signeR

This is the released version of signeR; for the devel version, see signeR.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4

Empirical Bayesian approach to mutational signature discovery

Bioconductor version: Release (3.23)

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 accamargo.org.br>

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

Rafael Rosales, Rodrigo Drummond, Renan Valieris, Alexandre Defelicibus, Israel Tojal da Silva. signeR: Empirical Bayesian approach to mutational signature discovery. doi:10.18129/B9.bioc.signeR, R package version 2.14.0, https://bioconductor.org/packages/signeR.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GenomicVariation, Software, SomaticMutation, StatisticalMethod, Visualization
Version	2.14.0
In Bioconductor since	BioC 3.4 (R-3.3) (10 years)
License	GPL-3
Depends	R (>= 4.1.0), NMF
Imports	BiocGenerics, Biostrings, class, grDevices, GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats, utils, PMCMRplus, parallel, pvclust, ppclust, clue, survival, maxstat, 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, broom, VariantAnnotation
System Requirements	C++14
URL	https://github.com/TojalLab/signeR

Suggests	knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, rmarkdown
Linking To	Rcpp, RcppArmadillo (>= 0.7.100)
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	signeR_2.14.0.tar.gz
Windows Binary (x86_64)	signeR_2.14.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	signeR_2.14.0.tgz
macOS Binary (sonoma-arm64)	signeR_2.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/signeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/signeR
Package Short Url	https://bioconductor.org/packages/signeR/
Package Downloads Report	Download Stats