To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MutationalPatterns")

In most cases, you don't need to download the package archive at all.

MutationalPatterns

This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see MutationalPatterns.

Studying patterns in base substitution catalogues

Bioconductor version: 3.4

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

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

Maintainer: Francis Blokzijl <F.Blokzijl at umcutrecht.nl>, Roel Janssen <R.R.E.Janssen-10 at umcutrecht.nl>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MutationalPatterns")

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 1.0.0
In Bioconductor since BioC 3.4 (R-3.3) (0.5 years)
License MIT + file LICENSE
Depends R (>= 3.3.0), NMF (>= 0.20.6), GenomicRanges(>= 1.24.0)
Imports stats, 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(>= 1.8.1), Biostrings(>= 2.40.0), gridExtra (>= 2.2.1)
LinkingTo
Suggests BSgenome(>= 1.40.0), BiocStyle(>= 2.0.3), biomaRt(>= 2.28.0), BSgenome.Hsapiens.UCSC.hg19(>= 1.4.0), TxDb.Hsapiens.UCSC.hg19.knownGene(>= 3.2.2), rtracklayer(>= 1.32.2)
SystemRequirements
Enhances
URL https://github.com/CuppenResearch/MutationalPatterns
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source MutationalPatterns_1.0.0.tar.gz
Windows Binary MutationalPatterns_1.0.0.zip
Mac OS X 10.9 (Mavericks) MutationalPatterns_1.0.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/MutationalPatterns/tree/release-3.4
Package Short Url http://bioconductor.org/packages/MutationalPatterns/
Package Downloads Report Download Stats

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