HiLDA

DOI: 10.18129/B9.bioc.HiLDA    

Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation

Bioconductor version: Release (3.14)

A package built under the Bayesian framework of applying hierarchical latent Dirichlet allocation. It statistically tests whether the mutational exposures of mutational signatures (Shiraishi-model signatures) are different between two groups. The package also provides inference and visualization.

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

Maintainer: Zhi Yang <zyang895 at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("HiLDA")

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("HiLDA")

 

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

Details

biocViews	Bayesian, Sequencing, Software, SomaticMutation, StatisticalMethod
Version	1.8.0
In Bioconductor since	BioC 3.10 (R-3.6) (2.5 years)
License	GPL-3
Depends	R (>= 4.1), ggplot2
Imports	R2jags, abind, cowplot, grid, forcats, stringr, GenomicRanges, S4Vectors, XVector, Biostrings, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, BiocGenerics, tidyr, grDevices, stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, methods, Rcpp
LinkingTo	Rcpp
Suggests	knitr, rmarkdown, testthat, BiocStyle
SystemRequirements	JAGS 4.0.0
Enhances
URL	https://github.com/USCbiostats/HiLDA https://doi.org/10.1101/577452
BugReports	https://github.com/USCbiostats/HiLDA/issues
Depends On Me
Imports Me	selectKSigs
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	HiLDA_1.8.0.tar.gz
Windows Binary	HiLDA_1.8.0.zip
macOS 10.13 (High Sierra)	HiLDA_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HiLDA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HiLDA
Package Short Url	https://bioconductor.org/packages/HiLDA/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive