Package: MutationalPatterns 3.15.0

Mark van Roosmalen

MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

Mutational processes leave characteristic footprints in genomic DNA. This package provides a comprehensive set of flexible functions that allows researchers to easily evaluate and visualize a multitude of mutational patterns in base substitution catalogues of e.g. healthy samples, tumour samples, or DNA-repair deficient cells. The package covers a wide range of patterns including: mutational signatures, transcriptional and replicative strand bias, lesion segregation, genomic distribution and association with genomic features, which are collectively meaningful for studying the activity of mutational processes. The package works with single nucleotide variants (SNVs), insertions and deletions (Indels), double base substitutions (DBSs) and larger multi base substitutions (MBSs). The package provides functionalities for both extracting mutational signatures de novo and determining the contribution of previously identified mutational signatures on a single sample level. MutationalPatterns integrates with common R genomic analysis workflows and allows easy association with (publicly available) annotation data.

Authors:Freek Manders [aut], Francis Blokzijl [aut], Roel Janssen [aut], Jurrian de Kanter [ctb], Rurika Oka [ctb], Mark van Roosmalen [cre], Ruben van Boxtel [aut, cph], Edwin Cuppen [aut]

MutationalPatterns_3.15.0.tar.gz
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MutationalPatterns_3.15.0.tgz(r-4.4-any)MutationalPatterns_3.15.0.tgz(r-4.3-any)
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MutationalPatterns.pdf |MutationalPatterns.html✨
MutationalPatterns/json (API)
NEWS

# Install 'MutationalPatterns' in R:
install.packages('MutationalPatterns', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:MutationalPatterns-3.15.0(bioc 3.20)MutationalPatterns-3.14.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

70 exports 1.69 score 114 dependencies 1 dependents 32 mentions

Last updated 2 months agofrom:3141f4438f

Exports:bin_mutation_densitybinomial_testcalculate_lesion_segregationcluster_signaturescontext_potential_damage_analysisconvert_sigs_to_refcos_simcos_sim_matrixcount_dbs_contextscount_indel_contextscount_mbs_contextsdetermine_regional_similarityenrichment_depletion_testextract_signaturesfit_to_signaturesfit_to_signatures_bootstrappedfit_to_signatures_strictgenomic_distributionget_dbs_contextget_indel_contextget_known_signaturesget_mut_typeget_sim_tblengthen_mut_matrixmerge_signaturesmut_contextmut_matrixmut_matrix_strandedmut_strandmut_typemut_type_occurrencesmutations_from_vcfplot_192_profileplot_96_profileplot_bootstrapped_contributionplot_compare_dbsplot_compare_indelsplot_compare_mbsplot_compare_profilesplot_contributionplot_contribution_heatmapplot_correlation_bootstrapplot_cosine_heatmapplot_dbs_contextsplot_enrichment_depletionplot_indel_contextsplot_lesion_segregationplot_main_dbs_contextsplot_main_indel_contextsplot_mbs_contextsplot_original_vs_reconstructedplot_profile_heatmapplot_profile_regionplot_rainfallplot_regional_similarityplot_riverplot_signature_strand_biasplot_spectrumplot_spectrum_regionplot_strandplot_strand_biaspool_mut_matread_vcfs_as_grangesrename_nmf_signaturesshowsignature_potential_damage_analysissplit_muts_regionstrand_bias_teststrand_occurrencestype_context

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcliclustercodetoolscolorspacecowplotcpp11crayoncurlDBIDelayedArraydigestdoParalleldplyrfansifarverfastmapforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggalluvialggdendroggplot2gluegridBasegtablehttrIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeNMFopensslpillarpkgconfigplogrplyrpngpracmapurrrR6RColorBrewerRcppRCurlregistryreshape2restfulrRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrXMLXVectoryamlzlibbioc

Introduction to MutationalPatterns

Freek Manders, Francis Blokzijl, Roel Janssen, Rurika Oka, Jurrian de Kanter, Mark van Roosmalen, Ruben van Boxtel, Edwin Cuppen

Rendered fromIntroduction_to_MutationalPatterns.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-01-11
Started: 2020-07-02

