API Reference

The API reference is split by workflow layer so the sidebar stays short and predictable.

Public Entry Points

• High-Level API: one-call workflows, compare_networks and virtual_knockout.
• Workflow Classes: step-wise scTenifoldNet and scTenifoldKnk classes.

Lower-Level Functions

• Network Functions: PC network construction, manifold alignment, differential regulation, AnnData conversion, and edge-direction helpers.
• Pipeline Functions: QC, normalization, tensor decomposition, and knockout propagation internals.
• Data Helpers: loading and test-data generation.
• Plotting: network, histogram, embedding, and QQ plots.
• Utilities: small shared helpers.

For most users, start with High-Level API or Workflow Classes.