supersigs

Supervised mutational signatures

Bioconductor version: 3.23 · Package version: 1.19.0

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).

Installation

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

BiocManager::install("supersigs")

Details

Maintainer	Albert Kuo <albertkuo@jhu.edu>
Author	Albert Kuo [aut, cre] (ORCID: <https://orcid.org/0000-0001-5155-0748>), Yifan Zhang [aut], Bahman Afsari [aut], Cristian Tomasetti [aut]
License	GPL-3
URL	https://tomasettilab.github.io/supersigs/
Bug Reports	https://github.com/TomasettiLab/supersigs/issues
Status	Deprecated
Downloads rank	401
Source branch	RELEASE_3_23
biocViews	Classification, FeatureExtraction, Regression, Sequencing, Software, SomaticMutation, WholeGenome

Download

Follow the installation instructions to use this package in your R session.

Source package	supersigs_1.19.0.tar.gz
Windows binary (x86_64)	supersigs_1.19.0.zip
macOS binary (arm64)	supersigs_1.19.0.tgz
macOS binary (x86_64)	supersigs_1.19.0.tgz

Dependencies

Depends: R (>= 4.1)

Imports: assertthat, caret, dplyr, tidyr, rsample, methods, rlang, utils, Biostrings, stats, SummarizedExperiment

Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, testthat, VariantAnnotation