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selectKSigs

Selecting the number of mutational signatures using a perplexity-based measure and cross-validation


Bioconductor version: Release (3.18)

A package to suggest the number of mutational signatures in a collection of somatic mutations using calculating the cross-validated perplexity score.

Author: Zhi Yang [aut, cre], Yuichi Shiraishi [ctb]

Maintainer: Zhi Yang <zyang895 at gmail.com>

Citation (from within R, enter citation("selectKSigs")):

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("selectKSigs")

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("selectKSigs")
An introduction to HiLDA HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, Sequencing, Software, SomaticMutation, StatisticalMethod
Version 1.14.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL-3
Depends R (>= 3.6)
Imports HiLDA, magrittr, gtools, methods, Rcpp
System Requirements
URL https://github.com/USCbiostats/selectKSigs
Bug Reports https://github.com/USCbiostats/HiLDA/selectKSigs
See More
Suggests knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package selectKSigs_1.14.0.tar.gz
Windows Binary selectKSigs_1.14.0.zip
macOS Binary (x86_64) selectKSigs_1.14.0.tgz
macOS Binary (arm64) selectKSigs_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/selectKSigs
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/selectKSigs
Bioc Package Browser https://code.bioconductor.org/browse/selectKSigs/
Package Short Url https://bioconductor.org/packages/selectKSigs/
Package Downloads Report Download Stats