MicrobiomeAnalysis.jl

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.

Installation

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

using Pkg
Pkg.add("MicrobiomeAnalysis")
using MicrobiomeAnalysis

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

git clone [email protected]: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
> shannon (generic function with 3 methods)

Documentation

• Function reference manual
• Basic microbiome workflow examples

Data containers

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

• MultiAssayExperiments
• SummarizedExperiments

Microbiome data analysis packages

Simulate microbial community dynamics and time series:

• FdeSolver

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

• BiobakeryUtils
• EcoBase
• Microbiome

Suggested dependencies

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

• DataFrames
• DataStructures
• MultivariateStats