HiLDA

DOI: 10.18129/B9.bioc.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 (3.11)

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")):

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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")

 

HTML R Script An introduction to HiLDA
PDF   Reference Manual
Text   NEWS
Text   INSTALL

Details

biocViews Bayesian, Sequencing, Software, SomaticMutation, StatisticalMethod
Version 1.1.0
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
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  

Package Archives

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

Source Package HiLDA_1.1.0.tar.gz
Windows Binary HiLDA_1.1.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) HiLDA_1.1.0.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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