HiLDA
This package is for version 3.19 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: 3.19
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("HiLDA")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| INSTALL | Text |
Details
| biocViews | Bayesian, Sequencing, Software, SomaticMutation, StatisticalMethod |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (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
| 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_1.18.0.tar.gz |
| Windows Binary (x86_64) | HiLDA_1.18.0.zip (64-bit only) |
| macOS Binary (x86_64) | HiLDA_1.18.0.tgz |
| macOS Binary (arm64) | HiLDA_1.18.0.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 |