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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SomaticSignatures")
In most cases, you don't need to download the package archive at all.
SomaticSignatures
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This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see SomaticSignatures.
Somatic Signatures
Bioconductor version: 3.2
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 (EMBL Heidelberg)
Maintainer: Julian Gehring <jg-bioc at gmx.com>
Citation (from within R,
enter citation("SomaticSignatures")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SomaticSignatures")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SomaticSignatures")
| HTML | SomaticSignatures | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Clustering, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization |
| Version | 2.6.1 |
| In Bioconductor since | BioC 2.14 (R-3.1) (2 years) |
| License | GPL-3 |
| Depends | R (>= 3.1.0), VariantAnnotation, GenomicRanges |
| Imports | S4Vectors, IRanges, GenomeInfoDb, Biostrings, ggplot2, ggbio, reshape2, NMF, pcaMethods, Biobase, methods, proxy |
| LinkingTo | |
| Suggests | testthat, knitr, parallel, BSgenome.Hsapiens.UCSC.hg19, SomaticCancerAlterations, ggdendro, fastICA, sva |
| SystemRequirements | |
| Enhances | |
| URL | http://bioconductor.org/packages/release/bioc/html/SomaticSignatures.html https://github.com/julian-gehring/SomaticSignatures-release |
| Depends On Me | |
| Imports Me | Rariant |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | SomaticSignatures_2.6.1.tar.gz |
| Windows Binary | SomaticSignatures_2.6.1.zip |
| Mac OS X 10.6 (Snow Leopard) | SomaticSignatures_2.6.0.tgz |
| Mac OS X 10.9 (Mavericks) | SomaticSignatures_2.6.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/SomaticSignatures/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/SomaticSignatures/ |
| Package Downloads Report | Download Stats |
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