animalcules
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see animalcules.
Interactive microbiome analysis toolkit
Bioconductor version: 3.16
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("animalcules")):
Installation
To install this package, start R (version "4.2") 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 |
Details
| biocViews | Coverage, Metagenomics, Microbiome, Software, Visualization |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (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 |
| System Requirements | |
| URL | https://github.com/compbiomed/animalcules |
| Bug Reports | https://github.com/compbiomed/animalcules/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat, usethis |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | animalcules_1.14.0.tar.gz |
| Windows Binary | animalcules_1.14.0.zip |
| macOS Binary (x86_64) | animalcules_1.14.0.tgz |
| macOS Binary (arm64) | animalcules_1.14.0.tgz |
| 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 |
| Old Source Packages for BioC 3.16 | Source Archive |