borzoi-regulatory-prediction

name	borzoi-regulatory-prediction
description	Run pinned Borzoi models to predict RNA-seq and regulatory tracks from long DNA sequence and compare reference versus alternate alleles. Use for regulatory variant hypotheses with explicit genome assembly, sequence-window, tissue, and track provenance.
license	MIT

Borzoi Regulatory Prediction

Gate

Ask once before cloning/installing a pinned Borzoi revision, downloading model weights, or using GPU compute. Keep genomic sequence local unless remote use is approved. Follow $cx-compute-environment.

Workflow

1. Pin genome assembly, coordinates, strand, reference/alternate alleles, transcript/annotation release, tissue/track IDs, input length, and boundary handling. Verify reference alleles against the assembly.
2. Pin code commit, ensemble/checkpoint checksums, preprocessing, target metadata, shifts/reverse-complement ensemble, precision, hardware, and seeds.
3. Smoke-test an official example. Predict into artifacts/<run-id>/borzoi/; retain input windows, coordinate maps, target labels, raw tracks, reference/alternate differences, plots, logs, and failures.
4. Summarize effect direction/magnitude by declared tissues and transcripts; report ensemble variability and sensitivity to window placement. Compare simple conservation/motif and nearby-QTL baselines where relevant.
5. Record with $science-provenance; review with $science-review.

Boundaries

• Predicted expression effects are not causal, pathogenic, or clinical evidence.
• Prevent overlapping/LD-correlated windows and the same locus from crossing evaluation splits; audit training-data and annotation-release overlap.