animalcules

This is the development version of animalcules; for the stable release version, see animalcules.

Interactive microbiome analysis toolkit

Bioconductor version: Development (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: Yue Zhao [aut, cre] , Anthony Federico [aut] , W. Evan Johnson [aut]

Maintainer: Yue Zhao <yuezh at bu.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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("animalcules")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Details

biocViews	Coverage, Metagenomics, Microbiome, Software, Visualization
Version	1.17.0
In Bioconductor since	BioC 3.9 (R-3.6) (4.5 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, plotROC, DT, utils, limma, methods, stats, tibble, biomformat, umap, Matrix, GUniFrac
Linking To
Suggests	BiocStyle, knitr, rmarkdown, testthat, usethis
System Requirements
Enhances
URL	https://github.com/compbiomed/animalcules
Bug Reports	https://github.com/compbiomed/animalcules/issues

Depends On Me
Imports Me
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Links To Me
Build Report

Package Archives

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

Source Package
Windows Binary	animalcules_1.17.0.zip
macOS Binary (x86_64)	animalcules_1.17.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/animalcules
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/animalcules
Bioc Package Browser	https://code.bioconductor.org/browse/animalcules/
Package Short Url	https://bioconductor.org/packages/animalcules/
Package Downloads Report	Download Stats