList |

strand_bias_test | Significance test for strand asymmetry |

strand_from_vcf | This function has been renamed. Use 'mut_strand' instead. |

strand_occurrences | Count occurrences per base substitution type and strand |

type_context | Retrieve context of base substitution types |

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