MutationalPatterns
This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see MutationalPatterns.
Comprehensive genome-wide analysis of mutational processes
Bioconductor version: 3.8
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 "3.5") 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.
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 | 1.8.0 |
| 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MutationalPatterns_1.8.0.tar.gz |
| Windows Binary | MutationalPatterns_1.8.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | MutationalPatterns_1.8.0.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 3.8 | Source Archive |