SomaticSignatures
Somatic Signatures
Bioconductor version: Release (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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization |
| Version | 2.42.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (10.5 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 |
| 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_2.42.0.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 |