MutSeqR
Analysis of Error-Corrected Sequencing Data for Mutation Detection
Bioconductor version: 3.23 · Package version: 1.0.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MutSeqR")Details
| Maintainer | Matthew J. Meier <matthew.meier@hc-sc.gc.ca> |
| Author | Annette E. Dodge [aut] (ORCID: <https://orcid.org/0000-0002-0446-9055>), Andrew Williams [aut] (ORCID: <https://orcid.org/0000-0002-7637-7686>), Danielle P.M. LeBlanc [aut] (ORCID: <https://orcid.org/0000-0002-3847-8371>), David M. Schuster [aut] (ORCID: <https://orcid.org/0009-0001-6316-4358>), Elena Esina [aut] (ORCID: <https://orcid.org/0009-0002-3443-378X>), Clint C. Valentine [aut] (ORCID: <https://orcid.org/0000-0001-5630-7368>), Jesse J. Salk [aut] (ORCID: <https://orcid.org/0000-0002-7804-0550>), Alexander Y. Maslov [aut], Christopher Bradley [aut], Carole L. Yauk [aut] (ORCID: <https://orcid.org/0000-0002-6725-3454>), Francesco Marchetti [aut] (ORCID: <https://orcid.org/0000-0002-9435-4867>), Matthew J. Meier [aut, cre] (ORCID: <https://orcid.org/0000-0001-8199-8754>), Geronimo Matteo [ctb] (ORCID: <https://orcid.org/0000-0003-0819-4471>), Health Canada's Genomics Research and Development Initiative [fnd], Canada Research Chairs Program [fnd] (CRC-2020-00060), Burroughs Wellcome Fund [fnd] |
| License | MIT + file LICENSE |
| URL | https://ehsrb-bsrse-bioinformatics.github.io/MutSeqR/ |
| Bug Reports | https://github.com/EHSRB-BSRSE-Bioinformatics/MutSeqR/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DriverMutation, GeneTarget, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization |
| Package Short Url | https://bioconductor.org/packages/MutSeqR/ |
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 1.0.0, https://bioconductor.org/packages/MutSeqR.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the installation instructions to use this package in your R session.
| Source package | MutSeqR_1.0.0.tar.gz |
| Windows binary (x86_64) | MutSeqR_1.0.0.zip |
| macOS binary (arm64) | MutSeqR_1.0.0.tgz |
| macOS binary (x86_64) | MutSeqR_1.0.0.tgz |
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