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Empirical Bayesian approach to mutational signature discovery

Bioconductor version: Release (3.19)

The signeR package provides an empirical Bayesian approach to mutational signature discovery. It is designed to analyze single nucleotide variation (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, Alexandre Defelicibus, Israel Tojal da Silva

Maintainer: Renan Valieris <renan.valieris at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

signeR HTML R Script
signeRFlow HTML R Script
Reference Manual PDF


biocViews GenomicVariation, Software, SomaticMutation, StatisticalMethod, Visualization
Version 2.6.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 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
System Requirements C++11
See More
Suggests knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, rmarkdown
Linking To Rcpp, RcppArmadillo (>= 0.7.100)
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Package Archives

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

Source Package signeR_2.6.0.tar.gz
Windows Binary
macOS Binary (x86_64) signeR_2.6.0.tgz
macOS Binary (arm64) signeR_2.6.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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