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Bioconductor - signeR (development version)

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 (3.22)

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")

# 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")
Details biocViews GenomicVariation, Software, SomaticMutation, StatisticalMethod, Visualization Version 2.11.0 In Bioconductor since BioC 3.4 (R-3.3) (8.5 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 URL https://github.com/TojalLab/signeR See More Package Archives

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

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