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SomaticSignatures

Somatic Signatures


Bioconductor version: Release (3.19)

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

Details

biocViews Clustering, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization
Version 2.40.0
In Bioconductor since BioC 2.14 (R-3.1) (10 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
See More
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_2.40.0.tar.gz
Windows Binary SomaticSignatures_2.40.0.zip (64-bit only)
macOS Binary (x86_64) SomaticSignatures_2.40.0.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
Old Source Packages for BioC 3.19 Source Archive