signeR

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see signeR.

Empirical Bayesian approach to mutational signature discovery

Bioconductor version: 3.21

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")):

Installation

To install this package, start R (version "4.5") 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 2.10.0

In Bioconductor since BioC 3.4 (R-3.3) (9 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

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

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Package Archives

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

Source Package signeR_2.10.0.tar.gz

Windows Binary (x86_64) signeR_2.10.0.zip

macOS Binary (x86_64) signeR_2.10.0.tgz

macOS Binary (arm64) signeR_2.10.0.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/

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