Package: animalcules
Title: Interactive microbiome analysis toolkit
Version: 1.27.0
Authors@R: c(person(given="Jessica", family="McClintock",
                email="jessica.mcclintock@rutgers.edu", role=c("cre")),
            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=c("W.", "Evan"), family="Johnson", email="wej@bu.edu",
                role=c("aut"),
                comment = c(ORCID = "0000-0002-6247-6595")))
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, devtools, glmnet, knitr, rmarkdown,
        testthat, usethis
VignetteBuilder: knitr
biocViews: Microbiome, Metagenomics, Coverage, Visualization
Encoding: UTF-8
RoxygenNote: 7.3.0
Config/pak/sysreqs: libfontconfig1-dev libfreetype6-dev make libicu-dev
        libpng-dev libxml2-dev libssl-dev python3 zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:52:04 UTC
RemoteUrl: https://github.com/bioc/animalcules
RemoteRef: HEAD
RemoteSha: 30597c8d859a071727c1f89132b3b9e27eff5287
NeedsCompilation: no
Packaged: 2025-11-02 14:41:17 UTC; root
Author: Jessica McClintock [cre],
  Yue Zhao [aut] (ORCID: <https://orcid.org/0000-0001-5257-5103>),
  Anthony Federico [aut] (ORCID: <https://orcid.org/0000-0002-9200-1689>),
  W. Evan Johnson [aut] (ORCID: <https://orcid.org/0000-0002-6247-6595>)
Maintainer: Jessica McClintock <jessica.mcclintock@rutgers.edu>
Built: R 4.6.0; ; 2025-11-02 14:44:17 UTC; windows
