MutationalPatterns

DOI: 10.18129/B9.bioc.MutationalPatterns    

Comprehensive genome-wide analysis of mutational processes

Bioconductor version: Release (3.12)

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 [cre] , Ruben van Boxtel [aut, cph] , Edwin Cuppen [aut]

Maintainer: Rurika Oka <R.Oka at prinsesmaximacentrum.nl>

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

Installation

To install this package, start R (version "4.0") 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")

 

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

Details

biocViews Genetics, Software, SomaticMutation
Version 3.0.1
In Bioconductor since BioC 3.4 (R-3.3) (4 years)
License MIT + file LICENSE
Depends R (>= 4.0.0), 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)
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/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_3.0.1.tar.gz
Windows Binary MutationalPatterns_3.0.1.zip
macOS 10.13 (High Sierra) MutationalPatterns_3.0.1.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
Old Source Packages for BioC 3.12 Source Archive

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