MutationalPatterns

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see MutationalPatterns.

Comprehensive genome-wide analysis of mutational processes

Bioconductor version: 3.7

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

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

To install this package, start R (version "3.5") 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.

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

Version 1.6.1

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

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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