README.md

In animalcules: Interactive microbiome analysis toolkit

animalcules

What does animalcules do?

R shiny app for interactive microbiome analysis

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.

Documentation

Please check our website at https://compbiomed.github.io/animalcules-docs/

Before Installation

• Make sure R version is >= 4.0.0 and Bioconductor version is 3.11. Bioconductor could be updated by :

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.11")

Installation

• Install the release version of the package from Bioconductor

if (!requireNamespace("BiocManager", quietly=TRUE))
  install.packages("BiocManager")
BiocManager::install("compbiomed/animalcules")

• Install the development version of the package from Github

if (!requireNamespace("devtools", quietly=TRUE))
  install.packages("devtools")
devtools::install_github("compbiomed/animalcules")

Run animalcules shiny app

library(animalcules)
run_animalcules()

animalcules documentation built on Nov. 8, 2020, 6:47 p.m.