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MutationalPatterns

This is the development version of MutationalPatterns; for the stable release version, see MutationalPatterns.

Comprehensive genome-wide analysis of mutational processes


Bioconductor version: Development (3.19)

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 [ctb] , Mark van Roosmalen [cre], Ruben van Boxtel [aut, cph] , Edwin Cuppen [aut]

Maintainer: Mark van Roosmalen <vanBoxtelBioinformatics at prinsesmaximacentrum.nl>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("MutationalPatterns")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews Genetics, Software, SomaticMutation
Version 3.13.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License MIT + file LICENSE
Depends R (>= 4.2.0), 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), RColorBrewer, methods
System Requirements
URL https://doi.org/doi:10.1186/s12864-022-08357-3
See More
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
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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/
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