Package ‘ signeR ’ April 26 , 2017

April 26, 2017 Type Package Title Empirical Bayesian approach to mutational signature discovery Version 1.2.0 Author Rafael Rosales, Rodrigo Drummond, Renan Valieris, Israel Tojal da Silva Maintainer Renan Valieris Description 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. License GPL-3 Imports BiocGenerics, Biostrings, BSgenome (>= 1.36.3), class, graphics, grDevices, GenomicRanges, nloptr, methods, NMF, stats, utils, VariantAnnotation, PMCMR LinkingTo Rcpp, RcppArmadillo (>= 0.7.100) SystemRequirements C++11 NeedsCompilation yes ByteCompile TRUE biocViews GenomicVariation, SomaticMutation, StatisticalMethod, Visualization Suggests knitr, rtracklayer, BSgenome.Hsapiens.UCSC.hg19 VignetteBuilder knitr