HiLDA
Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation
Bioconductor version: 3.23 · Package version: 1.26.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("HiLDA")Details
| Maintainer | Zhi Yang <zyang895@gmail.com> |
| Author | Zhi Yang [aut, cre], Yuichi Shiraishi [ctb] |
| License | GPL-3 |
| URL | https://github.com/USCbiostats/HiLDA, https://doi.org/10.1101/577452 |
| Bug Reports | https://github.com/USCbiostats/HiLDA/issues |
| System Requirements | JAGS 4.0.0 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Bayesian, Sequencing, Software, SomaticMutation, StatisticalMethod |
| Package Short Url | https://bioconductor.org/packages/HiLDA/ |
Citation
From within R, enter citation("HiLDA"):
Zhi Yang. HiLDA: Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation. doi:10.18129/B9.bioc.HiLDA, R package version 1.26.0, https://bioconductor.org/packages/HiLDA.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | HiLDA_1.26.0.tar.gz |
| Windows binary (x86_64) | HiLDA_1.26.0.zip |
| macOS binary (arm64) | HiLDA_1.26.0.tgz |
| macOS binary (x86_64) | HiLDA_1.26.0.tgz |
Dependencies
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
Reverse dependencies
Imports Me (1): selectKSigs