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https://github.com/juliaturkudatascience/microbiomeanalysis.jl
Functions and workflows for the analysis of microbiome data.
https://github.com/juliaturkudatascience/microbiomeanalysis.jl
bioinformatics ecology julia mia microbiome multiassayexperiment otu-table simulation summarized-experiment
Last synced: 1 day ago
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Functions and workflows for the analysis of microbiome data.
- Host: GitHub
- URL: https://github.com/juliaturkudatascience/microbiomeanalysis.jl
- Owner: JuliaTurkuDataScience
- License: mit
- Created: 2022-03-02T09:13:51.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2023-06-06T19:05:20.000Z (over 1 year ago)
- Last Synced: 2024-10-28T19:19:41.128Z (21 days ago)
- Topics: bioinformatics, ecology, julia, mia, microbiome, multiassayexperiment, otu-table, simulation, summarized-experiment
- Language: Julia
- Homepage: https://juliaturkudatascience.github.io/MicrobiomeAnalysis.jl
- Size: 1.67 MB
- Stars: 3
- Watchers: 3
- Forks: 1
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# MicrobiomeAnalysis.jl
[](https://juliaturkudatascience.github.io/MicrobiomeAnalysis.jl/dev/readme/)
[](https://github.com/JuliaTurkuDataScience/MicrobiomeAnalysis.jl/actions/workflows/CI.yml)
[](https://codecov.io/gh/JuliaTurkuDataScience/MicrobiomeAnalysis.jl)
This package provides common methods for microbiome analysis based on the [SummarizedExperiment](https://ltla.github.io/SummarizedExperiments.jl/dev/) and [MultiAssayExperiment](https://ltla.github.io/MultiAssayExperiments.jl/dev/) data containers. This work in Julia language reflects [related developments in R](https://github.com/microbiome/mia/) and has its own presentation at [JuliaCon 2022](https://www.youtube.com/watch?v=3PYFqwEQAb8&t=158s).
## Installation
This package has been registered in the Julia [General Registry](https://github.com/JuliaRegistries/General), so it can be installed as follows:
```julia
using Pkg
Pkg.add("MicrobiomeAnalysis")
using MicrobiomeAnalysis
```
For the latest functionality, you can clone this repo locally and start Julia with:
```bash
git clone [email protected]:JuliaTurkuDataScience/MicrobiomeAnalysis.jl.git
cd MicrobiomeAnalysis.jl
julia --project=.
```
and then run this in the Julia REPL:
```julia
using MicrobiomeAnalysis
```
Now you should be able to access and use all exported functions, for instance:
```julia
shannon
> shannon (generic function with 3 methods)
```
## Documentation
- [Function reference manual](https://juliaturkudatascience.github.io/MicrobiomeAnalysis.jl/dev/)
- [Basic microbiome workflow examples](https://juliaturkudatascience.github.io/MicrobiomeAnalysis.jl/dev/example1/)
## Data containers
MicrobiomeAnalysis.jl supports the analysis based on specific data containers:
- [MultiAssayExperiments](https://github.com/LTLA/MultiAssayExperiments.jl)
- [SummarizedExperiments](https://github.com/LTLA/SummarizedExperiments.jl)
## Microbiome data analysis packages
Simulate microbial community dynamics and time series:
- [FdeSolver](https://github.com/JuliaTurkuDataScience/FdeSolver.jl)
Independently developed packages for microbiome analysis provide
additional utilities but require in some cases further integration
with the SE and MAE data containers.
- [BiobakeryUtils](https://github.com/EcoJulia/BiobakeryUtils.jl)
- [EcoBase](https://github.com/EcoJulia/EcoBase.jl)
- [Microbiome](https://github.com/EcoJulia/Microbiome.jl)
## Suggested dependencies
A few optional dependencies are recommended for
MicrobiomeAnalysis.jl to function properly:
- [DataFrames](https://github.com/JuliaData/DataFrames.jl)
- [DataStructures](https://github.com/JuliaCollections/DataStructures.jl)
- [MultivariateStats](https://github.com/JuliaStats/MultivariateStats.jl)