DOI: 10.18129/B9.bioc.animalcules    

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

Interactive microbiome analysis toolkit

Bioconductor version: Development (3.14)

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: Yue Zhao <yuezh at>, Anthony Federico <anfed at>, W. Johnson <wej at>, Evan Zhao <yuezh at>

Maintainer: Yue Zhao <yuezh at>

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


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biocViews Coverage, Metagenomics, Microbiome, Software, Visualization
Version 1.9.1
In Bioconductor since BioC 3.9 (R-3.6) (2 years)
License Artistic-2.0
Depends R (>= 4.0.0)
Imports assertthat, shiny, shinyjs, DESeq2, caret, plotly, ggplot2, rentrez, reshape2, covr, ape, vegan, dplyr, magrittr, MultiAssayExperiment, SummarizedExperiment, S4Vectors(>= 0.23.19), XML, forcats, scales, lattice, glmnet, tsne, plotROC, DT, reactable, utils, limma, methods, stats, tibble, biomformat, umap, Matrix, GUniFrac
Suggests BiocStyle, knitr, rmarkdown, testthat, usethis
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