MutSeqR
This is the released version of MutSeqR; for the devel version, see MutSeqR.
Analysis of Error-Corrected Sequencing Data for Mutation Detection
Bioconductor version: Release (3.23)
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("MutSeqR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MutSeqR")
For older versions of R, please refer to the appropriate Bioconductor release.
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 | |
| LICENSE | Text |
Details
| biocViews | DriverMutation, GeneTarget, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | MIT + file LICENSE |
| 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 |
| System Requirements | |
| URL | https://ehsrb-bsrse-bioinformatics.github.io/MutSeqR/ |
| Bug Reports | https://github.com/EHSRB-BSRSE-Bioinformatics/MutSeqR/issues |
See More
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow 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 (big-sur-x86_64) | MutSeqR_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | MutSeqR_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MutSeqR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MutSeqR |
| Bioc Package Browser | https://code.bioconductor.org/browse/MutSeqR/ |
| Package Short Url | https://bioconductor.org/packages/MutSeqR/ |
| Package Downloads Report | Download Stats |