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HiLDA

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


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews Bayesian, Sequencing, Software, SomaticMutation, StatisticalMethod
Version 1.16.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 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
See More
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_1.16.0.tar.gz
Windows Binary HiLDA_1.16.0.zip
macOS Binary (x86_64) HiLDA_1.16.0.tgz
macOS Binary (arm64) HiLDA_1.16.0.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