DirichletMultinomial

This is the development version of DirichletMultinomial; for the stable release version, see DirichletMultinomial.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11

Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data

Bioconductor version: Development (3.24)

Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed further in the man page for this package, ?DirichletMultinomial.

Author: Martin Morgan [aut, cre] ORCID: 0000-0002-5874-8148

Maintainer: Martin Morgan <mtmorgan.xyz at gmail.com>

Citation (from within R, enter citation("DirichletMultinomial")):

Martin Morgan. DirichletMultinomial: Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data. doi:10.18129/B9.bioc.DirichletMultinomial, R package version 1.55.1, https://bioconductor.org/packages/DirichletMultinomial.

Generated from the package metadata; it may differ from the package's own citation.

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("DirichletMultinomial")

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("DirichletMultinomial")

DirichletMultinomial for Clustering and Classification of Microbiome Data	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, Clustering, ImmunoOncology, Metagenomics, Microbiome, Sequencing, Software
Version	1.55.1
In Bioconductor since	BioC 2.11 (R-2.15) (14 years)
License	LGPL-3
Depends	S4Vectors, IRanges
Imports	stats4, methods, BiocGenerics
System Requirements	gsl
URL	https://mtmorgan.github.io/DirichletMultinomial/
Bug Reports	https://github.com/mtmorgan/DirichletMultinomial/issues

Suggests	lattice, parallel, MASS, RColorBrewer, DT, knitr, rmarkdown, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me	mia, miaViz, TFBSTools
Suggests Me	bluster, MicrobiotaProcess
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	DirichletMultinomial_1.55.1.tar.gz
Windows Binary (x86_64)	DirichletMultinomial_1.55.1.zip
macOS Binary (big-sur-x86_64)	DirichletMultinomial_1.55.1.tgz
macOS Binary (sonoma-arm64)	DirichletMultinomial_1.55.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DirichletMultinomial
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DirichletMultinomial
Package Short Url	https://bioconductor.org/packages/DirichletMultinomial/
Package Downloads Report	Download Stats