DOI: 10.18129/B9.bioc.signeR  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see signeR.

Empirical Bayesian approach to mutational signature discovery

Bioconductor version: 3.17

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>

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biocViews GenomicVariation, Software, SomaticMutation, StatisticalMethod, Visualization
Version 2.2.1
In Bioconductor since BioC 3.4 (R-3.3) (7 years)
License GPL-3
Depends R (>= 3.0.2), VariantAnnotation, NMF
Imports BiocGenerics, Biostrings, class, grDevices, GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats, utils, PMCMRplus, parallel, pvclust, ppclust, clue, survival, maxstat, survivalAnalysis, future, VGAM, MASS, kknn, glmnet, e1071, randomForest, ada, future.apply, ggplot2, pROC, pheatmap, RColorBrewer, listenv, reshape2, scales, survminer, dplyr, ggpubr, cowplot, tibble, readr, shiny, shinydashboard, shinycssloaders, shinyWidgets, bsplus, DT, magrittr, tidyr, BiocFileCache, proxy, rtracklayer, BSgenome
LinkingTo Rcpp, RcppArmadillo (>= 0.7.100)
Suggests knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, rmarkdown
SystemRequirements C++11
Depends On Me
Imports Me
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