selectKSigs
Selecting the number of mutational signatures using a perplexity-based measure and cross-validation
Bioconductor version: Release (3.20)
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 "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | Clustering, Sequencing, Software, SomaticMutation, StatisticalMethod |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4.5 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_1.18.0.tar.gz |
| Windows Binary (x86_64) | selectKSigs_1.18.0.zip (64-bit only) |
| macOS Binary (x86_64) | selectKSigs_1.18.0.tgz |
| macOS Binary (arm64) | selectKSigs_1.18.0.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 |