SomaticSignatures

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see SomaticSignatures.

Somatic Signatures

Bioconductor version: 3.20

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>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("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")

SomaticSignatures	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization
Version	2.42.0
In Bioconductor since	BioC 2.14 (R-3.1) (11 years)
License	MIT + file LICENSE
Depends	R (>= 3.5.0), VariantAnnotation, GenomicRanges, NMF
Imports	S4Vectors, IRanges, GenomeInfoDb, Biostrings, ggplot2, ggbio, reshape2, NMF, pcaMethods, Biobase, methods, proxy
System Requirements
URL	https://github.com/juliangehring/SomaticSignatures
Bug Reports	https://support.bioconductor.org

Suggests	testthat, knitr, parallel, BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations, ggdendro, fastICA, sva
Linking To
Enhances
Depends On Me
Imports Me	YAPSA
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	SomaticSignatures_2.42.0.tar.gz
Windows Binary (x86_64)	SomaticSignatures_2.42.0.zip
macOS Binary (x86_64)	SomaticSignatures_2.42.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/SomaticSignatures
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SomaticSignatures
Bioc Package Browser	https://code.bioconductor.org/browse/SomaticSignatures/
Package Short Url	https://bioconductor.org/packages/SomaticSignatures/
Package Downloads Report	Download Stats