signeR

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see signeR.

Empirical Bayesian approach to mutational signature discovery


Bioconductor version: 3.7

The signeR package provides an empirical Bayesian approach to mutational signature discovery. It is designed to analyze single nucleotide variaton (SNV) counts in cancer genomes, but can also be applied to other features as well. Functionalities to characterize signatures or genome samples according to exposure patterns are also provided.

Author: Rafael Rosales, Rodrigo Drummond, Renan Valieris, Israel Tojal da Silva

Maintainer: Renan Valieris <renan.valieris at accamargo.org.br>

Citation (from within R, enter citation("signeR")):

Installation

To install this package, start R (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("signeR")

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("signeR")
signeR HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GenomicVariation, Software, SomaticMutation, StatisticalMethod, Visualization
Version 1.6.1
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL-3
Depends VariantAnnotation, NMF
Imports BiocGenerics, Biostrings, class, graphics, grDevices, GenomicRanges, nloptr, methods, stats, utils, PMCMR
System Requirements C++11
URL https://github.com/rvalieris/signeR
See More
Suggests knitr, rtracklayer, BSgenome.Hsapiens.UCSC.hg19
Linking To Rcpp, RcppArmadillo (>= 0.7.100)
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package signeR_1.6.1.tar.gz
Windows Binary signeR_1.6.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) signeR_1.6.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/signeR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/signeR
Package Short Url https://bioconductor.org/packages/signeR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive