supersigs

DOI: 10.18129/B9.bioc.supersigs    

This is the development version of supersigs; for the stable release version, see supersigs.

Supervised mutational signatures

Bioconductor version: Development (3.15)

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 "4.2") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

HTML R Script Using supersigs
PDF   Reference Manual
Text   NEWS

Details

biocViews Classification, FeatureExtraction, Regression, Sequencing, Software, SomaticMutation, WholeGenome
Version 1.3.0
In Bioconductor since BioC 3.13 (R-4.1) (0.5 years)
License GPL-3
Depends R (>= 4.1)
Imports assertthat, caret, dplyr, tidyr, rsample, methods, rlang, utils, Biostrings, stats, SummarizedExperiment
LinkingTo
Suggests BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, testthat, VariantAnnotation
SystemRequirements
Enhances
URL https://tomasettilab.github.io/supersigs/
BugReports 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_1.3.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) supersigs_1.3.0.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

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