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.
Please check our website at https://wejlab.github.io/animalcules-docs/
Our paper on animalcules was published on the journal Microbiome in 2021!
You can find our paper here: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01013-0
Please cite:
Zhao, Y., Federico, A., Faits, T., Manimaran, S., Segrè, D., Monti, S. and Johnson, W.E., 2021. animalcules: interactive microbiome analytics and visualization in R. Microbiome, 9(1), pp.1-16.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.18")
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("wejlab/animalcules")
if (!requireNamespace("devtools", quietly=TRUE))
install.packages("devtools")
devtools::install_github("wejlab/animalcules")
Run the animalcules shiny app!
library(animalcules)
run_animalcules()
First, make sure you have Docker installed on your machine.
docker pull bucbm/animalcules:latest
git clone https://github.com/wejlab/animalcules
cd animalcules
docker build --tag bucbm/animalcules:latest .
Run with Docker
docker run -d -p 8787:8787 -e PASSWORD=animalcules bucbm/animalcules:latest
Go to http://localhost:8787/ in browser and enter username: rstudio / password: animalcules. Then enter the following:
library(animalcules)
run_animalcules()