SomaticSignatures
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see SomaticSignatures.
Somatic Signatures
Bioconductor version: 3.9
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("SomaticSignatures")):
Installation
To install this package, start R (version "3.6") 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 | 2.20.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (10 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.1.0), 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 | Rariant, 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_2.20.0.tar.gz |
| Windows Binary | SomaticSignatures_2.20.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | SomaticSignatures_2.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SomaticSignatures |
| Source Repository (Developer Access) | git clone [email protected]: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 3.9 | Source Archive |