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

Interactive microbiome analysis toolkit

Bioconductor version: Development (3.19)

animalcules is an R package for utilizing up-to-date data analytics, visualization methods, and machine learning models to provide users an easy-to-use interactive microbiome analysis framework. It can be used as a standalone software package or users can explore their data with the accompanying interactive R Shiny application. Traditional microbiome analysis such as alpha/beta diversity and differential abundance analysis are enhanced, while new methods like biomarker identification are introduced by animalcules. Powerful interactive and dynamic figures generated by animalcules enable users to understand their data better and discover new insights.

Author: Jessica McClintock [cre], Yue Zhao [aut] , Anthony Federico [aut] , W. Evan Johnson [aut]

Maintainer: Jessica McClintock <jessica.mcclintock at rutgers.edu>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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:

animalcules HTML R Script
Reference Manual PDF


biocViews Coverage, Metagenomics, Microbiome, Software, Visualization
Version 1.19.2
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License Artistic-2.0
Depends R (>= 4.3.0)
Imports ape, assertthat, caret, covr, DESeq2, dplyr, DT, forcats, ggplot2, GUniFrac, lattice, limma, magrittr, Matrix, methods, MultiAssayExperiment, plotly, rentrez, reshape2, ROCit, S4Vectors(>= 0.23.19), scales, shiny, shinyjs, stats, SummarizedExperiment, tibble, tsne, umap, utils, vegan, XML
System Requirements
URL https://github.com/compbiomed/animalcules
Bug Reports https://github.com/compbiomed/animalcules/issues
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Suggests BiocStyle, biomformat, devtools, glmnet, knitr, rmarkdown, testthat, usethis
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Package Archives

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

Source Package animalcules_1.19.2.tar.gz
Windows Binary animalcules_1.19.2.zip
macOS Binary (x86_64) animalcules_1.19.2.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/animalcules
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/animalcules
Bioc Package Browser https://code.bioconductor.org/browse/animalcules/
Package Short Url https://bioconductor.org/packages/animalcules/
Package Downloads Report Download Stats