animalcules

DOI: 10.18129/B9.bioc.animalcules    

Interactive microbiome analysis toolkit

Bioconductor version: Release (3.9)

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 bu.edu>, Anthony Federico <anfed at bu.edu>, W. Evan Johnson <wej at bu.edu>

Maintainer: Yue Zhao <yuezh at bu.edu>

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

Installation

To install this package, start R (version "3.6") 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 1.0.4
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
License Artistic-2.0
Depends R (>= 3.6.0)
Imports assertthat, shiny, shinyjs, DESeq2, caret, plotly, ggplot2, rentrez, reshape2, covr, ape, vegan, dplyr, magrittr, MultiAssayExperiment, SummarizedExperiment, S4Vectors, XML, forcats, scales, lattice, glmnet, tsne, DMwR, plotROC, DT, utils, limma, methods, stats, tibble, httr
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_1.0.4.tar.gz
Windows Binary animalcules_1.0.4.zip
Mac OS X 10.11 (El Capitan) animalcules_1.0.4.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 http://bioconductor.org/packages/animalcules/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive

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