MutSeqR
This is the development version of MutSeqR; to use it, please install the devel version of Bioconductor.
Analysis of Error-Corrected Sequencing Data for Mutation Detection
Bioconductor version: Development (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")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 |
Details
| biocViews | DriverMutation, GeneTarget, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization |
| Version | 0.99.8 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| 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, stringr, SummarizedExperiment, tidyr, 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_0.99.8.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |