selectKSigs

DOI: 10.18129/B9.bioc.selectKSigs    

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

Bioconductor version: Release (3.11)

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 "4.0") and enter:

if (!requireNamespace("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 1.0.0
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
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_1.0.0.tar.gz
Windows Binary selectKSigs_1.0.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) selectKSigs_1.0.0.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
Old Source Packages for BioC 3.11 Source Archive

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