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SomaticSignatures

Somatic Signatures

Bioconductor version: Release (3.17)

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 "4.3") 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

Details

biocViews Clustering, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization
Version 2.36.0
In Bioconductor since BioC 2.14 (R-3.1) (9.5 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
Linking To
Suggests testthat, knitr, parallel, BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations, ggdendro, fastICA, sva
System Requirements
Enhances
URL https://github.com/juliangehring/SomaticSignatures
Bug Reports https://support.bioconductor.org
See More
Depends On Me
Imports Me YAPSA
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package SomaticSignatures_2.36.0.tar.gz
Windows Binary SomaticSignatures_2.36.0.zip
macOS Binary (x86_64) SomaticSignatures_2.36.0.tgz
macOS Binary (arm64) SomaticSignatures_2.35.0.tgz
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