q2-gglasso

A QIIME 2 plugin for solving General Graphical Lasso (GGLasso) problems with microbiome data including:

• Single Graphical Lasso (SGL)
• Adaptive SGL
• SGL with latent variables
• Multiple Graphical Lasso (MGL)
• MGL with latent variables
• GGL in the nonconforming case

📚 Documentation | 📂 Tutorial & Examples

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Installation

First, make sure you have GGLasso is installed:

conda install -q gglasso

OR

pip install gglasso

Next to install the plugin:

pip install git+https://github.com/bio-datascience/q2-gglasso.git
qiime dev refresh-cache

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Usage Tutorial

A complete tutorial on using q2-gglasso for microbiome data analysis — including preprocessing, CLR transformation, model fitting, and visualization — is available at:

👉 Atacama Soil Microbiome Tutorial

This tutorial includes:

• Input formatting and CLR transformation
• Applications of SGL, adaptive SGL, and SGL with latent variables
• Network visualizations of ASV associations
• Covariate analysis and interpretation

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Citation

If you use q2-gglasso, please cite:

Schaipp, F., Vlasovets, O., & Müller, C. L. (2021). GGLasso – a Python package for General Graphical Lasso computation. Journal of Open Source Software, 6(68), 3865. https://doi.org/10.21105/joss.03865

Related Projects

• gglasso: Python solvers for graphical lasso problems
• atacama-soil-microbiome-tutorial: Full tutorial and example analyses

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License

BSD 3-Clause License. See LICENSE for details.