MutationalPatterns
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see MutationalPatterns.
Comprehensive genome-wide analysis of mutational processes
Bioconductor version: 3.9
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: Roel Janssen <R.R.E.Janssen-10 at umcutrecht.nl>, Francis Blokzijl <f.blokzijl at hubrecht.eu>
citation("MutationalPatterns")
):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | Genetics, Software, SomaticMutation |
Version | 1.10.0 |
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 | |
URL | https://doi.org/10.1186/s13073-018-0539-0 |
See More
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 |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
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Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | MutationalPatterns_1.10.0.tar.gz |
Windows Binary | MutationalPatterns_1.10.0.zip (32- & 64-bit) |
Mac OS X 10.11 (El Capitan) | MutationalPatterns_1.10.0.tgz |
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 |
Old Source Packages for BioC 3.9 | Source Archive |