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@companion-inc/borzoi

A

Use Borzoi-style regulatory genomics models for sequence-to-expression or variant-effect analysis. Use when the task asks for noncoding variant impact, regulatory sequence design, or expression prediction.

skillclaude

Install

agr install @companion-inc/borzoi --target claude

Writes 1 file into .claude/skills/, pinned to git-acb51874.

  • .claude/skills/borzoi/SKILL.md

Document

name: borzoi description: Use Borzoi-style regulatory genomics models for sequence-to-expression or variant-effect analysis. Use when the task asks for noncoding variant impact, regulatory sequence design, or expression prediction.

Borzoi

Use this skill for regulatory genomics modeling around sequence, variant, and expression effects.

Workflow:

  1. Pin genome build, interval coordinates, reference/alternate alleles, cell type or tissue, strand, and window size.
  2. Confirm the model route: local checkpoint, managed endpoint, notebook package, or external documented service. Record missing checkpoints as setup work, not as a completed model run.
  3. Build input FASTA/variant manifests with source URLs or accession IDs.
  4. Save prediction arrays, summary tables, plots, model version, and runtime metadata as Feynman artifacts.
  5. Compare predicted effects against GTEx, ENCODE, literature, or other source-backed evidence when available.

Keep source-owned genomic coordinates separate from model-owned effect predictions in every output.

Trustgrade A

  • passBody integrity

    Whether the stored document is plausibly the kind of file the artifact declares, rather than something fetched by mistake.

  • passType matchnot applicable to this artifact type

    Whether the artifact is really the kind of thing its metadata claims it is.

  • passFreshness

    How long since the source repository was last pushed to.

  • passPrompt injection

    Scans the artifact's own text for instructions aimed at your agent rather than at you.

  • passLicense

    Whether the source repository declares an SPDX license permissive enough to redistribute.

How the grade is calculated

Each check contributes 0 points when it passes, 1 when it warns, and 2 when it fails. The total maps to a letter:

  • Aevery check passed
  • Bone warning
  • Ctwo warnings
  • Dprompt injection or body integrity failed, or three warnings
  • Fone of those failed, and something else is wrong

These are automated hygiene checks, not a security audit, and not a dependency or vulnerability scan. A grade of A means nothing was flagged — not that the artifact is safe.

Versions

  • git-acb518747a6d2026-07-31