Resources¶
Downloads
Workshop Files
Data files, manifests, metadata, classifiers, and R scripts, everything needed to follow along on Alpine HPC.
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Glossary
Key Terms
Searchable definitions for metrics, methods, and file formats used throughout the workshop.
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Publication Plots in R
Self-Study
Full export reference for moving QIIME2 artifacts into R, plus the workshop's
Open Reference
visualizations.Rmd setup for publication-quality figures.Further Reading¶
| Resource | Description |
|---|---|
| QIIME2 Documentation | Official QIIME2 plugin and tutorial reference |
| QIIME2 Forum | Community support and Q&A |
| GreenGenes2 | Reference taxonomy and tree resources |
| DADA2 Paper | Callahan et al. 2016, original DADA2 publication |
| ANCOM-BC Paper | Lin & Peddada 2020, original ANCOM-BC publication |
| UniFrac Paper | Lozupone & Knight 2005, UniFrac distance metric |
Useful Tools¶
| Tool | Description |
|---|---|
| QIIME2 View | Browser-based viewer for .qzv visualization files |
| Microbiome Analyst | Web-based downstream analysis platform |
| phyloseq | R package for microbiome data analysis |
| vegan | R package for community ecology statistics |
Citation¶
If you use methods or materials from this workshop in your research, please cite QIIME2:
Bolyen E, Rideout JR, Dillon MR, et al. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37, 852–857. https://doi.org/10.1038/s41587-019-0209-9