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Bioconductor - HiLDA

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 (3.21)

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 "4.5") 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")
Details biocViews Bayesian, Sequencing, Software, SomaticMutation, StatisticalMethod Version 1.22.0 In Bioconductor since BioC 3.10 (R-3.6) (5.5 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 Package Archives

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

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