Package: animalcules
Title: Interactive microbiome analysis toolkit
Version: 1.29.2
Authors@R: c(person(given=c("W.", "Evan"), family="Johnson", email="wevanjohnson@gmail.com",
                role=c("aut", "cre"),
                comment = c(ORCID = "0000-0002-6247-6595")),
            person(given="Yue", family="Zhao", email="yuezh@bu.edu",
                role=c("aut"), comment = c(ORCID = "0000-0001-5257-5103")),
            person(given="Anthony", family="Federico", email="anfed@bu.edu",
                role=c("aut"), comment = c(ORCID = "0000-0002-9200-1689")),
            person(given="Jessica", family="Anderson",
                email="anderson.jessica@rutgers.edu", role=c("ctr"),
                comment = c(ORCID = "0000-0002-0542-9872")))
Description: 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.
License: Artistic-2.0
URL: https://github.com/wejlab/animalcules
BugReports: https://github.com/wejlab/animalcules/issues
Depends: R (>= 4.3.0)
Imports: ape, assertthat, caret, covr, DESeq2, dplyr, DT, forcats,
        ggforce, ggplot2, GUniFrac, lattice, limma, magrittr, Matrix,
        methods, MultiAssayExperiment, plotly, rentrez, reshape2,
        ROCit, S4Vectors (>= 0.23.19), scales, shiny, shinyjs, stats,
        SummarizedExperiment, tibble, tidyr, tsne, umap, utils, vegan,
        XML
Suggests: BiocStyle, biomformat, curl, devtools, glmnet, knitr,
        rmarkdown, testthat, usethis
VignetteBuilder: knitr
biocViews: Microbiome, Metagenomics, Coverage, Visualization
Encoding: UTF-8
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev make
        libicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev python3
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-09-18 19:30:45 UTC
RemoteUrl: https://github.com/bioc/animalcules
RemoteRef: HEAD
RemoteSha: e3b50bb63d1c8ed13d32a87533945db3ea4bd8d4
NeedsCompilation: no
Packaged: 2026-09-18 22:47:01 UTC; root
Author: W. Evan Johnson [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-6247-6595>),
  Yue Zhao [aut] (ORCID: <https://orcid.org/0000-0001-5257-5103>),
  Anthony Federico [aut] (ORCID: <https://orcid.org/0000-0002-9200-1689>),
  Jessica Anderson [ctr] (ORCID: <https://orcid.org/0000-0002-0542-9872>)
Maintainer: W. Evan Johnson <wevanjohnson@gmail.com>