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 (3.17)

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")):


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biocViews Bayesian, Sequencing, Software, SomaticMutation, StatisticalMethod
Version 1.14.0
In Bioconductor since BioC 3.10 (R-3.6) (4 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
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
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Source Package HiLDA_1.14.0.tar.gz
Windows Binary HiLDA_1.14.0.zip (64-bit only)
macOS Binary (x86_64) HiLDA_1.14.0.tgz
macOS Binary (arm64) HiLDA_1.14.0.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/
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Old Source Packages for BioC 3.17 Source Archive

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