External Notebook Examples
==========================

This page highlights external notebook exemplars from the `nmdc_notebooks <https://github.com/microbiomedata/nmdc_notebooks>`_ repository.
Use them as end-to-end learning paths for discovery, integration, and analysis workflows using this package.

If you find any issues with the notebooks, please consider contributing a fix or opening an issue in the `nmdc_notebooks <https://github.com/microbiomedata/nmdc_notebooks>`_ repository.

Discovery and Metadata Exploration
----------------------------------

- `Bioscales Biogeochemical Metadata <https://microbiomedata.github.io/nmdc_notebooks/bioscales_python.html>`_
- `NEON Soil Metadata <https://microbiomedata.github.io/nmdc_notebooks/neon_python.html>`_
- `Taxonomy and Metadata Analysis <https://microbiomedata.github.io/nmdc_notebooks/taxonomic_python.html>`_

Visualization and Data Interpretation
-------------------------------------

- `Visualization of NOM Data <https://microbiomedata.github.io/nmdc_notebooks/nom_python.html>`_

Multi-omics Integration and Enrichment
--------------------------------------

- `Integrating Metagenome-Metatranscriptome Data <https://microbiomedata.github.io/nmdc_notebooks/metagmetat_python.html>`_
- `Integrating 'Omics Types Analysis <https://microbiomedata.github.io/nmdc_notebooks/integration_python.html>`_
- `Over-representation Analysis <https://microbiomedata.github.io/nmdc_notebooks/overrepresentation_python.html>`_

Related Guides
--------------

- :doc:`usage` for quick class selection and workflow guidance
- :doc:`filters` for Python filter recipes and troubleshooting