SomaticSignatures

DOI: 10.18129/B9.bioc.SomaticSignatures    

Somatic Signatures

Bioconductor version: Release (3.6)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SomaticSignatures")

Documentation

HTML	R Script	SomaticSignatures
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Clustering, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization
Version	2.14.0
In Bioconductor since	BioC 2.14 (R-3.1) (4 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
Build Report

Package Archives

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

Source Package	SomaticSignatures_2.14.0.tar.gz
Windows Binary	SomaticSignatures_2.14.0.zip
Mac OS X 10.11 (El Capitan)	SomaticSignatures_2.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SomaticSignatures
Package Short Url	http://bioconductor.org/packages/SomaticSignatures/
Package Downloads Report	Download Stats