animalcules

DOI: 10.18129/B9.bioc.animalcules    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see animalcules.

Interactive microbiome analysis toolkit

Bioconductor version: 3.12

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 [aut, cre] , Anthony Federico [aut] , W. Evan Johnson [aut]

Maintainer: Yue Zhao <yuezh at bu.edu>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	animalcules
PDF		Reference Manual

Details

biocViews	Coverage, Metagenomics, Microbiome, Software, Visualization
Version	1.6.0
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, DMwR, plotROC, DT, reactable, utils, limma, methods, stats, tibble, biomformat, umap, Matrix
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat, usethis
SystemRequirements
Enhances
URL	https://github.com/compbiomed/animalcules
BugReports	https://github.com/compbiomed/animalcules/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	animalcules_1.6.0.tar.gz
Windows Binary	animalcules_1.6.0.zip
macOS 10.13 (High Sierra)	animalcules_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/animalcules
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/animalcules
Package Short Url	https://bioconductor.org/packages/animalcules/
Package Downloads Report	Download Stats