{ "_id": "6a1bdbf71d7bb097a0a1729c", "Package": "MutationalPatterns", "Type": "Package", "Title": "Comprehensive genome-wide analysis of mutational processes", "Description": "Mutational processes leave characteristic footprints in\ngenomic DNA. This package provides a comprehensive set of\nflexible functions that allows researchers to easily evaluate\nand visualize a multitude of mutational patterns in base\nsubstitution catalogues of e.g. healthy samples, tumour\nsamples, or DNA-repair deficient cells. The package covers a\nwide range of patterns including: mutational signatures,\ntranscriptional and replicative strand bias, lesion\nsegregation, genomic distribution and association with genomic\nfeatures, which are collectively meaningful for studying the\nactivity of mutational processes. The package works with single\nnucleotide variants (SNVs), insertions and deletions (Indels),\ndouble base substitutions (DBSs) and larger multi base\nsubstitutions (MBSs). The package provides functionalities for\nboth extracting mutational signatures de novo and determining\nthe contribution of previously identified mutational signatures\non a single sample level. MutationalPatterns integrates with\ncommon R genomic analysis workflows and allows easy association\nwith (publicly available) annotation data.", "Version": "3.23.0", "Date": "2025-07-30", "Authors@R": "c(\nperson(\"Freek\", \"Manders\", email = \"F.M.Manders@prinsesmaximacentrum.nl\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0001-6197-347X\")),\nperson(\"Francis\", \"Blokzijl\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-8084-8444\")),\nperson(\"Roel\", \"Janssen\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-4324-5350\")),\nperson(\"Jurrian\", \"de Kanter\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0001-5665-3711\")),\nperson(\"Rurika\", \"Oka\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-4107-7250\")),\nperson(\"Mark\", \"van Roosmalen\", email = \"vanBoxtelBioinformatics@prinsesmaximacentrum.nl\", role = \"cre\"),\nperson(\"Ruben\", \"van Boxtel\", role = c(\"aut\", \"cph\"),\ncomment = c(ORCID = \"0000-0003-1285-2836\")),\nperson(\"Edwin\", \"Cuppen\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-0400-9542\")))", "License": "MIT + file LICENSE", "URL": "https://doi.org/doi:10.1186/s12864-022-08357-3", "biocViews": "Genetics, SomaticMutation", "ZipData": "NA", "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:44:31 UTC", "RemoteUrl": "https://github.com/bioc/MutationalPatterns", "RemoteRef": "HEAD", "RemoteSha": "abb88a938dcd33f9bb7c420e30305675bae28e97", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-31 06:17:55 UTC", "User": "root" }, "Author": "Freek Manders [aut] (ORCID: ),\nFrancis Blokzijl [aut] (ORCID: ),\nRoel Janssen [aut] (ORCID: ),\nJurrian de Kanter [ctb] (ORCID:\n),\nRurika Oka [ctb] (ORCID: ),\nMark van Roosmalen [cre],\nRuben van Boxtel [aut, cph] (ORCID:\n),\nEdwin Cuppen [aut] (ORCID: )", "Maintainer": "Mark van Roosmalen ", "MD5sum": "f6fc75b6f5403dfc3be37b361a0d3e4a", "_user": "bioc", "_type": "src", "_file": "MutationalPatterns_3.23.0.tar.gz", "_fileid": "8e1f2066150f35262db1c7618ed422711055b464c5a1a9698c071dd9611839f0", "_filesize": 6025169, "_sha256": "8e1f2066150f35262db1c7618ed422711055b464c5a1a9698c071dd9611839f0", "_created": "2026-05-31T06:17:55.000Z", "_published": "2026-05-31T06:57:59.148Z", "_jobs": [ { "job": 78704998893, "time": 289, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7314389038" }, { "job": 78704998898, "time": 604, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7314422713" }, { "job": 78704998897, "time": 693, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7314432400" }, { "job": 78704998912, "time": 389, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7314605365" }, { "job": 78704998903, "time": 386, "config": 