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signeR

This is the development version of signeR; for the stable release version, see signeR.

Empirical Bayesian approach to mutational signature discovery

Bioconductor version: Development (3.18)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 2.3.0
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_2.3.0.tar.gz
Windows Binary signeR_2.3.0.zip
macOS Binary (x86_64) signeR_2.3.0.tgz
macOS Binary (arm64) signeR_2.3.0.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