example-notebooks.md

Example Notebooks

Example notebooks live under Example_notebooks.

PBMC3k

The current notebook examples are under Example_notebooks/01_PBMC3k:

• 00_sctl_functions_preprocessing_PBMC3K.ipynb: function-based workflow operating on a separate AnnData object.
• 01_sctl_DATASET_class_preprocessing_PBMC3K.ipynb: class-based workflow using sctl.DATASET_class.

The notebooks cover QC, preprocessing, clustering, visualization, differential-expression analysis, and GSEA-style output.

Publishing Policy

The docs hub links to notebooks and generated results in GitHub instead of copying notebooks, PBMC data, generated tables, PDFs, or other large artifacts into the Pages build.