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selectKSigs

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

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

Bioconductor version: Development (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")

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

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 1.13.0
In Bioconductor since BioC 3.11 (R-4.0) (3.5 years)
License GPL-3
Depends R (>= 3.6)
Imports HiLDA, magrittr, gtools, methods, Rcpp
Linking To Rcpp
Suggests knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr
System Requirements
Enhances
URL https://github.com/USCbiostats/selectKSigs
Bug Reports https://github.com/USCbiostats/HiLDA/selectKSigs
See More
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_1.13.0.tar.gz
Windows Binary selectKSigs_1.13.0.zip
macOS Binary (x86_64) selectKSigs_1.13.0.tgz
macOS Binary (arm64) selectKSigs_1.13.0.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