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"plot_mbs_contexts", "plot_original_vs_reconstructed", "plot_profile_heatmap", "plot_profile_region", "plot_rainfall", "plot_regional_similarity", "plot_river", "plot_signature_strand_bias", "plot_spectrum", "plot_spectrum_region", "plot_strand", "plot_strand_bias", "pool_mut_mat", "read_vcfs_as_granges", "rename_nmf_signatures", "show", "signature_potential_damage_analysis", "split_muts_region", "strand_bias_test", "strand_occurrences", "type_context" ], "_help": [ { "page": "bin_mutation_density", "title": "Bin the genome based on mutation density", "concept": [ "genomic_regions" ], "topics": [ "bin_mutation_density" ] }, { "page": "binomial_test", "title": "Binomial test for enrichment or depletion testing", "topics": [ "binomial_test" ] }, { "page": "calculate_lesion_segregation", "title": "Calculate the amount of lesion segregation for a GRangesList or GRanges object.", "concept": [ "Lesion_segregation" ], "topics": [ "calculate_lesion_segregation" ] }, { "page": "cluster_signatures", "title": "Signature clustering function", "topics": [ "cluster_signatures" ] }, { "page": "context_potential_damage_analysis", "title": "Potential damage analysis for the supplied mutational contexts", "topics": [ "context_potential_damage_analysis" ] }, { "page": "convert_sigs_to_ref", "title": "Convert tissue specific signature exposures to reference", "topics": [ "convert_sigs_to_ref" ] }, { "page": "cos_sim", "title": "Cosine similarity function", "topics": [ "cos_sim" ] }, { "page": "cos_sim_matrix", "title": "Compute all pairwise cosine similarities between mutational profiles/signatures", "topics": [ "cos_sim_matrix" ] }, { "page": "count_dbs_contexts", "title": "Count DBS contexts", "concept": [ "DBS" ], "topics": [ "count_dbs_contexts" ] }, { "page": "count_indel_contexts", "title": "Count indel contexts", "concept": [ "Indels" ], "topics": [ "count_indel_contexts" ] }, { "page": "count_mbs_contexts", "title": "Count MBS variants grouped by length.", "concept": [ "MBS" ], "topics": [ "count_mbs_contexts" ] }, { "page": "determine_regional_similarity", "title": "Determine regional mutation pattern similarity", "concept": [ "regional_similarity" ], "topics": [ "determine_regional_similarity" ] }, { "page": "enrichment_depletion_test", "title": "Test for enrichment or depletion of mutations in genomic regions", "topics": [ "enrichment_depletion_test" ] }, { "page": "extract_signatures", "title": "Extract mutational signatures from 96 mutation matrix using NMF", "topics": [ "extract_signatures" ] }, { "page": "fit_to_signatures", "title": "Find optimal nonnegative linear combination of mutation signatures to reconstruct the mutation matrix.", "topics": [ "fit_to_signatures" ] }, { "page": "fit_to_signatures_bootstrapped", "title": "Fit mutational signatures to a mutation matrix with bootstrapping", "topics": [ "fit_to_signatures_bootstrapped" ] }, { "page": "fit_to_signatures_strict", "title": "Fit mutational signatures to a mutation matrix with less overfitting", "topics": [ "fit_to_signatures_strict" ] }, { "page": "genomic_distribution", "title": "Find overlaps between mutations and a genomic region.", "topics": [ "genomic_distribution" ] }, { "page": "get_dbs_context", "title": "Get DBS context", "concept": [ "DBS" ], "topics": [ "get_dbs_context" ] }, { "page": "get_indel_context", "title": "Get indel contexts", "concept": [ "Indels" ], "topics": [ "get_indel_context" ] }, { "page": "get_known_signatures", "title": "Get known signatures", "topics": [ "get_known_signatures" ] }, { "page": "get_mut_type", "title": "Get variants with mut_type from GRanges", "topics": [ "get_mut_type" ] }, { "page": "get_sim_tb", "title": "An S4 generic to get the sim_tb from a region_cossim object.", "topics": [ "get_sim_tb", "get_sim_tb,region_cossim-method" ] }, { "page": "lengthen_mut_matrix", "title": "A mutation_matrix calculated on a GRangesList or GR object modified by 'split_muts_region()', will contain a column per combination of sample and genomic region. In essence different regions are treated as different samples. This function will transform the matrix, so that these regions are instead treated as different mutation types. For example, instead of 'C[C>T]G', you might have the feature 'C[C>T]G Promoter'. The number of rows in the matrix will thus be multiplied by the number of regions. After using 'split_muts_region()', use 'mut_matrix()' to get a mut_matrix that can be used for this function. The result can be plotted with plot_profile_region, but could also be used for NMF, refitting ect.", "concept": [ "genomic_regions" ], "topics": [ "lengthen_mut_matrix" ] }, { "page": "merge_signatures", "title": "Merge signatures based on cosine similarity", "topics": [ "merge_signatures" ] }, { "page": "mut_192_occurrences", "title": "Count 192 trinucleotide mutation occurrences", "topics": [ "mut_192_occurrences" ] }, { "page": "mut_96_occurrences", "title": "Count 96 trinucleotide mutation occurrences", "topics": [ "mut_96_occurrences" ] }, { "page": "mut_context", "title": "Retrieve context of base substitutions", "topics": [ "mut_context" ] }, { "page": "mut_matrix", "title": "Make mutation count matrix of 96 trinucleotides", "topics": [ "mut_matrix" ] }, { "page": "mut_matrix_stranded", "title": "Make mutation count matrix of 96 trinucleotides with strand information", "topics": [ "mut_matrix_stranded" ] }, { "page": "mut_strand", "title": "Find strand of mutations", "topics": [ "mut_strand" ] }, { "page": "mut_type", "title": "Retrieve base substitution types from a VCF object", "topics": [ "mut_type" ] }, { "page": "mut_type_occurrences", "title": "Count the occurrences of each base substitution type", "topics": [ "mut_type_occurrences" ] }, { "page": "MutationalPatterns-package", "title": "MutationalPatterns: an integrative R package for studying patterns in base substitution catalogues", "topics": [ "MutationalPatterns-package", "MutationalPatterns" ] }, { "page": "MutationalPatterns-defunct", "title": "Defunct functions in package 'MutationalPattern'", "topics": [ "explained_by_signatures", "mutation_context", "mutation_types", "strand_from_vcf" ] }, { "page": "mutations_from_vcf", "title": "Retrieve base substitutions from vcf", "topics": [ "mutations_from_vcf" ] }, { "page": "plot_192_profile", "title": "Plot 192 trinucleotide profile", "topics": [ "plot_192_profile" ] }, { "page": "plot_96_profile", "title": "Plot 96 trinucleotide profile", "topics": [ "plot_96_profile" ] }, { "page": "plot_bootstrapped_contribution", "title": "Plot the bootstrapped signature contributions", "topics": [ "plot_bootstrapped_contribution" ] }, { "page": "plot_compare_dbs", "title": "Compare two DBS mutation profiles", "concept": [ "DBS" ], "topics": [ "plot_compare_dbs" ] }, { "page": "plot_compare_indels", "title": "Compare two indel mutation profiles", "concept": [ "Indels" ], "topics": [ "plot_compare_indels" ] }, { "page": "plot_compare_mbs", "title": "Compare two mbs mutation profiles", "concept": [ "MBS" ], "topics": [ "plot_compare_mbs" ] }, { "page": "plot_compare_profiles", "title": "Compare two 96 mutation profiles", "topics": [ "plot_compare_profiles" ] }, { "page": "plot_contribution", "title": "Plot signature contribution barplot", "topics": [ "plot_contribution" ] }, { "page": "plot_contribution_heatmap", "title": "Plot signature contribution heatmap", "topics": [ "plot_contribution_heatmap" ] }, { "page": "plot_correlation_bootstrap", "title": "Plots the correlation between bootstrapped signature contributions", "topics": [ "plot_correlation_bootstrap" ] }, { "page": "plot_cosine_heatmap", "title": "Plot cosine similarity heatmap", "topics": [ "plot_cosine_heatmap" ] }, { "page": "plot_dbs_contexts", "title": "Plot