To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("SomaticSignatures")

In most cases, you don't need to download the package archive at all.

SomaticSignatures

 

Somatic Signatures

Bioconductor version: Release (3.1)

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 (EMBL Heidelberg)

Maintainer: Julian Gehring <julian.gehring at embl.de>

Citation (from within R, enter citation("SomaticSignatures")):

Installation

To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("SomaticSignatures")

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

Details

biocViews Clustering, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization
Version 2.4.7
In Bioconductor since BioC 2.14 (R-3.1) (1.5 years)
License GPL-3
Depends R (>= 3.1.0), VariantAnnotation, GenomicRanges
Imports S4Vectors, IRanges, GenomeInfoDb, Biostrings, ggplot2, ggbio, reshape2, NMF, pcaMethods, Biobase, methods, proxy
LinkingTo
Suggests testthat, knitr, parallel, BSgenome.Hsapiens.UCSC.hg19, SomaticCancerAlterations, ggdendro, fastICA, sva
SystemRequirements
Enhances
URL http://bioconductor.org/packages/release/bioc/html/SomaticSignatures.html https://github.com/julian-gehring/SomaticSignatures-release
Depends On Me
Imports Me Rariant
Suggests Me
Build Report  

Package Archives

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

Package Source SomaticSignatures_2.4.7.tar.gz
Windows Binary SomaticSignatures_2.4.7.zip
Mac OS X 10.6 (Snow Leopard) SomaticSignatures_2.4.7.tgz
Mac OS X 10.9 (Mavericks) SomaticSignatures_2.4.7.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/SomaticSignatures/tree/release-3.1
Package Short Url http://bioconductor.org/packages/SomaticSignatures/
Package Downloads Report Download Stats

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