supersigs

DOI: 10.18129/B9.bioc.supersigs    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see supersigs.

Supervised mutational signatures

Bioconductor version: 3.15

Generate SuperSigs (supervised mutational signatures) from single nucleotide variants in the cancer genome. Functions included in the package allow the user to learn supervised mutational signatures from their data and apply them to new data. The methodology is based on the one described in Afsari (2021, ELife).

Author: Albert Kuo [aut, cre] , Yifan Zhang [aut], Bahman Afsari [aut], Cristian Tomasetti [aut]

Maintainer: Albert Kuo <albertkuo at jhu.edu>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("supersigs")

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("supersigs")

 

HTML	R Script	Using supersigs
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, FeatureExtraction, Regression, Sequencing, Software, SomaticMutation, WholeGenome
Version	1.4.0
In Bioconductor since	BioC 3.13 (R-4.1) (1.5 years)
License	GPL-3
Depends	R (>= 4.1)
Imports	assertthat, caret, dplyr, tidyr, rsample, methods, rlang, utils, Biostrings, stats, SummarizedExperiment
LinkingTo
Suggests	BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, testthat, VariantAnnotation
SystemRequirements
Enhances
URL	https://tomasettilab.github.io/supersigs/
BugReports	https://github.com/TomasettiLab/supersigs/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	supersigs_1.4.0.tar.gz
Windows Binary	supersigs_1.4.0.zip
macOS Binary (x86_64)	supersigs_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/supersigs
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/supersigs
Package Short Url	https://bioconductor.org/packages/supersigs/
Package Downloads Report	Download Stats