animalcules

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see animalcules.

Interactive microbiome analysis toolkit

Bioconductor version: 3.18

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")):

Installation

To install this package, start R (version "4.3") and enter:


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

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("animalcules")

animalcules HTML R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, Metagenomics, Microbiome, Software, Visualization

Version 1.18.3

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

Suggests BiocStyle, biomformat, devtools, glmnet, knitr, rmarkdown, testthat, usethis

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