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://compbiomed.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
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 = "3.14")
if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("compbiomed/animalcules")
if (!requireNamespace("devtools", quietly=TRUE)) install.packages("devtools") devtools::install_github("compbiomed/animalcules")
Run the animalcules shiny app!
First, make sure you have Docker installed on your machine.
docker pull bucbm/animalcules:latest
git clone https://github.com/compbiomed/animalcules cd animalcules docker build --tag bucbm/animalcules:latest .
docker run -d -p 8787:8787 -e PASSWORD=animalcules bucbm/animalcules:latest