HiLDA

This is the released version of HiLDA; for the devel version, see HiLDA.

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

Bioconductor version: Release (3.20)

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>

Citation (from within R, enter citation("HiLDA")):

Installation

To install this package, start R (version "4.4") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Bayesian, Sequencing, Software, SomaticMutation, StatisticalMethod
Version	1.20.0
In Bioconductor since	BioC 3.10 (R-3.6) (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
System Requirements	JAGS 4.0.0
URL	https://github.com/USCbiostats/HiLDA https://doi.org/10.1101/577452
Bug Reports	https://github.com/USCbiostats/HiLDA/issues

Suggests	knitr, rmarkdown, testthat, BiocStyle
Linking To	Rcpp
Enhances
Depends On Me
Imports Me	selectKSigs
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	HiLDA_1.20.0.tar.gz
Windows Binary (x86_64)	HiLDA_1.20.0.zip
macOS Binary (x86_64)	HiLDA_1.20.0.tgz
macOS Binary (arm64)	HiLDA_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HiLDA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HiLDA
Bioc Package Browser	https://code.bioconductor.org/browse/HiLDA/
Package Short Url	https://bioconductor.org/packages/HiLDA/
Package Downloads Report	Download Stats