Learning Paths

Tutorials

Choose the tutorial route that matches your starting point. Use the quick start when your input data are already prepared, or move to preprocessing and figure-level notebooks when you need deeper workflow coverage.

Open Quick Start Main Figures

• Start fast

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  Use the guided quick start notebook on prepared input data.

  Quick Start Notebook

• Prepare data

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  Generate spliced and unspliced layers from raw platform-specific data.

  Raw Data Preprocessing

• Reproduce figures

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  Follow the paper-oriented figure notebooks and analyses.

  Main Figures

Start here

If your .h5ad already contains spliced and unspliced, the recommended first notebook is:

• Quick Start Notebook

This notebook is the best entry point for first-time users. It explains the main workflow, key parameters, and the major training stages in a guided format.

Choose a path

• If you want to run STEER as quickly as possible, start with Quick Start Notebook.
• If you want to reproduce paper analyses, continue to Main Figures.
• If your data does not yet contain spliced and unspliced, begin with Raw Data Preprocessing.

Figure notebooks

For figure-level analyses, the following notebooks are available:

• Figure 2 Notebook
• Figure 3 Notebook
• Figure 4 Notebook
• Spatial Mouse Placentation Run
• scRNA Mouse Erythroid Run
• Figure 5 Notebook

Repository files

If you prefer to browse the original files on GitHub:

• quickstart.ipynb
• Figure2.ipynb
• Figure3.ipynb
• Figure4.ipynb
• run_Spatial_MousePlacentation.ipynb
• run_scRNA_Erythorid_slim.ipynb
• Figure5.ipynb