the DBS contexts", "concept": [ "DBS" ], "topics": [ "plot_dbs_contexts" ] }, { "page": "plot_enrichment_depletion", "title": "Plot enrichment/depletion of mutations in genomic regions", "topics": [ "plot_enrichment_depletion" ] }, { "page": "plot_indel_contexts", "title": "Plot the indel contexts", "concept": [ "Indels" ], "topics": [ "plot_indel_contexts" ] }, { "page": "plot_lesion_segregation", "title": "Plot the strands of variants to show lesion segregation", "concept": [ "Lesion_segregation" ], "topics": [ "plot_lesion_segregation" ] }, { "page": "plot_main_dbs_contexts", "title": "Plot the main DBS contexts", "concept": [ "DBS" ], "topics": [ "plot_main_dbs_contexts" ] }, { "page": "plot_main_indel_contexts", "title": "Plot the main indel contexts", "concept": [ "Indels" ], "topics": [ "plot_main_indel_contexts" ] }, { "page": "plot_mbs_contexts", "title": "Plot the MBS contexts", "concept": [ "MBS" ], "topics": [ "plot_mbs_contexts" ] }, { "page": "plot_original_vs_reconstructed", "title": "Plot the similarity between a mutation matrix and its reconstructed profile", "topics": [ "plot_original_vs_reconstructed" ] }, { "page": "plot_profile_heatmap", "title": "Plot a mutation matrix as a heatmap", "topics": [ "plot_profile_heatmap" ] }, { "page": "plot_profile_region", "title": "Plot 96 trinucleotide profile per subgroup", "concept": [ "genomic_regions" ], "topics": [ "plot_profile_region" ] }, { "page": "plot_rainfall", "title": "Plot genomic rainfall", "topics": [ "plot_rainfall" ] }, { "page": "plot_regional_similarity", "title": "Plot regional similarity", "concept": [ "regional_similarity" ], "topics": [ "plot_regional_similarity" ] }, { "page": "plot_river", "title": "Plot a riverplot", "topics": [ "plot_river" ] }, { "page": "plot_signature_strand_bias", "title": "Plot signature strand bias", "topics": [ "plot_signature_strand_bias" ] }, { "page": "plot_spectrum", "title": "Plot point mutation spectrum", "topics": [ "plot_spectrum" ] }, { "page": "plot_spectrum_region", "title": "Plot point mutation spectrum per genomic region", "concept": [ "genomic_regions" ], "topics": [ "plot_spectrum_region" ] }, { "page": "plot_strand", "title": "Plot strand per base substitution type", "topics": [ "plot_strand" ] }, { "page": "plot_strand_bias", "title": "Plot strand bias per base substitution type per group", "topics": [ "plot_strand_bias" ] }, { "page": "pool_mut_mat", "title": "Pool multiple samples from a mutation matrix together", "topics": [ "pool_mut_mat" ] }, { "page": "read_vcfs_as_granges", "title": "Read VCF files into a GRangesList", "topics": [ "read_vcfs_as_granges" ] }, { "page": "region_cossim-class", "title": "An S4 class to store the results of a regional mutation pattern similarity analysis", "topics": [ "region_cossim-class" ] }, { "page": "rename_nmf_signatures", "title": "Rename NMF signatures based on previously defined signatures", "topics": [ "rename_nmf_signatures" ] }, { "page": "show-region_cossim-method", "title": "An S4 method to show an instance of the region_cossim class.", "topics": [ "show,region_cossim-method" ] }, { "page": "signature_potential_damage_analysis", "title": "Potential damage analysis for the supplied mutational signatures", "topics": [ "signature_potential_damage_analysis" ] }, { "page": "split_muts_region", "title": "Split GRangesList or GRanges based on a list of regions.", "concept": [ "genomic_regions" ], "topics": [ "split_muts_region" ] }, { "page": "strand_bias_test", "title": "Significance test for strand asymmetry", "topics": [ "strand_bias_test" ] }, { "page": "strand_occurrences", "title": "Count occurrences per base substitution type and strand", 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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 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