SomaticSignatures

DOI: 10.18129/B9.bioc.SomaticSignatures    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see SomaticSignatures.

Somatic Signatures

Bioconductor version: 3.9

The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.

Author: Julian Gehring

Maintainer: Julian Gehring <jg-bioc at gmx.com>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("SomaticSignatures")

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("SomaticSignatures")

 

HTML	R Script	SomaticSignatures
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Clustering, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization
Version	2.20.0
In Bioconductor since	BioC 2.14 (R-3.1) (5.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.1.0), VariantAnnotation, GenomicRanges, NMF
Imports	S4Vectors, IRanges, GenomeInfoDb, Biostrings, ggplot2, ggbio, reshape2, NMF, pcaMethods, Biobase, methods, proxy
LinkingTo
Suggests	testthat, knitr, parallel, BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations, ggdendro, fastICA, sva
SystemRequirements
Enhances
URL	https://github.com/juliangehring/SomaticSignatures
BugReports	https://support.bioconductor.org
Depends On Me
Imports Me	Rariant, YAPSA
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	SomaticSignatures_2.20.0.tar.gz
Windows Binary	SomaticSignatures_2.20.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	SomaticSignatures_2.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SomaticSignatures
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SomaticSignatures
Package Short Url	https://bioconductor.org/packages/SomaticSignatures/
Package Downloads Report	Download Stats