supersigs

Supervised mutational signatures

Bioconductor version: Release (3.17)

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>

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

Installation

To install this package, start R (version "4.3") 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")

Using supersigs	HTML	R Script
Reference Manual	PDF
NEWS	Text

Details

biocViews	Classification, FeatureExtraction, Regression, Sequencing, Software, SomaticMutation, WholeGenome
Version	1.8.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 years)
License	GPL-3
Depends	R (>= 4.1)
Imports	assertthat, caret, dplyr, tidyr, rsample, methods, rlang, utils, Biostrings, stats, SummarizedExperiment
Linking To
Suggests	BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, testthat, VariantAnnotation
System Requirements
Enhances
URL	https://tomasettilab.github.io/supersigs/
Bug Reports	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_1.8.0.tar.gz
Windows Binary	supersigs_1.8.0.zip
macOS Binary (x86_64)	supersigs_1.8.0.tgz
macOS Binary (arm64)	supersigs_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/supersigs
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/supersigs
Bioc Package Browser	https://code.bioconductor.org/browse/supersigs/
Package Short Url	https://bioconductor.org/packages/supersigs/
Package Downloads Report	Download Stats