This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see HiLDA.
Bioconductor version: 3.13
A package built under the Bayesian framework of applying hierarchical latent Dirichlet allocation to statistically test whether the mutational exposures of mutational signatures (Shiraishi-model signatures) are different between two groups.
Author: Zhi Yang [aut, cre], Yuichi Shiraishi [ctb]
Maintainer: Zhi Yang <zyang895 at gmail.com>
Citation (from within R,
enter citation("HiLDA")
):
To install this package, start R (version "4.1") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("HiLDA")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("HiLDA")
HTML | R Script | An introduction to HiLDA |
Reference Manual | ||
Text | NEWS | |
Text | INSTALL |
biocViews | Bayesian, Sequencing, Software, SomaticMutation, StatisticalMethod |
Version | 1.6.0 |
In Bioconductor since | BioC 3.10 (R-3.6) (2 years) |
License | GPL-3 |
Depends | R (>= 3.6), 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 4.2.0 |
Enhances | |
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 | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | HiLDA_1.6.0.tar.gz |
Windows Binary | HiLDA_1.6.0.zip (32- & 64-bit) |
macOS 10.13 (High Sierra) | HiLDA_1.6.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/HiLDA |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HiLDA |
Package Short Url | https://bioconductor.org/packages/HiLDA/ |
Package Downloads Report | Download Stats |
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