selectKSigs

DOI: 10.18129/B9.bioc.selectKSigs    

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

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	An introduction to HiLDA
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, Sequencing, Software, SomaticMutation, StatisticalMethod
Version	1.8.0
In Bioconductor since	BioC 3.11 (R-4.0) (2.5 years)
License	GPL-3
Depends	R (>= 3.6)
Imports	HiLDA, magrittr, gtools, methods, Rcpp
LinkingTo	Rcpp
Suggests	knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr
SystemRequirements
Enhances
URL	https://github.com/USCbiostats/selectKSigs
BugReports	https://github.com/USCbiostats/HiLDA/selectKSigs
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	selectKSigs_1.8.0.tar.gz
Windows Binary	selectKSigs_1.8.0.zip
macOS Binary (x86_64)	selectKSigs_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/selectKSigs
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/selectKSigs
Package Short Url	https://bioconductor.org/packages/selectKSigs/
Package Downloads Report	Download Stats