MutationalPatterns
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see MutationalPatterns.
Comprehensive genome-wide analysis of mutational processes
Bioconductor version: 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("MutationalPatterns")):
Installation
To install this package, start R (version "4.4") 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 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Genetics, Software, SomaticMutation |
| Version | 3.14.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (8 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | RESOLVE |
| Suggests Me | SUITOR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MutationalPatterns_3.14.0.tar.gz |
| Windows Binary (x86_64) | MutationalPatterns_3.14.0.zip |
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/MutationalPatterns/ |
| Package Short Url | https://bioconductor.org/packages/MutationalPatterns/ |
| Package Downloads Report | Download Stats |