SomaticSignatures
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see SomaticSignatures.
Somatic Signatures
Bioconductor version: 3.7
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 "3.5") 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 | 2.16.0 |
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_2.16.0.tar.gz |
Windows Binary | SomaticSignatures_2.16.0.zip |
Mac OS X 10.11 (El Capitan) | SomaticSignatures_2.16.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/SomaticSignatures |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SomaticSignatures |
Package Short Url | https://bioconductor.org/packages/SomaticSignatures/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.7 | Source Archive |