HiLDA
This is the development version of HiLDA; for the stable release version, see HiLDA.
Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.27.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 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_1.27.0.tar.gz |
| Windows Binary (x86_64) | HiLDA_1.27.0.zip |
| macOS Binary (big-sur-x86_64) | HiLDA_1.27.0.tgz |
| macOS Binary (sonoma-arm64) | HiLDA_1.27.0.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 |