SomaticSignatures

This is thereleased version of SomaticSignatures; for the devel version, seeSomaticSignatures.

Somatic Signatures

DOI: 10.18129/B9.bioc.SomaticSignatures

Bioconductor version: Release (3.22)

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, entercitation("SomaticSignatures")):

Installation

To install this package, start R (version "4.5") and enter:

if (!require("BiocManager", quietly = TRUE))    install.packages("BiocManager")BiocManager::install("SomaticSignatures")

For older versions of R, please refer to the appropriateBioconductor 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	2.46.0
In Bioconductor since	BioC 2.14 (R-3.1) (11.5 years)
License	MIT + fileLICENSE
Depends	R (>= 3.5.0),VariantAnnotation,GenomicRanges,NMF
Imports	S4Vectors,IRanges,Seqinfo,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,GenomeInfoDb,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

FollowInstallation instructions to use this package in your R session.

Source Package	SomaticSignatures_2.46.0.tar.gz
Windows Binary (x86_64)	SomaticSignatures_2.46.0.zip
macOS Binary (x86_64)	SomaticSignatures_2.46.0.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

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SomaticSignatures