API Reference
This reference documents the user-facing public API of bolero — the symbols the
tutorials use and the paper figures reach through the
bolerodata companion. Import by fully-qualified
module path (only the top-level package and pp curate re-exports).
The pages are grouped to mirror the tutorial workflow:
| Page | What it covers | Tutorials |
|---|---|---|
| Genome & Sequence | Assembly handles, DNA one-hot, region utilities | all |
| Datasets & Pseudobulks | Metacells, pseudobulking, parquet build, streaming datasets | 01–05 |
| Training | The Bolero model (BorzoiLoRA) and its trainers |
06–08, 13 |
| Prediction & Variant Effect | Inference tasks, caQTL/eQTL, directed evolution | 09–11, 14, 15 |
| Interpretation | chromVAR, motif scanning, TF-MoDISco, finemo, TomTom | 12; Fig 5 |
| Plotting | Attribution sequence logos, IGV browser | 11; Fig 1b/2 |
!!! note This is a research code base that carries experimental/vestigial code; the pages here intentionally document only the finalized, published surface. See the tutorials for end-to-end, runnable examples.