This repository contains materials accompanying the workshop Microbiome-Based Tools: From Research to Application. To jump directly to the analysis notebooks, click on the badges for the corresponding tutorials below.
These notebooks describe simplified analyses of microbiome datasets using the with the bioinformatics platform QIIME 2. To learn more about the QIIME 2 project and applications in microbiome research, visit https://qiime2.org/. These materials have been adapted from the Advanced Block Course: Computational Biology; all source code is licensed under the Apache License 2.0.
In this notebook, we use 16S rRNA sequence data to evaluate bacterial composition of sample ecosystems. To launch, click on the badge above.
In this notebook, we use previously processed 16S rRNA sequence data to train and evaluate machine learning models. To launch, click on the badge above.
These analysis notebooks were adapted from the QIIME 2 Moving Pictures tutorial and q2-sample-classifier tutorial. A study based on these samples was originally published in Caporaso et al. (2011).
The Google Colab setup script was adapted from the 2023 ISB Virtual Microbiome Series workshop.
All source code is licensed under the Apache License 2.0.
