wave-crispr-signal

Focused CRISPR signal-analysis toolkit for guide scoring and disruption analysis.

Active Runtime Surfaces

• wave_crispr_signal/ (core sequence, spectral, and stats utilities)
• applications/phase_weighted_scorecard_cli.py
• applications/crispr_cli.py
• applications/genomic_disruption_api.py
• web_apps/demo_mvp/app.py

Quick Start

python3 -m pip install -r requirements.txt

python3 applications/phase_weighted_scorecard_cli.py --help
python3 applications/crispr_cli.py --help
python3 applications/genomic_disruption_api.py --help

Current CLI truth for applications/genomic_disruption_api.py:

• score is implemented.
• design is implemented.
• batch and offtarget are parser options, but CLI execution returns Command <name> not yet implemented in CLI.

Validation Model

• Validation is change-scoped.
• For behavior changes, default expectation is:
  • one targeted automated test, and
  • one manual verification command with observed outcome.

Validation Milestone (Gate v3)

• External comparator gate is active under validation/ontarget_gate/.
• Gate v3 uses two manifest lanes:
  • decision-grade clean manifest (authoritative),
  • raw exploratory manifest (non-authoritative).
• Current authoritative Gate v3 outcome on clean holdouts: NO-GO against baseline_c_crisprpred.
• Current model thesis status: closed (NO-GO) for incremental continuation.
• See:
  • validation/ontarget_gate/README.md
  • validation/ontarget_gate/PROTOCOL_V3.md
  • validation/ontarget_gate/BOARD_FUNDING_ADDENDUM.md
  • validation/ontarget_gate/CLOSEOUT_NO_GO.md
  • validation/ontarget_gate/outputs/gate_report_v3.md

Canonical Docs

• docs/INDEX.md
• docs/CURRENT_STATE_AND_DOC_GAPS.md
• docs/CONTRIBUTING.md
• docs/PRIMARY_CLI_VALIDATION.md
• docs/PHASE_WEIGHTED_SCORECARD.md
• docs/MODEL_NOVELTY_STATEMENT.md

License

MIT