MutationalPatterns

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see MutationalPatterns.

Comprehensive genome-wide analysis of mutational processes


Bioconductor version: 3.11

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: Rurika Oka <R.Oka at prinsesmaximacentrum.nl>, Freek Manders <F.M.Manders at prinsesmaximacentrum.nl>

Citation (from within R, enter citation("MutationalPatterns")):

Installation

To install this package, start R (version "4.0") 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")
Introduction to MutationalPatterns PDF R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Genetics, Software, SomaticMutation
Version 2.0.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 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)
System Requirements
URL https://doi.org/10.1186/s13073-018-0539-0
See More
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
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Package Archives

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

Source Package MutationalPatterns_2.0.0.tar.gz
Windows Binary MutationalPatterns_2.0.0.zip
macOS 10.13 (High Sierra) MutationalPatterns_2.0.0.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 3.11 Source Archive