supersigs

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see supersigs.

Supervised mutational signatures

Bioconductor version: 3.14

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 "4.1") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Classification, FeatureExtraction, Regression, Sequencing, Software, SomaticMutation, WholeGenome

Version 1.2.0

In Bioconductor since BioC 3.13 (R-4.1) (3 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

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

Linking To

Enhances

Depends On Me

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Build Report Build Report

Package Archives

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

Source Package supersigs_1.2.0.tar.gz

Windows Binary supersigs_1.2.0.zip

macOS 10.13 (High Sierra) supersigs_1.2.0.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

Old Source Packages for BioC 3.14 Source Archive