Package: MutSeqR 1.0.0

Matthew J. Meier

MutSeqR: Analysis of Error-Corrected Sequencing Data for Mutation Detection

Standard methods for analysis of mutation data following error- corrected sequencing (ECS) for the purpose of mutagencity assessment. Functions include importing the mutation lists provided by a variant caller, and a set of analytical tools for statistical testing and visualization of mutation data; comparison to COSMIC and/or germline signatures; etc.

Authors:Annette E. Dodge [aut], Andrew Williams [aut], Danielle P.M. LeBlanc [aut], David M. Schuster [aut], Elena Esina [aut], Clint C. Valentine [aut], Jesse J. Salk [aut], Alexander Y. Maslov [aut], Christopher Bradley [aut], Carole L. Yauk [aut], Francesco Marchetti [aut], Matthew J. Meier [aut, cre], Geronimo Matteo [ctb], Health Canada's Genomics Research and Development Initiative [fnd], Canada Research Chairs Program [fnd], Burroughs Wellcome Fund [fnd]

MutSeqR_1.0.0.tar.gz
MutSeqR_1.0.0.zip(r-4.7)MutSeqR_1.0.0.zip(r-4.6)MutSeqR_1.0.0.zip(r-4.5)
MutSeqR_1.0.0.tgz(r-4.6-any)MutSeqR_1.0.0.tgz(r-4.5-any)
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MutSeqR_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MutSeqR/json (API)
NEWS

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

Bug tracker:https://github.com/ehsrb-bsrse-bioinformatics/mutseqr/issues

Pkgdown/docs site:https://ehsrb-bsrse-bioinformatics.github.io

On BioConductor:MutSeqR-1.1.0(bioc 3.24)MutSeqR-1.0.0(bioc 3.23)

sequencingsomaticmutationvisualizationgenomicvariationdrivermutationstatisticalmethodgenetarget

6.84 score 10 stars 172 downloads 41 exports 94 dependencies

Last updated from:ec5b4d3b4b (on RELEASE_3_23). Checks:1 NOTE, 4 ERROR, 5 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE433
linux-devel-x86_64ERROR617
source / vignettesOK590
linux-release-x86_64OK602
macos-release-arm64OK333
macos-oldrel-arm64ERROR415
windows-develERROR467
windows-releaseOK425
windows-oldrelERROR509
wasm-releaseOK305

Exports:%>%bmd_proastBS_org_mapcalculate_mfcheck_required_columnsclassify_variationcontext_listdenominator_dictfilter_mutfind_BS_genomeget_binom_ciget_seqimport_mut_dataimport_vcf_dataload_regions_filemodel_mfopplot_bubblesplot_ciplot_lollipopplot_mean_mfplot_mfplot_model_mfplot_radarplot_spectraplot_trinucleotideplot_trinucleotide_heatmaprename_columnsrender_reportselect_optimal_lambdasidaksignature_fittingspectra_comparisonspectra_comparison_rpdmmsubtype_dictsubtype_listwrite_excelwrite_mutation_calling_filewrite_mutational_matrixwrite_reference_fastawrite_vcf_from_mut

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurldata.tableDBIDelayedArraydplyrfarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesggdendroggplot2gluegtableherehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplyrangespngpurrrR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangrprojrootRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8VariantAnnotationvctrsviridisLitewithrXMLXVectoryaml

MutSeqR: Error-Corrected Sequencing (ECS) Analysis For Mutagenicity Assessment

Annette E. Dodge, Matthew J. Meier

Rendered fromMutSeqR_introduction.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2026-02-06
Started: 2025-06-26

Readme and manuals

Help Manual

Help pageTopics
Annotate CpG sitesannotate_cpg_sites
BMD modeling using PROASTbmd_proast
BS genome organism dictionaryBS_org_map
Calculate mutation frequencycalculate_mf
Characterize Variantscharacterize_variants
Check that all required columns are present before proceeding with the functioncheck_required_columns
classify_variationclassify_variation
Cleveland Plotcleveland_plot
Hierarchical Clusteringcluster_spectra
A list of reference contexts at different resolutionscontext_list
Values used for denominators in frequency calculationsdenominator_dict
dm_loglik_ridge_stabledm_loglik_ridge_stable
Manages plotting for PROASTf.plot.gui
Plot the PROAST resultsf.plot.result
Run dose-response modeling using PROAST.f.proast
Filter your mutation datafilter_mut
Find the appropriate BS genome for the specified organism and genome.find_BS_genome
Add binomial confidence intervals to mutation frequencies.get_binom_ci
Get mutations at CpG sites.get_cpg_mutations
Get the coordinates of the CpG sites within your genomic regionsget_cpg_regions
A utility function that will return the reference context of a mutationget_ref_of_mut
Get sequence of genomic target regionsget_seq
Derive end coordinates from a VCF objectget_vcf_end_positions
Import tabular mutation dataimport_mut_data
Join Regions Metadataimport_regions_metadata
Import Sample Metadataimport_sample_data
Import a VCF fileimport_vcf_data
Imports the regions fileload_regions_file
Perform linear modelling on mutation frequency for given fixed and random effectsmodel_mf
Dictionary of column name synonyms for required mutation data columnsop
Generate Bubble Plotsplot_bubbles
plot_ciplot_ci
Plot recurrent mutations in a lollipop plot using ggplot2plot_lollipop
Plot the Mean Mutatation Frequencyplot_mean_mf
Plot the Mutation Frequencyplot_mf
Plot your mf modelplot_model_mf
Create a radar plotplot_radar
Plot spectraplot_spectra
Plot the trinucleotide spectrumplot_trinucleotide
Create a heatmap plot of mutation subtype proportions.plot_trinucleotide_heatmap
Populate Sequence contextpopulate_sequence_context
This function prints ASCII art when the package is loadedprint_ascii_art
rdm_fastrdm_fast
Map column names of mutation data to default column names. A utility function that renames columns of mutation data to default columns names.rename_columns
Read configuration file and render R Markdown documentrender_report
Get the reverse complement of a DNA or RNA sequence.reverseComplement
run_penalized_comparisonrun_penalized_comparison
select_optimal_lambdaselect_optimal_lambda
Set up Python environment for MutSeqRsetup_mutseqr_python
Correct p-values for multiple comparisonssidak
Run COSMIC signatures comparison using SigProfilerAssignmentsignature_fitting
Compare the overall mutation spectra between groupsspectra_comparison
spectra_comparison_rpdmmspectra_comparison_rpdmm
Subtype Resolution Dictionarysubtype_dict
A comprehensive list of mutation subtypes at different resolutionssubtype_list
Retrieve the sample column from VCF filesvcf_sample_fix
Write results to Excel tableswrite_excel
Write the mutation calling file to input into the SigProfiler Assignment web application.write_mutation_calling_file
Write a Mutational Matrix to input into the sigprofiler web applicationwrite_mutational_matrix
Write FASTA file of reference sequences.write_reference_fasta
Write mutation_data to a VCF filewrite_vcf_from_mut