Readme and manuals

Help Manual

Help pageTopics
Bin the genome based on mutation densitybin_mutation_density
Binomial test for enrichment or depletion testingbinomial_test
Calculate the amount of lesion segregation for a GRangesList or GRanges object.calculate_lesion_segregation
Signature clustering functioncluster_signatures
Potential damage analysis for the supplied mutational contextscontext_potential_damage_analysis
Convert tissue specific signature exposures to referenceconvert_sigs_to_ref
Cosine similarity functioncos_sim
Compute all pairwise cosine similarities between mutational profiles/signaturescos_sim_matrix
Count DBS contextscount_dbs_contexts
Count indel contextscount_indel_contexts
Count MBS variants grouped by length.count_mbs_contexts
Determine regional mutation pattern similaritydetermine_regional_similarity
Test for enrichment or depletion of mutations in genomic regionsenrichment_depletion_test
Extract mutational signatures from 96 mutation matrix using NMFextract_signatures
Find optimal nonnegative linear combination of mutation signatures to reconstruct the mutation matrix.fit_to_signatures
Fit mutational signatures to a mutation matrix with bootstrappingfit_to_signatures_bootstrapped
Fit mutational signatures to a mutation matrix with less overfittingfit_to_signatures_strict
Find overlaps between mutations and a genomic region.genomic_distribution
Get DBS contextget_dbs_context
Get indel contextsget_indel_context
Get known signaturesget_known_signatures
Get variants with mut_type from GRangesget_mut_type
An S4 generic to get the sim_tb from a region_cossim object.get_sim_tb get_sim_tb,region_cossim-method
Lengthen mutation matrixlengthen_mut_matrix
Merge signatures based on cosine similaritymerge_signatures
Count 192 trinucleotide mutation occurrencesmut_192_occurrences
Count 96 trinucleotide mutation occurrencesmut_96_occurrences
Retrieve context of base substitutionsmut_context
Make mutation count matrix of 96 trinucleotidesmut_matrix
Make mutation count matrix of 96 trinucleotides with strand informationmut_matrix_stranded
Find strand of mutationsmut_strand
Retrieve base substitution types from a VCF objectmut_type
Count the occurrences of each base substitution typemut_type_occurrences
MutationalPatterns: an integrative R package for studying patterns in base substitution cataloguesMutationalPatterns-package MutationalPatterns
Defunct functions in package 'MutationalPattern'explained_by_signatures mutation_context mutation_types strand_from_vcf
Retrieve base substitutions from vcfmutations_from_vcf
Plot 192 trinucleotide profileplot_192_profile
Plot 96 trinucleotide profileplot_96_profile
Plot the bootstrapped signature contributionsplot_bootstrapped_contribution
Compare two DBS mutation profilesplot_compare_dbs
Compare two indel mutation profilesplot_compare_indels
Compare two mbs mutation profilesplot_compare_mbs
Compare two 96 mutation profilesplot_compare_profiles
Plot signature contribution barplotplot_contribution
Plot signature contribution heatmapplot_contribution_heatmap
Plots the correlation between bootstrapped signature contributionsplot_correlation_bootstrap
Plot cosine similarity heatmapplot_cosine_heatmap
Plot the DBS contextsplot_dbs_contexts
Plot enrichment/depletion of mutations in genomic regionsplot_enrichment_depletion
Plot the indel contextsplot_indel_contexts
Plot the strands of variants to show lesion segregationplot_lesion_segregation
Plot the main DBS contextsplot_main_dbs_contexts
Plot the main indel contextsplot_main_indel_contexts
Plot the MBS contextsplot_mbs_contexts
Plot the similarity between a mutation matrix and its reconstructed profileplot_original_vs_reconstructed
Plot a mutation matrix as a heatmapplot_profile_heatmap
Plot 96 trinucleotide profile per subgroupplot_profile_region
Plot genomic rainfallplot_rainfall
Plot regional similarityplot_regional_similarity
Plot a riverplotplot_river
Plot signature strand biasplot_signature_strand_bias
Plot point mutation spectrumplot_spectrum
Plot point mutation spectrum per genomic regionplot_spectrum_region
Plot strand per base substitution typeplot_strand
Plot strand bias per base substitution type per groupplot_strand_bias
Pool multiple samples from a mutation matrix togetherpool_mut_mat
Read VCF files into a GRangesListread_vcfs_as_granges
An S4 class to store the results of a regional mutation pattern similarity analysisregion_cossim-class
Rename NMF signatures based on previously defined signaturesrename_nmf_signatures
An S4 method to show an instance of the region_cossim class.show,region_cossim-method
Potential damage analysis for the supplied mutational signaturessignature_potential_damage_analysis
Split GRangesList or GRanges based on a list of regions.split_muts_region
Significance test for strand asymmetrystrand_bias_test
Count occurrences per base substitution type and strandstrand_occurrences
Retrieve context of base substitution typestype_context