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

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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/

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