supersigs
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see supersigs.
Supervised mutational signatures
Bioconductor version: Release (3.23)
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("supersigs")):Albert Kuo, Yifan Zhang, Bahman Afsari, Cristian Tomasetti. supersigs: Supervised mutational signatures. doi:10.18129/B9.bioc.supersigs, R package version 1.19.0, https://bioconductor.org/packages/supersigs.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | Classification, FeatureExtraction, Regression, Sequencing, Software, SomaticMutation, WholeGenome |
| Version | 1.19.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.1) |
| Imports | assertthat, caret, dplyr, tidyr, rsample, methods, rlang, utils, Biostrings, stats, SummarizedExperiment |
| System Requirements | |
| URL | https://tomasettilab.github.io/supersigs/ |
| Bug Reports | https://github.com/TomasettiLab/supersigs/issues |
See More
| Suggests | BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, testthat, VariantAnnotation |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow 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 (big-sur-x86_64) | supersigs_1.19.0.tgz |
| macOS Binary (sonoma-arm64) | supersigs_1.19.0.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 |