Package: MutSeqR 1.1.0

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_1.1.0.tar.gz
MutSeqR_1.1.0.zip(r-4.7)MutSeqR_1.1.0.zip(r-4.6)MutSeqR_1.1.0.zip(r-4.5)
MutSeqR_1.1.0.tgz(r-4.6-any)MutSeqR_1.1.0.tgz(r-4.5-any)
MutSeqR_1.1.0.tar.gz(r-4.7-any)MutSeqR_1.1.0.tar.gz(r-4.6-any)
MutSeqR_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MutSeqR/json (API)

# Install 'MutSeqR' in R:

install.packages('MutSeqR', repos = c('https://bioc.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)

sequencing somaticmutation visualization genomicvariation drivermutation statisticalmethod genetarget

6.80 score 11 stars 8 scripts 41 exports 95 dependencies

Last updated from:99d54af33c. Checks:1 NOTE, 4 ERROR, 5 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	354
linux-devel-x86_64	ERROR	596
source / vignettes	OK	615
linux-release-x86_64	OK	642
macos-release-arm64	OK	403
macos-oldrel-arm64	ERROR	345
windows-devel	ERROR	424
windows-release	OK	444
windows-oldrel	ERROR	513
wasm-release	OK	331

Exports:%>%bmd_proast BS_org_map calculate_mf check_required_columns classify_variation context_list denominator_dict filter_mut find_BS_genome get_binom_ci get_seq import_mut_data import_vcf_data load_regions_file model_mf op plot_bubbles plot_ci plot_lollipop plot_mean_mf plot_mf plot_model_mf plot_radar plot_spectra plot_trinucleotide plot_trinucleotide_heatmap rename_columns render_report select_optimal_lambda sidak signature_fitting spectra_comparison spectra_comparison_rpdmm subtype_dict subtype_list write_excel write_mutation_calling_file write_mutational_matrix write_reference_fasta write_vcf_from_mut

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli codetools cpp11 crayon curl data.table DBI DelayedArray dplyr farver fastmap formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges ggdendro ggplot2 glue gtable here httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plyranges png purrr R6 RColorBrewer RCurl restfulr Rhtslib rjson rlang rprojroot Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 VariantAnnotation vctrs viridisLite withr XML XVector yaml

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

Rendered fromMutSeqR_introduction.Rmdusingknitr::rmarkdown

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

Help page	Topics
Annotate CpG sites	annotate_cpg_sites
BMD modeling using PROAST	bmd_proast
BS genome organism dictionary	BS_org_map
Calculate mutation frequency	calculate_mf
Characterize Variants	characterize_variants
Check that all required columns are present before proceeding with the function	check_required_columns
classify_variation	classify_variation
Cleveland Plot	cleveland_plot
Hierarchical Clustering	cluster_spectra
A list of reference contexts at different resolutions	context_list
Values used for denominators in frequency calculations	denominator_dict
dm_loglik_ridge_stable	dm_loglik_ridge_stable
Manages plotting for PROAST	f.plot.gui
Plot the PROAST results	f.plot.result
Run dose-response modeling using PROAST.	f.proast
Filter your mutation data	filter_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 regions	get_cpg_regions
A utility function that will return the reference context of a mutation	get_ref_of_mut
Get sequence of genomic target regions	get_seq
Derive end coordinates from a VCF object	get_vcf_end_positions
Import tabular mutation data	import_mut_data
Join Regions Metadata	import_regions_metadata
Import Sample Metadata	import_sample_data
Import a VCF file	import_vcf_data
Imports the regions file	load_regions_file
Perform linear modelling on mutation frequency for given fixed and random effects	model_mf
Dictionary of column name synonyms for required mutation data columns	op
Generate Bubble Plots	plot_bubbles
plot_ci	plot_ci
Plot recurrent mutations in a lollipop plot using ggplot2	plot_lollipop
Plot the Mean Mutatation Frequency	plot_mean_mf
Plot the Mutation Frequency	plot_mf
Plot your mf model	plot_model_mf
Create a radar plot	plot_radar
Plot spectra	plot_spectra
Plot the trinucleotide spectrum	plot_trinucleotide
Create a heatmap plot of mutation subtype proportions.	plot_trinucleotide_heatmap
Populate Sequence context	populate_sequence_context
This function prints ASCII art when the package is loaded	print_ascii_art
rdm_fast	rdm_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 document	render_report
Get the reverse complement of a DNA or RNA sequence.	reverseComplement
run_penalized_comparison	run_penalized_comparison
select_optimal_lambda	select_optimal_lambda
Set up Python environment for MutSeqR	setup_mutseqr_python
Correct p-values for multiple comparisons	sidak
Run COSMIC signatures comparison using SigProfilerAssignment	signature_fitting
Compare the overall mutation spectra between groups	spectra_comparison
spectra_comparison_rpdmm	spectra_comparison_rpdmm
Subtype Resolution Dictionary	subtype_dict
A comprehensive list of mutation subtypes at different resolutions	subtype_list
Retrieve the sample column from VCF files	vcf_sample_fix
Write results to Excel tables	write_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 application	write_mutational_matrix
Write FASTA file of reference sequences.	write_reference_fasta
Write mutation_data to a VCF file	write_vcf_from_mut

Package: MutSeqR 1.1.0

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

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)