This repository contains materials accompanying the Advanced Block Course: Computational Biology. To jump directly to the analysis notebook, click on the badge above ⬆️.
This notebook describes a simplified analysis of microbiome datasets using the bioinformatics software platform QIIME 2, as well as with several QIIME 2 plugins. In this case, 16S rRNA gene amplicon sequence data is used to take a "census" of the bacterial composition of several different ecosystems. For more information on QIIME 2 and its applications, see https://qiime2.org/.
The analysis notebook (including images), the setup script, and the corresponding data files were adapted from the ISB Virtual Microbiome Series workshop by the Gibbons Lab.
Minor modifications were made to the analysis notebook to introduce additional QIIME 2 plugins (e.g., q2-fondue) and to add or remove some other analysis and visualization steps.
All source code is licensed under the Apache License 2.0. This includes the notebooks deployed via Google Colaboratory.
Content and artwork is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
Illustrations embedded in the analysis notebook are used with license from https://github.com/Gibbons-Lab/isb_course_2021. Any reuse should cite the original source.
