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supersigs

Supervised mutational signatures

Bioconductor version: 3.23 · Package version: 1.20.0

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

MaintainerAlbert Kuo <albertkuo@jhu.edu>
AuthorAlbert Kuo [aut, cre] (ORCID: <https://orcid.org/0000-0001-5155-0748>), Yifan Zhang [aut], Bahman Afsari [aut], Cristian Tomasetti [aut]
LicenseGPL-3
URLhttps://tomasettilab.github.io/supersigs/
Bug Reportshttps://github.com/TomasettiLab/supersigs/issues
StatusDeprecated
Downloads rank288
Source branchRELEASE_3_23
biocViewsClassification, FeatureExtraction, Regression, Sequencing, Software, SomaticMutation, WholeGenome

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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