signeR

Empirical Bayesian approach to mutational signature discovery

Bioconductor version: Release (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 accamargo.org.br>

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

Installation

To install this package, start R (version "4.3") 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
signeRFlow	HTML	R Script
Reference Manual	PDF
NEWS	Text

Details

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
Linking To	Rcpp, RcppArmadillo (>= 0.7.100)
Suggests	knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, rmarkdown
System Requirements	C++11
Enhances
URL	https://github.com/rvalieris/signeR

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Build Report

Package Archives

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

Source Package	signeR_2.2.1.tar.gz
Windows Binary	signeR_2.2.1.zip
macOS Binary (x86_64)	signeR_2.2.1.tgz
macOS Binary (arm64)	signeR_2.2.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/signeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/signeR
Bioc Package Browser	https://code.bioconductor.org/browse/signeR/
Package Short Url	https://bioconductor.org/packages/signeR/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive