MutSeqRData
This is the development version of MutSeqRData; to use it, please install the devel version of Bioconductor.
Experimental Data for MutSeqR Examples
Bioconductor version: Development (3.23)
Experimental data for use with the MutSeqR vignette and examples. This dataset is taken from LeBlanc et al., 2022. 24 MutaMouse animals were exposed to one of three doses of benzo[a]pyrene or a vehicle control for 28 days by oral gavage. 28 days after the end of the exposure, bone marrow of the femurs was harvested from euthanized animals. DNA extraction was conducted via DNeasy Blood and Tissue kit. DNA samples were sequenced using TwinStrand's Duplex Sequencing on the Mouse Mutagenesis Panel at > 10,000 depth. The Mouse Mutagenesis Panel comprises 20 2.4kb genomic targets with one located on each mouse autosome (two on chromosome 1). Pre-processing of sequence reads was redone since publication using an updated version of TwinStrand's Mutagenesis App (v. 3.20.1) which produced tabular mutation data files for each sample. Data contained herein are only those required for running MutSeqR examples and vignette.
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]
Maintainer: Matthew J. Meier <matthew.meier at hc-sc.gc.ca>
citation("MutSeqRData")):
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("MutSeqRData")
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("MutSeqRData")| SUpporting data for the MutSeqR package | HTML | R Script |
| Reference Manual |
Details
| biocViews | ExperimentData, ExperimentHub, Genome, Mus_musculus_Data, SequencingData, Somatic |
| Version | 0.99.4 |
| License | MIT + file LICENSE |
| Depends | R (>= 3.5.0) |
| Imports | |
| System Requirements | |
| URL | https://github.com/EHSRB-BSRSE-Bioinformatics/MutSeqRData/ |
| Bug Reports | https://github.com/EHSRB-BSRSE-Bioinformatics/MutSeqRData/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown |
| 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 | MutSeqRData_0.99.4.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/MutSeqRData |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MutSeqRData |
| Package Short Url | https://bioconductor.org/packages/MutSeqRData/ |
| Package Downloads Report | Download Stats |