DirichletMultinomial

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see DirichletMultinomial.

Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data

DOI: 10.18129/B9.bioc.DirichletMultinomial

Bioconductor version: 3.21

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 This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed further in the man page for this package, ?DirichletMultinomial.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 iD ORCID: 0000-0002-5874-8148

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

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
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 1.50.0

In Bioconductor since BioC 2.11 (R-2.15) (13 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

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Package Archives

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

Source Package DirichletMultinomial_1.50.0.tar.gz

Windows Binary (x86_64) DirichletMultinomial_1.50.0.zip

macOS Binary (x86_64) DirichletMultinomial_1.50.0.tgz

macOS Binary (arm64) DirichletMultinomial_1.50.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/DirichletMultinomial

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DirichletMultinomial

Bioc Package Browser https://code.bioconductor.org/browse/DirichletMultinomial/

Package Short Url https://bioconductor.org/packages/DirichletMultinomial/

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