HiLDA

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see HiLDA.

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

Bioconductor version: 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>

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

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")

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 1.8.0

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

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_1.8.0.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

Bioc Package Browser https://code.bioconductor.org/browse/HiLDA/

Package Short Url https://bioconductor.org/packages/HiLDA/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.14 Source Archive