signeR
Empirical Bayesian approach to mutational signature discovery
Bioconductor version: Release (3.19)
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("signeR")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | GenomicVariation, Software, SomaticMutation, StatisticalMethod, Visualization |
| Version | 2.6.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (8 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
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | signeR_2.6.0.tar.gz |
| Windows Binary (x86_64) | signeR_2.6.0.zip |
| macOS Binary (x86_64) | signeR_2.6.0.tgz |
| macOS Binary (arm64) | signeR_2.6.0.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 |