Functions and workflows for the analysis of microbiome data.
Author JuliaTurkuDataScience
3 Stars
Updated Last
1 Year Ago
Started In
March 2022


Dev CI codecov

This package provides common methods for microbiome analysis based on the SummarizedExperiment and MultiAssayExperiment data containers. This work in Julia language reflects related developments in R and has its own presentation at JuliaCon 2022.


This package has been registered in the Julia General Registry, so it can be installed as follows:

using Pkg
using MicrobiomeAnalysis

For the latest functionality, you can clone this repo locally and start Julia with:

git clone git@github.com:JuliaTurkuDataScience/MicrobiomeAnalysis.jl.git
cd MicrobiomeAnalysis.jl
julia --project=.

and then run this in the Julia REPL:

using MicrobiomeAnalysis

Now you should be able to access and use all exported functions, for instance:

> shannon (generic function with 3 methods)


Data containers

MicrobiomeAnalysis.jl supports the analysis based on specific data containers:

Microbiome data analysis packages

Simulate microbial community dynamics and time series:

Independently developed packages for microbiome analysis provide additional utilities but require in some cases further integration with the SE and MAE data containers.

Suggested dependencies

A few optional dependencies are recommended for MicrobiomeAnalysis.jl to function properly: