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This is the development version of HiLDA; for the stable release version, see HiLDA.

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

Bioconductor version: Development (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>

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


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

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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An introduction to HiLDA HTML R Script
Reference Manual PDF


biocViews Bayesian, Sequencing, Software, SomaticMutation, StatisticalMethod
Version 1.19.0
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
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Suggests knitr, rmarkdown, testthat, BiocStyle
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Depends On Me
Imports Me selectKSigs
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Source Package HiLDA_1.19.0.tar.gz
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