MutationalPatterns

DOI: 10.18129/B9.bioc.MutationalPatterns    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see MutationalPatterns.

Comprehensive genome-wide analysis of mutational processes

Bioconductor version: 3.9

An extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution catalogs.

Author: Francis Blokzijl, Roel Janssen, Ruben van Boxtel, Edwin Cuppen

Maintainer: Roel Janssen <R.R.E.Janssen-10 at umcutrecht.nl>, Francis Blokzijl <f.blokzijl at hubrecht.eu>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	Genetics, Software, SomaticMutation
Version	1.10.0
In Bioconductor since	BioC 3.4 (R-3.3) (3 years)
License	MIT + file LICENSE
Depends	R (>= 3.4.0), GenomicRanges(>= 1.24.0), NMF (>= 0.20.6)
Imports	stats, parallel, S4Vectors, BiocGenerics(>= 0.18.0), VariantAnnotation(>= 1.18.1), reshape2 (>= 1.4.1), plyr (>= 1.8.3), ggplot2 (>= 2.1.0), pracma (>= 1.8.8), SummarizedExperiment(>= 1.2.2), IRanges(>= 2.6.0), GenomeInfoDb(>= 1.12.0), Biostrings(>= 2.40.0), ggdendro (>= 0.1-20), cowplot (>= 0.9.2)
LinkingTo
Suggests	BSgenome(>= 1.40.0), BSgenome.Hsapiens.1000genomes.hs37d5(>= 0.99.1), 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), testthat
SystemRequirements
Enhances
URL	https://doi.org/10.1186/s13073-018-0539-0
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	MutationalPatterns_1.10.0.tar.gz
Windows Binary	MutationalPatterns_1.10.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	MutationalPatterns_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MutationalPatterns
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MutationalPatterns
Package Short Url	https://bioconductor.org/packages/MutationalPatterns/
Package Downloads Report	Download Stats