MutSeqR
This is the development version of MutSeqR; for the stable release version, see MutSeqR.
All Bioconductor versions of MutSeqR
3.24 (devel), 3.23 (release)
Analysis of Error-Corrected Sequencing Data for Mutation Detection
Bioconductor version: 3.24 · Package version: 1.1.0
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.
Author: 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] (CRC-2020-00060), Burroughs Wellcome Fund [fnd]
Maintainer: Matthew J. Meier <matthew.meier at hc-sc.gc.ca>
Citation
From within R, enter citation("MutSeqR"):
Annette E. Dodge, Andrew Williams, Danielle P.M. LeBlanc, David M. Schuster, Elena Esina, Clint C. Valentine, Jesse J. Salk, Alexander Y. Maslov, Christopher Bradley, Carole L. Yauk, Francesco Marchetti, Matthew J. Meier. MutSeqR: Analysis of Error-Corrected Sequencing Data for Mutation Detection. doi:10.18129/B9.bioc.MutSeqR, R package version 1.1.0, https://bioconductor.org/packages/MutSeqR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("MutSeqR")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.1.0 |
| License | MIT + file LICENSE |
| URL | https://ehsrb-bsrse-bioinformatics.github.io/MutSeqR/ |
| Bug Reports | https://github.com/EHSRB-BSRSE-Bioinformatics/MutSeqR/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.23 (R-4.6) (less than a year) |
| Downloads rank | 2216 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DriverMutation, GeneTarget, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization |
| Package Short Url | https://bioconductor.org/packages/MutSeqR/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MutSeqR")| MutSeqR: Error-Corrected Sequencing (ECS) Analysis For Mutagenicity Assessment | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | MutSeqR_1.1.0.tar.gz |
| Windows binary (x86_64) | MutSeqR_1.1.0.zip |
| macOS binary (arm64) | MutSeqR_1.1.0.tgz |
| macOS binary (x86_64) | MutSeqR_1.1.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MutSeqR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MutSeqR |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.5.0)
Imports: BiocGenerics, Biostrings, BSgenome, data.table, dplyr, GenomicRanges, ggplot2, here, IRanges, ggdendro, magrittr, methods, plyranges, rlang, S4Vectors, Seqinfo, stats, stringr, SummarizedExperiment, tibble, tidyr, utils, VariantAnnotation
Suggests: binom, BiocManager, BiocStyle, bs4Dash, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, car, colorspace, dendsort, doBy, DT, ExperimentHub, fmsb, fs, ggrepel, gtools, htmltools, httr, knitr, lme4, magick, MutSeqRData, openxlsx, packcircles, patchwork, RColorBrewer, reticulate, rmarkdown, scales, shiny, testthat (>= 3.0.0), trackViewer, withr, yaml, xml2