MutationalPatterns

DOI: 10.18129/B9.bioc.MutationalPatterns  

Comprehensive genome-wide analysis of mutational processes

Bioconductor version: Release (3.17)

Mutational processes leave characteristic footprints in genomic DNA. This package provides a comprehensive set of flexible functions that allows researchers to easily evaluate and visualize a multitude of mutational patterns in base substitution catalogues of e.g. healthy samples, tumour samples, or DNA-repair deficient cells. The package covers a wide range of patterns including: mutational signatures, transcriptional and replicative strand bias, lesion segregation, genomic distribution and association with genomic features, which are collectively meaningful for studying the activity of mutational processes. The package works with single nucleotide variants (SNVs), insertions and deletions (Indels), double base substitutions (DBSs) and larger multi base substitutions (MBSs). The package provides functionalities for both extracting mutational signatures de novo and determining the contribution of previously identified mutational signatures on a single sample level. MutationalPatterns integrates with common R genomic analysis workflows and allows easy association with (publicly available) annotation data.

Author: Freek Manders [aut] , Francis Blokzijl [aut] , Roel Janssen [aut] , Jurrian de Kanter [ctb] , Rurika Oka [ctb] , Mark van Roosmalen [cre], Ruben van Boxtel [aut, cph] , Edwin Cuppen [aut]

Maintainer: Mark van Roosmalen <vanBoxtelBioinformatics at prinsesmaximacentrum.nl>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MutationalPatterns")

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("MutationalPatterns")

 

HTML	R Script	Introduction to MutationalPatterns
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Genetics, Software, SomaticMutation
Version	3.10.0
In Bioconductor since	BioC 3.4 (R-3.3) (7 years)
License	MIT + file LICENSE
Depends	R (>= 4.2.0), GenomicRanges(>= 1.24.0), NMF (>= 0.20.6)
Imports	stats, S4Vectors, BiocGenerics(>= 0.18.0), BSgenome(>= 1.40.0), VariantAnnotation(>= 1.18.1), dplyr (>= 0.8.3), tibble (>= 2.1.3), purrr (>= 0.3.2), tidyr (>= 1.0.0), stringr (>= 1.4.0), magrittr (>= 1.5), ggplot2 (>= 2.1.0), pracma (>= 1.8.8), IRanges(>= 2.6.0), GenomeInfoDb(>= 1.12.0), Biostrings(>= 2.40.0), ggdendro (>= 0.1-20), cowplot (>= 0.9.2), ggalluvial (>= 0.12.2), RColorBrewer, methods
LinkingTo
Suggests	BSgenome.Hsapiens.UCSC.hg19(>= 1.4.0), BiocStyle(>= 2.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene(>= 3.2.2), biomaRt(>= 2.28.0), gridExtra (>= 2.2.1), rtracklayer(>= 1.32.2), ccfindR(>= 1.6.0), GenomicFeatures, AnnotationDbi, testthat, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://doi.org/doi:10.1186/s12864-022-08357-3
Depends On Me
Imports Me	RESOLVE
Suggests Me	SUITOR
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	MutationalPatterns_3.10.0.tar.gz
Windows Binary	MutationalPatterns_3.10.0.zip (64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64)	MutationalPatterns_3.9.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MutationalPatterns
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MutationalPatterns
Bioc Package Browser	https://code.bioconductor.org/browse/MutationalPatterns/
Package Short Url	https://bioconductor.org/packages/MutationalPatterns/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive