JuliaTurkuDataScience / MicrobiomeAnalysis.jl

Functions and workflows for the analysis of microbiome data.

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 [e-mail]: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